From 9fda53d267ef08073f557058a4ec89703e5f513b Mon Sep 17 00:00:00 2001 From: Bennet Fauber Date: Mon, 24 Feb 2020 10:15:56 -0500 Subject: [PATCH 001/286] Updating WRF examples with output from EB 4.1.1 and foss/2018b This is separating out the changes for WRF example from other documentation changes that were accidentally bundled in PR #603. Repeating the summary here. I updated the example output in the Typical workflow example to use EB 4.1.1 and install WRF based on the foss/2018b toolchain. References in the text have been changed to match the updated output. --- docs/Typical_workflow_example_with_WRF.rst | 180 ++++++++++++--------- 1 file changed, 106 insertions(+), 74 deletions(-) diff --git a/docs/Typical_workflow_example_with_WRF.rst b/docs/Typical_workflow_example_with_WRF.rst index 2dc34ed9..4e1ba66d 100644 --- a/docs/Typical_workflow_example_with_WRF.rst +++ b/docs/Typical_workflow_example_with_WRF.rst @@ -26,30 +26,28 @@ Searching for build specification for a particular software package can be done for example, to get a list of available easyconfig files for WRF:: $ eb -S WRF - == temporary log file in case of crash /tmp/easybuild-MdAp7p/easybuild-zEBJMk.log - == Searching (case-insensitive) for 'WRF' in /home/example/.local/easybuild/software/EasyBuild/1.15.2/lib/python2.7/site-packages/easybuild_easyconfigs-1.15.2.0-py2.7.egg/easybuild/easyconfigs - CFGS1=/home/example/.local/easybuild/software/EasyBuild/1.15.2/lib/python2.7/site-packages/easybuild_easyconfigs-1.15.2.0-py2.7.egg/easybuild/easyconfigs/w/WRF - * $CFGS1/WRF-3.3.1-goalf-1.1.0-no-OFED-dmpar.eb - * $CFGS1/WRF-3.3.1-goolf-1.4.10-dmpar.eb - [...] - * $CFGS1/WRF-3.5-goolf-1.4.10-dmpar.eb - * $CFGS1/WRF-3.5-ictce-4.1.13-dmpar.eb - * $CFGS1/WRF-3.5-ictce-5.3.0-dmpar.eb - * $CFGS1/WRF-3.5.1-goolf-1.4.10-dmpar.eb - * $CFGS1/WRF-3.5.1-goolf-1.5.14-dmpar.eb - [...] - == temporary log file /tmp/easybuild-MdAp7p/easybuild-zEBJMk.log has been removed. - == temporary directory /tmp/easybuild-MdAp7p has been removed. - -Various easyconfig files are found: for different versions of WRF (e.g., v3.5 and v3.5.1), -for different (versions of) compiler toolchains (e.g., goolf v1.4.10, goolf v1.5.14, ictce), etc. - -For the remainder of this example, we will use the available ``WRF-3.5.1-goolf-1.4.10-dmpar.eb`` + CFGS1=/home/example/.local/easybuild/software/EasyBuild/4.1.1/easybuild/easyconfigs + * $CFGS1/w/WPS/WPS-4.0.1_find-wrfdir.patch + * $CFGS1/w/WPS/WPS-4.0.2_find-wrfdir.patch + [ . . . ] + * $CFGS1/w/WRF/WRF-4.0.1-intel-2018b-dmpar.eb + * $CFGS1/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb + [ . . . ] + + Note: 16 matching archived easyconfig(s) found, use --consider-archived-easyconfigs to see them + + + +Various easyconfig files are found: for different versions of WRF (e.g., v3.8 and v4.1.3), +for different (versions of) compiler toolchains (e.g., foss 2018b, intel 2018b), etc. + +For the remainder of this example, we will use the available ``WRF-4.0.2-foss-2018b-dmpar.eb`` easyconfig file to specify to EasyBuild to build and install -WRF v3.5.1 using version 1.4.10 of the ``goolf`` toolchain. +WRF v4.0.2 using version 2018b of the ``foss`` toolchain. -See :ref:`toolchains_table` for a list of available toolchains. The ``goolf`` toolchain -stands for ``GCC, OpenMPI, OpenBLAS, ScaLAPACK and FFTW``. +See :ref:`toolchains_table` for a list of available toolchains. The ``foss`` toolchain +stands for ``GCC, OpenMPI, OpenBLAS/LAPACK, ScaLAPACK, and FFTW``. The ``foss`` toolchain +is one of the :ref:`common_toolchains`. Getting an overview of planned installations -------------------------------------------- @@ -63,33 +61,58 @@ as well as their current availability (``[x]`` marks available modules). Note that EasyBuild will take care of all of the dependencies of WRF as well, and can even install the compiler toolchain as well if the corresponding modules are not available yet:: - $ eb WRF-3.5.1-goolf-1.4.10-dmpar.eb -Dr - == temporary log file in case of crash /tmp/easybuild-HqpcAZ/easybuild-uNzmpk.log + $ eb WRF-4.0.2-foss-2018b-dmpar.eb -Dr + == temporary log file in case of crash /tmp/eb-eEnBF5/easybuild-pvrvNP.log Dry run: printing build status of easyconfigs and dependencies - CFGS=/home/example/.local/easybuild/software/EasyBuild/1.15.2/lib/python2.7/site-packages/easybuild_easyconfigs-1.15.2.0-py2.7.egg/easybuild/easyconfigs - * [x] $CFGS/g/GCC/GCC-4.7.2.eb (module: GCC/4.7.2) - * [x] $CFGS/h/hwloc/hwloc-1.6.2-GCC-4.7.2.eb (module: hwloc/1.6.2-GCC-4.7.2) - * [x] $CFGS/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb (module: OpenMPI/1.6.4-GCC-4.7.2) - * [x] $CFGS/g/gompi/gompi-1.4.10.eb (module: gompi/1.4.10) - * [x] $CFGS/o/OpenBLAS/OpenBLAS-0.2.6-gompi-1.4.10-LAPACK-3.4.2.eb (module: OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2) - * [x] $CFGS/f/FFTW/FFTW-3.3.3-gompi-1.4.10.eb (module: FFTW/3.3.3-gompi-1.4.10) - * [x] $CFGS/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2.eb (module: ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2) - * [x] $CFGS/g/goolf/goolf-1.4.10.eb (module: goolf/1.4.10) - * [ ] $CFGS/s/Szip/Szip-2.1-goolf-1.4.10.eb (module: Szip/2.1-goolf-1.4.10) - * [ ] $CFGS/f/flex/flex-2.5.37-goolf-1.4.10.eb (module: flex/2.5.37-goolf-1.4.10) - * [ ] $CFGS/n/ncurses/ncurses-5.9-goolf-1.4.10.eb (module: ncurses/5.9-goolf-1.4.10) - * [ ] $CFGS/m/M4/M4-1.4.16-goolf-1.4.10.eb (module: M4/1.4.16-goolf-1.4.10) - * [ ] $CFGS/j/JasPer/JasPer-1.900.1-goolf-1.4.10.eb (module: JasPer/1.900.1-goolf-1.4.10) - * [ ] $CFGS/z/zlib/zlib-1.2.7-goolf-1.4.10.eb (module: zlib/1.2.7-goolf-1.4.10) - * [ ] $CFGS/t/tcsh/tcsh-6.18.01-goolf-1.4.10.eb (module: tcsh/6.18.01-goolf-1.4.10) - * [ ] $CFGS/b/Bison/Bison-2.7-goolf-1.4.10.eb (module: Bison/2.7-goolf-1.4.10) - * [ ] $CFGS/h/HDF5/HDF5-1.8.10-patch1-goolf-1.4.10.eb (module: HDF5/1.8.10-patch1-goolf-1.4.10) - * [ ] $CFGS/d/Doxygen/Doxygen-1.8.3.1-goolf-1.4.10.eb (module: Doxygen/1.8.3.1-goolf-1.4.10) - * [ ] $CFGS/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb (module: netCDF/4.2.1.1-goolf-1.4.10) - * [ ] $CFGS/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb (module: netCDF-Fortran/4.2-goolf-1.4.10) - * [ ] $CFGS/w/WRF/WRF-3.5.1-goolf-1.4.10-dmpar.eb (module: WRF/3.5.1-goolf-1.4.10-dmpar) - == temporary log file /tmp/easybuild-HqpcAZ/easybuild-uNzmpk.log has been removed. - == temporary directory /tmp/easybuild-HqpcAZ has been removed. + CFGS=/home/example/.local/easybuild/software/EasyBuild/4.1.1/easybuild/easyconfigs + * [x] $CFGS/m/M4/M4-1.4.18.eb (module: M4/1.4.18) + * [x] $CFGS/z/zlib/zlib-1.2.11.eb (module: zlib/1.2.11) + * [x] $CFGS/h/help2man/help2man-1.47.4.eb (module: help2man/1.47.4) + * [x] $CFGS/m/M4/M4-1.4.17.eb (module: M4/1.4.17) + * [x] $CFGS/b/Bison/Bison-3.0.4.eb (module: Bison/3.0.4) + * [x] $CFGS/f/flex/flex-2.6.4.eb (module: flex/2.6.4) + * [x] $CFGS/b/binutils/binutils-2.30.eb (module: binutils/2.30) + * [x] $CFGS/g/GCCcore/GCCcore-7.3.0.eb (module: GCCcore/7.3.0) + * [x] $CFGS/h/help2man/help2man-1.47.4-GCCcore-7.3.0.eb (module: help2man/1.47.4-GCCcore-7.3.0) + * [x] $CFGS/m/M4/M4-1.4.18-GCCcore-7.3.0.eb (module: M4/1.4.18-GCCcore-7.3.0) + * [x] $CFGS/z/zlib/zlib-1.2.11-GCCcore-7.3.0.eb (module: zlib/1.2.11-GCCcore-7.3.0) + * [x] $CFGS/b/Bison/Bison-3.0.4-GCCcore-7.3.0.eb (module: Bison/3.0.4-GCCcore-7.3.0) + * [x] $CFGS/b/Bison/Bison-3.0.5-GCCcore-7.3.0.eb (module: Bison/3.0.5-GCCcore-7.3.0) + * [x] $CFGS/f/flex/flex-2.6.4-GCCcore-7.3.0.eb (module: flex/2.6.4-GCCcore-7.3.0) + * [x] $CFGS/b/binutils/binutils-2.30-GCCcore-7.3.0.eb (module: binutils/2.30-GCCcore-7.3.0) + * [ ] $CFGS/n/ncurses/ncurses-6.1-GCCcore-7.3.0.eb (module: ncurses/6.1-GCCcore-7.3.0) + * [ ] $CFGS/c/CMake/CMake-3.11.4-GCCcore-7.3.0.eb (module: CMake/3.11.4-GCCcore-7.3.0) + * [x] $CFGS/a/Autoconf/Autoconf-2.69-GCCcore-7.3.0.eb (module: Autoconf/2.69-GCCcore-7.3.0) + * [x] $CFGS/a/Automake/Automake-1.16.1-GCCcore-7.3.0.eb (module: Automake/1.16.1-GCCcore-7.3.0) + * [x] $CFGS/g/GCC/GCC-7.3.0-2.30.eb (module: GCC/7.3.0-2.30) + * [ ] $CFGS/p/pkg-config/pkg-config-0.29.2-GCCcore-7.3.0.eb (module: pkg-config/0.29.2-GCCcore-7.3.0) + * [ ] $CFGS/c/cURL/cURL-7.60.0-GCCcore-7.3.0.eb (module: cURL/7.60.0-GCCcore-7.3.0) + * [x] $CFGS/l/libtool/libtool-2.4.6-GCCcore-7.3.0.eb (module: libtool/2.4.6-GCCcore-7.3.0) + * [ ] $CFGS/s/Szip/Szip-2.1.1-GCCcore-7.3.0.eb (module: Szip/2.1.1-GCCcore-7.3.0) + * [x] $CFGS/o/OpenBLAS/OpenBLAS-0.3.1-GCC-7.3.0-2.30.eb (module: OpenBLAS/0.3.1-GCC-7.3.0-2.30) + * [ ] $CFGS/t/tcsh/tcsh-6.20.00-GCCcore-7.3.0.eb (module: tcsh/6.20.00-GCCcore-7.3.0) + * [ ] $CFGS/j/JasPer/JasPer-2.0.14-GCCcore-7.3.0.eb (module: JasPer/2.0.14-GCCcore-7.3.0) + * [x] $CFGS/a/Autotools/Autotools-20180311-GCCcore-7.3.0.eb (module: Autotools/20180311-GCCcore-7.3.0) + * [ ] $CFGS/d/Doxygen/Doxygen-1.8.14-GCCcore-7.3.0.eb (module: Doxygen/1.8.14-GCCcore-7.3.0) + * [x] $CFGS/n/numactl/numactl-2.0.11-GCCcore-7.3.0.eb (module: numactl/2.0.11-GCCcore-7.3.0) + * [x] $CFGS/x/xorg-macros/xorg-macros-1.19.2-GCCcore-7.3.0.eb (module: xorg-macros/1.19.2-GCCcore-7.3.0) + * [x] $CFGS/l/libpciaccess/libpciaccess-0.14-GCCcore-7.3.0.eb (module: libpciaccess/0.14-GCCcore-7.3.0) + * [x] $CFGS/n/ncurses/ncurses-6.0.eb (module: ncurses/6.0) + * [x] $CFGS/g/gettext/gettext-0.19.8.1.eb (module: gettext/0.19.8.1) + * [x] $CFGS/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb (module: XZ/5.2.4-GCCcore-7.3.0) + * [x] $CFGS/l/libxml2/libxml2-2.9.8-GCCcore-7.3.0.eb (module: libxml2/2.9.8-GCCcore-7.3.0) + * [x] $CFGS/h/hwloc/hwloc-1.11.10-GCCcore-7.3.0.eb (module: hwloc/1.11.10-GCCcore-7.3.0) + * [x] $CFGS/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb (module: OpenMPI/3.1.1-GCC-7.3.0-2.30) + * [x] $CFGS/g/gompi/gompi-2018b.eb (module: gompi/2018b) + * [x] $CFGS/f/FFTW/FFTW-3.3.8-gompi-2018b.eb (module: FFTW/3.3.8-gompi-2018b) + * [x] $CFGS/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2018b-OpenBLAS-0.3.1.eb (module: ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1) + * [x] $CFGS/f/foss/foss-2018b.eb (module: foss/2018b) + * [ ] $CFGS/h/HDF5/HDF5-1.10.2-foss-2018b.eb (module: HDF5/1.10.2-foss-2018b) + * [ ] $CFGS/n/netCDF/netCDF-4.6.1-foss-2018b.eb (module: netCDF/4.6.1-foss-2018b) + * [ ] $CFGS/n/netCDF-Fortran/netCDF-Fortran-4.4.4-foss-2018b.eb (module: netCDF-Fortran/4.4.4-foss-2018b) + * [ ] $CFGS/w/WRF/WRF-4.0.2-foss-2018b-dmpar.eb (module: WRF/4.0.2-foss-2018b-dmpar) + == Temporary log file(s) /tmp/eb-eEnBF5/easybuild-pvrvNP.log* have been removed. + == Temporary directory /tmp/eb-eEnBF5 has been removed. @@ -101,49 +124,58 @@ To make EasyBuild build and install WRF, including all of its dependencies, a ** By using the ``--robot``/``-r`` (see :ref:`use_robot`) command line option, we enable dependency resolution such that the entire software stack is handled:: - $ eb WRF-3.5.1-goolf-1.4.10-dmpar.eb --robot + $ eb WRF-4.0.2-foss-2018b-dmpar.eb --robot + == temporary log file in case of crash /tmp/eb-LfQa8b/easybuild-TBXLTy.log + == resolving dependencies ... + == processing EasyBuild easyconfig /home/example/.local/easybuild/software/EasyBuild/4.1.1/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-7.3.0.eb + == building and installing ncurses/6.1-GCCcore-7.3.0... [...] - == building and installing zlib/1.2.7-goolf-1.4.10... + == building and installing tcsh/6.20.00-GCCcore-7.3.0... [...] - == building and installing Szip/2.1-goolf-1.4.10... + == building and installing CMake/3.11.4-GCCcore-7.3.0... [...] - == building and installing ncurses/5.9-goolf-1.4.10... + == building and installing JasPer/2.0.14-GCCcore-7.3.0... [...] - == building and installing flex/2.5.37-goolf-1.4.10... + == building and installing pkg-config/0.29.2-GCCcore-7.3.0... [...] - == building and installing M4/1.4.16-goolf-1.4.10... + == building and installing Doxygen/1.8.14-GCCcore-7.3.0... [...] - == building and installing JasPer/1.900.1-goolf-1.4.10... + == building and installing cURL/7.60.0-GCCcore-7.3.0... [...] - == building and installing HDF5/1.8.10-patch1-goolf-1.4.10... + == building and installing Szip/2.1.1-GCCcore-7.3.0... [...] - == building and installing tcsh/6.18.01-goolf-1.4.10... + == building and installing HDF5/1.10.2-foss-2018b... [...] - == building and installing Bison/2.7-goolf-1.4.10... + == building and installing netCDF/4.6.1-foss-2018b... [...] - == building and installing Doxygen/1.8.3.1-goolf-1.4.10... + == building and installing netCDF-Fortran/4.4.4-foss-2018b... [...] - == building and installing netCDF/4.2.1.1-goolf-1.4.10... + == building and installing WRF/4.0.2-foss-2018b-dmpar... [...] - == building and installing netCDF-Fortran/4.2-goolf-1.4.10... - [...] - == building and installing WRF/3.5.1-goolf-1.4.10-dmpar... - [...] - == Build succeeded for 13 out of 13 + == Build succeeded for 12 out of 12 + == Temporary log file(s) /tmp/eb-LfQa8b/easybuild-TBXLTy.log* have been removed. + == Temporary directory /tmp/eb-LfQa8b has been removed. + Once the installation has succeeded, modules will be available for WRF and all of its dependencies:: $ module load WRF $ module list - Currently Loaded Modulefiles: - 1) GCC/4.7.2 9) JasPer/1.900.1-goolf-1.4.10 - 2) hwloc/1.6.2-GCC-4.7.2 10) zlib/1.2.7-goolf-1.4.10 - 3) OpenMPI/1.6.4-GCC-4.7.2 11) Szip/2.1-goolf-1.4.10 - 4) gompi/1.4.10 12) HDF5/1.8.10-patch1-goolf-1.4.10 - 5) OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2 13) netCDF/4.2.1.1-goolf-1.4.10 - 6) FFTW/3.3.3-gompi-1.4.10 14) netCDF-Fortran/4.2-goolf-1.4.10 - 7) ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2 15) WRF/3.5.1-goolf-1.4.10-dmpar - 8) goolf/1.4.10 + $ module list + + Currently Loaded Modules: + 1) EasyBuild/4.1.1 13) gompi/2018b + 2) GCCcore/7.3.0 14) FFTW/3.3.8-gompi-2018b + 3) zlib/1.2.11-GCCcore-7.3.0 15) ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1 + 4) binutils/2.30-GCCcore-7.3.0 16) foss/2018b + 5) GCC/7.3.0-2.30 17) JasPer/2.0.14-GCCcore-7.3.0 + 6) numactl/2.0.11-GCCcore-7.3.0 18) Szip/2.1.1-GCCcore-7.3.0 + 7) XZ/5.2.4-GCCcore-7.3.0 19) HDF5/1.10.2-foss-2018b + 8) libxml2/2.9.8-GCCcore-7.3.0 20) cURL/7.60.0-GCCcore-7.3.0 + 9) libpciaccess/0.14-GCCcore-7.3.0 21) netCDF/4.6.1-foss-2018b + 10) hwloc/1.11.10-GCCcore-7.3.0 22) netCDF-Fortran/4.4.4-foss-2018b + 11) OpenMPI/3.1.1-GCC-7.3.0-2.30 23) WRF/4.0.2-foss-2018b-dmpar + 12) OpenBLAS/0.3.1-GCC-7.3.0-2.30 For more information, see the other topics discussed in the documentation (see :ref:`contents`). From a03fa2ae08e31ead949ec1e514a6d7b03bb245fa Mon Sep 17 00:00:00 2001 From: Bennet Fauber Date: Tue, 25 Feb 2020 14:52:55 -0500 Subject: [PATCH 002/286] Making corrections requested by K Hoste, PR 604 --- docs/Typical_workflow_example_with_WRF.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Typical_workflow_example_with_WRF.rst b/docs/Typical_workflow_example_with_WRF.rst index 4e1ba66d..6fd5e849 100644 --- a/docs/Typical_workflow_example_with_WRF.rst +++ b/docs/Typical_workflow_example_with_WRF.rst @@ -38,12 +38,12 @@ for example, to get a list of available easyconfig files for WRF:: -Various easyconfig files are found: for different versions of WRF (e.g., v3.8 and v4.1.3), +Various easyconfig files are found: for different versions of WRF (e.g., v4.0.1 and v4.4.0.2), for different (versions of) compiler toolchains (e.g., foss 2018b, intel 2018b), etc. For the remainder of this example, we will use the available ``WRF-4.0.2-foss-2018b-dmpar.eb`` easyconfig file to specify to EasyBuild to build and install -WRF v4.0.2 using version 2018b of the ``foss`` toolchain. +WRF v4.0.2 using version 2018b of the ``foss`` toolchain, which is one of the :ref:`common_toolchains`. See :ref:`toolchains_table` for a list of available toolchains. The ``foss`` toolchain stands for ``GCC, OpenMPI, OpenBLAS/LAPACK, ScaLAPACK, and FFTW``. The ``foss`` toolchain From 4a906efdfefcd9c2c9b4a7db97307517ed5c3b8b Mon Sep 17 00:00:00 2001 From: Bennet Fauber Date: Tue, 25 Feb 2020 15:06:53 -0500 Subject: [PATCH 003/286] Further corrections for PR #604 --- docs/Typical_workflow_example_with_WRF.rst | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/docs/Typical_workflow_example_with_WRF.rst b/docs/Typical_workflow_example_with_WRF.rst index 6fd5e849..50faa71e 100644 --- a/docs/Typical_workflow_example_with_WRF.rst +++ b/docs/Typical_workflow_example_with_WRF.rst @@ -38,16 +38,15 @@ for example, to get a list of available easyconfig files for WRF:: -Various easyconfig files are found: for different versions of WRF (e.g., v4.0.1 and v4.4.0.2), +Various easyconfig files are found: for different versions of WRF (e.g., v4.0.1 and v4.0.2), for different (versions of) compiler toolchains (e.g., foss 2018b, intel 2018b), etc. -For the remainder of this example, we will use the available ``WRF-4.0.2-foss-2018b-dmpar.eb`` -easyconfig file to specify to EasyBuild to build and install -WRF v4.0.2 using version 2018b of the ``foss`` toolchain, which is one of the :ref:`common_toolchains`. - -See :ref:`toolchains_table` for a list of available toolchains. The ``foss`` toolchain -stands for ``GCC, OpenMPI, OpenBLAS/LAPACK, ScaLAPACK, and FFTW``. The ``foss`` toolchain -is one of the :ref:`common_toolchains`. +For the remainder of this example, we will use the available +``WRF-4.0.2-foss-2018b-dmpar.eb`` easyconfig file to specify to EasyBuild +to build and install WRF v4.0.2 using version 2018b of the ``foss`` +toolchain, which is one of the :ref:`common_toolchains`. The ``foss`` +toolchain stands for ``GCC, OpenMPI, OpenBLAS/LAPACK, ScaLAPACK, and FFTW``. +See :ref:`toolchains_table` for a list of all available toolchains. Getting an overview of planned installations -------------------------------------------- From f1aa171d7321ad4b19d1bdf26b30b1df4b104753 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 11 Mar 2020 16:52:33 +0800 Subject: [PATCH 004/286] clarify usage of git_config --- docs/Writing_easyconfig_files.rst | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index f2c4dbd7..edd0aff4 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -408,28 +408,28 @@ If a recursive checkout should be made of the repository, the ``recursive`` key Examples: * creating a source tarball named ``example-master.tar.gz`` of the ``master`` branch of a (fictional) - ``test`` repository from ``https://github.com/example``: + ``test`` repository from ``https://agitserver.org/example``: .. code:: sources = [{ 'filename': 'example-master.tar.gz', 'git_config': { - 'url': 'https://github.com/example', + 'url': 'https://agitserver.org/example', 'repo_name': 'test', 'tag': 'master', }, }] * creating a source tarball named ``example-20180920.tar.gz`` of the recursive checkout of commit ``abcdef12`` - of the ``test`` repository from ``https://github.com/example``: + of the ``test`` repository from ``https://agitserver.org/example``: .. code:: sources = [{ 'filename': 'example-20180920.tar.gz', 'git_config': { - 'url': 'https://github.com/example', + 'url': 'https://agitserver.org/example', 'repo_name': 'test', 'commit': 'abcdef12', 'recursive': True, @@ -440,8 +440,9 @@ Examples: .. note:: Because the source tarball is created locally (by running ``tar cfvz`` on the directory containing the cloned repository), the (SHA256) checksum is not guaranteed to be the same across different systems. - Whenever you have the option to download a source tarball (or equivalent) directly (for example from GitHub), - we strongly recommend you to do so. + Whenever you have the option to download a source tarball (or equivalent) directly (for example from GitHub, + which also allows downloading a tarball of a specific commit), we strongly recommend you to do so, + ``git_config`` is intended for other Git repos. .. _dependency_specs: From cb4c6f831c7f03bff09a0f91eced00f473c50822 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 11 Mar 2020 18:32:10 +0800 Subject: [PATCH 005/286] add documentation for --include-easyblocks-from-pr --- docs/Integration_with_GitHub.rst | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/docs/Integration_with_GitHub.rst b/docs/Integration_with_GitHub.rst index 81eb29af..5b92410e 100644 --- a/docs/Integration_with_GitHub.rst +++ b/docs/Integration_with_GitHub.rst @@ -353,6 +353,37 @@ in that same pull request for netCDF, WRF, ...:: Again, note that locally available easyconfigs that are required to resolve dependencies are being picked up as needed. +.. _github_include_easyblocks_from_pr: + +Using easyblocks from pull requests (``--include-easyblocks-from-pr``) +---------------------------------------------------- + +*(supported since EasyBuild v4.2.0)* + +Via the ``--include-easyblocks-from-pr`` command line option (available since EasyBuild v4.2.0), easyblocks that are added or +modified by a particular pull request to the `easybuild-easyblocks GitHub repository +`_ can be used (regardless of whether the pull request is merged +or not). + +This can be useful to employ easyblocks that are not available yet in the active EasyBuild installation, +or to test new contributions by combining ``--include-easyblocks-from-pr`` with ``--from-pr`` and ``--upload-test-report`` +(see :ref:`github_upload_test_report`). + +When ``--include-easyblocks-from-pr`` is used, EasyBuild will download all modified easyblocks to a temporary +directory before processing them. + +For example, to use the LAMMPS easyblock contributed via `easyblocks pull request #1964 +`_ together with the LAMMPS v7Aug2019 easyconfigs contributed via +`easyconfigs pull request #9884 `_:: + + $ eb --from-pr 9884 --include-easyblocks 1964 --list-easyblocks=detailed + == temporary log file in case of crash /tmp/eb-Eq2zsJ/easybuild-1AaWf8.log + EasyBlock (easybuild.framework.easyblock) + ... + | | |-- EB_LAMMPS (easybuild.easyblocks.lammps @ /tmp/included-easyblocks-rD2HEQ/easybuild/easyblocks/lammps.py) + ... + + .. _github_upload_test_report: Uploading test reports (``--upload-test-report``) From 91fd9b1c2c5b150b606211a54357aab97f677b51 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 12 Mar 2020 10:31:32 +0800 Subject: [PATCH 006/286] update documentation for --include-easyblocks-from-pr --- docs/Including_additional_Python_modules.rst | 3 +++ docs/Integration_with_GitHub.rst | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/Including_additional_Python_modules.rst b/docs/Including_additional_Python_modules.rst index 67f172e7..4dd6d328 100644 --- a/docs/Including_additional_Python_modules.rst +++ b/docs/Including_additional_Python_modules.rst @@ -85,6 +85,9 @@ Generic easyblocks are expected to be located in a directory named ``generic``. To verify that the easyblocks you included are indeed being picked up, ``--list-easyblocks=detailed`` can be used (see also :ref:`list_easyblocks`). +Since EasyBuild 4.2.0, easyblocks from a PR can also be included with ``--include-easyblocks-from-pr``, +see :ref:`github_include_easyblocks_from_pr` + Example ~~~~~~~ diff --git a/docs/Integration_with_GitHub.rst b/docs/Integration_with_GitHub.rst index 5b92410e..e2e40e38 100644 --- a/docs/Integration_with_GitHub.rst +++ b/docs/Integration_with_GitHub.rst @@ -376,7 +376,7 @@ For example, to use the LAMMPS easyblock contributed via `easyblocks pull reques `_ together with the LAMMPS v7Aug2019 easyconfigs contributed via `easyconfigs pull request #9884 `_:: - $ eb --from-pr 9884 --include-easyblocks 1964 --list-easyblocks=detailed + $ eb --from-pr 9884 --include-easyblocks--from-pr 1964 --list-easyblocks=detailed == temporary log file in case of crash /tmp/eb-Eq2zsJ/easybuild-1AaWf8.log EasyBlock (easybuild.framework.easyblock) ... From 78c7db2f4bea09b8580be84757cf77863ed59acc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Mar 2020 12:00:21 +0100 Subject: [PATCH 007/286] release EasyBuild v4.1.2 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 30 ++++++++++++++++++++++++++++++ docs/conf.py | 4 ++-- setup.py | 18 +++++++++++++++--- 4 files changed, 48 insertions(+), 5 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 50e67e0c..967c3f0a 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20200316.01** (`Mar 16th 2020`): update release notes for EasyBuild v4.1.2 (see :ref:`release_notes_eb412`) * **release 20200116.01** (`Jan 16th 2020`): update release notes for EasyBuild v4.1.1 (see :ref:`release_notes_eb411`) * **release 20191204.01** (`Dec 4th 2019`): update release notes for EasyBuild v4.1.0 (see :ref:`release_notes_eb410`) * **release 20191015.01** (`Oct 15th 2019`): update release notes for EasyBuild v4.0.1 (see :ref:`release_notes_eb401`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 425d5776..bd584692 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -9,6 +9,36 @@ alongside 8,964 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb412: + +EasyBuild v4.1.2 (March 16th 2020) +---------------------------------- + +bugfix release + +.. note:: + + This release includes a bug fix for the leaking of your GitHub token in the EasyBuild (debug) log file. + + **We strongly encourage that you revoke the GitHub tokens you are using currently, via** https://github.com/settings/tokens, + **and to replace them using a new token (using** ``eb --install-github-token --force`` **).** + + More information in https://github.com/easybuilders/easybuild-framework/pull/3248 . + +**framework** + +* fix gitdb dependency on Python 2.6 in test configuration (`#3212 `_) +* fix broken test for --review-pr by using different PR to test with (`#3226 `_) +* censor authorization part of headers before logging ReST API request (`#3248 `_) + +**easyblocks** + +*(no changes)* + +**easyconfigs** + +*(no changes)* + .. _release_notes_eb411: EasyBuild v4.1.1 (January 16th 2020) diff --git a/docs/conf.py b/docs/conf.py index ff66c81c..1ed64c26 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.1.1' # this is meant to reference the version of EasyBuild +version = '4.1.2' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20200116.0' # this is meant to reference the version of the documentation itself +release = '20200316.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: diff --git a/setup.py b/setup.py index 8fa7e12e..92eb5c04 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.1.1' +VERSION = '4.1.2' # Utility function to read README file @@ -79,7 +79,19 @@ def read(fname): ], platforms="Linux", # for distutils - requires=['easybuild_%s(==%s)' % (x, VERSION) for x in ['framework', 'easyblocks', 'easyconfigs']], + requires=[ + 'easybuild_framework(==%s)' % VERSION, + # there is no 4.1.2 release for easyblocks/easyconfigs, + # only for framework (which includes an important security-related bug fix) + 'easybuild_easyblocks(==4.1.1)', + 'easybuild_easyconfigs(==4.1.1)', + ], # for setuptools/pip - install_requires=['easybuild-%s == %s' % (x, VERSION) for x in ['framework', 'easyblocks', 'easyconfigs']], + install_requires=[ + 'easybuild-framework == %s' % VERSION, + # there is no 4.1.2 release for easyblocks/easyconfigs, + # only for framework (which includes an important security-related bug fix) + 'easybuild-easyblocks == 4.1.1', + 'easybuild-easyconfigs == 4.1.1' + ], ) From d324614311ff3aa211713a82ed0fbf0654bef831 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Apr 2020 17:49:17 +0200 Subject: [PATCH 008/286] minor clarification to section on --include-easyblocks-from-pr --- docs/Including_additional_Python_modules.rst | 4 ++-- docs/Integration_with_GitHub.rst | 5 +++-- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/docs/Including_additional_Python_modules.rst b/docs/Including_additional_Python_modules.rst index 4dd6d328..7deedb46 100644 --- a/docs/Including_additional_Python_modules.rst +++ b/docs/Including_additional_Python_modules.rst @@ -85,8 +85,8 @@ Generic easyblocks are expected to be located in a directory named ``generic``. To verify that the easyblocks you included are indeed being picked up, ``--list-easyblocks=detailed`` can be used (see also :ref:`list_easyblocks`). -Since EasyBuild 4.2.0, easyblocks from a PR can also be included with ``--include-easyblocks-from-pr``, -see :ref:`github_include_easyblocks_from_pr` +Since EasyBuild 4.2.0, easyblocks from a pull request on GitHub can also be included, +using ``--include-easyblocks-from-pr`` (see :ref:`github_include_easyblocks_from_pr`). Example ~~~~~~~ diff --git a/docs/Integration_with_GitHub.rst b/docs/Integration_with_GitHub.rst index e2e40e38..d9c7770c 100644 --- a/docs/Integration_with_GitHub.rst +++ b/docs/Integration_with_GitHub.rst @@ -360,7 +360,7 @@ Using easyblocks from pull requests (``--include-easyblocks-from-pr``) *(supported since EasyBuild v4.2.0)* -Via the ``--include-easyblocks-from-pr`` command line option (available since EasyBuild v4.2.0), easyblocks that are added or +Via the ``--include-easyblocks-from-pr`` command line option, easyblocks that are added or modified by a particular pull request to the `easybuild-easyblocks GitHub repository `_ can be used (regardless of whether the pull request is merged or not). @@ -370,7 +370,8 @@ or to test new contributions by combining ``--include-easyblocks-from-pr`` with (see :ref:`github_upload_test_report`). When ``--include-easyblocks-from-pr`` is used, EasyBuild will download all modified easyblocks to a temporary -directory before processing them. +directory before processing them. Just like with ``--include-easyblocks`` (see :ref:`include_easyblocks`), +the easyblocks that are included are preferred over the ones included in the EasyBuild installation. For example, to use the LAMMPS easyblock contributed via `easyblocks pull request #1964 `_ together with the LAMMPS v7Aug2019 easyconfigs contributed via From 63353ef3929adc363c42716c4d9e412db739afb2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 12 Apr 2020 19:17:25 +0200 Subject: [PATCH 009/286] Add documentation for build locks --- docs/Build_locks.rst | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 docs/Build_locks.rst diff --git a/docs/Build_locks.rst b/docs/Build_locks.rst new file mode 100644 index 00000000..b7c500a5 --- /dev/null +++ b/docs/Build_locks.rst @@ -0,0 +1,37 @@ +.. _locks: + +Build locks +=========== + +Easybuild creates a lock during installation to avoid collision errors from multiple installations running in parallel. The lock is created in the installation path. By default, any new installation including any software package of an already running build will be automatically aborted with a ``lock already exists`` error. + +.. note:: Build locks support was added with EasyBuild v4.2.0. + + +.. contents:: + :depth: 3 + :backlinks: none + +.. _lock_system: + +Lock system characteristics +--------------------------- + +Easybuild will create a lock for each new easyconfig being installed if one does not already exists, being it the main software of the installation or any of its dependencies. These locks will only be removed by Easybuild whenever the original installation ends, successfully or not. Therefore, new installations will be aborted in the following circumstances (by default): + +* another installation for the same easyconfig is in progress +* previous installation of the same easyconfig was abruptly interrupted + +If a previous installation was abruptly interrupted and locks were left in the installation path, those can be easily removed with ``rmdir``. All locks of Easybuild are empty directories stored in a folder called ``.locks`` located in the root directory of the installation path. Each lock has a unique name identifying the installation it belongs to. + + +.. _lock_options: + +Lock system options +------------------- + +The behaviour of the lock system in Easybuild can be tuned with the following options + +* ``--ignore-locks``: Ignore any existing locks for the current installation. Default: False +* ``--wait-on-lock``: Wait for the lift of any existing locks for the current installation the given amount time (seconds). If set to 0 the installation will be automatically aborted if a lock exists. Default: 0 +* ``--locks-dir``: Path to the directory holding the installation locks. Default: ``.locks`` in installation path From b19cd85543dd49a31c5cd078c3160042a987915a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 12 Apr 2020 19:23:02 +0200 Subject: [PATCH 010/286] add build locks to the index --- docs/index.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/index.rst b/docs/index.rst index 8ef66668..7234432f 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -59,6 +59,7 @@ Advanced usage topics Archived-easyconfigs Backup_modules + Build_locks Containers Contributing Controlling_compiler_optimization_flags From 74e6873e1c665c5af9543e430ceb4e5cda1640d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Apr 2020 12:05:15 +0200 Subject: [PATCH 011/286] tweak documentation for installation locks --- docs/Build_locks.rst | 37 ---------------- docs/Locks.rst | 102 +++++++++++++++++++++++++++++++++++++++++++ docs/index.rst | 3 +- 3 files changed, 103 insertions(+), 39 deletions(-) delete mode 100644 docs/Build_locks.rst create mode 100644 docs/Locks.rst diff --git a/docs/Build_locks.rst b/docs/Build_locks.rst deleted file mode 100644 index b7c500a5..00000000 --- a/docs/Build_locks.rst +++ /dev/null @@ -1,37 +0,0 @@ -.. _locks: - -Build locks -=========== - -Easybuild creates a lock during installation to avoid collision errors from multiple installations running in parallel. The lock is created in the installation path. By default, any new installation including any software package of an already running build will be automatically aborted with a ``lock already exists`` error. - -.. note:: Build locks support was added with EasyBuild v4.2.0. - - -.. contents:: - :depth: 3 - :backlinks: none - -.. _lock_system: - -Lock system characteristics ---------------------------- - -Easybuild will create a lock for each new easyconfig being installed if one does not already exists, being it the main software of the installation or any of its dependencies. These locks will only be removed by Easybuild whenever the original installation ends, successfully or not. Therefore, new installations will be aborted in the following circumstances (by default): - -* another installation for the same easyconfig is in progress -* previous installation of the same easyconfig was abruptly interrupted - -If a previous installation was abruptly interrupted and locks were left in the installation path, those can be easily removed with ``rmdir``. All locks of Easybuild are empty directories stored in a folder called ``.locks`` located in the root directory of the installation path. Each lock has a unique name identifying the installation it belongs to. - - -.. _lock_options: - -Lock system options -------------------- - -The behaviour of the lock system in Easybuild can be tuned with the following options - -* ``--ignore-locks``: Ignore any existing locks for the current installation. Default: False -* ``--wait-on-lock``: Wait for the lift of any existing locks for the current installation the given amount time (seconds). If set to 0 the installation will be automatically aborted if a lock exists. Default: 0 -* ``--locks-dir``: Path to the directory holding the installation locks. Default: ``.locks`` in installation path diff --git a/docs/Locks.rst b/docs/Locks.rst new file mode 100644 index 00000000..f2a92f35 --- /dev/null +++ b/docs/Locks.rst @@ -0,0 +1,102 @@ +.. _locks: + +Locks to prevent duplicate installations running at the same time +================================================================= + +Easybuild creates a lock before starting the installation of an easyconfig file, +to avoid a collision between multiple installations running at the same time. + +If an EasyBuild session tries to install an easyconfig file when a lock for that installation already exists, +it will be automatically aborted with an error like "``Lock ... already exists, aborting!``". + +.. note:: Locking of installations was implemented in EasyBuild version 4.2.0 . + + +.. contents:: + :depth: 3 + :backlinks: none + +.. _locks_implementation: + +Locking implementation details +------------------------------ + +Easybuild will create a lock when starting an installation if no corresponding lock exists yet, +regardless of whether the installation was requested explicitly or is performed to resolve a dependency. + +The name of the lock corresponds to the *full* path of the installation directory, with slashes (``/``) and +dashes (``-``) replaced by underscores (``_``), and with an additional ``.lock`` added at the end. + +Locks are created in the :ref:`locks_dir`. + +The lock created by EasyBuild is an empty directory (rather than a file), +because that can be created more atomically on modern filesystems. + +For example, if ``OpenFOAM-7-foss-2019b.eb`` is being installed to ``/apps/easybuild/software``, +an empty directory that serves as a lock for this installation will be created at +``/apps/easybuild/software/.locks/_apps_easybuild_software_OpenFOAM_7_foss_2019b.lock`` +(assuming the default :ref:`locks_dir` is used). + +A lock is automatically removed by Easybuild when the installation ends, regardless of whether the installation +was successful or not. Therefore, new installations of the same easyconfig will be aborted in case of: + +* another installation for the same easyconfig is in progress; +* a previous installation of the same easyconfig was abruptly interrupted; + + +.. _locks_removing: + +Removing locks +-------------- + +If a previous installation was abruptly interrupted and a lock was left in place, +it can be easily removed using the ``rmdir`` command (since the lock is actually an empty directory). + + +.. _locks_configuration_options: + +Configuration options related to installation locks +--------------------------------------------------- + +The behaviour of the locking mechanism in Easybuild can be tuned with the following configuration options: + +.. _locks_ignore: + +Ignoring locks (``--ignore-locks``) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Using the ``--ignore-locks`` configuration option, you can instruct EasyBuild to ignore any existing locks. +Locks that exist are left untouched, even if the installation completes successfully. + +**Use this with caution, since installations may be (partially) overwritten if another EasyBuild session is also +performing those installations!** + + +.. _locks_wait: + +Waiting for locks to be removed (``--wait-on-lock``) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Using the ``--wait-on-lock`` configuration option, you can change how EasyBuild deals with existing locks, +by specifying how frequently EasyBuild should check whether an existing lock was removed. By specifying a non-zero value ``S``, +you can indicate how many seconds EasyBuild should wait before checking again whether the lock is still in place. + +.. note:: EasyBuild will wait indefinitely for an existing lock to be removed if ``--wait-on-lock`` is set to a non-zero value... + + If the lock is never removed, the EasyBuild session will never terminate; it will keep checking every ``S`` seconds whether the lock is still in place. + +By default, EasyBuild will *abort* the installation with an error like "``Lock ... already exists, aborting!``" +if a corresponding lock already exists, which is equivalent to setting ``--wait-on-lock`` to zero (``0``), +implying that no waiting should be done at all. + + +.. _locks_dir: + +Locks directory +--------------- + +If desired, an alternate location where locks should be created and checked for can be specified via the ``--locks-dir`` configuration option. + +.. note:: Keep in mind that a path on a *shared* filesystem should be used, to ensure that active EasyBuild sessions running on different systems use the same locks directory. + +By default, locks are created in a hidden subdirectory ``.locks`` in the top-level ``software`` installation directory; that is, the ``software`` subdirectory of the ``installpath`` configuration setting of the active EasyBuild session. diff --git a/docs/index.rst b/docs/index.rst index 7234432f..2c481a5d 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -4,7 +4,6 @@ .. EasyBuild documentation master file EasyBuild documentation -======================= Welcome to the documentation of `EasyBuild `_, a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. @@ -59,7 +58,6 @@ Advanced usage topics Archived-easyconfigs Backup_modules - Build_locks Containers Contributing Controlling_compiler_optimization_flags @@ -72,6 +70,7 @@ Advanced usage topics Implementing-easyblocks Including_additional_Python_modules Integration_with_GitHub + Locks Manipulating_dependencies Packaging_support Partial_installations From 74b3a788e2fb801ea1132a8c6b9bba745a601cb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Apr 2020 14:24:44 +0200 Subject: [PATCH 012/286] add doc page on easyconfigs index (WIP) --- docs/Easyconfigs_index.rst | 151 +++++++++++++++++++++++++++++++++++++ docs/index.rst | 1 + 2 files changed, 152 insertions(+) create mode 100644 docs/Easyconfigs_index.rst diff --git a/docs/Easyconfigs_index.rst b/docs/Easyconfigs_index.rst new file mode 100644 index 00000000..e94c32e4 --- /dev/null +++ b/docs/Easyconfigs_index.rst @@ -0,0 +1,151 @@ +.. _easyconfigs_index: + +Using an index to speed up searching for easyconfigs +==================================================== + +EasyBuild often needs to search for :ref:`easyconfig_files` (or accompanying files like patches), +either based on command line arguments (like the name of an easyconfig file) +or options to the ``eb`` command (like ``--search``, see :ref:`searching_for_easyconfigs`), +or to resolve dependencies for an particular easyconfig file that was parsed already. + +Searching for easyconfig files or patches make take a while, since it may involve weeding through +thousands of files, which may be located on a shared filesystem (where metadata-intensive operations like +file searching can be rather slow). + +If EasyBuild turns out to be rather sluggish when searching for easyconfig files in your setup, +using an *index* file could make a big difference. + +.. note:: Support for index files was implemented in EasyBuild version 4.2.0 . + + +.. contents:: + :depth: 3 + :backlinks: none + + +.. _easyconfigs_index_create: + +Creating an index (``--create-index``) +-------------------------------------- + +``eb --create-index`` can be used to create an index file for a particular directory +that holds a (large) set of easyconfig files. + +The index file (a hidden file named '``.eb-path-index``') will be created in the specified directory, +and will contain a list of (relative) paths of all files in that directory, +along with some metadata: the time at which the index file has created, +and a timestamp that indicates how long the index is considered to be valid (see :ref:`easyconfigs_index_max_age`). + +.. note:: + Make sure to create an index for the correct path. + + When searching for easyconfig files, EasyBuild will *not* recurse into subdirectories of the locations + it considers (see :ref:`robot_search_path`), other than the ones it considers based on the name of the + software for which it is trying to find an easyconfig file (like ``t/TensorFlow/`` when searching for an + easyconfig file for ``TensorFlow``). + + Hence, if the directory where your easyconfig files are housed in has an ``easybuild/easyconfigs`` subdirectory + (for example, a working copy of the ``easybuild-easyconfigs`` repository), create the index *in* that + subdirectory, rather than in the higher-level directory. + + +.. _easyconfigs_index_create_example: + +Example of creating an index +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code:: + + $ eb --create-index $HOME/easybuild-easyconfigs/easybuild/easyconfigs + == temporary log file in case of crash /tmp/eb-tUu6_w/easybuild-SKBnVO.log + Creating index for /home/example/easybuild-easyconfigs/easybuild/easyconfigs... + == found valid index for /home/example/easybuild-easyconfigs/easybuild/easyconfigs, so using it... + Index created at /home/example/easybuild-easyconfigs/easybuild/easyconfigs/.eb-path-index (738 files) + + $ head -n 5 $HOME/easybuild-easyconfigs/easybuild/easyconfigs/.eb-path-index + # created at: 2020-04-13 14:19:57.008981 + # valid until: 2020-04-20 14:19:57.008981 + a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb + b/Boost/Boost-1.71.0-gompi-2019b.eb + b/bokeh/bokeh-1.4.0-foss-2019b-Python-3.7.4.eb + + +.. note:: + The "``found valid index ...``" message being printed occurs because EasyBuild tries to load the index file + right after creating it, as a sanity check. + + +.. _easyconfigs_index_update: + +Updating an existing index (``--create-index --force``) +------------------------------------------------------- + +To update an existing index, you can use ``--create-index --force``. + +Without using ``--force``, EasyBuild will refuse to overwrite the existing index file:: + + $ eb --create-index $HOME/easybuild-easyconfigs/easybuild/easyconfigs + == temporary log file in case of crash /tmp/eb-tUu6_w/easybuild-SKBnVO.log + Creating index for /home/example/easybuild-easyconfigs/easybuild/easyconfigs... + ERROR: File exists, not overwriting it without --force: /home/example/easybuild-easyconfigs/easybuild/easyconfigs/.eb-path-index + + +.. _easyconfigs_index_use: + +Using index files +----------------- + +EasyBuild will automatically pick up & use an index file if it runs into it when searching for +easyconfig files or patches, rather than walking the directory to check whether the file it's looking for +is available in that directory, which is likely to significantly speed up the search operation. + +When a (valid) index file is found for a particular path, a message will be printed mentioning "``found valid index +for...``":: + + $ eb --search TensorFlow-2.1.0-foss-2019b + == found valid index for /home/example/easybuild-easyconfigs/easybuild/easyconfigs, so using it... + * /home/example/easybuild-easyconfigs/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0-foss-2019b-Python-3.7.4.eb + + +.. _easyconfigs_index_ignore: + +Ignoring indices (``--ignore-index``) +------------------------------------- + +One potential issue with having an index in place is that it may get outdated: +new files may have been added to the directory since the index was created or last updated. + +To deal with this, you can instruct EasyBuild to ignore any existing indices using the ``--ignore-index`` +configuration option. + +The only downside of this is that searching for easyconfig files may be significantly slower. +Any existing index files are left untouched (they will *not* be updated or removed). + + +.. _easyconfigs_index_max_age: + +Controlling how long the index is valid (``--index-max-age``) +------------------------------------------------------------- + +When creating an index file, you can specify how long the index should be considered valid. + +Using the ``--index-max-age`` configuration option, you can specify how longer after the creating time +the index remains valid (in seconds). + +By default, EasyBuild will consider index files to remain valid for 1 week (7 * 24 * 60 * 60 = 604,800 seconds). + +To create an index that *always* remains (never expires), use zero (``0``) as value for ``--index-max-age``:: + + $ eb --create-index --index-max-age=0 $HOME/easybuild-easyconfigs/easybuild/easyconfigs + + $ head -n 2 $HOME/easybuild-easyconfigs/easybuild/easyconfigs/.eb-path-index + # created at: 2020-04-13 15:10:07.173191 + # valid until: 9999-12-31 23:59:59.999999 + +.. note:: Trust us here, December 31st 9999 is the end of times. Better get prepared. + + +.. _easyconfigs_index_release: + +Index included with EasyBuild releases +-------------------------------------- diff --git a/docs/index.rst b/docs/index.rst index 2c481a5d..50f51df0 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -64,6 +64,7 @@ Advanced usage topics Cray-support Detecting_loaded_modules Easyconfig-files-local-variables + Easyconfigs_index Experimental_features Extended_dry_run Hooks From 3401c9407844ee45de0d9cc06f507b1380f0a043 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Apr 2020 18:07:23 +0200 Subject: [PATCH 013/286] add script to create source tarballs for EasyBuild releases --- scripts/create_source_tarball.sh | 210 +++++++++++++++++++++++++++++++ 1 file changed, 210 insertions(+) create mode 100755 scripts/create_source_tarball.sh diff --git a/scripts/create_source_tarball.sh b/scripts/create_source_tarball.sh new file mode 100755 index 00000000..35491a15 --- /dev/null +++ b/scripts/create_source_tarball.sh @@ -0,0 +1,210 @@ +#!/bin/bash + +# -u: consider use of undefined variables as an error +set -u + +# ================================================================================================= + +function error() { + # error message in red + echo -e "\033[31mERROR: $1\033[0m" >&2 + exit 1 +} + +function ok() { + # OK in green + echo -e "\033[32mOK\033[0m" +} + +function success() { + # success message in green + echo -e "\033[32mSUCCESS!\033[0m" +} + +# ================================================================================================= + +if [ $# -ne 2 ]; then + error "Usage $0 " +fi +repo=$1 +version=$2 + +echo ">> (start: `date`)" +echo ">> creating source tarball for $repo $version..." + +# ================================================================================================= + +# create temporary directory +tmpdir=`mktemp -d` + +# we need to create an index file when composing the source tarball for easybuild-easyconfigs, +# which requires running 'eb --create-index' +if [[ "$repo" == "easybuild-easyconfigs" ]]; then + + # 'eb' command must be available, and it must support '--create-index' + echo -n ">> checking whether 'eb' command is available ... " + which eb > /dev/null + if [ $? -eq 0 ]; then + ok + else + error "'eb' command not found!" + fi + + echo -n ">> checking whether 'eb --create-index' is supported ... " + eb --help | grep create-index &> /dev/null + if [ $? -eq 0 ]; then + ok + else + error "'eb --create-index' not supported!" + fi + +fi + +# check whether this script is being run from the expected directory +cwd=`pwd` +echo -n ">> current working directory: $cwd ... " + +if [[ "`basename $cwd`" == "$repo" ]]; then + ok +else + echo + error "Expected to be in $repo directory, found myself in $cwd" +fi + +# make sure source tarball doesn't already exist in dist/ subdirectory +sdist_tar_gz=dist/${repo}-${version}.tar.gz +echo -n ">> making sure $sdist_tar_gz doesn't exist yet ... " +if [ -f $sdist_tar_gz ]; then + error "Found $sdist_tar_gz, which will be blindly overwritten by this script, please (re)move first!" +else + ok +fi + +# check that the working directory is clean +out=$tmpdir/git_status.out +echo -n ">> checking for clean working directory... " +git status &> $out +grep "nothing to commit, working tree clean" $tmpdir/git_status.out > /dev/null +if [[ $? -eq 0 ]]; then + ok +else + error "Working directory not clean: `cat $out`" +fi + +if [[ "$repo" == "easybuild-easyconfigs" ]]; then + + # create index file + create_index_cmd="eb --create-index easybuild/easyconfigs --force" + out=$tmpdir/eb_create_index.out + echo -n ">> creating index file with '$create_index_cmd'... " + eval $create_index_cmd > $out + if [ $? -eq 0 ]; then + ok + else + error "Creating index file failed, output in $out" + fi + + expected_index_file=easybuild/easyconfigs/.eb-path-index + echo -n ">> checking for $expected_index_file ... " + if [ -f $expected_index_file ]; then + ok + else + error "Expected to find index file $expected_index_file, not found! (output: $out)" + fi + +fi + +# create source tarball +sdist_cmd="python setup.py sdist" +out=$tmpdir/sdist.out +echo -n ">> running '$sdist_cmd'... " +eval $sdist_cmd &> $out +if [ $? -eq 0 ]; then + ok + echo ">> output of '$sdist_cmd' in $out" +else + error "Creating source tarball failed, output in $out" +fi + +echo -n ">> checking for $sdist_tar_gz ... " +if [ -f $sdist_tar_gz ]; then + ok +else + error "Expected file $sdist_tar_gz not found!" +fi + +# sanity checks on source tarball +cd $tmpdir; tar xfz $cwd/$sdist_tar_gz; cd - > /dev/null +unpacked_sdist=$tmpdir/${repo}-${version} +echo -n ">> checking for unpacked source tarball at $unpacked_sdist ... " +if [ -d $unpacked_sdist ]; then + ok +else + error "Expected unpacked source tarball at $unpacked_sdist, not found!" +fi + +if [[ "$repo" == "easybuild-easyconfigs" ]]; then + + index_in_sdist=$unpacked_sdist/easybuild/easyconfigs/.eb-path-index + echo -n ">> checking for $index_in_sdist ... " + if [ -f $index_in_sdist ]; then + ok + else + error "Expected to found index file in unpacked source tarball at $index_in_sdist, not found!" + fi + + # make sure all files are included in index + # (this take a couple of minutes, since we're running 'grep' thousands of times...) + file_list=$tmpdir/files.txt + echo -n ">> checking whether all files are included in index ... " + cd $cwd/easybuild/easyconfigs + find . -type f | sed 's@^\./@@g' | grep -v '^\.eb-path-index$' > $file_list + cd - > /dev/null + file_cnt=`cat $file_list | wc -l | sed 's/ //g'` + idx=1 + for file in `cat $file_list`; do + echo -e -n "\r>> checking whether all files are included in index ... $idx/$file_cnt" + grep $file $index_in_sdist > /dev/null + if [ $? -ne 0 ]; then + error "File $file not listed in index $index_in_sdist!" + fi + idx=$(($idx + 1)) + done + echo -e -n "\r>> checking whether all files are included in index ... $idx/$file_cnt " + ok + + # make sure all files listed in index actually exist in unpacked source tarball + echo -n ">> checking whether all files in index actually exist in unpacked source tarball ... " + file_cnt=`cat $index_in_sdist | grep -v '^#' | wc -l | sed 's/ //g'` + idx=1 + for file in `cat $index_in_sdist | grep -v '^#'`; do + echo -e -n "\r>> checking whether all files in index actually exist in unpacked source tarball ... $idx/$file_cnt" + if [ ! -f $unpacked_sdist/easybuild/easyconfigs/$file ]; then + error "File $file listed in index, but not found in $cwd!" + fi + idx=$(($idx + 1)) + done + echo -e -n "\r>> checking whether all files in index actually exist in unpacked source tarball ... $idx/$file_cnt " + ok + + # cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/10325 + echo -n ">> checking for CVS easyconfigs in source tarball... " + CVS_easyconfigs=`ls $unpacked_sdist/easybuild/easyconfigs/c/CVS/*.eb 2> /dev/null` + if [ -z "$CVS_easyconfigs" ]; then + error "No CVS easyconfigs found in source tarball!" + else + ok + fi + +fi + +# all done checking, if no checks failed up until now, we're done! +echo +success +echo "Source tarball for $repo $version is ready for publishing with:" +echo " twine upload $sdist_tar_gz" +echo +echo ">> (end: `date`)" + +# cleanup +rm -rf $tmpdir From 27b35aa7aedccb2f0beeb9b4ba68da65c37b7499 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Apr 2020 18:30:25 +0200 Subject: [PATCH 014/286] fix typos & process suggestions made by @lexming --- docs/Easyconfigs_index.rst | 33 +++++++++++++++++---------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/docs/Easyconfigs_index.rst b/docs/Easyconfigs_index.rst index e94c32e4..54adf71d 100644 --- a/docs/Easyconfigs_index.rst +++ b/docs/Easyconfigs_index.rst @@ -6,13 +6,13 @@ Using an index to speed up searching for easyconfigs EasyBuild often needs to search for :ref:`easyconfig_files` (or accompanying files like patches), either based on command line arguments (like the name of an easyconfig file) or options to the ``eb`` command (like ``--search``, see :ref:`searching_for_easyconfigs`), -or to resolve dependencies for an particular easyconfig file that was parsed already. +or to resolve dependencies for a particular easyconfig file that was parsed already. -Searching for easyconfig files or patches make take a while, since it may involve weeding through +Searching for easyconfig files or patches may take a while, since it can potentially involve weeding through thousands of files, which may be located on a shared filesystem (where metadata-intensive operations like file searching can be rather slow). -If EasyBuild turns out to be rather sluggish when searching for easyconfig files in your setup, +If EasyBuild turns out to be sluggish when searching for easyconfig files in your setup, using an *index* file could make a big difference. .. note:: Support for index files was implemented in EasyBuild version 4.2.0 . @@ -31,20 +31,20 @@ Creating an index (``--create-index``) ``eb --create-index`` can be used to create an index file for a particular directory that holds a (large) set of easyconfig files. -The index file (a hidden file named '``.eb-path-index``') will be created in the specified directory, -and will contain a list of (relative) paths of all files in that directory, -along with some metadata: the time at which the index file has created, +The index file (a hidden file named ``.eb-path-index``) will be created in the specified directory. +It will contain a list of (relative) paths for all files in that directory, +along with some metadata: the time at which the index file has created and a timestamp that indicates how long the index is considered to be valid (see :ref:`easyconfigs_index_max_age`). .. note:: Make sure to create an index for the correct path. - When searching for easyconfig files, EasyBuild will *not* recurse into subdirectories of the locations - it considers (see :ref:`robot_search_path`), other than the ones it considers based on the name of the + The search for easyconfig files performed by EasyBuild will *not* recurse into subdirectories of the locations + it considers (see :ref:`robot_search_path`), other than those with a name matching the software for which it is trying to find an easyconfig file (like ``t/TensorFlow/`` when searching for an easyconfig file for ``TensorFlow``). - Hence, if the directory where your easyconfig files are housed in has an ``easybuild/easyconfigs`` subdirectory + Hence, if the directory housing your easyconfig files has an ``easybuild/easyconfigs`` subdirectory (for example, a working copy of the ``easybuild-easyconfigs`` repository), create the index *in* that subdirectory, rather than in the higher-level directory. @@ -95,9 +95,9 @@ Without using ``--force``, EasyBuild will refuse to overwrite the existing index Using index files ----------------- -EasyBuild will automatically pick up & use an index file if it runs into it when searching for -easyconfig files or patches, rather than walking the directory to check whether the file it's looking for -is available in that directory, which is likely to significantly speed up the search operation. +EasyBuild will automatically pick up and use any index file that it runs into while searching for +easyconfig files or patches. If an index file is found, it will be preferred over walking through +the directory tree to check for the target file, which is likely to significantly speed up the search operation. When a (valid) index file is found for a particular path, a message will be printed mentioning "``found valid index for...``":: @@ -115,10 +115,11 @@ Ignoring indices (``--ignore-index``) One potential issue with having an index in place is that it may get outdated: new files may have been added to the directory since the index was created or last updated. -To deal with this, you can instruct EasyBuild to ignore any existing indices using the ``--ignore-index`` +If updating the indexes is not an option (see :ref:`easyconfigs_index_update`), +you can instruct EasyBuild to ignore any existing indices using the ``--ignore-index`` configuration option. -The only downside of this is that searching for easyconfig files may be significantly slower. +The only downside of this option is that searching for easyconfig files may be significantly slower. Any existing index files are left untouched (they will *not* be updated or removed). @@ -129,12 +130,12 @@ Controlling how long the index is valid (``--index-max-age``) When creating an index file, you can specify how long the index should be considered valid. -Using the ``--index-max-age`` configuration option, you can specify how longer after the creating time +Using the ``--index-max-age`` configuration option, you can specify how long after the creation time the index remains valid (in seconds). By default, EasyBuild will consider index files to remain valid for 1 week (7 * 24 * 60 * 60 = 604,800 seconds). -To create an index that *always* remains (never expires), use zero (``0``) as value for ``--index-max-age``:: +To create an index that *always* remains valid (never expires), use zero (``0``) as value for ``--index-max-age``:: $ eb --create-index --index-max-age=0 $HOME/easybuild-easyconfigs/easybuild/easyconfigs From 97f5cfc95f96e49592a3b56a99ea3a622acab0d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Apr 2020 18:42:41 +0200 Subject: [PATCH 015/286] add subsections in docs page for easyconfig index on index included in EasyBuild releases + 'Should I create an index?' --- docs/Easyconfigs_index.rst | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/docs/Easyconfigs_index.rst b/docs/Easyconfigs_index.rst index 54adf71d..b203a9f0 100644 --- a/docs/Easyconfigs_index.rst +++ b/docs/Easyconfigs_index.rst @@ -150,3 +150,26 @@ To create an index that *always* remains valid (never expires), use zero (``0``) Index included with EasyBuild releases -------------------------------------- + +Each EasyBuild release (since EasyBuild v4.2.0) comes with a index file for the easyconfig (and patch) files +that are included with that release. + +Hence, you only need to use ``--create-index`` to create/update the index file for any additional directories +with easyconfig files you may have on the side (and only if searching those easyconfig files is rather slow). + + +.. _easyconfigs_index_should_use: + +Should I create an index? +------------------------- + +Whether or not you should create an index file for your directories housing additional easyconfig files depends on a number of factors, including: + +* how often files or added and/or removed in those directories, since files listed in the index are assumed to be there and any files not included in the index will be overlooked by EasyBuild when it's searching for files; + +* the filesystem on which those directories are located, since an index file will only make a significant difference on filesystems where metadata-intensive operations are relatively slow; + +* how many files there are in those directories, since performance benefits will only be apparent if the number if files is sufficiently large; + +.. note:: Keep in mind that creating an index implies also updating it frequently, + to ensure that EasyBuild will take all available files in account. From 6b59ee53ce981d1fefdfbffb023ef1794d723332 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Apr 2020 18:49:10 +0200 Subject: [PATCH 016/286] create index file with --index-max-age=0, and make sure index file is valid indefinitely --- scripts/create_source_tarball.sh | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/scripts/create_source_tarball.sh b/scripts/create_source_tarball.sh index 35491a15..9ed4a7af 100755 --- a/scripts/create_source_tarball.sh +++ b/scripts/create_source_tarball.sh @@ -94,7 +94,7 @@ fi if [[ "$repo" == "easybuild-easyconfigs" ]]; then # create index file - create_index_cmd="eb --create-index easybuild/easyconfigs --force" + create_index_cmd="eb --create-index easybuild/easyconfigs --index-max-age=0 --force" out=$tmpdir/eb_create_index.out echo -n ">> creating index file with '$create_index_cmd'... " eval $create_index_cmd > $out @@ -112,6 +112,15 @@ if [[ "$repo" == "easybuild-easyconfigs" ]]; then error "Expected to find index file $expected_index_file, not found! (output: $out)" fi + # make sure index file is valid indefinitely + echo -n ">> checking whether index file is valid indefinitely ... " + grep "^# valid until: 9999-12-31" $expected_index_file > /dev/null + if [[ $? -eq 0 ]]; then + ok + else + error "Index file $expected_index_file is not valid indefinitely!" + fi + fi # create source tarball From 9c12114ee1aa4279f44a4ee0e53f9ffaadd879b6 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Apr 2020 19:18:24 +0200 Subject: [PATCH 017/286] fix typos in doc/easyconfig_index --- docs/Easyconfigs_index.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/Easyconfigs_index.rst b/docs/Easyconfigs_index.rst index b203a9f0..333c9dd0 100644 --- a/docs/Easyconfigs_index.rst +++ b/docs/Easyconfigs_index.rst @@ -33,7 +33,7 @@ that holds a (large) set of easyconfig files. The index file (a hidden file named ``.eb-path-index``) will be created in the specified directory. It will contain a list of (relative) paths for all files in that directory, -along with some metadata: the time at which the index file has created +along with some metadata: the time at which the index file was created and a timestamp that indicates how long the index is considered to be valid (see :ref:`easyconfigs_index_max_age`). .. note:: @@ -151,7 +151,7 @@ To create an index that *always* remains valid (never expires), use zero (``0``) Index included with EasyBuild releases -------------------------------------- -Each EasyBuild release (since EasyBuild v4.2.0) comes with a index file for the easyconfig (and patch) files +Each EasyBuild release (since EasyBuild v4.2.0) comes with an index file for the easyconfig (and patch) files that are included with that release. Hence, you only need to use ``--create-index`` to create/update the index file for any additional directories @@ -165,7 +165,7 @@ Should I create an index? Whether or not you should create an index file for your directories housing additional easyconfig files depends on a number of factors, including: -* how often files or added and/or removed in those directories, since files listed in the index are assumed to be there and any files not included in the index will be overlooked by EasyBuild when it's searching for files; +* how often files are added and/or removed in those directories, since files listed in the index are assumed to be there and any files not included in the index will be overlooked by EasyBuild when it's searching for files; * the filesystem on which those directories are located, since an index file will only make a significant difference on filesystems where metadata-intensive operations are relatively slow; From 153e8da945560e5f50789029ac28c5a4ffaf7919 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Apr 2020 19:50:22 +0200 Subject: [PATCH 018/286] add test for create_source_tarball.sh script --- .github/workflows/doc_build.yml | 111 +++++++++++++++++++++++++++++++- 1 file changed, 108 insertions(+), 3 deletions(-) diff --git a/.github/workflows/doc_build.yml b/.github/workflows/doc_build.yml index 60c44888..e61d7c7d 100644 --- a/.github/workflows/doc_build.yml +++ b/.github/workflows/doc_build.yml @@ -3,10 +3,8 @@ name: Docs build and installation end-to-end tests on: [push, pull_request] jobs: - build: - + docs: runs-on: ubuntu-latest - steps: - uses: actions/checkout@v2 - name: Set up Python 3.8 @@ -39,3 +37,110 @@ jobs: # test installation too (using options that don't require to have a modules tool installed) eb --list-easyblocks | grep EB_bzip2 eb --fetch bzip2-1.0.6.eb + scripts: + runs-on: ubuntu-latest + strategy: + matrix: + repo: [easybuild-framework, easybuild-easyblocks, easybuild-easyconfigs, easybuild] + fail-fast: false + steps: + - uses: actions/checkout@v2 + - name: Set up Python 3.8 + uses: actions/setup-python@v1 + with: + python-version: 3.8 + - name: install EasyBuild (framework-only) + run: | + pip install easybuild-framework + eb --version + - name: clone repo + run: | + cd $HOME + git clone https://github.com/easybuilders/${{matrix.repo}}.git + cd ${{matrix.repo}} + git checkout master + - name: test create_source_tarball.sh script + run: | + cd $HOME/${{matrix.repo}} + + # file to figure out the version from depends on repo + if [[ ${{matrix.repo}} == "easybuild-framework" ]]; then + version_file=easybuild/tools/version.py + elif [[ ${{matrix.repo}} == "easybuild-easyblocks" ]]; then + version_file=easybuild/easyblocks/__init__.py + else + version_file=setup.py + fi + version=$(grep '^VERSION' $version_file | sed 's/[^0-9]*\([0-9a-zA-Z.]*\).*/\1/g') + echo "${{matrix.repo}} version: $version" + + echo "testing with '$GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version'" + + out=$HOME/out.txt + + echo "================================================================================================" + + # check use of script outside correct directory + cd $HOME + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true + grep "ERROR: Expected to be in ${{matrix.repo}} directory" $out + echo "Expected error found in output: OK!" + + echo "================================================================================================" + + # existing source tarball in dist should result in an error + cd ${{matrix.repo}} + mkdir -p dist + touch dist/${{matrix.repo}}-${version}.tar.gz + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true + grep "ERROR: Found dist/${{matrix.repo}}-${version}.tar.gz" $out + echo "Expected error found in output: OK!" + rm dist/${{matrix.repo}}-${version}.tar.gz + + echo "================================================================================================" + + # check for error when script is run in a dirty working copy + touch dirty.txt + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true + grep "ERROR: Working directory not clean" $out + echo "Expected error found in output: OK!" + rm dirty.txt + + echo "================================================================================================" + + # script should fail if expected source tarball did not get created in dist/ + mkdir -p /tmp/$USER/bin + echo '#!/bin/bash' > /tmp/$USER/bin/python + chmod u+x /tmp/$USER/bin/python + export PATH=/tmp/$USER/bin:$PATH + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true + grep "ERROR: Expected file dist/${{matrix.repo}}-${version}.tar.gz not found!" $out + echo "Expected error found in output: OK!" + + echo "================================================================================================" + + # script should deal well with failing 'python setup.py sdist' + echo 'exit 1' >> /tmp/$USER/bin/python + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true + grep "ERROR: Creating source tarball failed" $out + echo "Expected error found in output: OK!" + rm /tmp/$USER/bin/python + + echo "================================================================================================" + + # using of script with incorrect version should result in an error + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} 0.0.0 2>&1 | tee $out) || true + grep "ERROR: Expected file dist/${{matrix.repo}}-0.0.0.tar.gz not found!" $out + echo "Expected error found in output: OK!" + rm -f dist/${{matrix.repo}}-${version}.tar.gz MANIFEST + + echo "================================================================================================" + + # check use of script in correct way, should yield "SUCCESS" in output + $GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out + grep SUCCESS $out + # no errors in output + errors=$(grep ERROR $out || true) + if [ ! -z $errors ]; then "Errors found: $errors"; fi + + echo "Correct run of script OK!" From 1bdf0ff6034e299c533210e6256d221b7c34398c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 08:56:37 +0200 Subject: [PATCH 019/286] add check to make sure we're on master branch --- .github/workflows/doc_build.yml | 12 +++++++++--- scripts/create_source_tarball.sh | 9 +++++++++ 2 files changed, 18 insertions(+), 3 deletions(-) diff --git a/.github/workflows/doc_build.yml b/.github/workflows/doc_build.yml index e61d7c7d..4131773f 100644 --- a/.github/workflows/doc_build.yml +++ b/.github/workflows/doc_build.yml @@ -57,8 +57,6 @@ jobs: run: | cd $HOME git clone https://github.com/easybuilders/${{matrix.repo}}.git - cd ${{matrix.repo}} - git checkout master - name: test create_source_tarball.sh script run: | cd $HOME/${{matrix.repo}} @@ -88,8 +86,16 @@ jobs: echo "================================================================================================" - # existing source tarball in dist should result in an error cd ${{matrix.repo}} + + # script should make sure we're on master branch + git checkout develop + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true + grep "develop ERROR: Not on master branch!" $out + echo "Expected error found in output: OK!" + git checkout master + + # existing source tarball in dist should result in an error mkdir -p dist touch dist/${{matrix.repo}}-${version}.tar.gz ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true diff --git a/scripts/create_source_tarball.sh b/scripts/create_source_tarball.sh index 9ed4a7af..255b9a68 100755 --- a/scripts/create_source_tarball.sh +++ b/scripts/create_source_tarball.sh @@ -80,6 +80,15 @@ else ok fi +# make sure we're on the master branch +curr_branch=$(git status -b --porcelain | grep '^##' | cut -f2 -d' ' | cut -f1 -d'.') +echo -n ">> checking current Git branch ... ${curr_branch} " +if [ "$curr_branch" == "master" ]; then + ok +else + error "Not on master branch!" +fi + # check that the working directory is clean out=$tmpdir/git_status.out echo -n ">> checking for clean working directory... " From 3575e159de77db60712e1609747a066fb9d262c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 09:05:53 +0200 Subject: [PATCH 020/286] check version before creating sdist --- .github/workflows/doc_build.yml | 17 +++++++++-------- scripts/create_source_tarball.sh | 16 ++++++++++++++++ 2 files changed, 25 insertions(+), 8 deletions(-) diff --git a/.github/workflows/doc_build.yml b/.github/workflows/doc_build.yml index 4131773f..0a51a7cc 100644 --- a/.github/workflows/doc_build.yml +++ b/.github/workflows/doc_build.yml @@ -95,6 +95,15 @@ jobs: echo "Expected error found in output: OK!" git checkout master + echo "================================================================================================" + + # specified version should match with current version + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} 0.0.0 2>&1 | tee $out) || true + grep "specified version '0.0.0' ... ERROR: Found version '${version}'" $out + echo "Expected error found in output: OK!" + + echo "================================================================================================" + # existing source tarball in dist should result in an error mkdir -p dist touch dist/${{matrix.repo}}-${version}.tar.gz @@ -134,14 +143,6 @@ jobs: echo "================================================================================================" - # using of script with incorrect version should result in an error - ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} 0.0.0 2>&1 | tee $out) || true - grep "ERROR: Expected file dist/${{matrix.repo}}-0.0.0.tar.gz not found!" $out - echo "Expected error found in output: OK!" - rm -f dist/${{matrix.repo}}-${version}.tar.gz MANIFEST - - echo "================================================================================================" - # check use of script in correct way, should yield "SUCCESS" in output $GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out grep SUCCESS $out diff --git a/scripts/create_source_tarball.sh b/scripts/create_source_tarball.sh index 255b9a68..d998e2b9 100755 --- a/scripts/create_source_tarball.sh +++ b/scripts/create_source_tarball.sh @@ -100,6 +100,22 @@ else error "Working directory not clean: `cat $out`" fi +# check whether specified version matches current version +echo -n ">> checking whether current version matches specified version '$version' ... " +if [[ "$repo" == "easybuild-framework" ]]; then + curr_version_file='easybuild/tools/version.py' +elif [[ "$repo" == "easybuild-easyblocks" ]]; then + curr_version_file='easybuild/easyblocks/__init__.py' +else + curr_version_file='setup.py' +fi +curr_version=$(grep '^VERSION' $curr_version_file | sed 's/[^0-9]*\([0-9a-zA-Z.]*\).*/\1/g') +if [[ "$curr_version" == "$version" ]]; then + ok +else + error "Found version '$curr_version'" +fi + if [[ "$repo" == "easybuild-easyconfigs" ]]; then # create index file From 45de91c0715461977891644a42281a7edbb1bd41 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 09:20:55 +0200 Subject: [PATCH 021/286] fix 'master' branch test for create_source_tarball.sh script --- .github/workflows/doc_build.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/doc_build.yml b/.github/workflows/doc_build.yml index 0a51a7cc..975cbd08 100644 --- a/.github/workflows/doc_build.yml +++ b/.github/workflows/doc_build.yml @@ -89,11 +89,11 @@ jobs: cd ${{matrix.repo}} # script should make sure we're on master branch - git checkout develop + git checkout develop &> /dev/null ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true - grep "develop ERROR: Not on master branch!" $out + grep "ERROR: Not on master branch" $out echo "Expected error found in output: OK!" - git checkout master + git checkout master > /dev/null echo "================================================================================================" From c8635a58e28ddd4d8c9f6c2ae6dcee9359958f0e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 09:36:22 +0200 Subject: [PATCH 022/286] checkout master before determining version in test for create_source_tarball.sh script --- .github/workflows/doc_build.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/doc_build.yml b/.github/workflows/doc_build.yml index 975cbd08..c9c72b24 100644 --- a/.github/workflows/doc_build.yml +++ b/.github/workflows/doc_build.yml @@ -60,6 +60,7 @@ jobs: - name: test create_source_tarball.sh script run: | cd $HOME/${{matrix.repo}} + git checkout master # file to figure out the version from depends on repo if [[ ${{matrix.repo}} == "easybuild-framework" ]]; then @@ -93,7 +94,7 @@ jobs: ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true grep "ERROR: Not on master branch" $out echo "Expected error found in output: OK!" - git checkout master > /dev/null + git checkout master &> /dev/null echo "================================================================================================" From 5c2a495929eb26c931099488b2aa287aacf049fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 09:40:18 +0200 Subject: [PATCH 023/286] fix version check test for create_source_tarball.sh script --- .github/workflows/doc_build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/doc_build.yml b/.github/workflows/doc_build.yml index c9c72b24..118d5378 100644 --- a/.github/workflows/doc_build.yml +++ b/.github/workflows/doc_build.yml @@ -100,7 +100,7 @@ jobs: # specified version should match with current version ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} 0.0.0 2>&1 | tee $out) || true - grep "specified version '0.0.0' ... ERROR: Found version '${version}'" $out + grep "ERROR: Found version '${version}'" $out echo "Expected error found in output: OK!" echo "================================================================================================" From 1cc06a4e255b672cb8d293f84fa9145d79781676 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 12:20:48 +0200 Subject: [PATCH 024/286] auto-update documentation for EasyBuild v4.2.0 --- docs/version-specific/Supported_software.rst | 3881 +++++++++++++---- docs/version-specific/easyblocks.rst | 8 + .../version-specific/easyconfig_templates.rst | 2 + docs/version-specific/generic_easyblocks.rst | 27 +- docs/version-specific/help.rst | 12 +- 5 files changed, 3000 insertions(+), 930 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index af1167be..0e08fd78 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 1798 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 1912 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_ALPS_304` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_APBS_294` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_ARCH_286` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_ART_231` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_ALPS_304` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_ART_231` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -115,6 +115,39 @@ version versionsuffix toolchain ========== ======================== =============================== +.. _list_software_ABRA2_328: + +*ABRA2* ++++++++ + +Assembly Based ReAligner + +*homepage*: https://github.com/mozack/abra2 + +======== ======================= +version toolchain +======== ======================= +``2.22`` ``iccifort/2019.5.281`` +======== ======================= + + +.. _list_software_ABRicate_731: + +*ABRicate* +++++++++++ + +Mass screening of contigs for antimicrobial and virulence genes + +*homepage*: https://github.com/tseemann/abricate + +========= ================ =============== +version versionsuffix toolchain +========= ================ =============== +``0.9.9`` ``gompi/2019b`` +``0.9.9`` ``-Perl-5.28.1`` ``gompi/2019a`` +========= ================ =============== + + .. _list_software_ABySS_418: *ABySS* @@ -122,7 +155,7 @@ version versionsuffix toolchain Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler -*homepage*: http://www.bcgsc.ca/platform/bioinfo/software/abyss +*homepage*: https://www.bcgsc.ca/platform/bioinfo/software/abyss ========= ================================================================ version toolchain @@ -130,6 +163,7 @@ version toolchain ``1.9.0`` ``foss/2016a`` ``2.0.2`` ``foss/2016b``, ``foss/2018a``, ``gompi/2019a``, ``intel/2016b`` ``2.0.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.5`` ``foss/2019b`` ========= ================================================================ @@ -251,6 +285,22 @@ version toolchain ================================ =============== +.. _list_software_ADIOS_368: + +*ADIOS* ++++++++ + +The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation. + +*homepage*: https://www.olcf.ornl.gov/center-projects/adios/ + +========== ================== ============== +version versionsuffix toolchain +========== ================== ============== +``1.13.1`` ``-Python-2.7.15`` ``foss/2019a`` +========== ================== ============== + + .. _list_software_adjustText_1072: *adjustText* @@ -706,6 +756,22 @@ version toolchain =========== ========== +.. _list_software_aNCI_315: + +*aNCI* +++++++ + +Non-covalent interaction (NCI) for MD trajectories + +*homepage*: https://www.lct.jussieu.fr/pagesperso/contrera/nci-MD.html + +======= ======================= +version toolchain +======= ======================= +``2.0`` ``iccifort/2019.5.281`` +======= ======================= + + .. _list_software_angsd_525: *angsd* @@ -853,7 +919,7 @@ version versionsuffix toolchain ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. -*homepage*: http://stnava.github.io/ANTs/ +*homepage*: https://stnava.github.io/ANTs/ ========= ================== =============================== version versionsuffix toolchain @@ -861,6 +927,7 @@ version versionsuffix toolchain ``2.2.0`` ``-Python-2.7.12`` ``foss/2016b`` ``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2.3.1`` ``-Python-3.6.6`` ``foss/2018b`` +``2.3.2`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== =============================== @@ -880,6 +947,23 @@ version versionsuffix toolchain ======= ================= =============== +.. _list_software_any2fasta_905: + +*any2fasta* ++++++++++++ + +Convert various sequence formats to FASTA + +*homepage*: https://github.com/tseemann/any2fasta + +========= ================ ================= +version versionsuffix toolchain +========= ================ ================= +``0.4.2`` ``GCCcore/8.3.0`` +``0.4.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +========= ================ ================= + + .. _list_software_APBS_294: *APBS* @@ -896,6 +980,22 @@ version versionsuffix toolchain ======= ======================== ========== +.. _list_software_apex_430: + +*apex* +++++++ + +A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch + +*homepage*: https://github.com/nvidia/apex + +============ ================= ================== +version versionsuffix toolchain +============ ================= ================== +``20200325`` ``-Python-3.7.4`` ``fosscuda/2019b`` +============ ================= ================== + + .. _list_software_APR_227: *APR* @@ -977,6 +1077,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_archspec_841: + +*archspec* +++++++++++ + +A library for detecting, labeling, and reasoning about microarchitectures + +*homepage*: https://github.com/archspec/archspec + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``0.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= + + .. _list_software_ARGoS_412: *ARGoS* @@ -1002,11 +1118,11 @@ Argtable is an ANSI C library for parsing GNU style command line options with a *homepage*: http://argtable.sourceforge.net/ -======== =================================================================================== -version toolchain -======== =================================================================================== -``2.13`` ``GCCcore/8.2.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -======== =================================================================================== +======== ====================================================================================================== +version toolchain +======== ====================================================================================================== +``2.13`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +======== ====================================================================================================== .. _list_software_Armadillo_917: @@ -1062,7 +1178,7 @@ version toolchain ``3.4.0`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b``, ``intel/2017a`` ``3.5.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b`` ``3.6.2`` ``intel/2018a`` -``3.7.0`` ``foss/2019a``, ``foss/2019b`` +``3.7.0`` ``foss/2019a``, ``foss/2019b``, ``intel/2019b`` ========= ================================================================================ @@ -1114,6 +1230,7 @@ version versionsuffix toolchain ``0.7.1`` ``-Python-3.6.3`` ``intel/2017b`` ``0.12.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.12.0`` ``-Python-3.6.6`` ``intel/2018b`` +``0.16.0`` ``-Python-3.7.4`` ``intel/2019b`` ========== ================== =============================== @@ -1133,6 +1250,22 @@ version toolchain ============== ================================== +.. _list_software_ArviZ_492: + +*ArviZ* ++++++++ + +Exploratory analysis of Bayesian models with Python + +*homepage*: https://github.com/arviz-devs/arviz + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.7.0`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + .. _list_software_ARWEN_381: *ARWEN* @@ -1199,6 +1332,8 @@ version versionsuffix toolchain ``3.17.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``3.18.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.18.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ============== ================== ================================================ @@ -1315,6 +1450,7 @@ version toolchain ========== ================== ``2.26.3`` ``fosscuda/2018b`` ``2.32.0`` ``GCCcore/8.2.0`` +``2.34.1`` ``GCCcore/8.3.0`` ========== ================== @@ -1332,6 +1468,7 @@ version toolchain ========== ================== ``2.26.3`` ``fosscuda/2018b`` ``2.32.0`` ``GCCcore/8.2.0`` +``2.34.0`` ``GCCcore/8.3.0`` ========== ================== @@ -1342,7 +1479,7 @@ version toolchain ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. -*homepage*: https://developer.gnome.org/ATK/stable/ +*homepage*: https://developer.gnome.org/atk/ ========== =================================================================== version toolchain @@ -1355,6 +1492,7 @@ version toolchain ``2.27.1`` ``foss/2017b``, ``intel/2017b`` ``2.28.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a`` ``2.32.0`` ``GCCcore/8.2.0`` +``2.34.1`` ``GCCcore/8.3.0`` ========== =================================================================== @@ -1476,6 +1614,7 @@ version versionsuffix toolchain ``3.3.2`` ``-Python-2.7.13`` ``intel/2017a`` ``3.3.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``3.3.2`` ``-Python-2.7.15`` ``intel/2018b`` +``3.3.3`` ``foss/2019b`` ========= ================== =============================== @@ -1581,6 +1720,22 @@ version toolchain ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +.. _list_software_autopep8_822: + +*autopep8* +++++++++++ + +A tool that automatically formats Python code to conform to the PEP 8 style guide. + +*homepage*: https://github.com/hhatto/autopep8 + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``1.4.4`` ``-Python-3.6.4`` ``intel/2018a`` +========= ================= =============== + + .. _list_software_Autotools_970: *Autotools* @@ -1609,13 +1764,14 @@ Universal Command Line Environment for AWS *homepage*: https://pypi.python.org/pypi/awscli -============ ================== =============== -version versionsuffix toolchain -============ ================== =============== -``1.11.1`` ``-Python-2.7.12`` ``intel/2016b`` -``1.11.56`` ``-Python-2.7.12`` ``foss/2016b`` -``1.16.290`` ``-Python-3.6.6`` ``foss/2018b`` -============ ================== =============== +============ ================== ================= +version versionsuffix toolchain +============ ================== ================= +``1.11.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.11.56`` ``-Python-2.7.12`` ``foss/2016b`` +``1.16.290`` ``-Python-3.6.6`` ``foss/2018b`` +``1.17.7`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +============ ================== ================= .. _list_software_letter_b: @@ -1624,7 +1780,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_Biopython_956` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` +:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_Biopython_956` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` .. _list_software_Bader_478: @@ -1709,6 +1865,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_BAMSurgeon_947: + +*BAMSurgeon* +++++++++++++ + +Tools for adding mutations to existing .bam files, used for testing mutation callers + +*homepage*: https://github.com/adamewing/bamsurgeon + +======= ================== ============= +version versionsuffix toolchain +======= ================== ============= +``1.2`` ``-Python-2.7.16`` ``GCC/8.3.0`` +======= ================== ============= + + .. _list_software_BamTools_801: *BamTools* @@ -1718,14 +1890,14 @@ BamTools provides both a programmer's API and an end-user's toolkit for handling *homepage*: https://github.com/pezmaster31/bamtools -========= ================================================================================================================================================ -version toolchain -========= ================================================================================================================================================ -``2.4.0`` ``foss/2016b`` -``2.4.1`` ``intel/2017a`` -``2.5.0`` ``foss/2016b``, ``intel/2017b`` -``2.5.1`` ``GCC/8.2.0-2.31.1``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b`` -========= ================================================================================================================================================ +========= ======================================================================================================================================================================================== +version toolchain +========= ======================================================================================================================================================================================== +``2.4.0`` ``foss/2016b`` +``2.4.1`` ``intel/2017a`` +``2.5.0`` ``foss/2016b``, ``intel/2017b`` +``2.5.1`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017b``, ``intel/2018b`` +========= ======================================================================================================================================================================================== .. _list_software_BamUtil_686: @@ -1829,6 +2001,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_BatMeth2_727: + +*BatMeth2* +++++++++++ + +An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping. + +*homepage*: https://github.com/GuoliangLi-HZAU/BatMeth2 + +======= ============== +version toolchain +======= ============== +``2.1`` ``foss/2019b`` +======= ============== + + .. _list_software_BayesAss_795: *BayesAss* @@ -1870,11 +2058,11 @@ BayeScEnv is a Fst-based, genome-scan method that uses environmental variables t *homepage*: https://github.com/devillemereuil/bayescenv -======= ============== -version toolchain -======= ============== -``1.1`` ``foss/2016a`` -======= ============== +======= ====================================================== +version toolchain +======= ====================================================== +``1.1`` ``GCC/8.3.0``, ``foss/2016a``, ``iccifort/2019.5.281`` +======= ====================================================== .. _list_software_BayesTraits_1131: @@ -1970,6 +2158,7 @@ version versionsuffix toolchain ``37.93`` ``foss/2018a``, ``intel/2018a`` ``38.26`` ``foss/2018b`` ``38.50b`` ``GCC/8.2.0-2.31.1`` +``38.76`` ``GCC/8.2.0-2.31.1`` ========== =================== =============================== @@ -2030,13 +2219,14 @@ Samtools is a suite of programs for interacting with high-throughput sequencing *homepage*: http://www.htslib.org/ -======= ========================================================================================= -version toolchain -======= ========================================================================================= -``1.3`` ``foss/2016a``, ``intel/2016a`` -``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` -``1.9`` ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -======= ========================================================================================= +========== ========================================================================================= +version toolchain +========== ========================================================================================= +``1.3`` ``foss/2016a``, ``intel/2016a`` +``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` +``1.9`` ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` +``1.10.2`` ``GCC/8.3.0`` +========== ========================================================================================= .. _list_software_bcgTree_700: @@ -2195,9 +2385,9 @@ version toolchain *BEDTools* ++++++++++ -The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. +BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. -*homepage*: https://github.com/arq5x/bedtools2 +*homepage*: https://bedtools.readthedocs.io/ ========== ==================================================================================== version toolchain @@ -2206,6 +2396,7 @@ version toolchain ``2.26.0`` ``GCCcore/6.4.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``2.27.1`` ``GCCcore/6.4.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` ``2.28.0`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.29.2`` ``GCC/8.3.0`` ========== ==================================================================================== @@ -2233,16 +2424,17 @@ version versionsuffix toolchain The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. -*homepage*: http://www.berkeleygw.org +*homepage*: https://www.berkeleygw.org -============= ================================================================ -version toolchain -============= ================================================================ -``1.0.6`` ``intel/2016.02-GCC-4.9`` -``1.1-beta2`` ``intel/2016.02-GCC-4.9`` -``1.2.0`` ``intel/2017a``, ``intel/2018a`` -``2.0.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` -============= ================================================================ +============= ================= ================================================================ +version versionsuffix toolchain +============= ================= ================================================================ +``1.0.6`` ``intel/2016.02-GCC-4.9`` +``1.1-beta2`` ``intel/2016.02-GCC-4.9`` +``1.2.0`` ``intel/2017a``, ``intel/2018a`` +``2.0.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` +``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +============= ================= ================================================================ .. _list_software_BFAST_368: @@ -2293,6 +2485,38 @@ version toolchain ========= ================= +.. _list_software_BiG-SCAPE_651: + +*BiG-SCAPE* ++++++++++++ + +BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. + +*homepage*: https://bigscape-corason.secondarymetabolites.org/index.html + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``1.0.1`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + +.. _list_software_BinSanity_913: + +*BinSanity* ++++++++++++ + +BinSanity contains a suite a scripts designed to cluster contigs generated from metagenomic assembly into putative genomes. + +*homepage*: https://github.com/edgraham/BinSanity/wiki + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.3.5`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_binutils_874: *binutils* @@ -2314,6 +2538,7 @@ version toolchain ``2.30`` ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``system`` ``2.31.1`` ``GCCcore/7.4.0``, ``GCCcore/8.2.0``, ``system`` ``2.32`` ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` +``2.34`` ``GCCcore/9.3.0``, ``system`` ========== ======================================================================================================================================================================================== @@ -2451,6 +2676,7 @@ version versionsuffix toolchain ``1.73`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``1.73`` ``-Python-3.6.6`` ``foss/2018b`` ``1.74`` ``foss/2019a`` +``1.75`` ``-Python-2.7.16`` ``foss/2019b`` ``1.75`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ======== ================== =================================================== @@ -2495,7 +2721,7 @@ version toolchain Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. -*homepage*: http://www.gnu.org/software/bison +*homepage*: https://www.gnu.org/software/bison ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain @@ -2506,7 +2732,9 @@ version toolchain ``3.0.4`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``GCCcore/system``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``3.0.5`` ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/system``, ``system`` ``3.2.2`` ``GCCcore/7.4.0`` -``3.3.2`` ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` +``3.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` +``3.5.2`` ``system`` +``3.5.3`` ``GCCcore/9.3.0``, ``system`` ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -2591,6 +2819,7 @@ version versionsuffix toolchain ========== ================= ========== ``2.2.26`` ``-Linux_x86_64`` ``system`` ``2.8.1`` ``-Linux_x86_64`` ``system`` +``2.10.0`` ``-Linux_x86_64`` ``system`` ========== ================= ========== @@ -2601,21 +2830,21 @@ version versionsuffix toolchain Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. -*homepage*: http://blast.ncbi.nlm.nih.gov/ +*homepage*: https://blast.ncbi.nlm.nih.gov/ -========== ================== ================================================================ -version versionsuffix toolchain -========== ================== ================================================================ -``2.2.31`` ``system`` -``2.3.0`` ``-Python-2.7.11`` ``foss/2016a`` -``2.6.0`` ``-Python-2.7.12`` ``foss/2016b`` -``2.6.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` -``2.6.0`` ``-Python-2.7.14`` ``intel/2017b`` -``2.7.1`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -``2.7.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.8.1`` ``foss/2018b`` -``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a`` -========== ================== ================================================================ +========== ================== ================================================================== +version versionsuffix toolchain +========== ================== ================================================================== +``2.2.31`` ``system`` +``2.3.0`` ``-Python-2.7.11`` ``foss/2016a`` +``2.6.0`` ``-Python-2.7.12`` ``foss/2016b`` +``2.6.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``2.6.0`` ``-Python-2.7.14`` ``intel/2017b`` +``2.7.1`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +``2.7.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.8.1`` ``foss/2018b`` +``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a``, ``iimpi/2019b`` +========== ================== ================================================================== .. _list_software_BLAT_291: @@ -2627,11 +2856,11 @@ BLAT on DNA is designed to quickly find sequences of 95% and greater similarity *homepage*: http://genome.ucsc.edu/FAQ/FAQblat.html -======= ====================================================================================== -version toolchain -======= ====================================================================================== -``3.5`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a`` -======= ====================================================================================== +======= ===================================================================================================== +version toolchain +======= ===================================================================================================== +``3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a`` +======= ===================================================================================================== .. _list_software_Blender_700: @@ -2711,7 +2940,7 @@ version versionsuffix toolchain Blosc, an extremely fast, multi-threaded, meta-compressor library -*homepage*: http://www.blosc.org/ +*homepage*: https://www.blosc.org/ ========== ================================================================== version toolchain @@ -2721,6 +2950,7 @@ version toolchain ``1.14.2`` ``GCCcore/6.4.0``, ``foss/2016a`` ``1.14.4`` ``GCCcore/7.3.0`` ``1.17.0`` ``GCCcore/8.2.0`` +``1.17.1`` ``GCCcore/8.3.0`` ========== ================================================================== @@ -2781,16 +3011,16 @@ Statistical and novel interactive HTML plots for Python *homepage*: https://github.com/bokeh/bokeh -=========== ================== =============================== -version versionsuffix toolchain -=========== ================== =============================== -``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` -``0.12.3`` ``-Python-3.5.2`` ``intel/2016b`` -``0.12.15`` ``-Python-3.6.4`` ``intel/2018a`` -``1.0.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.3.4`` ``-Python-3.7.2`` ``foss/2019a`` -``1.4.0`` ``-Python-3.7.4`` ``foss/2019b`` -=========== ================== =============================== +=========== ================== ================================== +version versionsuffix toolchain +=========== ================== ================================== +``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` +``0.12.3`` ``-Python-3.5.2`` ``intel/2016b`` +``0.12.15`` ``-Python-3.6.4`` ``intel/2018a`` +``1.0.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.3.4`` ``-Python-3.7.2`` ``foss/2019a`` +``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +=========== ================== ================================== .. _list_software_BoltzTraP_898: @@ -2809,6 +3039,22 @@ version toolchain ========= =============== +.. _list_software_Bonito_619: + +*Bonito* +++++++++ + +Convolution Basecaller for Oxford Nanopore Reads + +*homepage*: https://github.com/nanoporetech/bonito + +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``0.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========= ================= ================================== + + .. _list_software_Bonmin_611: *Bonmin* @@ -2892,7 +3138,7 @@ version versionsuffix toolchain ``1.68.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.69.0`` ``intel/2019.01`` ``1.70.0`` ``gompi/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` -``1.71.0`` ``gompi/2019b``, ``iimpi/2019b`` +``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b`` ========== ================== ==================================================================== @@ -2944,14 +3190,14 @@ Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DN *homepage*: http://bowtie-bio.sourceforge.net/index.shtml -=========== ======================================================================================================= -version toolchain -=========== ======================================================================================================= -``1.1.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a`` -``1.2.1.1`` ``foss/2016b``, ``intel/2017b`` -``1.2.2`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` -``1.2.3`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -=========== ======================================================================================================= +=========== ====================================================================================================================== +version toolchain +=========== ====================================================================================================================== +``1.1.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a`` +``1.2.1.1`` ``foss/2016b``, ``intel/2017b`` +``1.2.2`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` +``1.2.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` +=========== ====================================================================================================================== .. _list_software_Bowtie2_668: @@ -2963,19 +3209,19 @@ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads *homepage*: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml -=========== ============================================================== -version toolchain -=========== ============================================================== -``2.2.8`` ``foss/2016a`` -``2.2.9`` ``foss/2016a``, ``intel/2016b`` -``2.3.2`` ``foss/2016b``, ``foss/2017a``, ``intel/2017a`` -``2.3.3.1`` ``intel/2017b`` -``2.3.4`` ``intel/2017b`` -``2.3.4.1`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``2.3.4.2`` ``foss/2018b``, ``intel/2018b`` -``2.3.4.3`` ``foss/2017b`` -``2.3.5.1`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -=========== ============================================================== +=========== ====================================================================================================== +version toolchain +=========== ====================================================================================================== +``2.2.8`` ``foss/2016a`` +``2.2.9`` ``foss/2016a``, ``intel/2016b`` +``2.3.2`` ``foss/2016b``, ``foss/2017a``, ``intel/2017a`` +``2.3.3.1`` ``intel/2017b`` +``2.3.4`` ``intel/2017b`` +``2.3.4.1`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``2.3.4.2`` ``foss/2018b``, ``intel/2018b`` +``2.3.4.3`` ``foss/2017b`` +``2.3.5.1`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` +=========== ====================================================================================================== .. _list_software_Bpipe_496: @@ -3107,6 +3353,38 @@ version versionsuffix toolchain ========= ================== ================== +.. _list_software_BSMAPz_493: + +*BSMAPz* +++++++++ + +Updated and optimized fork of BSMAP. BSMAPz is a short reads mapping program for bisulfite sequencing in DNA methylation study. + +*homepage*: https://github.com/zyndagj/BSMAPz + +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``1.1.1`` ``-Python-2.7.16`` ``intel/2019b`` +========= ================== =============== + + +.. _list_software_BSseeker2_838: + +*BSseeker2* ++++++++++++ + +BS-Seeker2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated reads. + +*homepage*: http://pellegrini-legacy.mcdb.ucla.edu/bs_seeker2 + +========= ================== ====================================== +version versionsuffix toolchain +========= ================== ====================================== +``2.1.8`` ``-Python-2.7.16`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +========= ================== ====================================== + + .. _list_software_buildenv_857: *buildenv* @@ -3146,7 +3424,7 @@ version toolchain BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs -*homepage*: http://busco.ezlab.org/ +*homepage*: https://busco.ezlab.org/ ========= ================== =============== version versionsuffix toolchain @@ -3154,9 +3432,26 @@ version versionsuffix toolchain ``1.22`` ``-Python-2.7.13`` ``intel/2017a`` ``2.0.1`` ``-Python-2.7.13`` ``intel/2017a`` ``3.0.2`` ``-Python-2.7.15`` ``intel/2018b`` +``4.0.5`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== =============== +.. _list_software_BUStools_795: + +*BUStools* +++++++++++ + +bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow. + +*homepage*: https://github.com/BUStools/bustools + +========== ============== +version toolchain +========== ============== +``0.40.0`` ``foss/2018b`` +========== ============== + + .. _list_software_BWA_218: *BWA* @@ -3166,15 +3461,15 @@ Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively sh *homepage*: http://bio-bwa.sourceforge.net/ -=========== ================================================================================================================================================================= -version toolchain -=========== ================================================================================================================================================================= -``0.7.12`` ``foss/2016b`` -``0.7.13`` ``foss/2016a``, ``intel/2016a`` -``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``0.7.16a`` ``foss/2016b``, ``intel/2017a`` -``0.7.17`` ``GCC/8.2.0-2.31.1``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -=========== ================================================================================================================================================================= +=========== ========================================================================================================================================================================================================= +version toolchain +=========== ========================================================================================================================================================================================================= +``0.7.12`` ``foss/2016b`` +``0.7.13`` ``foss/2016a``, ``intel/2016a`` +``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``0.7.16a`` ``foss/2016b``, ``intel/2017a`` +``0.7.17`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +=========== ========================================================================================================================================================================================================= .. _list_software_bwa-meth_789: @@ -3186,11 +3481,11 @@ Fast and accurante alignment of BS-Seq reads. *homepage*: https://github.com/brentp/bwa-meth -========= ======================================== -version toolchain -========= ======================================== -``0.2.2`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -========= ======================================== +========= ================================================================= +version toolchain +========= ================================================================= +``0.2.2`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` +========= ================================================================= .. _list_software_bwakit_642: @@ -3222,6 +3517,7 @@ The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl version toolchain ========== ================= ``1.9.13`` ``GCCcore/8.2.0`` +``1.9.14`` ``GCCcore/8.3.0`` ========== ================= @@ -3318,7 +3614,7 @@ version toolchain --- -:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_charmm_632` - :ref:`list_software_CHARMM_440` - :ref:`list_software_CHASE_356` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Commet_613` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_charmm_632` - :ref:`list_software_CHARMM_440` - :ref:`list_software_CHASE_356` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_C3D_186: @@ -3454,7 +3750,7 @@ version versionsuffix toolchain Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing -*homepage*: http://canu.readthedocs.io +*homepage*: https://canu.readthedocs.io ======= ================ =============================== version versionsuffix toolchain @@ -3464,6 +3760,7 @@ version versionsuffix toolchain ``1.8`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``1.8`` ``-Perl-5.28.0`` ``foss/2018b`` ``1.8`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``1.9`` ``-Java-11`` ``GCCcore/8.3.0`` ======= ================ =============================== @@ -3616,6 +3913,22 @@ version toolchain ========== ============== +.. _list_software_Cbc_264: + +*Cbc* ++++++ + +Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable. + +*homepage*: https://github.com/coin-or/Cbc + +========== ============== +version toolchain +========== ============== +``2.10.3`` ``foss/2018b`` +========== ============== + + .. _list_software_CBLAS_357: *CBLAS* @@ -3887,7 +4200,7 @@ version versionsuffix toolchain ``4.11.1`` ``-Python-3.6.4`` ``foss/2018a`` ``4.11.1`` ``-Python-3.6.6`` ``foss/2018b`` ``4.14`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``4.14.1`` ``-Python-3.7.4`` ``foss/2019b`` +``4.14.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========== ================== =============================== @@ -3907,6 +4220,38 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_Cgl_278: + +*Cgl* ++++++ + +The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver. + +*homepage*: https://github.com/coin-or/Cgl + +========== ============== +version toolchain +========== ============== +``0.60.2`` ``foss/2018b`` +========== ============== + + +.. _list_software_CGmapTools_985: + +*CGmapTools* +++++++++++++ + +Command-line Toolset for Bisulfite Sequencing Data Analysis + +*homepage*: https://cgmaptools.github.io/ + +========= =============== +version toolchain +========= =============== +``0.1.2`` ``intel/2019b`` +========= =============== + + .. _list_software_CGNS_299: *CGNS* @@ -3936,6 +4281,7 @@ CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-los version toolchain ========= ==================================== ``2.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.1.0`` ``GCCcore/8.2.0`` ========= ==================================== @@ -4003,6 +4349,7 @@ version versionsuffix toolchain ``1.0.13`` ``-Python-2.7.15`` ``foss/2018b`` ``1.0.13`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.0.18`` ``-Python-2.7.15`` ``foss/2019a`` +``1.1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========== ================== =============================== @@ -4201,29 +4548,30 @@ C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard lib *homepage*: https://clang.llvm.org/ -========= ================== ====================================== -version versionsuffix toolchain -========= ================== ====================================== -``3.3`` ``GCC/4.8.1`` -``3.4`` ``GCC/4.8.2`` -``3.4.1`` ``GCC/4.8.2`` -``3.4.2`` ``GCC/4.8.2`` -``3.6.0`` ``GCC/4.9.2`` -``3.6.1`` ``GCC/4.9.2`` -``3.7.0`` ``GNU/4.9.3-2.25`` -``3.7.1`` ``GCC/4.9.3-2.25``, ``foss/2016a`` -``3.8.0`` ``GCC/4.9.3-2.25`` -``3.8.1`` ``GCC/5.4.0-2.26``, ``foss/2016b`` -``5.0.0`` ``GCC/6.4.0-2.28`` -``5.0.1`` ``GCC/6.4.0-2.28`` -``6.0.1`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30`` -``7.0.0`` ``GCC/6.4.0-2.28`` -``7.0.1`` ``GCC/7.3.0-2.30`` -``8.0.0`` ``GCCcore/8.2.0`` -``8.0.0`` ``-CUDA-10.1.105`` ``GCCcore/8.2.0`` -``9.0.1`` ``GCCcore/8.3.0`` -``9.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` -========= ================== ====================================== +========== ================== ====================================== +version versionsuffix toolchain +========== ================== ====================================== +``3.3`` ``GCC/4.8.1`` +``3.4`` ``GCC/4.8.2`` +``3.4.1`` ``GCC/4.8.2`` +``3.4.2`` ``GCC/4.8.2`` +``3.6.0`` ``GCC/4.9.2`` +``3.6.1`` ``GCC/4.9.2`` +``3.7.0`` ``GNU/4.9.3-2.25`` +``3.7.1`` ``GCC/4.9.3-2.25``, ``foss/2016a`` +``3.8.0`` ``GCC/4.9.3-2.25`` +``3.8.1`` ``GCC/5.4.0-2.26``, ``foss/2016b`` +``5.0.0`` ``GCC/6.4.0-2.28`` +``5.0.1`` ``GCC/6.4.0-2.28`` +``6.0.1`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30`` +``7.0.0`` ``GCC/6.4.0-2.28`` +``7.0.1`` ``GCC/7.3.0-2.30`` +``8.0.0`` ``GCCcore/8.2.0`` +``8.0.0`` ``-CUDA-10.1.105`` ``GCCcore/8.2.0`` +``9.0.1`` ``GCCcore/8.3.0`` +``9.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` +``10.0.0`` ``GCCcore/8.3.0`` +========== ================== ====================================== .. _list_software_Clang-Python-bindings_2063: @@ -4328,6 +4676,22 @@ version toolchain ========== ============= +.. _list_software_Clp_287: + +*Clp* ++++++ + +Clp (Coin-or linear programming) is an open-source linear programming solver. It is primarily meant to be used as a callable library, but a basic, stand-alone executable version is also available. + +*homepage*: https://github.com/coin-or/Clp + +========== ============== +version toolchain +========== ============== +``1.17.3`` ``foss/2018b`` +========== ============== + + .. _list_software_Clustal-Omega_1262: *Clustal-Omega* @@ -4337,12 +4701,12 @@ Clustal Omega is a multiple sequence alignment program for proteins. It produce *homepage*: http://www.clustal.org/omega/ -========= ================================================ -version toolchain -========= ================================================ -``1.2.0`` ``foss/2016b`` -``1.2.4`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -========= ================================================ +========= =============================================================== +version toolchain +========= =============================================================== +``1.2.0`` ``foss/2016b`` +``1.2.4`` ``GCC/8.3.0``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +========= =============================================================== .. _list_software_ClustalW2_865: @@ -4505,6 +4869,22 @@ version versionsuffix toolchain ============ ============= =============== +.. _list_software_CoinUtils_922: + +*CoinUtils* ++++++++++++ + +CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project. + +*homepage*: https://github.com/coin-or/CoinUtils + +========== ================= +version toolchain +========== ================= +``2.11.3`` ``GCCcore/7.3.0`` +========== ================= + + .. _list_software_Commet_613: *Commet* @@ -4798,14 +5178,15 @@ version toolchain *CppUnit* +++++++++ -CppUnit is the C++ port of the famous JUnit framework for unit testing. +CppUnit is the C++ port of the famous JUnit framework for unit testing. -*homepage*: http://sourceforge.net/projects/cppunit/ +*homepage*: https://freedesktop.org/wiki/Software/cppunit/ ========== ==================================================== version toolchain ========== ==================================================== ``1.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a`` +``1.15.1`` ``GCCcore/8.3.0`` ========== ==================================================== @@ -4915,11 +5296,12 @@ Conditional Reciprocal Best BLAST - high confidence ortholog assignment. CRB-BL *homepage*: https://github.com/cboursnell/crb-blast -========= =============== -version toolchain -========= =============== -``0.6.9`` ``intel/2017a`` -========= =============== +========= =============== =============== +version versionsuffix toolchain +========= =============== =============== +``0.6.9`` ``intel/2017a`` +``0.6.9`` ``-Ruby-2.6.1`` ``foss/2018b`` +========= =============== =============== .. _list_software_CRF++_305: @@ -5295,7 +5677,7 @@ version versionsuffix toolchain Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. -*homepage*: http://opensource.scilifelab.se/projects/cutadapt/ +*homepage*: https://opensource.scilifelab.se/projects/cutadapt/ ========= ================== ================================================ version versionsuffix toolchain @@ -5307,10 +5689,12 @@ version versionsuffix toolchain ``1.16`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``1.16`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.16`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.18`` ``GCCcore/8.2.0`` +``1.18`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``1.18`` ``-Python-2.7.15`` ``foss/2018b`` ``1.18`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``2.1`` ``-Python-3.6.6`` ``foss/2018b`` +``2.7`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.8`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========= ================== ================================================ @@ -5357,11 +5741,12 @@ CVXPY is a Python-embedded modeling language for convex optimization problems. *homepage*: https://www.cvxpy.org/ -========== ============== -version toolchain -========== ============== -``1.0.24`` ``foss/2019a`` -========== ============== +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``1.0.24`` ``foss/2019a`` +``1.0.28`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== .. _list_software_cysignals_973: @@ -5458,7 +5843,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dxpy_453` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` .. _list_software_dadi_402: @@ -5585,7 +5970,7 @@ version versionsuffix toolchain ``1.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.1.4`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``2.3.0`` ``-Python-3.7.2`` ``foss/2019a`` -``2.8.0`` ``-Python-3.7.4`` ``foss/2019b`` +``2.8.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========== ================== =================================================== @@ -5612,13 +5997,14 @@ version toolchain The davix project aims to make file management over HTTP-based protocols simple. The focus is on high-performance remote I/O and data management of large collections of files. Currently, there is support for the WebDav (link is external), Amazon S3 (link is external), Microsoft Azure (link is external), and HTTP (link is external) protocols. -*homepage*: http://dmc.web.cern.ch/projects/davix/home +*homepage*: https://dmc.web.cern.ch/projects/davix/home -========= =============== -version toolchain -========= =============== -``0.6.6`` ``intel/2017a`` -========= =============== +========= ================= +version toolchain +========= ================= +``0.6.6`` ``intel/2017a`` +``0.7.5`` ``GCCcore/8.3.0`` +========= ================= .. _list_software_DB_134: @@ -5630,15 +6016,15 @@ Berkeley DB enables the development of custom data management solutions, withou *homepage*: http://www.oracle.com/technetwork/products/berkeleydb -=========== ================================== -version toolchain -=========== ================================== -``4.8.30`` ``intel/2016a`` -``6.2.23`` ``foss/2016a`` -``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` -``18.1.25`` ``GCCcore/7.3.0`` -``18.1.32`` ``GCCcore/8.2.0`` -=========== ================================== +=========== ==================================== +version toolchain +=========== ==================================== +``4.8.30`` ``intel/2016a`` +``6.2.23`` ``foss/2016a`` +``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` +``18.1.25`` ``GCCcore/7.3.0`` +``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +=========== ==================================== .. _list_software_DB_File_613: @@ -5751,7 +6137,7 @@ dcm2niix is a designed to convert neuroimaging data from the DICOM format to the version toolchain ================ ==================================== ``1.0.20180622`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.0.20190902`` ``GCCcore/7.3.0`` +``1.0.20190902`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ================ ==================================== @@ -5929,12 +6315,12 @@ A Python library for phylogenetics and phylogenetic computing: reading, writing *homepage*: https://pypi.python.org/pypi/DendroPy/ -========= ================== ================================== -version versionsuffix toolchain -========= ================== ================================== -``4.4.0`` ``GCCcore/8.2.0``, ``intel/2019a`` -``4.4.0`` ``-Python-2.7.15`` ``intel/2018b`` -========= ================== ================================== +========= ================== ===================================================== +version versionsuffix toolchain +========= ================== ===================================================== +``4.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2019a`` +``4.4.0`` ``-Python-2.7.15`` ``intel/2018b`` +========= ================== ===================================================== .. _list_software_destiny_768: @@ -5978,11 +6364,11 @@ DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock *homepage*: http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english -========= =============== -version toolchain -========= =============== -``3.2.0`` ``intel/2019a`` -========= =============== +========= ============================== +version toolchain +========= ============================== +``3.2.0`` ``GCC/8.3.0``, ``intel/2019a`` +========= ============================== .. _list_software_DFTB+_331: @@ -6032,6 +6418,7 @@ version toolchain ========== ================================================================ ``0.9.22`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` ``0.9.24`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``0.9.30`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ========== ================================================================ @@ -6323,6 +6710,23 @@ version toolchain ========= ================================ +.. _list_software_dtcwt_550: + +*dtcwt* ++++++++ + +Dual-Tree Complex Wavelet Transform library for Python + +*homepage*: https://github.com/rjw57/dtcwt + +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``0.12.0`` ``-Python-2.7.15`` ``foss/2018b`` +``0.12.0`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================== =============== + + .. _list_software_dxpy_453: *dxpy* @@ -6345,7 +6749,7 @@ version versionsuffix toolchain --- -:ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_ea-utils_804: @@ -6463,6 +6867,8 @@ version toolchain ``4.0.0`` ``system`` ``4.0.1`` ``system`` ``4.1.0`` ``system`` +``4.1.1`` ``system`` +``4.1.2`` ``system`` ========== ========== @@ -6637,7 +7043,7 @@ version toolchain Eigenvalue SoLvers for Petaflop-Applications . -*homepage*: http://elpa.rzg.mpg.de +*homepage*: https://elpa.rzg.mpg.de =================== ================================================ version toolchain @@ -6648,6 +7054,7 @@ version toolchain ``2017.11.001`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` ``2018.05.001`` ``foss/2018b``, ``intel/2018b`` ``2018.11.001`` ``intel/2019a`` +``2019.11.001`` ``foss/2019b``, ``intel/2019b`` =================== ================================================ @@ -6667,6 +7074,23 @@ version toolchain ========= ============== +.. _list_software_ELSI_301: + +*ELSI* +++++++ + +ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems. + +*homepage*: https://wordpress.elsi-interchange.org/ + +========= ============= =============== +version versionsuffix toolchain +========= ============= =============== +``2.5.0`` ``intel/2019b`` +``2.5.0`` ``-PEXSI`` ``intel/2019b`` +========= ============= =============== + + .. _list_software_Emacs_489: *Emacs* @@ -6719,6 +7143,7 @@ EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a fre version versionsuffix toolchain ========= ================= ================================================================================================================================ ``6.6.0`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` +``6.6.0`` ``-Java-11`` ``GCC/8.3.0`` ``6.6.0`` ``-X11-20170314`` ``intel/2017a`` ========= ================= ================================================================================================================================ @@ -6773,6 +7198,22 @@ version toolchain ========= =============== +.. _list_software_EnsEMBLCoreAPI_1193: + +*EnsEMBLCoreAPI* +++++++++++++++++ + +The Ensembl Core Perl API and SQL schema + +*homepage*: https://www.ensembl.org/info/docs/api/index.html + +================== ================ ============== +version versionsuffix toolchain +================== ================ ============== +``96.0-r20190601`` ``-Perl-5.28.1`` ``foss/2019a`` +================== ================ ============== + + .. _list_software_entrypoints_1231: *entrypoints* @@ -7068,7 +7509,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FIAT_292` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FIAT_292` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -7128,11 +7569,12 @@ Falcon: a set of tools for fast aligning long reads for consensus and assembly *homepage*: https://github.com/PacificBiosciences/FALCON -========= =============== -version toolchain -========= =============== -``1.8.8`` ``intel/2017b`` -========= =============== +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``1.8.8`` ``intel/2017b`` +``1.8.8`` ``-Python-2.7.16`` ``intel/2019b`` +========= ================== =============== .. _list_software_FANN_291: @@ -7213,6 +7655,7 @@ version toolchain ======= ============================================================== ``1.1`` ``foss/2018b``, ``intel/2018b`` ``1.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``1.3`` ``iccifort/2019.5.281`` ======= ============================================================== @@ -7225,12 +7668,12 @@ FastME: a comprehensive, accurate and fast distance-based phylogeny inference pr *homepage*: http://www.atgc-montpellier.fr/fastme/ -=========== ================================ -version toolchain -=========== ================================ -``2.1.5`` ``foss/2016a`` -``2.1.6.1`` ``intel/2018a``, ``intel/2018b`` -=========== ================================ +=========== ======================================================================== +version toolchain +=========== ======================================================================== +``2.1.5`` ``foss/2016a`` +``2.1.6.1`` ``GCC/8.3.0``, ``iccifort/2019.5.281``, ``intel/2018a``, ``intel/2018b`` +=========== ======================================================================== .. _list_software_fastp_542: @@ -7242,12 +7685,12 @@ A tool designed to provide fast all-in-one preprocessing for FastQ files. This *homepage*: https://github.com/OpenGene/fastp -========== ============================================= -version toolchain -========== ============================================= -``0.19.7`` ``foss/2018b`` -``0.20.0`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.5.281`` -========== ============================================= +========== ============================================================ +version toolchain +========== ============================================================ +``0.19.7`` ``foss/2018b`` +``0.20.0`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.5.281`` +========== ============================================================ .. _list_software_fastPHASE_799: @@ -7266,6 +7709,22 @@ version toolchain ========= ========== +.. _list_software_fastq-pair_1016: + +*fastq-pair* +++++++++++++ + +Match up paired end fastq files quickly and efficiently. + +*homepage*: https://github.com/linsalrob/fastq-pair + +======= ================= +version toolchain +======= ================= +``1.0`` ``GCCcore/8.2.0`` +======= ================= + + .. _list_software_fastq-tools_1149: *fastq-tools* @@ -7324,6 +7783,7 @@ version versionsuffix toolchain ``0.11.7`` ``-Java-1.8.0_162`` ``system`` ``0.11.8`` ``-Java-1.8`` ``system`` ``0.11.8`` ``-Java-11`` ``system`` +``0.11.9`` ``-Java-11`` ``system`` ========== =================== ========== @@ -7407,7 +7867,7 @@ FastTree infers approximately-maximum-likelihood phylogenetic trees from alignme version toolchain ========== ================================================================= ``2.1.10`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``2.1.11`` ``GCCcore/8.2.0`` +``2.1.11`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========== ================================================================= @@ -7553,13 +8013,14 @@ version toolchain Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets. -*homepage*: http://ferret.pmel.noaa.gov/ +*homepage*: https://ferret.pmel.noaa.gov/Ferret/ -======= =============== -version toolchain -======= =============== -``7.3`` ``intel/2017b`` -======= =============== +========= =============== +version toolchain +========= =============== +``7.3`` ``intel/2017b`` +``7.5.0`` ``foss/2019b`` +========= =============== .. _list_software_FFC_207: @@ -7697,6 +8158,22 @@ version versionsuffix toolchain ============ ================== =============================== +.. _list_software_FigureGen_892: + +*FigureGen* ++++++++++++ + +FigureGen is a Fortran program that creates images for ADCIRC files. It reads mesh files (fort.14, etc.), nodal attributes files (fort.13, etc.) and output files (fort.63, fort.64, maxele.63, etc.). It plots contours, contour lines, and vectors. Using FigureGen, you can go directly from the ADCIRC input and output files to a presentation-quality figure, for one or multiple time snaps. + +*homepage*: https://ccht.ccee.ncsu.edu/category/software/figuregen/ + +=============== ============== +version toolchain +=============== ============== +``51-20190516`` ``foss/2019a`` +=============== ============== + + .. _list_software_Fiji_386: *Fiji* @@ -7831,6 +8308,22 @@ version toolchain ========= =============== +.. _list_software_Fiona_493: + +*Fiona* ++++++++ + +Fiona is designed to be simple and dependable. It focuses on reading and writing data in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS packages such as pyproj, Rtree, and Shapely. + +*homepage*: https://github.com/Toblerity/Fiona + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``1.8.13`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_Firefox_723: *Firefox* @@ -7954,17 +8447,17 @@ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, some *homepage*: http://flex.sourceforge.net/ -========== ================================================================================================================================================================================================================================================================================================================================================= -version toolchain -========== ================================================================================================================================================================================================================================================================================================================================================= -``2.5.35`` ``system`` -``2.5.38`` ``GCC/4.8.2`` -``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` -``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.6.2`` ``intel/2016b`` -``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` -``2.6.4`` ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/system``, ``system`` -========== ================================================================================================================================================================================================================================================================================================================================================= +========== ==================================================================================================================================================================================================================================================================================================================================================================== +version toolchain +========== ==================================================================================================================================================================================================================================================================================================================================================================== +``2.5.35`` ``system`` +``2.5.38`` ``GCC/4.8.2`` +``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` +``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +``2.6.2`` ``intel/2016b`` +``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` +``2.6.4`` ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` +========== ==================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_FlexiDot_799: @@ -8052,6 +8545,7 @@ version versionsuffix toolchain ======= ================== =============== ``2.4`` ``-Python-2.7.15`` ``intel/2018b`` ``2.6`` ``-Python-3.7.2`` ``foss/2019a`` +``2.6`` ``-Python-3.7.4`` ``intel/2019b`` ======= ================== =============== @@ -8353,11 +8847,11 @@ FreeImage is an Open Source library project for developers who would like to sup *homepage*: http://freeimage.sourceforge.net -========== ================= -version toolchain -========== ================= -``3.18.0`` ``GCCcore/7.3.0`` -========== ================= +========== ==================================== +version toolchain +========== ==================================== +``3.18.0`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +========== ==================================== .. _list_software_FreeSurfer_1017: @@ -8549,6 +9043,22 @@ version toolchain ========= =============== +.. _list_software_FuSeq_484: + +*FuSeq* ++++++++ + +FuSeq is a novel method to discover fusion genes from paired-end RNA sequencing data. + +*homepage*: https://github.com/nghiavtr/FuSeq + +========= =============== +version toolchain +========= =============== +``1.1.2`` ``gompi/2019b`` +========= =============== + + .. _list_software_future_667: *future* @@ -8590,7 +9100,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gblocks_709` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_gtest_551` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gblocks_709` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_gtest_551` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -8635,11 +9145,11 @@ g2log, efficient asynchronous logger using C++11 *homepage*: https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11 -======= ============== -version toolchain -======= ============== -``1.0`` ``foss/2016b`` -======= ============== +======= ================================= +version toolchain +======= ================================= +``1.0`` ``GCCcore/8.3.0``, ``foss/2016b`` +======= ================================= .. _list_software_Gaia_370: @@ -8821,6 +9331,7 @@ version versionsuffix toolchain ``4.1.0.0`` ``-Python-3.6.6`` ``foss/2018b`` ``4.1.2.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` ``4.1.3.0`` ``-Java-1.8`` ``GCCcore/8.3.0`` +``4.1.4.1`` ``-Java-11`` ``GCCcore/8.3.0`` ============ =================== ================= @@ -8953,6 +9464,7 @@ version versionsuffix toolchain ``8.3.0`` ``system`` ``8.3.0`` ``-2.32`` ``system`` ``9.1.0`` ``-2.32`` ``system`` +``9.2.0`` ``system`` ``9.2.0`` ``-2.32`` ``system`` ``system`` ``system`` ``system`` ``-2.29`` ``system`` @@ -8991,6 +9503,7 @@ version toolchain ``8.3.0`` ``system`` ``9.1.0`` ``system`` ``9.2.0`` ``system`` +``9.3.0`` ``system`` ``system`` ``system`` ========== ========== @@ -9098,7 +9611,7 @@ version versionsuffix toolchain ``2.2.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.0.0`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ``3.0.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.0.2`` ``-Python-3.7.4`` ``intel/2019b`` +``3.0.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========= ============================== ================================================================ @@ -9109,7 +9622,7 @@ version versionsuffix toolchain The GNU Project Debugger -*homepage*: http://www.gnu.org/software/gdb/gdb.html +*homepage*: https://www.gnu.org/software/gdb/gdb.html ========== ================== =============================== version versionsuffix toolchain @@ -9124,6 +9637,7 @@ version versionsuffix toolchain ``8.1`` ``-Python-2.7.14`` ``foss/2018a`` ``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` ``8.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``9.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========== ================== =============================== @@ -9248,6 +9762,7 @@ version toolchain ``2.36.11`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2018b``, ``intel/2017b``, ``intel/2018a`` ``2.36.12`` ``foss/2018b``, ``fosscuda/2018b`` ``2.38.1`` ``GCCcore/8.2.0`` +``2.38.2`` ``GCCcore/8.3.0`` =========== ==================================================================================== @@ -9402,6 +9917,25 @@ version versionsuffix toolchain ========= ======================= ========== +.. _list_software_GenomeTools_1132: + +*GenomeTools* ++++++++++++++ + +A comprehensive software library for efficient processing of structured genome annotations. + +*homepage*: http://genometools.org + +========== ================== ============== +version versionsuffix toolchain +========== ================== ============== +``1.5.10`` ``foss/2018b`` +``1.5.10`` ``-Python-2.7.15`` ``foss/2018b`` +``1.6.1`` ``GCC/8.3.0`` +``1.6.1`` ``-Python-2.7.16`` ``GCC/8.3.0`` +========== ================== ============== + + .. _list_software_GenotypeHarmonizer_1898: *GenotypeHarmonizer* @@ -9475,7 +10009,7 @@ version versionsuffix toolchain ``3.6.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.7.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ``3.7.2`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.8.0`` ``-Python-3.7.4`` ``iccifort/2019.5.281`` +``3.8.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ========= ================== ================================================================ @@ -9899,13 +10433,13 @@ GL2PS: an OpenGL to PostScript printing library *homepage*: http://www.geuz.org/gl2ps/ -========= ================ ================================================================================================= -version versionsuffix toolchain -========= ================ ================================================================================================= -``1.3.9`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``1.3.9`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` -``1.4.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -========= ================ ================================================================================================= +========= ================ ==================================================================================================================================== +version versionsuffix toolchain +========= ================ ==================================================================================================================================== +``1.3.9`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``1.3.9`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` +``1.4.0`` ``GCCcore/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +========= ================ ==================================================================================================================================== .. _list_software_Glade_477: @@ -10129,14 +10663,14 @@ The GLPK (GNU Linear Programming Kit) package is intended for solving large-sca *homepage*: https://www.gnu.org/software/glpk/ -======== ======================================================= -version toolchain -======== ======================================================= -``4.58`` ``foss/2016a``, ``intel/2016a`` -``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` -``4.61`` ``intel/2017a`` -``4.65`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -======== ======================================================= +======== ========================================================================== +version toolchain +======== ========================================================================== +``4.58`` ``foss/2016a``, ``intel/2016a`` +``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` +``4.61`` ``intel/2017a`` +``4.65`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +======== ========================================================================== .. _list_software_glproto_775: @@ -10172,6 +10706,7 @@ version toolchain ``2018-05-11`` ``intel/2018a`` ``2018-07-04`` ``intel/2018a`` ``2019-03-15`` ``foss/2018b`` +``2019-09-12`` ``GCC/8.3.0`` ============== =============== @@ -10347,7 +10882,7 @@ version toolchain Portable interactive, function plotting utility -*homepage*: http://gnuplot.sourceforge.net/ +*homepage*: https://gnuplot.sourceforge.net/ ========= ================================================================ version toolchain @@ -10358,6 +10893,7 @@ version toolchain ``5.2.2`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``5.2.5`` ``foss/2018b`` ``5.2.6`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b`` +``5.2.8`` ``GCCcore/8.3.0`` ========= ================================================================ @@ -10399,6 +10935,8 @@ version toolchain ``1.12`` ``system`` ``1.12.1`` ``GCCcore/7.3.0`` ``1.13.1`` ``system`` +``1.14`` ``system`` +``1.14.1`` ``system`` ========== ================= @@ -10424,7 +10962,9 @@ version versionsuffix toolchain ``1.54.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``1.54.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` ``1.54.1`` ``-Python-3.6.6`` ``fosscuda/2018b`` +``1.58.3`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` ``1.60.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``1.63.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========== ================== ================================== @@ -10573,6 +11113,7 @@ version versionsuffix toolchain ``1.4.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``19.8.1`` ``-ASE-3.18.0-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``19.8.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``20.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========== ============================ =============================== @@ -10619,14 +11160,15 @@ version toolchain gperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C++ with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. -*homepage*: http://github.com/gperftools/gperftools +*homepage*: https://github.com/gperftools/gperftools -========= =============================== -version toolchain -========= =============================== -``2.5`` ``foss/2016a``, ``intel/2016b`` -``2.6.3`` ``GCCcore/6.4.0`` -========= =============================== +========== =============================== +version toolchain +========== =============================== +``2.5`` ``foss/2016a``, ``intel/2016b`` +``2.6.3`` ``GCCcore/6.4.0`` +``2.7.90`` ``GCCcore/8.3.0`` +========== =============================== .. _list_software_gpustat_776: @@ -10652,13 +11194,13 @@ version versionsuffix toolchain Grace is a WYSIWYG tool to make two-dimensional plots of numerical data. -*homepage*: http://plasma-gate.weizmann.ac.il/Grace/ +*homepage*: https://plasma-gate.weizmann.ac.il/Grace/ -========== ============= =============================================== -version versionsuffix toolchain -========== ============= =============================================== -``5.1.25`` ``-5build1`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` -========== ============= =============================================== +========== ============= ================================================================================================================= +version versionsuffix toolchain +========== ============= ================================================================================================================= +``5.1.25`` ``-5build1`` ``foss/2017b``, ``foss/2018a``, ``foss/2019a``, ``foss/2019b``, ``intel/2017b``, ``intel/2019a``, ``intel/2019b`` +========== ============= ================================================================================================================= .. _list_software_grace_514: @@ -10690,6 +11232,7 @@ Complete Gradle install. From mobile apps to microservices, from small startups version toolchain ========= ========== ``4.5.1`` ``system`` +``6.1.1`` ``system`` ========= ========== @@ -10749,7 +11292,7 @@ version toolchain GraphicsMagick is the swiss army knife of image processing. -*homepage*: http://www.graphicsmagick.org/ +*homepage*: https://www.graphicsmagick.org/ ========== ================================ version toolchain @@ -10758,9 +11301,26 @@ version toolchain ``1.3.25`` ``intel/2016b``, ``intel/2017a`` ``1.3.28`` ``foss/2018a`` ``1.3.31`` ``foss/2018b`` +``1.3.34`` ``foss/2019a``, ``foss/2019b`` ========== ================================ +.. _list_software_GraphMap2_834: + +*GraphMap2* ++++++++++++ + +A highly sensitive and accurate mapper for long, error-prone reads + +*homepage*: https://github.com/lbcb-sci/graphmap2 + +========= ============== +version toolchain +========= ============== +``0.6.4`` ``foss/2019b`` +========= ============== + + .. _list_software_Graphviz_843: *Graphviz* @@ -10768,14 +11328,17 @@ version toolchain Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains. -*homepage*: http://www.graphviz.org/ +*homepage*: https://www.graphviz.org/ -========== =============================== -version toolchain -========== =============================== -``2.38.0`` ``foss/2016b``, ``intel/2016b`` -``2.40.1`` ``intel/2018a`` -========== =============================== +========== ================== =============================== +version versionsuffix toolchain +========== ================== =============================== +``2.38.0`` ``foss/2016b``, ``intel/2016b`` +``2.40.1`` ``foss/2018b``, ``intel/2018a`` +``2.40.1`` ``-Python-2.7.15`` ``foss/2018b`` +``2.42.2`` ``foss/2019b`` +``2.42.2`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================== =============================== .. _list_software_graphviz_875: @@ -10796,6 +11359,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_GRASP_381: + +*GRASP* ++++++++ + +The General Relativistic Atomic Structure Package (GRASP) is a set of Fortran 90 programs for performing fully-relativistic electron structure calculations of atoms. + +*homepage*: https://compas.github.io/grasp/ + +======== ============== +version toolchain +======== ============== +``2018`` ``foss/2019b`` +======== ============== + + .. _list_software_GRASS_384: *GRASS* @@ -10947,6 +11526,7 @@ version versionsuffix toolchain ``2019.2`` ``fosscuda/2019a`` ``2019.3`` ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019a``, ``fosscuda/2019b`` ``2019.4`` ``foss/2019b`` +``2020`` ``foss/2019b``, ``fosscuda/2019b`` ========== ================= ============================================================================================================ @@ -10982,6 +11562,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_Groovy_646: + +*Groovy* +++++++++ + +Groovy is a powerful, optionally typed and dynamic language, with static-typing and static compilation capabilities, for the Java platform aimed at improving developer productivity thanks to a concise, familiar and easy to learn syntax. + +*homepage*: https://groovy-lang.org + +========= ============= ========== +version versionsuffix toolchain +========= ============= ========== +``2.5.9`` ``-Java-11`` ``system`` +========= ============= ========== + + .. _list_software_gsettings-desktop-schemas_2576: *gsettings-desktop-schemas* @@ -11029,11 +11625,28 @@ The gSOAP toolkit is a C and C++ software development toolkit for SOAP and REST *homepage*: http://www.cs.fsu.edu/~engelen/soap.html -========== ================= -version toolchain -========== ================= -``2.8.48`` ``GCCcore/6.3.0`` -========== ================= +=========== ================= +version toolchain +=========== ================= +``2.8.48`` ``GCCcore/6.3.0`` +``2.8.100`` ``GCCcore/8.3.0`` +=========== ================= + + +.. _list_software_gsport_671: + +*gsport* +++++++++ + +GSPORT command-line tool for accessing GenomeScan Customer Portal + +*homepage*: https://github.com/genomescan/gsport + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``1.4.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= .. _list_software_GST-plugins-base_1509: @@ -11089,6 +11702,7 @@ version versionsuffix toolchain ========= ================== =============================== ``0.2.2`` ``-Python-2.7.15`` ``intel/2018b`` ``0.3.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` +``1.0.2`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================== =============================== @@ -11101,12 +11715,13 @@ Google's framework for writing C++ tests on a variety of platforms *homepage*: https://github.com/google/googletest -========= ==================================== -version toolchain -========= ==================================== -``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``1.8.1`` ``GCCcore/8.2.0`` -========= ==================================== +========== ==================================== +version toolchain +========== ==================================== +``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``1.8.1`` ``GCCcore/8.2.0`` +``1.10.0`` ``GCCcore/8.3.0`` +========== ==================================== .. _list_software_GTK+_273: @@ -11127,6 +11742,7 @@ version toolchain ``2.24.32`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ``3.22.30`` ``fosscuda/2018b`` ``3.24.8`` ``GCCcore/8.2.0`` +``3.24.13`` ``GCCcore/8.3.0`` =========== ================================================================================ @@ -11180,20 +11796,36 @@ version toolchain ============ ================================================================================================================= -.. _list_software_guenomu_768: +.. _list_software_gubbins_746: -*guenomu* +*gubbins* +++++++++ -guenomu is a software written in C that estimates the species tree for a given set of gene families. +Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences. -*homepage*: https://bitbucket.org/leomrtns/guenomu +*homepage*: https://sanger-pathogens.github.io/gubbins -============== ============= =============== -version versionsuffix toolchain -============== ============= =============== -``2019.07.05`` ``-mpi`` ``iimpi/2019a`` -============== ============= =============== +========= ========== +version toolchain +========= ========== +``2.4.0`` ``system`` +========= ========== + + +.. _list_software_guenomu_768: + +*guenomu* ++++++++++ + +guenomu is a software written in C that estimates the species tree for a given set of gene families. + +*homepage*: https://bitbucket.org/leomrtns/guenomu + +============== ============= =============== +version versionsuffix toolchain +============== ============= =============== +``2019.07.05`` ``-mpi`` ``iimpi/2019a`` +============== ============= =============== .. _list_software_Guile_502: @@ -11251,6 +11883,8 @@ version versionsuffix toolchain ``8.1.1`` ``system`` ``9.0.0`` ``system`` ``9.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``9.0.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``9.0.1`` ``system`` ========= ================= =============================== @@ -11268,7 +11902,7 @@ version toolchain ======== ======================================================= ``1.8`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.9`` ``GCCcore/7.3.0`` -``1.10`` ``GCCcore/8.2.0`` +``1.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ======== ======================================================= @@ -11450,6 +12084,7 @@ version toolchain ``1.9.0`` ``fosscuda/2018b`` ``2.2.0`` ``foss/2018b``, ``fosscuda/2018b`` ``2.4.0`` ``GCCcore/8.2.0`` +``2.6.4`` ``GCCcore/8.3.0`` ========= ================================================ @@ -11494,11 +12129,12 @@ HDDM is a Puthon toolbox for hierarchical Bayesian parameter estimation of the *homepage*: http://ski.clps.brown.edu/hddm_docs -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``0.6.1`` ``-Python-3.6.6`` ``intel/2018b`` -========= ================= =============== +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``0.6.1`` ``-Python-3.6.6`` ``intel/2018b`` +``0.7.5`` ``-Python-2.7.16`` ``intel/2019b`` +========= ================== =============== .. _list_software_HDF_210: @@ -11651,6 +12287,7 @@ version toolchain ``1.47.7`` ``GCCcore/8.2.0`` ``1.47.8`` ``GCCcore/7.4.0``, ``GCCcore/8.3.0`` ``1.47.10`` ``GCCcore/9.1.0``, ``GCCcore/9.2.0`` +``1.47.12`` ``GCCcore/9.3.0`` =========== ================================================================================================================================================================================== @@ -11818,7 +12455,9 @@ version versionsuffix toolchain ``0.9.10`` ``-Python-3.6.3`` ``intel/2017b`` ``0.18.1`` ``-Python-3.7.2`` ``foss/2019a`` ``0.18.2`` ``-TensorFlow-1.15.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.18.2`` ``-TensorFlow-1.15.2-Python-3.7.4`` ``fosscuda/2019b`` ``0.18.2`` ``-TensorFlow-2.0.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.19.1`` ``-TensorFlow-2.1.0-Python-3.7.4`` ``fosscuda/2019b`` ========== =================================== ================== @@ -11969,6 +12608,7 @@ version versionsuffix toolchain ``1.7`` ``intel/2018a`` ``1.8`` ``foss/2018a``, ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` +``1.10.2`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ``20160107`` ``-PacBio`` ``intel/2017a`` ============ ============= =========================================================================================================================================================== @@ -12123,6 +12763,7 @@ version toolchain ``2.11.1`` ``foss/2016a``, ``intel/2016a`` ``2.14.0`` ``foss/2018a``, ``intel/2018a`` ``2.15.1`` ``foss/2019a``, ``intel/2019a`` +``2.18.2`` ``foss/2019b``, ``intel/2019b`` ========== =============================== @@ -12132,7 +12773,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_ITSTool_654` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_ITSTool_654` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -12280,6 +12921,7 @@ version versionsuffix toolchain ``2019.4.243`` ``system`` ``2019.5.281`` ``system`` ``2020.0.166`` ``system`` +``2020.0.166`` ``-GCC-9.2.0`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ============== ===================== ========== @@ -12449,12 +13091,13 @@ version toolchain igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. -*homepage*: http://igraph.org +*homepage*: https://igraph.org ========= ================================================ version toolchain ========= ================================================ ``0.7.1`` ``foss/2018b``, ``intel/2016b``, ``intel/2017b`` +``0.8.0`` ``foss/2019b`` ========= ================================================ @@ -12465,7 +13108,7 @@ version toolchain This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. -*homepage*: http://www.broadinstitute.org/software/igv/ +*homepage*: https://www.broadinstitute.org/software/igv/ ========== ================== ========== version versionsuffix toolchain @@ -12473,9 +13116,26 @@ version versionsuffix toolchain ``2.3.68`` ``-Java-1.7.0_80`` ``system`` ``2.3.80`` ``-Java-1.7.0_80`` ``system`` ``2.5.0`` ``-Java-11`` ``system`` +``2.8.0`` ``-Java-11`` ``system`` ========== ================== ========== +.. _list_software_igv-reports_1154: + +*igv-reports* ++++++++++++++ + +Python application to generate self-contained igv.js pages that can be opened within a browser with "file" protocol. + +*homepage*: https://github.com/igvteam/igv-reports + +========= ================= ============= +version versionsuffix toolchain +========= ================= ============= +``0.9.8`` ``-Python-3.7.4`` ``GCC/8.3.0`` +========= ================= ============= + + .. _list_software_IGVTools_759: *IGVTools* @@ -12836,7 +13496,7 @@ version versionsuffix toolchain ``2019.1.144`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2019.2.187`` ``iccifort/2019.2.187-GCC-8.2.0-2.31.1`` ``2019.3.199`` ``iccifort/2019.3.199-GCC-8.3.0-2.32`` -``2019.6.166`` ``iccifort/2020.0.166`` +``2019.6.166`` ``iccifort/2020.0.166-GCC-9.2.0`` ``system`` ``iccifort/system-GCC-system-2.29`` ============== ============= ================================================================================================================================================================================================================================ @@ -12876,6 +13536,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_inferCNV_763: + +*inferCNV* +++++++++++ + +InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence for somatic large-scale chromosomal copy number alterations, such as gains or deletions of entire chromosomes or large segments of chromosomes. + +*homepage*: https://github.com/broadinstitute/inferCNV/wiki + +========= ========================= ============== +version versionsuffix toolchain +========= ========================= ============== +``1.0.4`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` +========= ========================= ============== + + .. _list_software_Infernal_815: *Infernal* @@ -13346,7 +14022,7 @@ version versionsuffix toolchain ``6.4.0`` ``-Python-3.6.4`` ``foss/2018a`` ``7.2.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``7.7.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` -``7.9.0`` ``-Python-3.7.4`` ``foss/2019b`` +``7.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ========= ================== ======================================================================================= @@ -13359,12 +14035,13 @@ Efficient phylogenomic software by maximum likelihood *homepage*: http://www.iqtree.org/ -========= ============= =============== -version versionsuffix toolchain -========= ============= =============== -``1.5.5`` ``-omp-mpi`` ``foss/2016a`` -``1.6.6`` ``intel/2018a`` -========= ============= =============== +========== ============= =============== +version versionsuffix toolchain +========== ============= =============== +``1.5.5`` ``-omp-mpi`` ``foss/2016a`` +``1.6.6`` ``intel/2018a`` +``1.6.12`` ``intel/2019b`` +========== ============= =============== .. _list_software_IRkernel_796: @@ -13376,11 +14053,12 @@ The R kernel for the 'Jupyter' environment executes R code which the front-end *homepage*: https://irkernel.github.io -========== ========================== =============================== -version versionsuffix toolchain -========== ========================== =============================== -``0.8.15`` ``-R-3.4.3-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -========== ========================== =============================== +========== ========================== ================================== +version versionsuffix toolchain +========== ========================== ================================== +``0.8.15`` ``-R-3.4.3-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``1.1`` ``-R-3.6.2-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========== ========================== ================================== .. _list_software_IronPython_1050: @@ -13432,6 +14110,7 @@ version toolchain ========== ========== ``1.6.0`` ``system`` ``1.10.0`` ``system`` +``1.12.0`` ``system`` ========== ========== @@ -13477,6 +14156,7 @@ version versionsuffix toolchain ``4.13.1`` ``-Python-3.6.4`` ``foss/2018a`` ``4.13.1`` ``-Python-3.6.6`` ``foss/2018b`` ``5.0.1`` ``-Python-3.7.2`` ``foss/2019a`` +``5.0.1`` ``-Python-3.7.4`` ``foss/2019b`` ``5.0b01`` ``-Python-3.6.6`` ``foss/2018b`` ========== ================== ============== @@ -13499,13 +14179,29 @@ version versionsuffix toolchain ========= ================== ================= +.. _list_software_iVar_402: + +*iVar* +++++++ + +iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. + +*homepage*: https://github.com/andersen-lab/ivar + +========= ============== +version toolchain +========= ============== +``1.0.1`` ``foss/2018b`` +========= ============== + + .. _list_software_letter_j: *J* --- -:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_jq_219` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyterhub_1106` - :ref:`list_software_JWM_238` +:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyterhub_1106` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` .. _list_software_JAGS_293: @@ -13517,12 +14213,12 @@ JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian *homepage*: http://mcmc-jags.sourceforge.net/ -========= ================================================ -version toolchain -========= ================================================ -``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` -``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b`` -========= ================================================ +========= =============================================================== +version toolchain +========= =============================================================== +``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` +``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b`` +========= =============================================================== .. _list_software_Jansson_732: @@ -13567,54 +14263,58 @@ version toolchain Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. -*homepage*: http://java.com/ - -======================= ========== -version toolchain -======================= ========== -``1.6.0_24`` ``system`` -``1.7.0_10`` ``system`` -``1.7.0_15`` ``system`` -``1.7.0_21`` ``system`` -``1.7.0_40`` ``system`` -``1.7.0_45`` ``system`` -``1.7.0_60`` ``system`` -``1.7.0_75`` ``system`` -``1.7.0_76`` ``system`` -``1.7.0_79`` ``system`` -``1.7.0_80`` ``system`` -``1.8`` ``system`` -``1.8.0_20`` ``system`` -``1.8.0_25`` ``system`` -``1.8.0_31`` ``system`` -``1.8.0_40`` ``system`` -``1.8.0_45`` ``system`` -``1.8.0_60`` ``system`` -``1.8.0_65`` ``system`` -``1.8.0_66`` ``system`` -``1.8.0_72`` ``system`` -``1.8.0_74`` ``system`` -``1.8.0_77`` ``system`` -``1.8.0_92`` ``system`` -``1.8.0_112`` ``system`` -``1.8.0_121`` ``system`` -``1.8.0_131`` ``system`` -``1.8.0_141`` ``system`` -``1.8.0_144`` ``system`` -``1.8.0_152`` ``system`` -``1.8.0_162`` ``system`` -``1.8.0_172`` ``system`` -``1.8.0_181`` ``system`` -``1.8.0_192`` ``system`` -``1.8.0_202`` ``system`` -``1.8.0_212`` ``system`` -``1.8.0_221`` ``system`` -``1.8.0_231`` ``system`` -``1.8_191-b26-OpenJDK`` ``system`` -``1.9.0.4`` ``system`` -``11`` ``system`` -``11.0.2`` ``system`` -======================= ========== +*homepage*: https://java.com/ + +======================= ============= ========== +version versionsuffix toolchain +======================= ============= ========== +``1.6.0_24`` ``system`` +``1.7.0_10`` ``system`` +``1.7.0_15`` ``system`` +``1.7.0_21`` ``system`` +``1.7.0_40`` ``system`` +``1.7.0_45`` ``system`` +``1.7.0_60`` ``system`` +``1.7.0_75`` ``system`` +``1.7.0_76`` ``system`` +``1.7.0_79`` ``system`` +``1.7.0_80`` ``system`` +``1.8`` ``system`` +``1.8.0_20`` ``system`` +``1.8.0_25`` ``system`` +``1.8.0_31`` ``system`` +``1.8.0_40`` ``system`` +``1.8.0_45`` ``system`` +``1.8.0_60`` ``system`` +``1.8.0_65`` ``system`` +``1.8.0_66`` ``system`` +``1.8.0_72`` ``system`` +``1.8.0_74`` ``system`` +``1.8.0_77`` ``system`` +``1.8.0_92`` ``system`` +``1.8.0_112`` ``system`` +``1.8.0_121`` ``system`` +``1.8.0_131`` ``system`` +``1.8.0_141`` ``system`` +``1.8.0_144`` ``system`` +``1.8.0_152`` ``system`` +``1.8.0_162`` ``system`` +``1.8.0_172`` ``system`` +``1.8.0_181`` ``system`` +``1.8.0_192`` ``system`` +``1.8.0_202`` ``system`` +``1.8.0_212`` ``system`` +``1.8.0_221`` ``system`` +``1.8.0_231`` ``system`` +``1.8.0_241`` ``system`` +``1.8_191-b26-OpenJDK`` ``system`` +``1.9.0.4`` ``system`` +``11`` ``system`` +``11.0.2`` ``system`` +``11.0.6`` ``-ppc64le`` ``system`` +``13`` ``system`` +``13.0.2`` ``system`` +======================= ============= ========== .. _list_software_JAXFrontCE_884: @@ -13658,15 +14358,15 @@ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. *homepage*: http://www.genome.umd.edu/jellyfish.html -========== =============================== -version toolchain -========== =============================== -``1.1.11`` ``foss/2016a``, ``foss/2016b`` -``1.1.12`` ``foss/2018b``, ``intel/2018a`` -``2.2.6`` ``foss/2016b``, ``intel/2017a`` -``2.2.10`` ``foss/2018b``, ``intel/2018a`` -``2.3.0`` ``GCC/8.2.0-2.31.1`` -========== =============================== +========== =================================== +version toolchain +========== =================================== +``1.1.11`` ``foss/2016a``, ``foss/2016b`` +``1.1.12`` ``foss/2018b``, ``intel/2018a`` +``2.2.6`` ``foss/2016b``, ``intel/2017a`` +``2.2.10`` ``foss/2018b``, ``intel/2018a`` +``2.3.0`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` +========== =================================== .. _list_software_jemalloc_839: @@ -13741,6 +14441,22 @@ version versionsuffix toolchain =================== ================== ========== +.. _list_software_joypy_571: + +*joypy* ++++++++ + +Joyplots in Python with matplotlib & pandas + +*homepage*: https://github.com/sbebo/joypy + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.2.2`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + .. _list_software_jq_219: *jq* @@ -13822,6 +14538,7 @@ version versionsuffix toolchain ``1.1.1`` ``-linux-x86_64`` ``system`` ``1.2.0`` ``-linux-x86_64`` ``system`` ``1.3.1`` ``-linux-x86_64`` ``system`` +``1.4.0`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -13875,6 +14592,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_JupyterLab_1026: + +*JupyterLab* +++++++++++++ + +JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook. + +*homepage*: https://jupyter.org/ + +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``1.2.5`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========= ================= ================================== + + .. _list_software_JWM_238: *JWM* @@ -13897,7 +14630,7 @@ version toolchain --- -:ref:`list_software_Kaiju_500` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` +:ref:`list_software_Kaiju_500` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_kma_313` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` .. _list_software_Kaiju_500: @@ -13914,6 +14647,7 @@ version versionsuffix toolchain ========= ================= =============== ``1.5.0`` ``intel/2016b`` ``1.7.2`` ``-Python-3.7.2`` ``iimpi/2019a`` +``1.7.3`` ``-Python-3.7.4`` ``gompi/2019b`` ========= ================= =============== @@ -13924,7 +14658,7 @@ version versionsuffix toolchain kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. -*homepage*: http://pachterlab.github.io/kallisto/ +*homepage*: https://pachterlab.github.io/kallisto/ ========== ================================================ version toolchain @@ -13936,6 +14670,7 @@ version toolchain ``0.45.0`` ``foss/2018b`` ``0.45.1`` ``foss/2019a`` ``0.46.0`` ``intel/2019a`` +``0.46.1`` ``foss/2019b`` ========== ================================================ @@ -14021,6 +14756,7 @@ version versionsuffix toolchain ``2.2.4`` ``-Python-3.6.4`` ``intel/2018a`` ``2.2.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``2.2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` +``2.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========= ================== ================================== @@ -14054,9 +14790,26 @@ Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collec version toolchain ========= =============================== ``2.1.2`` ``foss/2019a``, ``intel/2019a`` +``2.1.3`` ``foss/2019b``, ``intel/2019b`` ========= =============================== +.. _list_software_kma_313: + +*kma* ++++++ + +KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. + +*homepage*: https://bitbucket.org/genomicepidemiology/kma + +========== =============== +version toolchain +========== =============== +``1.2.22`` ``intel/2019b`` +========== =============== + + .. _list_software_KMC_219: *KMC* @@ -14152,12 +14905,13 @@ Kraken is a system for assigning taxonomic labels to short DNA sequences, usual *homepage*: http://www.ccb.jhu.edu/software/kraken2/ -============== ================ ============== -version versionsuffix toolchain -============== ================ ============== -``2.0.6-beta`` ``-Perl-5.26.1`` ``foss/2018a`` -``2.0.7-beta`` ``-Perl-5.28.0`` ``foss/2018b`` -============== ================ ============== +============== ================ =============== +version versionsuffix toolchain +============== ================ =============== +``2.0.6-beta`` ``-Perl-5.26.1`` ``foss/2018a`` +``2.0.7-beta`` ``-Perl-5.28.0`` ``foss/2018b`` +``2.0.8-beta`` ``-Perl-5.30.0`` ``gompi/2019b`` +============== ================ =============== .. _list_software_Kratos_628: @@ -14263,7 +15017,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libpsml_755` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -14299,6 +15053,39 @@ version toolchain ========== =========================================================================================== +.. _list_software_LAMMPS_458: + +*LAMMPS* +++++++++ + +LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. + +*homepage*: https://lammps.sandia.gov/ + +============ ======================== =============================== +version versionsuffix toolchain +============ ======================== =============================== +``3Mar2020`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` +``7Aug2019`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` +============ ======================== =============================== + + +.. _list_software_lancet_631: + +*lancet* +++++++++ + +Lancet is a somatic variant caller (SNVs and indels) for short read data. + +*homepage*: https://github.com/nygenome/lancet + +========= ======================= +version toolchain +========= ======================= +``1.1.0`` ``iccifort/2019.5.281`` +========= ======================= + + .. _list_software_LAST_308: *LAST* @@ -14308,12 +15095,13 @@ LAST finds similar regions between sequences. *homepage*: http://last.cbrc.jp/ -======= =============== -version toolchain -======= =============== -``869`` ``intel/2017a`` -``914`` ``intel/2017b`` -======= =============== +======== =============== +version toolchain +======== =============== +``869`` ``intel/2017a`` +``914`` ``intel/2017b`` +``1045`` ``intel/2019b`` +======== =============== .. _list_software_LASTZ_398: @@ -14323,12 +15111,13 @@ version toolchain LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. -*homepage*: http://www.bx.psu.edu/~rsharris/lastz/ +*homepage*: https://www.bx.psu.edu/~rsharris/lastz/ =========== ============== version toolchain =========== ============== ``1.02.00`` ``foss/2016a`` +``1.04.03`` ``foss/2019b`` =========== ============== @@ -14496,6 +15285,22 @@ version toolchain ========= ================= +.. _list_software_libBigWig_880: + +*libBigWig* ++++++++++++ + +A C library for handling bigWig files + +*homepage*: https://github.com/dpryan79/libBigWig + +========= ================= +version toolchain +========= ================= +``0.4.4`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_libbitmask_1058: *libbitmask* @@ -14657,7 +15462,7 @@ version versionsuffix toolchain Direct Rendering Manager runtime library. -*homepage*: http://dri.freedesktop.org +*homepage*: https://dri.freedesktop.org ========== ================================================== version toolchain @@ -14738,6 +15543,7 @@ Epoxy is a library for handling OpenGL function pointer management for you version toolchain ========= ===================================== ``1.5.3`` ``GCCcore/8.2.0``, ``fosscuda/2018b`` +``1.5.4`` ``GCCcore/8.3.0`` ========= ===================================== @@ -14750,13 +15556,13 @@ The libevent API provides a mechanism to execute a callback function when a spec *homepage*: http://libevent.org/ -========== ======================================================================== -version toolchain -========== ======================================================================== -``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` -``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` -``2.1.11`` ``GCCcore/8.3.0`` -========== ======================================================================== +========== ====================================================================================== +version toolchain +========== ====================================================================================== +``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` +``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` +``2.1.11`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +========== ====================================================================================== .. _list_software_libffcall_927: @@ -14961,9 +15767,26 @@ version versionsuffix toolchain ``0.7.6`` ``fosscuda/2019a`` ``0.7.6`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``0.7.6`` ``-Python-3.6.6`` ``fosscuda/2018b`` +``0.7.6`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ================== ======================================================== +.. _list_software_libGridXC_856: + +*libGridXC* ++++++++++++ + +A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems. It is based on SiestaXC. + +*homepage*: https://launchpad.net/libgridxc + +========= =============== +version toolchain +========= =============== +``0.8.5`` ``iimpi/2019b`` +========= =============== + + .. _list_software_libgtextutils_1428: *libgtextutils* @@ -14989,11 +15812,11 @@ libHaru is a free, cross platform, open source library for generating PDF files. *homepage*: http://libharu.org/ -========= ====================================================================================================== -version toolchain -========= ====================================================================================================== -``2.3.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2017a``, ``intel/2018b`` -========= ====================================================================================================== +========= ========================================================================================================================= +version toolchain +========= ========================================================================================================================= +``2.3.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2017a``, ``intel/2018b`` +========= ========================================================================================================================= .. _list_software_libibmad_820: @@ -15075,7 +15898,7 @@ version toolchain ======== ====================================================================================== ``1.32`` ``GCCcore/5.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` ``1.34`` ``GCCcore/6.4.0`` -``1.35`` ``GCCcore/7.3.0`` +``1.35`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ======== ====================================================================================== @@ -15203,6 +16026,7 @@ libpng is the official PNG reference library version toolchain ========== ===================================================================== ``1.2.58`` ``system`` +``1.2.59`` ``system`` ``1.6.21`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``1.6.23`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``1.6.24`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` @@ -15250,6 +16074,22 @@ version toolchain ========= ============================== +.. _list_software_libPSML_627: + +*libPSML* ++++++++++ + +A library to handle PSML, the pseudopotential markup language. + +*homepage*: https://launchpad.net/libpsml + +========= ======================= +version toolchain +========= ======================= +``1.1.8`` ``iccifort/2019.5.281`` +========= ======================= + + .. _list_software_libpsortb_977: *libpsortb* @@ -15529,13 +16369,13 @@ version toolchain LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification. -*homepage*: http://www.csie.ntu.edu.tw/~cjlin/libsvm/ +*homepage*: https://www.csie.ntu.edu.tw/~cjlin/libsvm/ ======== ================================ version toolchain ======== ================================ ``3.22`` ``intel/2016b``, ``intel/2017b`` -``3.23`` ``intel/2018b`` +``3.23`` ``foss/2018b``, ``intel/2018b`` ======== ================================ @@ -15704,14 +16544,14 @@ version toolchain libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes. -*homepage*: http://libvdwxc.org +*homepage*: https://libvdwxc.org -========= ============== -version toolchain -========= ============== -``0.3.2`` ``foss/2018b`` -``0.4.0`` ``foss/2019a`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``0.3.2`` ``foss/2018b`` +``0.4.0`` ``foss/2019a``, ``foss/2019b`` +========= ============================== .. _list_software_libwebp_741: @@ -15782,7 +16622,7 @@ version toolchain ``4.0.1`` ``foss/2017b``, ``intel/2017b`` ``4.0.3`` ``foss/2016b``, ``foss/2017a`` ``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` -``4.3.4`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``4.3.4`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` ========= ======================================================================================================================================= @@ -16266,6 +17106,7 @@ version toolchain ``4.1.0`` ``GCCcore/4.9.3`` ``4.2.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2017a``, ``intel/2017a`` ``4.3.2`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``5.0.1`` ``GCCcore/8.3.0`` ========= ===================================================================== @@ -16310,25 +17151,28 @@ version toolchain The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. -*homepage*: http://llvm.org/ +*homepage*: https://llvm.org/ -========= ======================================================================== -version toolchain -========= ======================================================================== -``3.7.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``3.8.0`` ``foss/2016a``, ``intel/2016a`` -``3.8.1`` ``GCCcore/4.9.3``, ``foss/2016b``, ``intel/2016b`` -``3.9.0`` ``foss/2016b``, ``intel/2016b`` -``3.9.1`` ``foss/2017a`` -``4.0.0`` ``foss/2017a``, ``intel/2017a`` -``4.0.1`` ``intel/2017a``, ``intel/2017b`` -``5.0.0`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``5.0.1`` ``GCCcore/6.4.0`` -``6.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``7.0.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``7.0.1`` ``GCCcore/8.2.0`` -``9.0.0`` ``GCCcore/8.3.0`` -========= ======================================================================== +========== ======================================================================== +version toolchain +========== ======================================================================== +``3.7.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``3.8.0`` ``foss/2016a``, ``intel/2016a`` +``3.8.1`` ``GCCcore/4.9.3``, ``foss/2016b``, ``intel/2016b`` +``3.9.0`` ``foss/2016b``, ``intel/2016b`` +``3.9.1`` ``foss/2017a`` +``4.0.0`` ``foss/2017a``, ``intel/2017a`` +``4.0.1`` ``intel/2017a``, ``intel/2017b`` +``5.0.0`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``5.0.1`` ``GCCcore/6.4.0`` +``6.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``7.0.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``7.0.1`` ``GCCcore/8.2.0`` +``8.0.1`` ``GCCcore/8.3.0`` +``9.0.0`` ``GCCcore/8.3.0`` +``9.0.1`` ``GCCcore/8.3.0`` +``10.0.0`` ``GCCcore/8.3.0`` +========== ======================================================================== .. _list_software_LMDB_287: @@ -16360,11 +17204,12 @@ Lmfit provides a high-level interface to non-linear optimization and curve fitti *homepage*: https://lmfit.github.io/lmfit-py -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``0.9.9`` ``-Python-3.6.4`` ``intel/2018a`` -========= ================= =============== +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``0.9.9`` ``-Python-3.6.4`` ``intel/2018a`` +``0.9.14`` ``-Python-2.7.15`` ``intel/2018b`` +========== ================== =============== .. _list_software_Lmod_396: @@ -16535,12 +17380,13 @@ LS-PrePost is an advanced pre and post-processor that is delivered free with LS- *homepage*: http://lstc.com/products/ls-prepost -======= ============= ========== -version versionsuffix toolchain -======= ============= ========== -``4.6`` ``-centos6`` ``system`` -``4.6`` ``-centos7`` ``system`` -======= ============= ========== +========= ============= ========== +version versionsuffix toolchain +========= ============= ========== +``4.6`` ``-centos6`` ``system`` +``4.6`` ``-centos7`` ``system`` +``4.7.8`` ``system`` +========= ============= ========== .. _list_software_LSMS_319: @@ -16559,6 +17405,22 @@ version toolchain ============ ============== +.. _list_software_LtrDetector_1132: + +*LtrDetector* ++++++++++++++ + +A modern tool-suite for detectinglong terminal repeat retrotransposons de-novo onthe genomic scale + +*homepage*: https://github.com/TulsaBioinformaticsToolsmith/LtrDetector + +======= ================= =============== +version versionsuffix toolchain +======= ================= =============== +``1.0`` ``-Python-3.7.4`` ``intel/2019b`` +======= ================= =============== + + .. _list_software_Lua_290: *Lua* @@ -16568,16 +17430,16 @@ Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combin *homepage*: http://www.lua.org/ -=========== ======================================== -version toolchain -=========== ======================================== -``5.1.4-5`` ``GCC/4.8.2`` -``5.1.4-8`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``system`` -``5.1.5`` ``GCCcore/7.3.0`` -``5.2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``5.3.4`` ``GCCcore/7.2.0``, ``system`` -``5.3.5`` ``GCCcore/8.2.0``, ``system`` -=========== ======================================== +=========== ================================================ +version toolchain +=========== ================================================ +``5.1.4-5`` ``GCC/4.8.2`` +``5.1.4-8`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``system`` +``5.1.5`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +``5.2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``5.3.4`` ``GCCcore/7.2.0``, ``system`` +``5.3.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` +=========== ================================================ .. _list_software_LuaJIT_521: @@ -16730,12 +17592,12 @@ Portable lossless data compression library *homepage*: http://www.oberhumer.com/opensource/lzo/ -======== ========================================================================================================================================================= -version toolchain -======== ========================================================================================================================================================= -``2.09`` ``intel/2016b``, ``intel/2017b`` -``2.10`` ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` -======== ========================================================================================================================================================= +======== ============================================================================================================================================================================ +version toolchain +======== ============================================================================================================================================================================ +``2.09`` ``intel/2016b``, ``intel/2017b`` +``2.10`` ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` +======== ============================================================================================================================================================================ .. _list_software_letter_m: @@ -16744,7 +17606,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_magma_515` - :ref:`list_software_MAGMA_355` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_Mako_392` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_mordecai_836` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_magma_515` - :ref:`list_software_MAGMA_355` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -16761,7 +17623,7 @@ version toolchain ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.4.16`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.4.18`` ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/system``, ``system`` +``1.4.18`` ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -16825,14 +17687,15 @@ MAFFT is a multiple sequence alignment program for unix-like operating systems *homepage*: https://mafft.cbrc.jp/alignment/software/source.html -========= ==================== ==================== -version versionsuffix toolchain -========= ==================== ==================== -``7.305`` ``-with-extensions`` ``foss/2016b`` -``7.397`` ``-with-extensions`` ``intel/2018a`` -``7.427`` ``-with-extensions`` ``intel/2018b`` -``7.429`` ``-with-extensions`` ``GCC/8.2.0-2.31.1`` -========= ==================== ==================== +========= ==================== ====================================== +version versionsuffix toolchain +========= ==================== ====================================== +``7.305`` ``-with-extensions`` ``foss/2016b`` +``7.397`` ``-with-extensions`` ``intel/2018a`` +``7.427`` ``-with-extensions`` ``intel/2018b`` +``7.429`` ``-with-extensions`` ``GCC/8.2.0-2.31.1`` +``7.453`` ``-with-extensions`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +========= ==================== ====================================== .. _list_software_magick_620: @@ -17009,6 +17872,23 @@ version versionsuffix toolchain ========= ================== ================================================================================================================================================================= +.. _list_software_manta_529: + +*manta* ++++++++ + +Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow. + +*homepage*: https://github.com/Illumina/manta + +========= ========== +version toolchain +========= ========== +``1.1.1`` ``system`` +``1.6.0`` ``system`` +========= ========== + + .. _list_software_Maple_495: *Maple* @@ -17092,13 +17972,13 @@ MariaDB Connector/C is used to connect applications developed in C/C++ to MariaD *homepage*: https://downloads.mariadb.org/connector-c/ -========= ================================= -version toolchain -========= ================================= -``2.3.4`` ``foss/2017b``, ``intel/2017b`` -``2.3.5`` ``intel/2018a``, ``iomkl/2018a`` -``2.3.7`` ``GCCcore/8.2.0``, ``foss/2018b`` -========= ================================= +========= ==================================================== +version toolchain +========= ==================================================== +``2.3.4`` ``foss/2017b``, ``intel/2017b`` +``2.3.5`` ``intel/2018a``, ``iomkl/2018a`` +``2.3.7`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` +========= ==================================================== .. _list_software_Mash_393: @@ -17202,7 +18082,7 @@ version toolchain MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. -*homepage*: http://www.mathworks.com/products/matlab +*homepage*: https://www.mathworks.com/products/matlab.html ========= ========== version toolchain @@ -17213,6 +18093,7 @@ version toolchain ``2016a`` ``system`` ``2017a`` ``system`` ``2018b`` ``system`` +``2019b`` ``system`` ========= ========== @@ -17273,10 +18154,12 @@ version versionsuffix toolchain ``2.2.3`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.2.3`` ``-Python-3.6.6`` ``intel/2018b`` ``2.2.4`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` +``2.2.4`` ``-Python-2.7.16`` ``foss/2019b``, ``intel/2019b`` +``2.2.5`` ``-Python-2.7.16`` ``foss/2019b`` ``3.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` ``3.0.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ========= ================================= ======================================================================== @@ -17314,6 +18197,7 @@ version toolchain ``3.5.0`` ``system`` ``3.5.2`` ``system`` ``3.6.0`` ``system`` +``3.6.3`` ``system`` ========= ========== @@ -17380,6 +18264,7 @@ The Mayavi scientific data 3-dimensional visualizer version versionsuffix toolchain ========= ================== =============== ``4.4.4`` ``-Python-2.7.11`` ``intel/2016a`` +``4.7.1`` ``-Python-2.7.15`` ``foss/2019a`` ``4.7.1`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================== =============== @@ -17409,14 +18294,14 @@ The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable *homepage*: http://micans.org/mcl/ -========== ================ =============================== -version versionsuffix toolchain -========== ================ =============================== -``02.063`` ``intel/2016b`` -``14.137`` ``foss/2016a``, ``intel/2016b`` -``14.137`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``14.137`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -========== ================ =============================== +========== ================ ================================================== +version versionsuffix toolchain +========== ================ ================================================== +``02.063`` ``intel/2016b`` +``14.137`` ``GCCcore/8.3.0``, ``foss/2016a``, ``intel/2016b`` +``14.137`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``14.137`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +========== ================ ================================================== .. _list_software_MCR_226: @@ -17521,17 +18406,51 @@ medaka is a tool to create a consensus sequence of nanopore sequencing data. *homepage*: https://nanoporetech.github.io/medaka +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.4.3`` ``-Python-3.6.6`` ``foss/2018b`` +``0.11.4`` ``-Python-3.6.6`` ``foss/2018b`` +``0.12.0`` ``-Python-3.6.6`` ``foss/2018b`` +========== ================= ============== + + +.. _list_software_medImgProc_999: + +*medImgProc* +++++++++++++ + +Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation. + +*homepage*: https://github.com/WeiXuanChan/motionSegmentation + ========= ================= ============== version versionsuffix toolchain ========= ================= ============== -``0.4.3`` ``-Python-3.6.6`` ``foss/2018b`` +``2.5.7`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== -.. _list_software_Meep_391: +.. _list_software_MedPy_479: -*Meep* -++++++ +*MedPy* ++++++++ + +MedPy is a library and script collection for medical image processing in Python, providing basic functionalities for reading, writing and manipulating large images of arbitrary dimensionality. Its main contributions are n-dimensional versions of popular image filters, a collection of image feature extractors, ready to be used with scikit-learn, and an exhaustive n-dimensional graph-cut package. + +*homepage*: https://pypi.org/project/MedPy/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.4.0`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + +.. _list_software_Meep_391: + +*Meep* +++++++ Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. @@ -17772,6 +18691,7 @@ version versionsuffix toolchain ``0.48.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``0.50.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``0.51.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.53.1`` ``-Python-3.6.3`` ``intel/2017b`` ========== ================= ================================== @@ -17919,6 +18839,7 @@ A (mostly) universal methylation extractor for BS-seq experiments. version toolchain ========= ======================================== ``0.4.0`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``0.5.0`` ``iccifort/2019.5.281`` ========= ======================================== @@ -18021,6 +18942,22 @@ version toolchain ========== =============================================== +.. _list_software_Mini-XML_683: + +*Mini-XML* +++++++++++ + +Mini-XML is a tiny XML library that you can use to read and write XML and XML-like data files in your application without requiring large non-standard libraries. + +*homepage*: https://www.msweet.org/mxml/ + +======= ================= +version toolchain +======= ================= +``2.9`` ``GCCcore/8.2.0`` +======= ================= + + .. _list_software_Miniconda2_964: *Miniconda2* @@ -18217,6 +19154,22 @@ version toolchain ========= =============== +.. _list_software_mkl_fft_739: + +*mkl_fft* ++++++++++ + +NumPy-based Python interface to Intel(R) MKL FFT functionality + +*homepage*: https://github.com/IntelPython/mkl_fft + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``1.0.14`` ``-Python-3.6.6`` ``intel/2018b`` +========== ================= =============== + + .. _list_software_MLC_220: *MLC* @@ -18274,13 +19227,14 @@ MMseqs2: ultra fast and sensitive search and clustering suite *homepage*: https://mmseqs.com -=========== =============== -version toolchain -=========== =============== -``1-c7a89`` ``foss/2016b`` -``5-9375b`` ``intel/2018a`` -``8-fac81`` ``intel/2018b`` -=========== =============== +============ ================================ +version toolchain +============ ================================ +``1-c7a89`` ``foss/2016b`` +``5-9375b`` ``intel/2018a`` +``8-fac81`` ``intel/2018b`` +``10-6d92c`` ``gompi/2019b``, ``iimpi/2019b`` +============ ================================ .. _list_software_modred_635: @@ -18372,7 +19326,7 @@ version versionsuffix toolchain ``1.4.4`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``1.4.4`` ``-Python-2.7.15`` ``intel/2018b`` ``1.4.4`` ``-Python-3.7.2`` ``intel/2019a`` -``1.4.5`` ``-Python-3.7.4`` ``intel/2019b`` +``1.4.5`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========= ================== =============================== @@ -18414,9 +19368,26 @@ version toolchain ``5.10.0.160`` ``foss/2018a`` ``5.18.1.0`` ``foss/2018a`` ``6.4.0.198`` ``foss/2018b`` +``6.8.0.105`` ``GCCcore/8.3.0`` ============== =============================== +.. _list_software_Monocle3_768: + +*Monocle3* +++++++++++ + +An analysis toolkit for single-cell RNA-seq. + +*homepage*: https://cole-trapnell-lab.github.io/monocle3/ + +========= ========================= ============== +version versionsuffix toolchain +========= ========================= ============== +``0.2.0`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` +========= ========================= ============== + + .. _list_software_mordecai_836: *mordecai* @@ -18433,6 +19404,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_MoreRONN_720: + +*MoreRONN* +++++++++++ + +MoreRONN is the spiritual successor of RONN and is useful for surveying disorder in proteins as well as designing expressible constructs for X-ray crystallography. + +*homepage*: https://github.com/varun-ramraj/MoreRONN + +======= ============= +version toolchain +======= ============= +``4.9`` ``GCC/8.3.0`` +======= ============= + + .. _list_software_mosdepth_868: *mosdepth* @@ -18476,15 +19463,15 @@ version versionsuffix toolchain Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix. -*homepage*: http://motif.ics.com/ +*homepage*: https://motif.ics.com/ -========= ================================================================================ -version toolchain -========= ================================================================================ -``2.3.5`` ``foss/2016a``, ``intel/2016a`` -``2.3.7`` ``intel/2017a`` -``2.3.8`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` -========= ================================================================================ +========= ==================================================================================================================================== +version toolchain +========= ==================================================================================================================================== +``2.3.5`` ``foss/2016a``, ``intel/2016a`` +``2.3.7`` ``intel/2017a`` +``2.3.8`` ``GCCcore/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` +========= ==================================================================================================================================== .. _list_software_MotionCor2_972: @@ -18503,6 +19490,22 @@ version toolchain ========= ================= +.. _list_software_motionSegmentation_1924: + +*motionSegmentation* +++++++++++++++++++++ + +Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation. + +*homepage*: https://github.com/WeiXuanChan/motionSegmentation + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``2.7.9`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_MoviePy_713: *MoviePy* @@ -18880,13 +19883,13 @@ A parallel sparse direct solver *homepage*: http://graal.ens-lyon.fr/MUMPS/ -========= ============== =============================== -version versionsuffix toolchain -========= ============== =============================== -``5.1.2`` ``-metis`` ``foss/2017b`` -``5.2.1`` ``-metis`` ``foss/2019a``, ``intel/2019a`` -``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` -========= ============== =============================== +========= ============== ================================================================================ +version versionsuffix toolchain +========= ============== ================================================================================ +``5.1.2`` ``-metis`` ``foss/2017b`` +``5.2.1`` ``-metis`` ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``intel/2019a``, ``intel/2019b`` +``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` +========= ============== ================================================================================ .. _list_software_muParser_847: @@ -18935,7 +19938,7 @@ version versionsuffix toolchain ============ =============== ================================================================================================================== ``3.8.31`` ``foss/2016a``, ``foss/2017b``, ``foss/2018a``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ``3.8.31`` ``-i86linux64`` ``system`` -``3.8.1551`` ``GCC/8.2.0-2.31.1`` +``3.8.1551`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` ============ =============== ================================================================================================================== @@ -19149,7 +20152,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanonet_755` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -19204,6 +20207,22 @@ version versionsuffix toolchain ======== ============= ================================================================ +.. _list_software_NanoComp_795: + +*NanoComp* +++++++++++ + +Comparing runs of Oxford Nanopore sequencing data and alignments + +*homepage*: https://github.com/wdecoster/NanoComp + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``1.10.1`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================= =============== + + .. _list_software_nanofilt_859: *nanofilt* @@ -19220,6 +20239,54 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_NanoFilt_795: + +*NanoFilt* +++++++++++ + +Filtering and trimming of Oxford Nanopore Sequencing data + +*homepage*: https://github.com/wdecoster/nanofilt + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``2.6.0`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + +.. _list_software_nanoget_748: + +*nanoget* ++++++++++ + +Functions to extract information from Oxford Nanopore sequencing data and alignments + +*homepage*: https://github.com/wdecoster/nanoget + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``1.12.1`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================= =============== + + +.. _list_software_nanomath_854: + +*nanomath* +++++++++++ + +A few simple math function for other Oxford Nanopore processing scripts + +*homepage*: https://github.com/wdecoster/nanomath + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``0.23.1`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================= =============== + + .. _list_software_nanonet_755: *nanonet* @@ -19236,6 +20303,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_NanoPlot_811: + +*NanoPlot* +++++++++++ + +Plotting suite for long read sequencing data and alignments + +*homepage*: https://github.com/wdecoster/NanoPlot + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``1.28.4`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================= =============== + + .. _list_software_nanopolish_1083: *nanopolish* @@ -19364,6 +20447,7 @@ version versionsuffix toolchain ``1.16`` ``-R-3.4.4`` ``intel/2018a`` ``1.16.1`` ``-R-3.5.1`` ``foss/2018b``, ``intel/2018b`` ``1.16.1`` ``-R-3.6.0`` ``foss/2019a`` +``1.17`` ``foss/2019b`` ========== ============= =============================== @@ -19480,7 +20564,7 @@ version toolchain The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. -*homepage*: http://www.gnu.org/software/ncurses/ +*homepage*: https://www.gnu.org/software/ncurses/ ======= ============================================================================================================================================================================================================================================================================================================================================================================= version toolchain @@ -19654,7 +20738,7 @@ version versionsuffix toolchain ``4.4.4`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.4.4`` ``-HDF5-1.8.19`` ``foss/2017b``, ``intel/2017b`` ``4.4.5`` ``gompi/2019a``, ``iimpi/2019a`` -``4.5.2`` ``iimpi/2019b`` +``4.5.2`` ``gompi/2019b``, ``iimpi/2019b`` ========= ================ ==================================================================================================================================================================================================================================================================================================================================== @@ -19680,6 +20764,7 @@ version versionsuffix toolchain ``1.4.2`` ``-Python-3.6.4`` ``foss/2018a`` ``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` ``1.5.2`` ``intel/2019a`` +``1.5.3`` ``-Python-3.7.4`` ``intel/2019b`` ========= ============================= =============== @@ -19810,21 +20895,21 @@ NetworkX is a Python package for the creation, manipulation, and study of the st *homepage*: https://pypi.python.org/pypi/networkx -======== ================== =============================== -version versionsuffix toolchain -======== ================== =============================== -``1.1`` ``-Python-2.7.12`` ``intel/2016b`` -``1.11`` ``-Python-2.7.11`` ``foss/2016a`` -``1.11`` ``-Python-2.7.14`` ``intel/2017b`` -``1.11`` ``-Python-3.5.1`` ``foss/2016a`` -``2.0`` ``-Python-2.7.14`` ``intel/2017b`` -``2.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.2`` ``-Python-2.7.15`` ``intel/2018b`` -``2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``2.4`` ``-Python-3.7.4`` ``foss/2019b`` -======== ================== =============================== +======== ================== =============================================== +version versionsuffix toolchain +======== ================== =============================================== +``1.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.11`` ``-Python-2.7.11`` ``foss/2016a`` +``1.11`` ``-Python-2.7.14`` ``intel/2017b`` +``1.11`` ``-Python-3.5.1`` ``foss/2016a`` +``2.0`` ``-Python-2.7.14`` ``intel/2017b`` +``2.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b`` +``2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``2.4`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +======== ================== =============================================== .. _list_software_NeuroKit_817: @@ -19867,13 +20952,15 @@ version versionsuffix toolchain Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data -*homepage*: https://www.nextflow.io/ +*homepage*: https://www.nextflow.io =========== ========== version toolchain =========== ========== ``19.04.0`` ``system`` ``19.07.0`` ``system`` +``19.12.0`` ``system`` +``20.01.0`` ``system`` =========== ========== @@ -19979,6 +21066,22 @@ version toolchain ======= ================== +.. _list_software_ngspice_745: + +*ngspice* ++++++++++ + +Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice. + +*homepage*: https://ngspice.sourceforge.net + +======= ============== +version toolchain +======= ============== +``31`` ``foss/2019b`` +======= ============== + + .. _list_software_NiBabel_653: *NiBabel* @@ -20172,6 +21275,7 @@ version toolchain ``8.9.4`` ``foss/2017a`` ``10.15.1`` ``foss/2018b`` ``10.15.3`` ``GCCcore/8.2.0`` +``12.16.1`` ``GCCcore/8.3.0`` =========== ================= @@ -20310,6 +21414,38 @@ version toolchain ========== ==================================== +.. _list_software_ntEdit_616: + +*ntEdit* +++++++++ + +ntEdit is a fast and scalable genomics application for polishing genome assembly drafts. + +*homepage*: https://github.com/bcgsc/ntEdit + +========= ====================================== +version toolchain +========= ====================================== +``1.3.1`` ``iccifort/2018.3.222-GCC-7.3.0-2.30`` +========= ====================================== + + +.. _list_software_ntHits_634: + +*ntHits* +++++++++ + +ntHits is a method for identifying repeats in high-throughput DNA sequencing data. + +*homepage*: https://github.com/bcgsc/ntHits + +========= ====================================== +version toolchain +========= ====================================== +``0.0.1`` ``iccifort/2018.3.222-GCC-7.3.0-2.30`` +========= ====================================== + + .. _list_software_numactl_756: *numactl* @@ -20339,18 +21475,19 @@ Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by *homepage*: https://numba.pydata.org/ -========== ================== =============================== -version versionsuffix toolchain -========== ================== =============================== -``0.24.0`` ``-Python-2.7.11`` ``intel/2016a`` -``0.24.0`` ``-Python-3.5.1`` ``intel/2016a`` -``0.26.0`` ``-Python-2.7.11`` ``intel/2016a`` -``0.32.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.37.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` -``0.37.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``0.43.1`` ``intel/2019a`` -``0.46.0`` ``foss/2019a`` -========== ================== =============================== +========== ================== ================================== +version versionsuffix toolchain +========== ================== ================================== +``0.24.0`` ``-Python-2.7.11`` ``intel/2016a`` +``0.24.0`` ``-Python-3.5.1`` ``intel/2016a`` +``0.26.0`` ``-Python-2.7.11`` ``intel/2016a`` +``0.32.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.37.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` +``0.37.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.43.1`` ``intel/2019a`` +``0.46.0`` ``foss/2019a`` +``0.47.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========== ================== ================================== .. _list_software_numexpr_783: @@ -20360,7 +21497,7 @@ version versionsuffix toolchain The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime. -*homepage*: https://numexpr.readthedocs.io +*homepage*: https://numexpr.readthedocs.io/en/latest/ ========= ================== ================================== version versionsuffix toolchain @@ -20377,6 +21514,8 @@ version versionsuffix toolchain ``2.6.5`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.6.5`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``2.7.0`` ``intel/2019a`` +``2.7.1`` ``-Python-2.7.16`` ``intel/2019b`` +``2.7.1`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== ================================== @@ -20458,7 +21597,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenPyXL_767` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_orca_421` - :ref:`list_software_ORCA_293` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -20511,6 +21650,38 @@ version toolchain ========== ============== +.. _list_software_occt_425: + +*occt* +++++++ + +Open CASCADE Technology (OCCT) is an object-oriented C++ class library designed for rapid production of sophisticated domain-specific CAD/CAM/CAE applications. + +*homepage*: https://www.opencascade.com/ + +=========== ============== +version toolchain +=========== ============== +``7.3.0p4`` ``foss/2019b`` +=========== ============== + + +.. _list_software_OCNet_441: + +*OCNet* ++++++++ + +Generate and analyze Optimal Channel Networks (OCNs): oriented spanning trees reproducing all scaling features characteristic of real, natural river networks. As such, they can be used in a variety of numerical experiments in the fields of hydrology, ecology and epidemiology. + +*homepage*: https://cran.r-project.org/web/packages/OCNet + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``0.2.0`` ``-R-3.6.0`` ``foss/2019a`` +========= ============= ============== + + .. _list_software_Octave_610: *Octave* @@ -20518,7 +21689,7 @@ version toolchain GNU Octave is a high-level interpreted language, primarily intended for numerical computations. -*homepage*: http://www.gnu.org/software/octave/ +*homepage*: https://www.gnu.org/software/octave/ ========= ============= ================================================ version versionsuffix toolchain @@ -20529,6 +21700,7 @@ version versionsuffix toolchain ``4.2.1`` ``-mt`` ``intel/2017a`` ``4.2.2`` ``foss/2018a`` ``4.4.1`` ``foss/2018b`` +``5.1.0`` ``foss/2019a``, ``foss/2019b`` ========= ============= ================================================ @@ -20581,6 +21753,22 @@ version toolchain ========= ================= +.. _list_software_OpenAI-Gym_886: + +*OpenAI-Gym* +++++++++++++ + +A toolkit for developing and comparing reinforcement learning algorithms. + +*homepage*: https://gym.openai.com + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.17.1`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_OpenBabel_872: *OpenBabel* @@ -20588,7 +21776,7 @@ version toolchain Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. -*homepage*: http://openbabel.org +*homepage*: https://openbabel.org ========= ================== =============== version versionsuffix toolchain @@ -20597,6 +21785,8 @@ version versionsuffix toolchain ``2.4.1`` ``-Python-2.7.14`` ``intel/2017b`` ``2.4.1`` ``-Python-2.7.15`` ``intel/2018b`` ``2.4.1`` ``-Python-3.6.6`` ``intel/2018b`` +``2.4.1`` ``-Python-3.7.2`` ``intel/2019a`` +``3.0.0`` ``-Python-3.7.4`` ``gompi/2019b`` ========= ================== =============== @@ -20607,7 +21797,7 @@ version versionsuffix toolchain OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. -*homepage*: http://xianyi.github.com/OpenBLAS/ +*homepage*: https://xianyi.github.com/OpenBLAS/ ========== ================= ========================================================== version versionsuffix toolchain @@ -20629,6 +21819,7 @@ version versionsuffix toolchain ``0.3.5`` ``GCC/8.2.0-2.31.1`` ``0.3.6`` ``GCC/8.3.0-2.32`` ``0.3.7`` ``GCC/8.3.0`` +``0.3.8`` ``GCC/9.2.0`` ========== ================= ========================================================== @@ -20673,7 +21864,7 @@ version toolchain OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. -*homepage*: http://opencv.org/ +*homepage*: https://opencv.org/ ========== ================== ================================================================ version versionsuffix toolchain @@ -20691,6 +21882,7 @@ version versionsuffix toolchain ``3.4.7`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``4.0.1`` ``-Python-2.7.15`` ``foss/2018b`` ``4.0.1`` ``-Python-3.6.6`` ``foss/2018b`` +``4.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========== ================== ================================================================ @@ -20701,7 +21893,7 @@ version versionsuffix toolchain OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. -*homepage*: http://opencv.org/ +*homepage*: https://opencv.org/ ========= ================= ============== version versionsuffix toolchain @@ -20742,7 +21934,7 @@ version toolchain ================ ================================================ ``2.2.2`` ``intel/2016a``, ``intel/2017a`` ``2.2.x`` ``intel/2019a`` -``2.3.1`` ``intel/2017a`` +``2.3.1`` ``intel/2017a``, ``intel/2019b`` ``2.4.0`` ``intel/2017a``, ``intel/2019a`` ``3.0.0`` ``foss/2016a`` ``3.0.1`` ``intel/2016b``, ``intel/2018a`` @@ -20758,7 +21950,7 @@ version toolchain ``v1806`` ``foss/2018b`` ``v1812`` ``foss/2018b`` ``v1906`` ``foss/2019b`` -``v1912`` ``foss/2019b`` +``v1912`` ``foss/2019b``, ``intel/2019b`` ================ ================================================ @@ -20771,14 +21963,15 @@ OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive *homepage*: http://www.extend-project.de/ -======= ================== ================================= -version versionsuffix toolchain -======= ================== ================================= -``3.1`` ``gimkl/2.11.5`` -``3.2`` ``gimkl/2.11.5``, ``intel/2016a`` -``4.0`` ``intel/2017a`` -``4.0`` ``-Python-2.7.16`` ``intel/2019b`` -======= ================== ================================= +================ ================== ================================= +version versionsuffix toolchain +================ ================== ================================= +``3.1`` ``gimkl/2.11.5`` +``3.2`` ``gimkl/2.11.5``, ``intel/2016a`` +``4.0`` ``intel/2017a`` +``4.0`` ``-Python-2.7.16`` ``intel/2019b`` +``4.1-20191120`` ``-Python-2.7.16`` ``intel/2019b`` +================ ================== ================================= .. _list_software_OpenImageIO_1037: @@ -20844,11 +22037,11 @@ Open Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of *homepage*: https://openkim.org/ -============ =============================== -version toolchain -============ =============================== -``20190725`` ``foss/2019a``, ``intel/2019a`` -============ =============================== +============ ================================================================ +version toolchain +============ ================================================================ +``20190725`` ``foss/2019a``, ``foss/2019b``, ``intel/2019a``, ``intel/2019b`` +============ ================================================================ .. _list_software_OpenMM_556: @@ -20963,6 +22156,22 @@ version toolchain =========== ============================================================================================================================================================================= +.. _list_software_OpenPIV_641: + +*OpenPIV* ++++++++++ + +OpenPIV is an open source Particle Image Velocimetry analysis software + +*homepage*: http://www.openpiv.net + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``0.21.8`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================= =============== + + .. _list_software_openpyxl_895: *openpyxl* @@ -20979,6 +22188,22 @@ version toolchain ========= ================= +.. _list_software_OpenPyXL_767: + +*OpenPyXL* +++++++++++ + +A Python library to read/write Excel 2010 xlsx/xlsm files + +*homepage*: https://openpyxl.readthedocs.io + +========= ================= +version toolchain +========= ================= +``2.6.4`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_OpenRefine_1003: *OpenRefine* @@ -21118,6 +22343,22 @@ version versionsuffix toolchain ======= ================= ============== +.. _list_software_orca_421: + +*orca* +++++++ + +Orca is an Electron app that generates images and reports of Plotly things like plotly.js graphs, dash apps, dashboards from the command line. + +*homepage*: https://github.com/plotly/orca + +========= ================= +version toolchain +========= ================= +``1.3.0`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_ORCA_293: *ORCA* @@ -21165,12 +22406,14 @@ OrthoFinder is a fast, accurate and comprehensive platform for comparative genom *homepage*: https://github.com/davidemms/OrthoFinder -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``2.2.7`` ``-Python-2.7.14`` ``intel/2018a`` -``2.3.3`` ``-Python-2.7.15`` ``intel/2018b`` -========= ================== =============== +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``2.2.7`` ``-Python-2.7.14`` ``intel/2018a`` +``2.3.3`` ``-Python-2.7.15`` ``intel/2018b`` +``2.3.8`` ``-Python-2.7.16`` ``foss/2019b`` +``2.3.11`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================== =============== .. _list_software_OrthoMCL_744: @@ -21190,14 +22433,30 @@ version versionsuffix toolchain ========= ================ =============== -.. _list_software_OSU-Micro-Benchmarks_1865: +.. _list_software_Osi_299: -*OSU-Micro-Benchmarks* -++++++++++++++++++++++ +*Osi* ++++++ -OSU Micro-Benchmarks +Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver. That is, programs written to the OSI standard may be linked to any solver with an OSI interface and should produce correct results. The OSI has been significantly extended compared to its first incarnation. Currently, the OSI supports linear programming solvers and has rudimentary support for integer programming. -*homepage*: http://mvapich.cse.ohio-state.edu/benchmarks/ +*homepage*: https://github.com/coin-or/Osi + +=========== ================= +version toolchain +=========== ================= +``0.108.5`` ``GCCcore/7.3.0`` +=========== ================= + + +.. _list_software_OSU-Micro-Benchmarks_1865: + +*OSU-Micro-Benchmarks* +++++++++++++++++++++++ + +OSU Micro-Benchmarks + +*homepage*: http://mvapich.cse.ohio-state.edu/benchmarks/ ========= ============================== version toolchain @@ -21263,7 +22522,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_pip_329` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_pip_329` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -21464,6 +22723,7 @@ version toolchain ``1.41.1`` ``foss/2018a``, ``intel/2018a`` ``1.42.4`` ``foss/2018b``, ``fosscuda/2018b`` ``1.43.0`` ``GCCcore/8.2.0`` +``1.44.7`` ``GCCcore/8.3.0`` =========== ================================== @@ -21555,12 +22815,13 @@ parasail is a SIMD C (C99) library containing implementations of the Smith-Wate *homepage*: https://github.com/jeffdaily/parasail -======= =============== -version toolchain -======= =============== -``2.2`` ``intel/2018a`` -``2.4`` ``foss/2018b`` -======= =============== +========= =============== +version toolchain +========= =============== +``2.2`` ``intel/2018a`` +``2.4`` ``foss/2018b`` +``2.4.1`` ``intel/2019b`` +========= =============== .. _list_software_Paraver_721: @@ -21598,7 +22859,7 @@ version versionsuffix toolchain ``5.3.0`` ``-mpi`` ``foss/2016b`` ``5.4.1`` ``-mpi`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``5.5.2`` ``-Python-2.7.15-mpi`` ``foss/2018b`` -``5.6.2`` ``-Python-3.7.4-mpi`` ``foss/2019b`` +``5.6.2`` ``-Python-3.7.4-mpi`` ``foss/2019b``, ``intel/2019b`` ========= ====================== ================================================================================================= @@ -21643,11 +22904,11 @@ ParMETIS is an MPI-based parallel library that implements a variety of algorithm *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview -========= ========================================================================================================================================================================================================================================================================= -version toolchain -========= ========================================================================================================================================================================================================================================================================= -``4.0.3`` ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``iimpi/2019a``, ``iimpi/2019b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -========= ========================================================================================================================================================================================================================================================================= +========= ========================================================================================================================================================================================================================================================================================== +version toolchain +========= ========================================================================================================================================================================================================================================================================================== +``4.0.3`` ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +========= ========================================================================================================================================================================================================================================================================================== .. _list_software_ParMGridGen_1040: @@ -21666,6 +22927,22 @@ version toolchain ======= =================================================================== +.. _list_software_PartitionFinder_1554: + +*PartitionFinder* ++++++++++++++++++ + +PartitionFinder 2 is a Python program for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data. You can PartitionFinder 2 before running a phylogenetic analysis, in order to decide how to divide up your sequence data into separate blocks before analysis, and to simultaneously perform model selection on each of those blocks. + +*homepage*: https://www.robertlanfear.com/partitionfinder + +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``2.1.1`` ``-Python-2.7.16`` ``intel/2019b`` +========= ================== =============== + + .. _list_software_pasta_537: *pasta* @@ -21736,6 +23013,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_pauvre_659: + +*pauvre* +++++++++ + +Tools for plotting Oxford Nanopore and other long-read data + +*homepage*: https://github.com/conchoecia/pauvre + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``0.1923`` ``-Python-3.7.4`` ``intel/2019b`` +========== ================= =============== + + .. _list_software_pbbam_514: *pbbam* @@ -22075,6 +23368,8 @@ version versionsuffix toolchain ``3.9.3`` ``foss/2018a``, ``intel/2018a`` ``3.11.0`` ``-downloaded-deps`` ``foss/2018b`` ``3.11.1`` ``foss/2019a``, ``intel/2019a`` +``3.12.3`` ``foss/2019b`` +``3.12.4`` ``foss/2019b``, ``intel/2019b`` ========== ==================== =============================== @@ -22173,6 +23468,7 @@ version versionsuffix toolchain ``19.1`` ``-GCC-8.2.0-2.31.1`` ``system`` ``19.4`` ``-GCC-8.2.0-2.31.1`` ``system`` ``19.7`` ``-GCC-8.3.0-2.32`` ``system`` +``19.10`` ``-GCC-8.3.0-2.32`` ``system`` ========= ======================= ========== @@ -22401,7 +23697,7 @@ version toolchain A set of tools (in Java) for working with next generation sequencing data in the BAM format. -*homepage*: http://sourceforge.net/projects/picard +*homepage*: https://sourceforge.net/projects/picard =========== =================== ========== version versionsuffix toolchain @@ -22427,6 +23723,7 @@ version versionsuffix toolchain ``2.18.17`` ``-Java-1.8`` ``system`` ``2.18.27`` ``-Java-1.8`` ``system`` ``2.21.1`` ``-Java-11`` ``system`` +``2.21.6`` ``-Java-11`` ``system`` =========== =================== ========== @@ -22439,13 +23736,13 @@ pigz, which stands for parallel implementation of gzip, is a fully functional *homepage*: https://zlib.net/pigz/ -========= ======================================================================= -version toolchain -========= ======================================================================= -``2.3.3`` ``foss/2016b`` -``2.3.4`` ``GCCcore/6.4.0`` -``2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2018a`` -========= ======================================================================= +========= ========================================================================================== +version toolchain +========= ========================================================================================== +``2.3.3`` ``foss/2016b`` +``2.3.4`` ``GCCcore/6.4.0`` +``2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018a`` +========= ========================================================================================== .. _list_software_PIL_229: @@ -22702,7 +23999,7 @@ version toolchain ``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` ``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``0.29.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``system`` +``0.29.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``system`` ========== =========================================================================================================================================================================== @@ -22945,7 +24242,7 @@ version versionsuffix toolchain ``2.5.1`` ``foss/2019a``, ``intel/2018b`` ``2.5.1`` ``-PathCV`` ``intel/2018b`` ``2.5.2`` ``-Python-3.7.2`` ``intel/2019a`` -``2.5.3`` ``-Python-3.7.4`` ``intel/2019b`` +``2.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``2.5b`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== ================================================ @@ -22979,7 +24276,9 @@ Process Management for Exascale Environments PMI Exascale (PMIx) represents an a version toolchain ========= ======================================================= ``1.2.5`` ``GCCcore/6.4.0`` -``2.1.3`` ``GCCcore/7.3.0`` +``2.1.3`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``2.2.1`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``2.2.3`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``3.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``3.0.2`` ``GCCcore/8.2.0`` ``3.1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` @@ -23023,6 +24322,22 @@ version toolchain ======= ================================ +.. _list_software_polymake_866: + +*polymake* +++++++++++ + +polymake is open source software for research in polyhedral geometry. It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, graphs, tropical hypersurfaces, and other objects. + +*homepage*: https://polymake.org + +========= ============== +version toolchain +========= ============== +``4.0r1`` ``foss/2019b`` +========= ============== + + .. _list_software_pomkl_547: *pomkl* @@ -23101,12 +24416,13 @@ Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. *homepage*: https://github.com/rrwick/Porechop -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``0.2.3`` ``-Python-3.5.2`` ``foss/2016b`` -``0.2.4`` ``-Python-3.6.6`` ``foss/2018b`` -========= ================= ============== +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.2.3`` ``-Python-3.5.2`` ``foss/2016b`` +``0.2.4`` ``-Python-3.6.6`` ``foss/2018b`` +``0.2.4`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== .. _list_software_poretools_999: @@ -23312,6 +24628,22 @@ version toolchain ========= =============================== +.. _list_software_pretty-yaml_1160: + +*pretty-yaml* ++++++++++++++ + +PyYAML-based python module to produce pretty and readable YAML-serialized data. This module is for serialization only, see ruamel.yaml module for literate YAML parsing (keeping track of comments, spacing, line/column numbers of values, etc). + +*homepage*: https://github.com/mk-fg/pretty-yaml + +=========== ================= +version toolchain +=========== ================= +``19.12.0`` ``GCCcore/8.3.0`` +=========== ================= + + .. _list_software_Primer3_674: *Primer3* @@ -23589,6 +24921,22 @@ version versionsuffix toolchain ========= ================== ================================== +.. _list_software_PRSice_550: + +*PRSice* +++++++++ + +PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses. + +*homepage*: https://www.prsice.info/ + +========== ================= +version toolchain +========== ================= +``2.2.12`` ``GCCcore/8.3.0`` +========== ================= + + .. _list_software_pscom_546: *pscom* @@ -23988,7 +25336,7 @@ version versionsuffix toolchain Python bindings for the cairo library -*homepage*: https://cairographics.org/pycairo/ +*homepage*: https://pycairo.readthedocs.io/ ========== ================== ================= version versionsuffix toolchain @@ -24000,6 +25348,7 @@ version versionsuffix toolchain ``1.18.0`` ``-Python-2.7.15`` ``foss/2018b`` ``1.18.0`` ``-Python-3.6.6`` ``foss/2018b`` ``1.18.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``1.18.2`` ``GCCcore/8.3.0`` ========== ================== ================= @@ -24036,6 +25385,22 @@ version toolchain ========= =============== +.. _list_software_pycodestyle_1205: + +*pycodestyle* ++++++++++++++ + +pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8. + +*homepage*: https://pycodestyle.readthedocs.io + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``2.5.0`` ``-Python-3.6.4`` ``intel/2018a`` +========= ================= =============== + + .. _list_software_PyCogent_809: *PyCogent* @@ -24102,6 +25467,7 @@ version versionsuffix toolchain ========= ================== ================= ``0.9.9`` ``-Python-2.7.11`` ``intel/2016a`` ``1.2.2`` ``GCCcore/8.2.0`` +``1.4.2`` ``GCCcore/8.3.0`` ========= ================== ================= @@ -24122,6 +25488,22 @@ version versionsuffix toolchain ============ ================== =============== +.. _list_software_pydot_560: + +*pydot* ++++++++ + +Python interface to Graphviz's Dot language. + +*homepage*: https://github.com/pydot/pydot + +========= ============== +version toolchain +========= ============== +``1.4.1`` ``foss/2019b`` +========= ============== + + .. _list_software_pyEGA3_489: *pyEGA3* @@ -24180,11 +25562,12 @@ A pythonic wrapper around FFTW, the FFT library, presenting a unified interface *homepage*: https://github.com/pyFFTW/pyFFTW -========== =============== -version toolchain -========== =============== -``0.11.1`` ``intel/2019a`` -========== =============== +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``0.11.1`` ``intel/2019a`` +``0.11.1`` ``-Python-3.6.6`` ``foss/2018b`` +========== ================= =============== .. _list_software_pyfits_671: @@ -24291,9 +25674,9 @@ version versionsuffix toolchain *PyGObject* +++++++++++ -Python Bindings for GLib/GObject/GIO/GTK+ +PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more. -*homepage*: http://www.pygtk.org/ +*homepage*: https://pygobject.readthedocs.io/ ========== ================== ================= version versionsuffix toolchain @@ -24302,10 +25685,28 @@ version versionsuffix toolchain ``2.28.6`` ``-Python-2.7.14`` ``intel/2017b`` ``2.28.7`` ``-Python-2.7.14`` ``intel/2018a`` ``2.28.7`` ``-Python-2.7.15`` ``foss/2018b`` +``3.34.0`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` ``3.34.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``3.34.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========== ================== ================= +.. _list_software_pygraphviz_1108: + +*pygraphviz* +++++++++++++ + +PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz graph data structure and layout algorithms. + +*homepage*: https://pygraphviz.github.io/ + +======= ============== +version toolchain +======= ============== +``1.5`` ``foss/2019b`` +======= ============== + + .. _list_software_pygrib_653: *pygrib* @@ -24427,6 +25828,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_pylift_664: + +*pylift* +++++++++ + +pylift is an uplift library that provides, primarily: (1) Fast uplift modeling implementations and (2) Evaluation tools (UpliftEval class). + +*homepage*: https://github.com/df-foundation/pylift + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.1.5`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_Pylint_640: *Pylint* @@ -24496,6 +25913,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_PyMC3_396: + +*PyMC3* ++++++++ + +Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano + +*homepage*: https://docs.pymc.io/ + +======= ================= =============== +version versionsuffix toolchain +======= ================= =============== +``3.8`` ``-Python-3.7.4`` ``intel/2019b`` +======= ================= =============== + + .. _list_software_pymemcache_1052: *pymemcache* @@ -24567,6 +26000,22 @@ version versionsuffix toolchain =========== ================== =============================== +.. _list_software_pyparsing_989: + +*pyparsing* ++++++++++++ + +The pyparsing module is an alternative approach to creating and executing simple grammars, vs. the traditional lex/yacc approach, or the use of regular expressions. The pyparsing module provides a library of classes that client code uses to construct the grammar directly in Python code. + +*homepage*: https://github.com/pyparsing/pyparsing + +========= ================== ================= +version versionsuffix toolchain +========= ================== ================= +``2.4.6`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +========= ================== ================= + + .. _list_software_pyplusplus_1137: *pyplusplus* @@ -24593,11 +26042,12 @@ Python interface to PROJ4 library for cartographic transformations *homepage*: https://pyproj4.github.io/pyproj -========= ================= -version toolchain -========= ================= -``2.1.3`` ``GCCcore/8.2.0`` -========= ================= +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``2.1.3`` ``GCCcore/8.2.0`` +``2.4.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= .. _list_software_pyqstem_787: @@ -24654,7 +26104,7 @@ version versionsuffix toolchain ``5.8.2`` ``-Python-2.7.13`` ``intel/2017a`` ``5.9.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``5.9.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``5.11.3`` ``-Python-3.6.6`` ``foss/2018b`` +``5.11.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================== =============================== @@ -24669,12 +26119,29 @@ PyQtGraph is a pure-python graphics and GUI library built on PyQt4/PySide and nu *homepage*: http://www.pyqtgraph.org/ -========== ================= =============== -version versionsuffix toolchain -========== ================= =============== -``0.10.0`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.0`` ``-Python-3.7.2`` ``intel/2019a`` -========== ================= =============== +========== ================= =============================== +version versionsuffix toolchain +========== ================= =============================== +``0.10.0`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.10.0`` ``-Python-3.7.2`` ``intel/2019a`` +========== ================= =============================== + + +.. _list_software_PyRe_384: + +*PyRe* +++++++ + +PyRe (Python Reliability) is a Python module for structural reliability analysis. + +*homepage*: https://hackl.science/pyre + +================== ================= =============================== +version versionsuffix toolchain +================== ================= =============================== +``5.0.3-20190221`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +================== ================= =============================== .. _list_software_PyRETIS_592: @@ -24879,7 +26346,7 @@ version versionsuffix toolchain PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases. -*homepage*: http://www.pytables.org +*homepage*: https://www.pytables.org =========== ================== ================================== version versionsuffix toolchain @@ -24897,6 +26364,8 @@ version versionsuffix toolchain ``3.4.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``3.5.2`` ``intel/2019a`` ``3.5.2`` ``-Python-2.7.14`` ``intel/2018a`` +``3.5.2`` ``-Python-2.7.16`` ``intel/2019b`` +``3.6.1`` ``-Python-3.7.4`` ``foss/2019b`` =========== ================== ================================== @@ -24989,13 +26458,14 @@ version versionsuffix toolchain Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis. -*homepage*: http://igraph.org/python +*homepage*: https://igraph.org/python =============== ================== =============== version versionsuffix toolchain =============== ================== =============== ``0.7.1.post6`` ``-Python-2.7.14`` ``intel/2017b`` ``0.7.1.post6`` ``-Python-3.6.6`` ``foss/2018b`` +``0.8.0`` ``foss/2019b`` =============== ================== =============== @@ -25020,18 +26490,35 @@ version versionsuffix toolchain *python-parasail* +++++++++++++++++ -This package contains Python bindings for parasail. +Python Bindings for the Parasail C Library -*homepage*: https://pypi.org/project/parasail/ +*homepage*: https://github.com/jeffdaily/parasail-python ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``1.1.12`` ``-Python-2.7.14`` ``intel/2018a`` ``1.1.16`` ``-Python-3.6.6`` ``foss/2018b`` +``1.2`` ``-Python-3.7.4`` ``intel/2019b`` ========== ================== =============== +.. _list_software_python-weka-wrapper3_2008: + +*python-weka-wrapper3* +++++++++++++++++++++++ + +Python3 wrapper for the Weka Machine Learning Workbench + +*homepage*: https://github.com/fracpete/python-weka-wrapper3 + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.1.11`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_pythran_774: *pythran* @@ -25069,9 +26556,27 @@ version versionsuffix toolchain ``1.1.0`` ``-Python-3.7.2`` ``foss/2019a`` ``1.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``1.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========= ============================= ================================== +.. _list_software_PyTorch-Geometric_1685: + +*PyTorch-Geometric* ++++++++++++++++++++ + +PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch. + +*homepage*: https://github.com/rusty1s/pytorch_geometric + +========= =============================== ============== +version versionsuffix toolchain +========= =============================== ============== +``1.3.2`` ``-Python-3.7.4`` ``foss/2019b`` +``1.4.2`` ``-Python-3.7.4-PyTorch-1.4.0`` ``foss/2019b`` +========= =============================== ============== + + .. _list_software_PyYAML_508: *PyYAML* @@ -25134,7 +26639,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcint_543` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` +:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcat_425` - :ref:`list_software_qcint_543` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` .. _list_software_Q6_135: @@ -25170,6 +26675,22 @@ version toolchain ========= ================================================== +.. _list_software_qcat_425: + +*qcat* +++++++ + +qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files + +*homepage*: https://github.com/nanoporetech/qcat/releases + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``1.1.0`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + .. _list_software_qcint_543: *qcint* @@ -25241,7 +26762,7 @@ version versionsuffix toolchain *Qhull* +++++++ -Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. +Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. *homepage*: http://www.qhull.org @@ -25249,6 +26770,7 @@ Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspa version toolchain ========== ============================================================================================================================================================================= ``2015.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``2019.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========== ============================================================================================================================================================================= @@ -25361,11 +26883,11 @@ qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions *homepage*: https://sourceforge.net/projects/qrupdate/ -========= ======================================================================================================================================== -version toolchain -========= ======================================================================================================================================== -``1.1.2`` ``GCC/5.4.0-2.26``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -========= ======================================================================================================================================== +========= ================================================================================================================================================================================= +version toolchain +========= ================================================================================================================================================================================= +``1.1.2`` ``GCC/5.4.0-2.26``, ``GCC/8.2.0-2.31.1``, ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +========= ================================================================================================================================================================================= .. _list_software_QScintilla_1012: @@ -25414,20 +26936,20 @@ Qt is a comprehensive cross-platform C++ application framework. *homepage*: http://qt.io/ -========== ================================================================================= -version toolchain -========== ================================================================================= -``5.6.0`` ``foss/2016a``, ``intel/2016a`` -``5.7.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``5.7.1`` ``intel/2016b`` -``5.8.0`` ``foss/2017a``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``5.9.3`` ``foss/2017b`` -``5.9.8`` ``fosscuda/2018b`` -``5.10.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a`` -``5.11.2`` ``foss/2018b`` -``5.12.3`` ``GCCcore/8.2.0`` -``5.13.1`` ``GCCcore/8.3.0`` -========== ================================================================================= +========== ==================================================================================== +version toolchain +========== ==================================================================================== +``5.6.0`` ``foss/2016a``, ``intel/2016a`` +``5.7.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``5.7.1`` ``intel/2016b`` +``5.8.0`` ``foss/2017a``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +``5.9.3`` ``foss/2017b`` +``5.9.8`` ``fosscuda/2018b`` +``5.10.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` +``5.11.2`` ``foss/2018b`` +``5.12.3`` ``GCCcore/8.2.0`` +``5.13.1`` ``GCCcore/8.3.0`` +========== ==================================================================================== .. _list_software_Qt5Webkit_864: @@ -25548,6 +27070,7 @@ version versionsuffix toolchain ``6.2.1`` ``iomkl/2017b`` ``6.3`` ``foss/2018b``, ``intel/2018b`` ``6.4.1`` ``intel/2019a`` +``6.5`` ``intel/2019a`` ========= ============= =============================== @@ -25693,7 +27216,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_RAxML_420` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray_300` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -25735,19 +27258,20 @@ Bioconductor provides tools for the analysis and coprehension of high-throughpu *homepage*: https://bioconductor.org -======= ============= =============================== -version versionsuffix toolchain -======= ============= =============================== -``3.2`` ``-R-3.2.3`` ``foss/2016a``, ``intel/2016a`` -``3.3`` ``-R-3.3.1`` ``intel/2016b`` -``3.5`` ``-R-3.4.0`` ``intel/2017a`` -``3.6`` ``-R-3.4.3`` ``foss/2017b``, ``intel/2017b`` -``3.6`` ``-R-3.4.4`` ``intel/2018a`` -``3.7`` ``-R-3.5.0`` ``iomkl/2018a`` -``3.7`` ``-R-3.5.1`` ``foss/2018b`` -``3.8`` ``-R-3.5.1`` ``foss/2018b`` -``3.9`` ``-R-3.6.0`` ``foss/2019a`` -======= ============= =============================== +======== ============= =============================== +version versionsuffix toolchain +======== ============= =============================== +``3.2`` ``-R-3.2.3`` ``foss/2016a``, ``intel/2016a`` +``3.3`` ``-R-3.3.1`` ``intel/2016b`` +``3.5`` ``-R-3.4.0`` ``intel/2017a`` +``3.6`` ``-R-3.4.3`` ``foss/2017b``, ``intel/2017b`` +``3.6`` ``-R-3.4.4`` ``intel/2018a`` +``3.7`` ``-R-3.5.0`` ``iomkl/2018a`` +``3.7`` ``-R-3.5.1`` ``foss/2018b`` +``3.8`` ``-R-3.5.1`` ``foss/2018b`` +``3.9`` ``-R-3.6.0`` ``foss/2019a`` +``3.10`` ``foss/2019b`` +======== ============= =============================== .. _list_software_R-keras_661: @@ -25764,6 +27288,7 @@ version versionsuffix toolchain =========== ========================= ================================== ``2.1.6`` ``-R-3.4.4`` ``foss/2018a`` ``2.2.5.0`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a``, ``fosscuda/2019a`` +``2.2.5.0`` ``-Python-3.7.4-R-3.6.2`` ``foss/2019b``, ``fosscuda/2019b`` =========== ========================= ================================== @@ -25788,16 +27313,17 @@ version versionsuffix toolchain *Racon* +++++++ -Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. +Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads -*homepage*: https://github.com/lbcb-sci/racon +*homepage*: https://github.com/clara-genomics/racon-gpu -========= ================= -version toolchain -========= ================= -``1.3.2`` ``GCCcore/8.2.0`` -``1.4.7`` ``GCCcore/8.2.0`` -========= ================= +========== ==================================== +version toolchain +========== ==================================== +``1.3.2`` ``GCCcore/8.2.0`` +``1.4.7`` ``GCCcore/8.2.0``, ``gcccuda/2019b`` +``1.4.10`` ``GCC/7.3.0-2.30`` +========== ==================================== .. _list_software_Ragout_626: @@ -25857,11 +27383,11 @@ A fast JSON parser/generator for C++ with both SAX/DOM style API *homepage*: https://rapidjson.org -========= ================= -version toolchain -========= ================= -``1.1.0`` ``GCCcore/8.2.0`` -========= ================= +========= ==================================== +version toolchain +========= ==================================== +``1.1.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ==================================== .. _list_software_rapidtide_950: @@ -25930,10 +27456,42 @@ version versionsuffix toolchain ``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` ``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` -``8.2.12`` ``-hybrid-avx2`` ``intel/2019a`` +``8.2.12`` ``-hybrid-avx2`` ``iimpi/2019b``, ``intel/2019a`` ========== ================ ================================================ +.. _list_software_RAxML-NG_614: + +*RAxML-NG* +++++++++++ + +RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. + +*homepage*: https://github.com/amkozlov/raxml-ng + +========= =============== +version toolchain +========= =============== +``0.9.0`` ``gompi/2019b`` +========= =============== + + +.. _list_software_Ray_300: + +*Ray* ++++++ + +Parallel genome assemblies for parallel DNA sequencing + +*homepage*: http://denovoassembler.sourceforge.net/ + +========= =============== +version toolchain +========= =============== +``2.3.1`` ``iimpi/2019a`` +========= =============== + + .. _list_software_RBFOpt_525: *RBFOpt* @@ -25951,6 +27509,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_rclone_643: + +*rclone* +++++++++ + +Rclone is a command line program to sync files and directories to and from a variety of online storage services + +*homepage*: https://rclone.org/ + +======== ============= ========== +version versionsuffix toolchain +======== ============= ========== +``1.42`` ``-amd64`` ``system`` +======== ============= ========== + + .. _list_software_Rcorrector_1061: *Rcorrector* @@ -25993,11 +27567,11 @@ RDFLib is a Python library for working with RDF, a simple yet powerful language *homepage*: https://github.com/RDFLib/rdflib -========= ============== -version toolchain -========= ============== -``4.2.2`` ``foss/2019a`` -========= ============== +========= ================================= +version toolchain +========= ================================= +``4.2.2`` ``GCCcore/8.3.0``, ``foss/2019a`` +========= ================================= .. _list_software_RDKit_446: @@ -26013,6 +27587,7 @@ RDKit is a collection of cheminformatics and machine-learning software written i version versionsuffix toolchain ============= ================= =============== ``2018.09.3`` ``-Python-3.6.6`` ``intel/2018b`` +``2019.09.3`` ``-Python-3.7.4`` ``foss/2019b`` ============= ================= =============== @@ -26066,6 +27641,22 @@ version toolchain ======= ========== +.. _list_software_Red_283: + +*Red* ++++++ + +Red (REpeat Detector) + +*homepage*: http://toolsmith.ens.utulsa.edu/ + +============== ======================================== +version toolchain +============== ======================================== +``2015-05-22`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +============== ======================================== + + .. _list_software_Redundans_932: *Redundans* @@ -26097,6 +27688,7 @@ version toolchain ``2.18`` ``system`` ``2.19`` ``system`` ``2.20`` ``system`` +``2.21`` ``system`` ======== ========== @@ -26238,6 +27830,7 @@ Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11 version versionsuffix toolchain ========= ============= ============== ``1.4-4`` ``-R-3.6.0`` ``foss/2019a`` +``1.4-8`` ``-R-3.6.2`` ``foss/2019b`` ========= ============= ============== @@ -26255,6 +27848,7 @@ version versionsuffix toolchain ========== ============= =============== ``0.3-17`` ``-R-3.2.3`` ``intel/2016a`` ``0.5-1`` ``-R-3.6.0`` ``foss/2019a`` +``0.5-2`` ``-R-3.6.2`` ``foss/2019b`` ========== ============= =============== @@ -26298,7 +27892,7 @@ version versionsuffix toolchain The rjags package is an interface to the JAGS library. -*homepage*: http://cran.r-project.org/web/packages/rjags +*homepage*: https://cran.r-project.org/web/packages/rjags ======= ============= =============== version versionsuffix toolchain @@ -26306,6 +27900,7 @@ version versionsuffix toolchain ``4-6`` ``-R-3.4.0`` ``intel/2017a`` ``4-6`` ``-R-3.4.3`` ``intel/2017b`` ``4-8`` ``-R-3.5.1`` ``foss/2018b`` +``4-9`` ``-R-3.6.0`` ``foss/2019a`` ======= ============= =============== @@ -26505,6 +28100,7 @@ version versionsuffix toolchain ``6.10.04`` ``-Python-2.7.13`` ``intel/2017a`` ``6.10.08`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``6.14.06`` ``-Python-2.7.15`` ``foss/2018b`` +``6.14.06`` ``-Python-3.6.6`` ``foss/2018b`` ``v5.34.34`` ``-Python-2.7.11`` ``intel/2016a`` ``v5.34.36`` ``-Python-2.7.11`` ``intel/2016a`` ``v6.06.02`` ``-Python-2.7.12`` ``intel/2016b`` @@ -26567,15 +28163,16 @@ version toolchain *rpy2* ++++++ -rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions. +rpy2 is an interface to R running embedded in a Python process. -*homepage*: http://rpy.sourceforge.net/ +*homepage*: https://rpy2.bitbucket.io/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.7.9`` ``-Python-2.7.12`` ``foss/2016b`` ``2.8.2`` ``-Python-2.7.13`` ``intel/2017a`` +``3.2.6`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== =============== @@ -26650,6 +28247,22 @@ version versionsuffix toolchain ========== ============= =============================== +.. _list_software_rstanarm_872: + +*rstanarm* +++++++++++ + +Estimates previously compiled regression models using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation. + +*homepage*: https://r-forge.r-project.org/projects/rstanarm + +========== ============= ============== +version versionsuffix toolchain +========== ============= ============== +``2.19.3`` ``-R-3.6.2`` ``foss/2019b`` +========== ============= ============== + + .. _list_software_RTG-Tools_811: *RTG-Tools* @@ -26687,7 +28300,7 @@ version versionsuffix toolchain *Ruby* ++++++ -Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. +Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. *homepage*: https://www.ruby-lang.org @@ -26703,6 +28316,7 @@ version toolchain ``2.5.1`` ``intel/2018a`` ``2.6.1`` ``GCCcore/7.3.0`` ``2.6.3`` ``GCCcore/8.2.0`` +``2.7.1`` ``GCCcore/8.3.0`` ========= ================================================ @@ -26737,7 +28351,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL2_277` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_segemehl_842` - :ref:`list_software_SelEstim_806` - :ref:`list_software_sep_328` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_Shannon_725` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singularity_1179` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_splitRef_841` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_Stata_509` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STIR_322` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_SymEngine_911` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL2_277` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_Shannon_725` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_Singularity_1179` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_Stata_509` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_SymEngine_911` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -26798,11 +28412,12 @@ Sailfish is a software tool that implements a novel, alignment-free algorithm fo *homepage*: http://www.cs.cmu.edu/~ckingsf/software/sailfish/ -========== ================== ============== -version versionsuffix toolchain -========== ================== ============== -``0.10.1`` ``-Python-2.7.12`` ``foss/2016b`` -========== ================== ============== +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``0.10.1`` ``gompi/2019b`` +``0.10.1`` ``-Python-2.7.12`` ``foss/2016b`` +========== ================== =============== .. _list_software_SALib_427: @@ -26830,17 +28445,18 @@ Salmon is a wicked-fast program to produce a highly-accurate, transcript-level *homepage*: https://github.com/COMBINE-lab/salmon -========== ================== =============== -version versionsuffix toolchain -========== ================== =============== -``0.8.2`` ``system`` -``0.8.2`` ``-Python-2.7.12`` ``foss/2016b`` -``0.11.2`` ``intel/2018a`` -``0.12.0`` ``foss/2018b`` -``0.14.1`` ``foss/2018b`` -``0.14.2`` ``gompi/2019a`` -``1.0.0`` ``gompi/2019a`` -========== ================== =============== +========== ================== ================================ +version versionsuffix toolchain +========== ================== ================================ +``0.8.2`` ``system`` +``0.8.2`` ``-Python-2.7.12`` ``foss/2016b`` +``0.11.2`` ``intel/2018a`` +``0.12.0`` ``foss/2018b`` +``0.14.1`` ``foss/2018b`` +``0.14.2`` ``gompi/2019a`` +``1.0.0`` ``gompi/2019a``, ``gompi/2019b`` +``1.1.0`` ``gompi/2019b`` +========== ================== ================================ .. _list_software_SALMON-TDDFT_877: @@ -26922,7 +28538,7 @@ version versionsuffix toolchain ========== ================= ======================================================================================================================================= ``0.1.17`` ``intel/2017a`` ``0.1.19`` ``foss/2016a``, ``foss/2016b`` -``0.1.20`` ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``0.1.20`` ``GCC/8.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b`` ``1.2`` ``foss/2016b`` ``1.3`` ``foss/2016a``, ``intel/2016a`` ``1.3.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` @@ -26934,7 +28550,7 @@ version versionsuffix toolchain ``1.7`` ``foss/2018a``, ``intel/2018a`` ``1.8`` ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``1.10`` ``GCC/8.2.0-2.31.1`` +``1.10`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.5.281`` ========== ================= ======================================================================================================================================= @@ -27110,6 +28726,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_scikit-build_1220: + +*scikit-build* +++++++++++++++ + +Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions. + +*homepage*: https://scikit-build.github.io + +========== ================= =============================== +version versionsuffix toolchain +========== ================= =============================== +``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +========== ================= =============================== + + .. _list_software_scikit-image_1207: *scikit-image* @@ -27134,7 +28766,7 @@ version versionsuffix toolchain ``0.14.0`` ``-Python-3.6.4`` ``intel/2018a`` ``0.14.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``0.15.0`` ``-Python-3.7.2`` ``foss/2019a`` -``0.16.2`` ``-Python-3.7.4`` ``foss/2019b`` +``0.16.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========== ================== =================================================== @@ -27172,7 +28804,8 @@ version versionsuffix toolchain ``0.20.2`` ``-Python-2.7.15`` ``foss/2018b`` ``0.20.2`` ``-Python-3.6.6`` ``foss/2018b`` ``0.20.3`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` -``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.20.4`` ``-Python-2.7.16`` ``intel/2019b`` +``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ========== ================================= ======================================================================== @@ -27205,6 +28838,7 @@ Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) version versionsuffix toolchain ========= ================= =============== ``0.5.2`` ``-Python-3.6.6`` ``intel/2018b`` +``0.7.4`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= =============== @@ -27255,7 +28889,7 @@ Bundle of Python packages for scientific software version versionsuffix toolchain =========== ================== ======================================================================== ``2019.03`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``2019.10`` ``-Python-2.7.16`` ``foss/2019b`` +``2019.10`` ``-Python-2.7.16`` ``foss/2019b``, ``intel/2019b`` ``2019.10`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` =========== ================== ======================================================================== @@ -27413,6 +29047,22 @@ version toolchain ========= =============== +.. _list_software_scVelo_620: + +*scVelo* +++++++++ + +scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using dynamical modeling. + +*homepage*: https://scvelo.org + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.1.24`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_SDCC_285: *SDCC* @@ -27456,19 +29106,20 @@ Seaborn is a Python visualization library based on matplotlib. It provides a h *homepage*: http://stanford.edu/~mwaskom/software/seaborn/ -========= ================== ========================================================================================= -version versionsuffix toolchain -========= ================== ========================================================================================= -``0.7.1`` ``-Python-2.7.12`` ``intel/2016b`` -``0.8.1`` ``-Python-2.7.13`` ``foss/2017a`` -``0.8.1`` ``-Python-2.7.14`` ``intel/2018a`` -``0.9.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a``, ``intelcuda/2017b`` -``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` -``0.9.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``0.9.0`` ``-Python-3.6.4`` ``intel/2018a`` -``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.9.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -========= ================== ========================================================================================= +========== ================== ========================================================================================= +version versionsuffix toolchain +========== ================== ========================================================================================= +``0.7.1`` ``-Python-2.7.12`` ``intel/2016b`` +``0.8.1`` ``-Python-2.7.13`` ``foss/2017a`` +``0.8.1`` ``-Python-2.7.14`` ``intel/2018a`` +``0.9.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a``, ``intelcuda/2017b`` +``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` +``0.9.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``0.9.0`` ``-Python-3.6.4`` ``intel/2018a`` +``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.9.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``0.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +========== ================== ========================================================================================= .. _list_software_SearchGUI_827: @@ -27487,6 +29138,22 @@ version versionsuffix toolchain ========= =================== ========== +.. _list_software_SECAPR_446: + +*SECAPR* +++++++++ + +SECAPR is a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments + +*homepage*: https://github.com/AntonelliLab/seqcap_processor + +========== ================== ============== +version versionsuffix toolchain +========== ================== ============== +``1.1.15`` ``-Python-2.7.16`` ``foss/2019b`` +========== ================== ============== + + .. _list_software_segemehl_842: *segemehl* @@ -27504,6 +29171,22 @@ version toolchain ========= ================================================ +.. _list_software_segmentation-models_1983: + +*segmentation-models* ++++++++++++++++++++++ + +Python library with Neural Networks for Image Segmentation based on Keras and TensorFlow. + +*homepage*: https://github.com/qubvel/segmentation_models + +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``1.0.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========= ================= ================================== + + .. _list_software_SelEstim_806: *SelEstim* @@ -27520,6 +29203,22 @@ version versionsuffix toolchain ========= ================= ========== +.. _list_software_SentencePiece_1307: + +*SentencePiece* ++++++++++++++++ + +Unsupervised text tokenizer for Neural Network-based text generation. + +*homepage*: https://github.com/google/sentencepiece + +========== ================= ============= +version versionsuffix toolchain +========== ================= ============= +``0.1.85`` ``-Python-3.7.4`` ``GCC/8.3.0`` +========== ================= ============= + + .. _list_software_sep_328: *sep* @@ -27536,6 +29235,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_SEPP_312: + +*SEPP* +++++++ + +SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees. + +*homepage*: https://github.com/smirarab/sepp + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``4.3.10`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_Seq-Gen_624: *Seq-Gen* @@ -27578,12 +29293,13 @@ SeqAn is an open source C++ library of efficient algorithms and data structures *homepage*: https://www.seqan.de/ -========= ===================================================== -version toolchain -========= ===================================================== -``2.3.2`` ``foss/2016b`` -``2.4.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` -========= ===================================================== +========= ============= ===================================================== +version versionsuffix toolchain +========= ============= ===================================================== +``1.4.2`` ``-library`` ``system`` +``2.3.2`` ``foss/2016b`` +``2.4.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` +========= ============= ===================================================== .. _list_software_SeqAn3_523: @@ -27644,12 +29360,12 @@ Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FA *homepage*: https://github.com/lh3/seqtk/ -======= ==================================================== -version toolchain -======= ==================================================== -``1.2`` ``foss/2016b``, ``intel/2017a`` -``1.3`` ``GCC/8.2.0-2.31.1``, ``foss/2018a``, ``foss/2018b`` -======= ==================================================== +======= =================================================================== +version toolchain +======= =================================================================== +``1.2`` ``foss/2016b``, ``intel/2017a`` +``1.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2018a``, ``foss/2018b`` +======= =================================================================== .. _list_software_Serf_400: @@ -27692,7 +29408,7 @@ version versionsuffix toolchain Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. -*homepage*: http://satijalab.org/seurat +*homepage*: https://satijalab.org/seurat ============ ============= =============== version versionsuffix toolchain @@ -27700,6 +29416,7 @@ version versionsuffix toolchain ``1.4.0.16`` ``-R-3.4.0`` ``intel/2017a`` ``2.3.4`` ``-R-3.4.4`` ``intel/2018a`` ``2.3.4`` ``-R-3.5.1`` ``foss/2018b`` +``3.1.2`` ``-R-3.6.0`` ``foss/2019a`` ============ ============= =============== @@ -27752,6 +29469,22 @@ version versionsuffix toolchain ========== =============== ========== +.. _list_software_Shapely_726: + +*Shapely* ++++++++++ + +Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries. + +*homepage*: https://github.com/Toblerity/Shapely + +========= ================= ====================================== +version versionsuffix toolchain +========= ================= ====================================== +``1.7.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +========= ================= ====================================== + + .. _list_software_sharutils_991: *sharutils* @@ -27891,15 +29624,17 @@ SIESTA is both a method and its computer program implementation, to perform effi *homepage*: http://departments.icmab.es/leem/siesta -========== =============================== -version toolchain -========== =============================== -``4.0`` ``intel/2017a`` -``4.0.1`` ``intel/2017a`` -``4.1-b2`` ``intel/2017a`` -``4.1-b3`` ``intel/2017a`` -``4.1-b4`` ``foss/2018b``, ``intel/2018b`` -========== =============================== +=============== ============= =============================== +version versionsuffix toolchain +=============== ============= =============================== +``4.0`` ``intel/2017a`` +``4.0.1`` ``intel/2017a`` +``4.1-b2`` ``intel/2017a`` +``4.1-b3`` ``intel/2017a`` +``4.1-b4`` ``foss/2018b``, ``intel/2018b`` +``4.1-MaX-1.0`` ``intel/2019b`` +``4.1-MaX-1.0`` ``-PEXSI`` ``intel/2019b`` +=============== ============= =============================== .. _list_software_SimPEG_517: @@ -27939,15 +29674,16 @@ version toolchain *SimpleElastix* +++++++++++++++ -Multi-lingual medical image registration library. +Multi-lingual medical image registration library. -*homepage*: http://simpleelastix.github.io/ +*homepage*: https://simpleelastix.github.io ========== ================= ============== version versionsuffix toolchain ========== ================= ============== ``0.10.0`` ``-Python-3.6.3`` ``foss/2017b`` ``0.10.0`` ``-Python-3.6.4`` ``foss/2018a`` +``1.1.0`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================= ============== @@ -27966,6 +29702,7 @@ version versionsuffix toolchain ``1.1.0`` ``-Python-2.7.15`` ``foss/2018b`` ``1.1.0`` ``-Python-3.6.4`` ``foss/2018a`` ``1.1.0`` ``-Python-3.6.6`` ``foss/2018b`` +``1.2.4`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== ============== @@ -28018,6 +29755,22 @@ version versionsuffix toolchain ========== ================== =============== +.. _list_software_Singular_837: + +*Singular* +++++++++++ + +Singular is a computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory. + +*homepage*: https://www.singular.uni-kl.de/ + +========= ========== +version toolchain +========= ========== +``4.1.2`` ``system`` +========= ========== + + .. _list_software_Singularity_1179: *Singularity* @@ -28129,6 +29882,22 @@ version toolchain ========= =============== +.. _list_software_SLATEC_444: + +*SLATEC* +++++++++ + +SLATEC Common Mathematical Library, a comprehensive software library containing over 1400 general purpose mathematical and statistical routines written in Fortran 77. + +*homepage*: https://www.netlib.org/slatec/ + +======= ========================================================== +version toolchain +======= ========================================================== +``4.1`` ``GCC/6.4.0-2.28``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` +======= ========================================================== + + .. _list_software_SLEPc_407: *SLEPc* @@ -28136,15 +29905,16 @@ version toolchain SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. -*homepage*: http://www.grycap.upv.es/slepc/ +*homepage*: https://www.grycap.upv.es/slepc/ -========== ============== -version toolchain -========== ============== -``3.8.3`` ``foss/2017b`` -``3.9.2`` ``foss/2018a`` -``3.11.0`` ``foss/2018b`` -========== ============== +========== =============================== +version toolchain +========== =============================== +``3.8.3`` ``foss/2017b`` +``3.9.2`` ``foss/2018a`` +``3.11.0`` ``foss/2018b`` +``3.12.2`` ``foss/2019b``, ``intel/2019b`` +========== =============================== .. _list_software_slepc4py_820: @@ -28555,16 +30325,18 @@ Genome assembler for single-cell and isolates data sets *homepage*: http://bioinf.spbau.ru/en/spades -========== ============================================== -version toolchain -========== ============================================== -``3.9.0`` ``foss/2016a``, ``foss/2016b`` -``3.10.1`` ``foss/2016b``, ``foss/2017a`` -``3.11.1`` ``foss/2017b``, ``foss/2018a`` -``3.12.0`` ``foss/2016b``, ``foss/2018a``, ``foss/2018b`` -``3.13.0`` ``foss/2018b`` -``3.13.1`` ``GCC/8.2.0-2.31.1`` -========== ============================================== +========== ================= ============================================== +version versionsuffix toolchain +========== ================= ============================================== +``3.9.0`` ``foss/2016a``, ``foss/2016b`` +``3.10.1`` ``foss/2016b``, ``foss/2017a`` +``3.11.1`` ``foss/2017b``, ``foss/2018a`` +``3.12.0`` ``foss/2016b``, ``foss/2018a``, ``foss/2018b`` +``3.13.0`` ``foss/2018b`` +``3.13.1`` ``GCC/8.2.0-2.31.1`` +``3.14.0`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` +``3.14.0`` ``-Python-3.7.4`` ``GCC/8.3.0`` +========== ================= ============================================== .. _list_software_spaln_542: @@ -28622,12 +30394,28 @@ An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! T *homepage*: https://github.com/sparsehash/sparsehash -========= =========================================================================================================== -version toolchain -========= =========================================================================================================== -``2.0.2`` ``foss/2016a`` -``2.0.3`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2017a`` -========= =========================================================================================================== +========= ============================================================================================================================== +version toolchain +========= ============================================================================================================================== +``2.0.2`` ``foss/2016a`` +``2.0.3`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``intel/2017a`` +========= ============================================================================================================================== + + +.. _list_software_spatialreg_1068: + +*spatialreg* +++++++++++++ + +A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up to now in 'spdep', 'sphet' and 'spse'. + +*homepage*: https://cran.r-project.org/package=spatialreg + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``1.1-5`` ``-R-3.6.2`` ``foss/2019b`` +========= ============= ============== .. _list_software_spectral.methods_1664: @@ -28776,6 +30564,22 @@ version toolchain =========== ================== +.. _list_software_split-seq_930: + +*split-seq* ++++++++++++ + +Analysis tools for split-seq. + +*homepage*: https://github.com/yjzhang/split-seq-pipeline + +============ ================= ============== +version versionsuffix toolchain +============ ================= ============== +``20190717`` ``-Python-3.6.6`` ``foss/2018b`` +============ ================= ============== + + .. _list_software_splitRef_841: *splitRef* @@ -28792,6 +30596,22 @@ version toolchain ========= ========== +.. _list_software_spoa_435: + +*spoa* +++++++ + +Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences + +*homepage*: https://github.com/rvaser/spoa + +========= ================== +version toolchain +========= ================== +``3.0.1`` ``GCC/7.3.0-2.30`` +========= ================== + + .. _list_software_SPRNG_394: *SPRNG* @@ -28927,6 +30747,22 @@ version versionsuffix toolchain ========= ============= ========== +.. _list_software_SSN_244: + +*SSN* ++++++ + +Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included. + +*homepage*: https://cran.r-project.org/web/packages/SSN + +========== ============= ============== +version versionsuffix toolchain +========== ============= ============== +``1.1.14`` ``-R-3.6.0`` ``foss/2019a`` +========== ============= ============== + + .. _list_software_SSPACE_Basic_1024: *SSPACE_Basic* @@ -28971,6 +30807,7 @@ version toolchain ``2.2`` ``foss/2018a`` ``2.3b`` ``foss/2018a`` ``2.3e`` ``foss/2018b`` +``2.5`` ``iccifort/2019.5.281`` ``2.41`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ============== ============================================================================== @@ -29048,6 +30885,8 @@ version toolchain ``2.7.0d`` ``foss/2018b`` ``2.7.0f`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` ``2.7.1a`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` +``2.7.2b`` ``GCC/8.3.0`` +``2.7.3a`` ``GCC/8.3.0`` ========== =============================================== @@ -29056,7 +30895,7 @@ version toolchain *STAR-Fusion* +++++++++++++ -STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set. +STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set. *homepage*: https://github.com/STAR-Fusion/STAR-Fusion @@ -29065,6 +30904,7 @@ version versionsuffix toolchain ========= ============================= ==================== ``1.5.0`` ``-Perl-5.28.0`` ``foss/2018b`` ``1.6.0`` ``-Perl-5.28.1-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` +``1.8.1`` ``-Python-3.7.4`` ``foss/2019b`` ========= ============================= ==================== @@ -29077,11 +30917,12 @@ Stata is a complete, integrated statistical software package that provides every *homepage*: https://www.stata.com/ -======= ========== -version toolchain -======= ========== -``15`` ``system`` -======= ========== +======= ============= ========== +version versionsuffix toolchain +======= ============= ========== +``15`` ``system`` +``16`` ``-legacy`` ``system`` +======= ============= ========== .. _list_software_statsmodels_1203: @@ -29101,10 +30942,28 @@ version versionsuffix toolchain ``0.6.1`` ``-Python-3.5.2`` ``intel/2016b`` ``0.8.0`` ``-Python-2.7.13`` ``intel/2017a`` ``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.9.0`` ``-Python-3.6.6`` ``intel/2018b`` ``0.10.1`` ``foss/2019a`` +``0.11.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========== ================== =============================== +.. _list_software_STEAK_376: + +*STEAK* ++++++++ + +Detects integrations of any sort in high-throughput sequencing (HTS) data. STEAK was built for validating and discovering transposable element (TE) and retroviral integrations in a variety of HTS data. The software performs on both single-end (SE) and paired-end ( PE) libraries and on a variety of HTS sequencing strategies. It can be applied to a broad range of research interests and clinical uses such as population genetic studies and detecting polymorphic integrations. + +*homepage*: https://omictools.com/steak-tool + +============== ================== ============== +version versionsuffix toolchain +============== ================== ============== +``2019.09.12`` ``-Python-2.7.16`` ``foss/2019b`` +============== ================== ============== + + .. _list_software_STIR_322: *STIR* @@ -29121,6 +30980,23 @@ version toolchain ======= =============== +.. _list_software_stpipeline_1085: + +*stpipeline* +++++++++++++ + +The ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format to generated datasets for down-stream analysis. The ST pipeline can also be used to process single cell data as long as a file with barcodes identifying each cell is provided. The ST Pipeline can also process RNA-Seq datasets generated with or without UMIs. + +*homepage*: https://github.com/SpatialTranscriptomicsResearch/st_pipeline + +========= ================== ============== +version versionsuffix toolchain +========= ================== ============== +``1.7.3`` ``-Python-2.7.15`` ``foss/2018b`` +``1.7.6`` ``-Python-3.7.2`` ``foss/2019a`` +========= ================== ============== + + .. _list_software_STREAM_460: *STREAM* @@ -29160,9 +31036,9 @@ version versionsuffix toolchain *StringTie* +++++++++++ -StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. +StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts -*homepage*: http://ccb.jhu.edu/software/%(namelower)/ +*homepage*: https://ccb.jhu.edu/software/stringtie/ ========== ================================== version toolchain @@ -29172,6 +31048,7 @@ version toolchain ``1.3.3b`` ``foss/2016b`` ``1.3.5`` ``GCCcore/8.2.0``, ``foss/2018b`` ``2.0.3`` ``GCCcore/7.3.0`` +``2.1.0`` ``foss/2018b`` ========== ================================== @@ -29184,11 +31061,11 @@ The program structure is a free software package for using multi-locus genotype *homepage*: https://web.stanford.edu/group/pritchardlab/structure.html -========= ====================================== -version toolchain -========= ====================================== -``2.3.4`` ``iccifort/2019.3.199-GCC-8.3.0-2.32`` -========= ====================================== +========= ============================================================ +version toolchain +========= ============================================================ +``2.3.4`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.3.199-GCC-8.3.0-2.32`` +========= ============================================================ .. _list_software_Subread_710: @@ -29200,14 +31077,14 @@ High performance read alignment, quantification and mutation discovery *homepage*: http://subread.sourceforge.net/ -============ ============================== -version toolchain -============ ============================== -``1.5.0-p1`` ``foss/2016a``, ``foss/2016b`` -``1.6.3`` ``foss/2018b`` -``1.6.4`` ``foss/2018b`` -``2.0.0`` ``GCC/7.3.0-2.30`` -============ ============================== +============ ================================= +version toolchain +============ ================================= +``1.5.0-p1`` ``foss/2016a``, ``foss/2016b`` +``1.6.3`` ``foss/2018b`` +``1.6.4`` ``foss/2018b`` +``2.0.0`` ``GCC/7.3.0-2.30``, ``GCC/8.3.0`` +============ ================================= .. _list_software_Subversion_1072: @@ -29267,7 +31144,7 @@ version versionsuffix toolchain ``5.1.2`` ``-METIS-5.1.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ``5.1.2`` ``-ParMETIS-4.0.3`` ``foss/2017b``, ``intel/2017b`` ``5.4.0`` ``-METIS-5.1.0`` ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` -``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b`` +``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b``, ``intel/2019b`` ========= =================== ================================================================================================= @@ -29347,11 +31224,11 @@ Very simple MPI sanity code. Nothing more, nothing less. *homepage*: https://github.com/hpc/supermagic -============ ============== -version toolchain -============ ============== -``20170824`` ``foss/2017a`` -============ ============== +============ =============================== +version toolchain +============ =============================== +``20170824`` ``foss/2017a``, ``gompi/2019b`` +============ =============================== .. _list_software_supernova_995: @@ -29403,6 +31280,22 @@ version toolchain ============ =============== +.. _list_software_SVG_240: + +*SVG* ++++++ + +Perl binding for SVG + +*homepage*: https://metacpan.org/pod/SVG + +======== ================ ============== +version versionsuffix toolchain +======== ================ ============== +``2.84`` ``-Perl-5.30.0`` ``foss/2019b`` +======== ================ ============== + + .. _list_software_swarm_554: *swarm* @@ -29528,7 +31421,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_texinfo_765` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` +:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_texinfo_765` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` .. _list_software_tabix_536: @@ -29640,6 +31533,7 @@ version toolchain ``2018_U5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2019_U4`` ``GCCcore/8.2.0`` ``2019_U9`` ``GCCcore/8.3.0`` +``2020.2`` ``GCCcore/8.3.0`` ============== ================================================== @@ -29777,9 +31671,12 @@ version versionsuffix toolchain ``1.13.1`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``1.14.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``1.15.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.15.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.0.0`` ``-Python-3.7.2`` ``foss/2019a`` ``2.0.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``2.1.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2.0.1`` ``-Python-3.7.2`` ``foss/2019a`` +``2.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========== ============================= =================================================== @@ -29929,26 +31826,27 @@ Theano is a Python library that allows you to define, optimize, and evaluate mat *homepage*: https://deeplearning.net/software/theano -========= ================== ======================================= -version versionsuffix toolchain -========= ================== ======================================= -``0.8.2`` ``-Python-2.7.11`` ``foss/2016a`` -``0.8.2`` ``-Python-3.5.1`` ``foss/2016a`` -``0.8.2`` ``-Python-3.5.2`` ``intel/2016b`` -``0.9.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.9.0`` ``-Python-3.6.1`` ``intel/2017a`` -``1.0.0`` ``-Python-2.7.14`` ``intel/2017b`` -``1.0.0`` ``-Python-3.6.3`` ``intel/2017b`` -``1.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.0.2`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` -``1.0.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``1.0.2`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intelcuda/2017b`` -``1.0.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``1.0.4`` ``foss/2019a``, ``fosscuda/2019a`` -``1.0.4`` ``-Python-3.6.4`` ``foss/2018a`` -``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` -========= ================== ======================================= +========= ================== =================================================== +version versionsuffix toolchain +========= ================== =================================================== +``0.8.2`` ``-Python-2.7.11`` ``foss/2016a`` +``0.8.2`` ``-Python-3.5.1`` ``foss/2016a`` +``0.8.2`` ``-Python-3.5.2`` ``intel/2016b`` +``0.9.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.9.0`` ``-Python-3.6.1`` ``intel/2017a`` +``1.0.0`` ``-Python-2.7.14`` ``intel/2017b`` +``1.0.0`` ``-Python-3.6.3`` ``intel/2017b`` +``1.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``1.0.2`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``1.0.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``1.0.2`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``1.0.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``1.0.4`` ``foss/2019a``, ``fosscuda/2019a`` +``1.0.4`` ``-Python-3.6.4`` ``foss/2018a`` +``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` +``1.0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +========= ================== =================================================== .. _list_software_THetA_438: @@ -30122,6 +32020,7 @@ version versionsuffix toolchain ``2.7.14`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a``, ``intelcuda/2017b`` ``2.7.15`` ``GCCcore/8.2.0`` ``2.7.15`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``2.7.16`` ``GCCcore/8.3.0`` ``3.6.1`` ``-Python-3.6.1`` ``foss/2017a``, ``intel/2017a`` ``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` ``3.6.3`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` @@ -30186,6 +32085,22 @@ version versionsuffix toolchain ========== ================== =============================== +.. _list_software_Togl_406: + +*Togl* +++++++ + +A Tcl/Tk widget for OpenGL rendering. + +*homepage*: https://sourceforge.net/projects/togl/ + +======= ================= +version toolchain +======= ================= +``2.0`` ``GCCcore/8.3.0`` +======= ================= + + .. _list_software_TopHat_592: *TopHat* @@ -30204,6 +32119,22 @@ version versionsuffix toolchain ========= ================== ================================================================================ +.. _list_software_torchtext_997: + +*torchtext* ++++++++++++ + +Data loaders and abstractions for text and NLP + +*homepage*: https://github.com/pytorch/text + +========= ================================ ================== +version versionsuffix toolchain +========= ================================ ================== +``0.5.0`` ``-PyTorch-1.4.0--Python-3.7.4`` ``fosscuda/2019b`` +========= ================================ ================== + + .. _list_software_torchvision_1208: *torchvision* @@ -30247,18 +32178,20 @@ version versionsuffix toolchain *tqdm* ++++++ -A fast, extensible progress bar for Python and CLI +Instantly make your loops show a smart progress meter. *homepage*: https://github.com/tqdm/tqdm -========== ================== ================= -version versionsuffix toolchain -========== ================== ================= -``4.24.0`` ``-Python-2.7.15`` ``foss/2018b`` -``4.24.0`` ``-Python-3.5.1`` ``foss/2016a`` -``4.29.0`` ``-Python-3.6.4`` ``intel/2018a`` -``4.32.1`` ``GCCcore/8.2.0`` -========== ================== ================= +========== ================== =============================== +version versionsuffix toolchain +========== ================== =============================== +``4.24.0`` ``-Python-2.7.15`` ``foss/2018b`` +``4.24.0`` ``-Python-3.5.1`` ``foss/2016a`` +``4.29.0`` ``-Python-3.6.4`` ``intel/2018a`` +``4.32.1`` ``GCCcore/8.2.0`` +``4.41.1`` ``GCCcore/8.3.0`` +``4.41.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +========== ================== =============================== .. _list_software_Tracer_609: @@ -30412,25 +32345,26 @@ version versionsuffix toolchain *Trim_Galore* +++++++++++++ -Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. +Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. *homepage*: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ -========= ================== =============================== -version versionsuffix toolchain -========= ================== =============================== -``0.4.2`` ``foss/2016b`` -``0.4.4`` ``foss/2016b``, ``intel/2017a`` -``0.5.0`` ``foss/2018b`` -``0.5.0`` ``-Python-3.6.6`` ``intel/2018b`` -``0.6.0`` ``-Python-2.7.15`` ``foss/2018b`` -``0.6.0`` ``-Python-3.6.6`` ``foss/2018b`` -``0.6.1`` ``-Python-2.7.15`` ``foss/2018b`` -``0.6.1`` ``-Python-3.6.6`` ``foss/2018b`` -``0.6.2`` ``-Java-11`` ``GCCcore/8.2.0`` -``0.6.2`` ``-Python-2.7.15`` ``foss/2018b`` -``0.6.2`` ``-Python-3.6.6`` ``foss/2018b`` -========= ================== =============================== +========= ========================= =============================== +version versionsuffix toolchain +========= ========================= =============================== +``0.4.2`` ``foss/2016b`` +``0.4.4`` ``foss/2016b``, ``intel/2017a`` +``0.5.0`` ``foss/2018b`` +``0.5.0`` ``-Python-3.6.6`` ``intel/2018b`` +``0.6.0`` ``-Python-2.7.15`` ``foss/2018b`` +``0.6.0`` ``-Python-3.6.6`` ``foss/2018b`` +``0.6.1`` ``-Python-2.7.15`` ``foss/2018b`` +``0.6.1`` ``-Python-3.6.6`` ``foss/2018b`` +``0.6.2`` ``-Java-11`` ``GCCcore/8.2.0`` +``0.6.2`` ``-Python-2.7.15`` ``foss/2018b`` +``0.6.2`` ``-Python-3.6.6`` ``foss/2018b`` +``0.6.5`` ``-Java-11-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ========================= =============================== .. _list_software_trimAl_617: @@ -30465,6 +32399,7 @@ version versionsuffix toolchain ``0.36`` ``-Java-1.8.0_92`` ``system`` ``0.38`` ``-Java-1.8`` ``system`` ``0.38`` ``-Java-1.8.0_162`` ``system`` +``0.39`` ``-Java-11`` ``system`` ======== =================== ========== @@ -30477,16 +32412,20 @@ Trinity represents a novel method for the efficient and robust de novo reconstru *homepage*: https://trinityrnaseq.github.io -========= ======================================== -version toolchain -========= ======================================== -``2.2.0`` ``foss/2016a`` -``2.4.0`` ``foss/2017a`` -``2.5.1`` ``intel/2017a``, ``intel/2017b`` -``2.6.6`` ``intel/2018a`` -``2.8.4`` ``foss/2018b`` -``2.8.5`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -========= ======================================== +========== ================== ======================================== +version versionsuffix toolchain +========== ================== ======================================== +``2.2.0`` ``foss/2016a`` +``2.4.0`` ``foss/2017a`` +``2.5.1`` ``intel/2017a``, ``intel/2017b`` +``2.6.6`` ``intel/2018a`` +``2.8.4`` ``foss/2018b`` +``2.8.5`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.8.5`` ``-Java-11`` ``GCC/8.3.0`` +``2.9.1`` ``-Python-2.7.16`` ``foss/2019b`` +``2.9.1`` ``-Python-3.7.4`` ``foss/2019b`` +``2.10.0`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================== ======================================== .. _list_software_TRIQS_403: @@ -30676,7 +32615,7 @@ version versionsuffix toolchain --- -:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` +:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` .. _list_software_UCLUST_480: @@ -30831,6 +32770,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_units_563: + +*units* ++++++++ + +GNU Units converts quantities expressed in various systems of measurement to their equivalents in other systems of measurement. Like many similar programs, it can handle multiplicative scale changes. It can also handle nonlinear conversions such as Fahrenheit to Celsius or wire gauge, and it can convert from and to sums of units, such as converting between meters and feet plus inches. + +*homepage*: https://www.gnu.org/software/units/ + +======== ================= +version toolchain +======== ================= +``2.19`` ``GCCcore/8.2.0`` +======== ================= + + .. _list_software_unixODBC_732: *unixODBC* @@ -30873,11 +32828,27 @@ UnZip is an extraction utility for archives compressed in .zip format (also call *homepage*: http://www.info-zip.org/UnZip.html -======= ======================================================= -version toolchain -======= ======================================================= -``6.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -======= ======================================================= +======= ========================================================================== +version toolchain +======= ========================================================================== +``6.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +======= ========================================================================== + + +.. _list_software_UQTk_357: + +*UQTk* +++++++ + +The UQ Toolkit (UQTk) is a collection of libraries and tools for the quantification of uncertainty in numerical model predictions. + +*homepage*: https://www.sandia.gov/UQToolkit/ + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``3.1.0`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== .. _list_software_USEARCH_523: @@ -31164,6 +33135,7 @@ version versionsuffix toolchain ``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` ``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` +``0.1.16`` ``GCC/8.3.0`` ``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` ========== ================ =============================== @@ -31193,12 +33165,12 @@ Sequence assembler for very short reads *homepage*: http://www.ebi.ac.uk/~zerbino/velvet/ -========== ================ ============================== -version versionsuffix toolchain -========== ================ ============================== -``1.2.10`` ``-mt-kmer_191`` ``foss/2018a``, ``foss/2018b`` -``1.2.10`` ``-mt-kmer_37`` ``intel/2017a`` -========== ================ ============================== +========== ================ ============================================= +version versionsuffix toolchain +========== ================ ============================================= +``1.2.10`` ``-mt-kmer_191`` ``GCC/8.3.0``, ``foss/2018a``, ``foss/2018b`` +``1.2.10`` ``-mt-kmer_37`` ``intel/2017a`` +========== ================ ============================================= .. _list_software_VEP_235: @@ -31351,11 +33323,11 @@ Voro++ is a software library for carrying out three-dimensional computations of *homepage*: http://math.lbl.gov/voro++/ -========= ================================================== -version toolchain -========= ================================================== -``0.4.6`` ``GCCcore/6.4.0``, ``foss/2016a``, ``intel/2016a`` -========= ================================================== +========= =================================================================================== +version toolchain +========= =================================================================================== +``0.4.6`` ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2019b``, ``intel/2016a``, ``intel/2019b`` +========= =================================================================================== .. _list_software_vsc-base_788: @@ -31606,7 +33578,7 @@ version toolchain --- -:ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` +:ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` .. _list_software_Wannier90_829: @@ -31722,13 +33694,13 @@ GNU Wget is a free software package for retrieving files using HTTP, HTTPS and F *homepage*: https://www.gnu.org/software/wget/ -========== ============================== -version toolchain -========== ============================== -``1.17.1`` ``foss/2016a``, ``foss/2016b`` -``1.19.4`` ``GCCcore/6.4.0`` -``1.20.1`` ``GCCcore/7.3.0`` -========== ============================== +========== ==================================== +version toolchain +========== ==================================== +``1.17.1`` ``foss/2016a``, ``foss/2016b`` +``1.19.4`` ``GCCcore/6.4.0`` +``1.20.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +========== ==================================== .. _list_software_wheel_533: @@ -31773,6 +33745,38 @@ version toolchain ======== ================================================ +.. _list_software_WildMagic_881: + +*WildMagic* ++++++++++++ + +Wild Magic 5.17 + +*homepage*: https://www.geometrictools.com/index.html + +======== ============== +version toolchain +======== ============== +``5.17`` ``foss/2018b`` +======== ============== + + +.. _list_software_Winnowmap_960: + +*Winnowmap* ++++++++++++ + +Winnowmap is a long-read mapping algorithm, and a result of our exploration into superior minimizer sampling techniques. + +*homepage*: https://github.com/marbl/Winnowmap + +======= ============= +version toolchain +======= ============= +``1.0`` ``GCC/8.3.0`` +======= ============= + + .. _list_software_WISExome_753: *WISExome* @@ -31961,7 +33965,7 @@ version toolchain --- -:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCfun_484` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtrans_672` - :ref:`list_software_XZ_178` +:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCfun_484` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_XZ_178` .. _list_software_X11_186: @@ -32045,20 +34049,21 @@ xarray (formerly xray) is an open source project and Python package that aims to *homepage*: https://github.com/pydata/xarray -========== ================== =============== -version versionsuffix toolchain -========== ================== =============== -``0.9.5`` ``-Python-2.7.13`` ``intel/2017a`` -``0.9.5`` ``-Python-3.6.1`` ``intel/2017a`` -``0.9.6`` ``-Python-2.7.13`` ``intel/2017a`` -``0.10.0`` ``-Python-2.7.14`` ``intel/2017b`` -``0.10.0`` ``-Python-3.6.3`` ``intel/2017b`` -``0.10.3`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.4`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.8`` ``-Python-3.6.4`` ``intel/2018a`` -``0.12.1`` ``-Python-3.6.6`` ``intel/2018b`` -``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` -========== ================== =============== +========== ================== =============================== +version versionsuffix toolchain +========== ================== =============================== +``0.9.5`` ``-Python-2.7.13`` ``intel/2017a`` +``0.9.5`` ``-Python-3.6.1`` ``intel/2017a`` +``0.9.6`` ``-Python-2.7.13`` ``intel/2017a`` +``0.10.0`` ``-Python-2.7.14`` ``intel/2017b`` +``0.10.0`` ``-Python-3.6.3`` ``intel/2017b`` +``0.10.3`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.4`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.8`` ``-Python-3.6.4`` ``intel/2018a`` +``0.12.1`` ``-Python-3.6.6`` ``intel/2018b`` +``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` +``0.15.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +========== ================== =============================== .. _list_software_xbitmaps_872: @@ -32216,11 +34221,12 @@ XCrySDen is a crystalline and molecular structure visualisation program aiming *homepage*: http://www.xcrysden.org/ -========== =============== -version toolchain -========== =============== -``1.5.60`` ``intel/2019a`` -========== =============== +========== =============================== +version toolchain +========== =============================== +``1.5.60`` ``intel/2019a`` +``1.6.2`` ``foss/2019b``, ``intel/2019b`` +========== =============================== .. _list_software_Xerces-C++_816: @@ -32289,6 +34295,7 @@ version versionsuffix toolchain ``0.6a2`` ``-Python-3.5.2`` ``intel/2016b`` ``0.6a2`` ``-Python-3.6.1`` ``intel/2017a`` ``0.72.1`` ``-Python-2.7.14`` ``intel/2017b`` +``0.90`` ``-Python-3.7.4`` ``foss/2019b`` ``20171120`` ``-Java-1.8.0_152`` ``intel/2017b`` ============ =================== =============== @@ -32414,6 +34421,7 @@ xmlf90 is a basic XML parsing library written in Fortran. version toolchain ========= ============================== ``1.5.3`` ``foss/2016b``, ``foss/2017a`` +``1.5.4`` ``iccifort/2019.5.281`` ========= ============================== @@ -32552,6 +34560,23 @@ version toolchain ============== ========================================================== +.. _list_software_xtb_334: + +*xtb* ++++++ + +xtb - An extended tight-binding semi-empirical program package. + +*homepage*: https://xtb-docs.readthedocs.io + +================ ================= =============== +version versionsuffix toolchain +================ ================= =============== +``6.2.2-hotfix`` ``-Python-3.6.3`` ``intel/2017b`` +``6.2.3`` ``foss/2019b`` +================ ================= =============== + + .. _list_software_xtrans_672: *xtrans* @@ -32638,7 +34663,7 @@ version versionsuffix toolchain ``1.5.0`` ``-Python-2.7.15`` ``intel/2018b`` ``1.5.0`` ``-Python-3.7.2`` ``intel/2019a`` ``1.6.0`` ``-Python-3.7.2`` ``intel/2019a`` -``1.6.0`` ``-Python-3.7.4`` ``intel/2019b`` +``1.6.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ==================== ============================== ================================================ @@ -32715,7 +34740,7 @@ version toolchain --- -:ref:`list_software_zarr_447` - :ref:`list_software_ZeroMQ_574` - :ref:`list_software_zingeR_623` - :ref:`list_software_zlib_433` - :ref:`list_software_zlibbioc_846` - :ref:`list_software_ZPAQ_316` - :ref:`list_software_zsh_341` - :ref:`list_software_zstd_453` +:ref:`list_software_zarr_447` - :ref:`list_software_ZeroMQ_574` - :ref:`list_software_zingeR_623` - :ref:`list_software_Zip_307` - :ref:`list_software_zlib_433` - :ref:`list_software_zlibbioc_846` - :ref:`list_software_ZPAQ_316` - :ref:`list_software_zsh_341` - :ref:`list_software_zstd_453` .. _list_software_zarr_447: @@ -32771,6 +34796,22 @@ version versionsuffix toolchain ============ ============= ============== +.. _list_software_Zip_307: + +*Zip* ++++++ + +Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality + +*homepage*: http://www.info-zip.org/Zip.html + +======= ==================================== +version toolchain +======= ==================================== +``3.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +======= ==================================== + + .. _list_software_zlib_433: *zlib* @@ -32786,7 +34827,7 @@ version toolchain ``1.2.7`` ``GCC/4.8.1``, ``GCC/4.8.2`` ``1.2.8`` ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.2.10`` ``system`` -``1.2.11`` ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` +``1.2.11`` ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index 6325e2d8..6505e118 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -69,9 +69,11 @@ * EB_DIRAC * EB_Doxygen * EB_Eigen + * EB_ELSI * EB_GATE * EB_Geant4 * EB_GROMACS + * EB_LAMMPS * EB_netCDF * EB_OpenBabel * EB_OpenCV @@ -84,6 +86,7 @@ * EB_Amber * EB_ARB * EB_ATLAS + * EB_BerkeleyGW * EB_binutils * EB_BLACS * EB_Bowtie @@ -91,6 +94,7 @@ * EB_bzip2 * EB_CBLAS * EB_Chapel + * EB_CMake * EB_cppcheck * EB_Cufflinks * EB_DB @@ -119,6 +123,7 @@ * EB_HPL * EB_Hypre * EB_LAPACK + * EB_libdrm * EB_Libint * EB_libQGLViewer * EB_libxml2 @@ -251,6 +256,7 @@ * EB_PyQuante * EB_python_minus_meep * EB_PyZMQ + * EB_SEPP * EB_TensorFlow * EB_TensorRT * EB_VSC_minus_tools @@ -308,6 +314,7 @@ * MesonNinja * CMakeNinja + * EB_Mesa * ModuleRC * PackedBinary @@ -372,6 +379,7 @@ * EB_PyQuante * EB_python_minus_meep * EB_PyZMQ + * EB_SEPP * EB_TensorFlow * EB_TensorRT * EB_VSC_minus_tools diff --git a/docs/version-specific/easyconfig_templates.rst b/docs/version-specific/easyconfig_templates.rst index c41fee53..b838bfe3 100644 --- a/docs/version-specific/easyconfig_templates.rst +++ b/docs/version-specific/easyconfig_templates.rst @@ -24,6 +24,8 @@ Template names/values for (short) software versions ==================== ========================================== Template name Template value ==================== ========================================== +``%(cudashortver)s`` short version for CUDA (.) +``%(cudaver)s`` full version for CUDA ``%(javashortver)s`` short version for Java (.) ``%(javaver)s`` full version for Java ``%(perlshortver)s`` short version for Perl (.) diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index 19d45027..478218ec 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -173,13 +173,14 @@ easyconfig parameter description ``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` ``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` ``build_cmd`` Build command to use ``"make"`` -``build_type`` Build type for CMake, e.g. Release or Debug.Use None to not specify -DCMAKE_BUILD_TYPE ``None`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``configure_cmd`` Configure command to use ``"cmake"`` ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``install_cmd`` Build command to use ``"make install"`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``separate_build_dir`` Perform build in a separate directory ``False`` +``separate_build_dir`` Perform build in a separate directory ``True`` ``srcdir`` Source directory location to provide to cmake command ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` ======================== ================================================================================================================================================================================================== ================== @@ -246,14 +247,15 @@ easyconfig parameter description ``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` ``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` ``build_cmd`` Build command to use ``"make"`` -``build_type`` Build type for CMake, e.g. Release or Debug.Use None to not specify -DCMAKE_BUILD_TYPE ``None`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``configure_cmd`` Configure command to use ``"cmake"`` ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``files_to_copy`` List of files or dirs to copy ``None`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``install_cmd`` Build command to use ``"make install"`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``separate_build_dir`` Perform build in a separate directory ``False`` +``separate_build_dir`` Perform build in a separate directory ``True`` ``srcdir`` Source directory location to provide to cmake command ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` ``with_configure`` Run configure script before building ``False`` @@ -282,13 +284,14 @@ easyconfig parameter description ``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` ``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` ``build_cmd`` Build command to use ``"make"`` -``build_type`` Build type for CMake, e.g. Release or Debug.Use None to not specify -DCMAKE_BUILD_TYPE ``None`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``configure_cmd`` Configure command to use ``"cmake"`` ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``install_cmd`` Build command to use ``"make install"`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``separate_build_dir`` Perform build in a separate directory ``False`` +``separate_build_dir`` Perform build in a separate directory ``True`` ``srcdir`` Source directory location to provide to cmake command ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` ======================== ================================================================================================================================================================================================== ================== @@ -325,7 +328,8 @@ easyconfig parameter description ``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` ``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` ``build_cmd`` Build command to use ``"make"`` -``build_type`` Build type for CMake, e.g. Release or Debug.Use None to not specify -DCMAKE_BUILD_TYPE ``None`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` ``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` ``configure_cmd`` Configure command to use ``"cmake"`` @@ -341,13 +345,14 @@ easyconfig parameter description ``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` ``runtest`` Run unit tests. ``True`` ``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed ``False`` -``separate_build_dir`` Perform build in a separate directory ``False`` +``separate_build_dir`` Perform build in a separate directory ``True`` ``srcdir`` Source directory location to provide to cmake command ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` ``unpack_sources`` Unpack sources prior to build/install ``True`` ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` @@ -537,6 +542,7 @@ easyconfig parameter description ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` @@ -635,6 +641,7 @@ easyconfig parameter description ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` @@ -904,6 +911,7 @@ easyconfig parameter description ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` @@ -938,6 +946,7 @@ easyconfig parameter description ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` @@ -1225,6 +1234,7 @@ easyconfig parameter description ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` @@ -1259,6 +1269,7 @@ easyconfig parameter description ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index d7075cdb..0af240bb 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -58,7 +58,9 @@ Option flag Option description ``-x, --extended-dry-run`` Print build environment and (expected) build procedure that will be performed (default: False) ``--extended-dry-run-ignore-errors`` Ignore errors that occur during dry run (default: True; disable with --disable-extended-dry-run-ignore-errors) ``-f, --force`` Force to rebuild software even if it's already installed (i.e. if it can be found as module), and skipping check for OS dependencies (default: False) +``--ignore-locks`` Ignore locks that prevent two identical installations running in parallel (default: False) ``--job`` Submit the build as a job (default: False) +``--locks-dir=LOCKS-DIR`` Directory to store lock files (should be on a shared filesystem); None implies .locks subdirectory of software installation directory ``-l, --logtostdout`` Redirect main log to stdout (default: False) ``-M, --missing-modules`` Print list of missing modules for dependencies of specified easyconfigs (default: False) ``-b BLOCKS, --only-blocks=BLOCKS`` Only build listed blocks (type comma-separated list) @@ -105,7 +107,7 @@ Option flag Option desc ``--packagepath=PACKAGEPATH`` The destination path for the packages built by package-tool (default: /home/example/.local/easybuild/packages) ``--prefix=PREFIX`` Change prefix for buildpath, installpath, sourcepath and repositorypath (used prefix for defaults /home/example/.local/easybuild) ``--recursive-module-unload`` Enable generating of modules that unload recursively. (default: False) -``--repository=REPOSITORY`` Repository type, using repositorypath (type choice; default: FileRepository) (choices: FileRepository, GitRepository, HgRepository) +``--repository=REPOSITORY`` Repository type, using repositorypath (type choice; default: FileRepository) (choices: FileRepository, GitRepository) ``--repositorypath=REPOSITORYPATH`` Repository path, used by repository (is passed as list of arguments to create the repository instance). For more info, use --avail-repositories. (type comma-separated list; default: /home/example/.local/easybuild/ebfiles_repo) ``--sourcepath=SOURCEPATH`` Path(s) to where sources should be downloaded (string, colon-separated) (default: /home/example/.local/easybuild/sources) ``--subdir-modules=SUBDIR-MODULES`` Installpath subdir for modules (default: modules) @@ -138,7 +140,10 @@ Options for Easyconfigs =================================================== ===================================================================================================================================================================================================================================================== Option flag Option description =================================================== ===================================================================================================================================================================================================================================================== +``--create-index=CREATE-INDEX`` Create index for files in specified directory ``--fix-deprecated-easyconfigs`` Fix use of deprecated functionality in specified easyconfig files. (default: False) +``--ignore-index`` Ignore index when searching for files (default: False) +``--index-max-age=INDEX-MAX-AGE`` Maximum age for index before it is considered stale (in seconds) (type ; default: 604800) ``--inject-checksums=INJECT-CHECKSUMS`` Inject checksums of specified type for sources/patches into easyconfig file(s) (type choice; default: sha256) (choices: adler32, crc32, md5, sha1, sha256, sha512, size) ``--local-var-naming-check=LOCAL-VAR-NAMING-CHECK`` Mode to use when checking whether local variables follow the recommended naming scheme ('log': only log warnings (no printed messages); 'warn': print warnings; 'error': fail with an error) (type choice; default: warn) (choices: error, log, warn) =================================================== ===================================================================================================================================================================================================================================================== @@ -161,6 +166,7 @@ Option flag Option description ``--git-working-dirs-path=GIT-WORKING-DIRS-PATH`` Path to Git working directories for EasyBuild repositories (type ) ``--github-org=GITHUB-ORG`` GitHub organization (type ) ``--github-user=GITHUB-USER`` GitHub username (type ) +``--include-easyblocks-from-pr=PR#`` Include easyblocks from specified PR (type ) ``--install-github-token`` Install GitHub token (requires --github-user) (default: False) ``--list-prs=STATE,ORDER,DIRECTION`` List pull requests (type ; default: open,created,desc) ``--merge-pr=PR#`` Merge pull request (type ) @@ -172,7 +178,7 @@ Option flag Option description ``--pr-descr=PR-DESCR`` Description for new pull request created with --new-pr (type ) ``--pr-target-account=PR-TARGET-ACCOUNT`` Target account for new PRs (type ; default: easybuilders) ``--pr-target-branch=PR-TARGET-BRANCH`` Target branch for new PRs (type ; default: develop) -``--pr-target-repo=PR-TARGET-REPO`` Target repository for new/updating PRs (type ; default: easybuild-easyconfigs) +``--pr-target-repo=PR-TARGET-REPO`` Target repository for new/updating PRs (default: auto-detect based on provided files) (type ) ``--pr-title=PR-TITLE`` Title for new pull request created with --new-pr (type ) ``--preview-pr`` Preview a new pull request (default: False) ``--review-pr=PR#`` Review specified pull request (type ) @@ -305,6 +311,7 @@ Option flag Opt ``--use-existing-modules`` Use existing modules when resolving dependencies with minimal toolchains (default: False) ``--use-f90cache=PATH`` Enable use of f90cache to speed up compilation, with specified cache dir (type ; default: False) ``--verify-easyconfig-filenames`` Verify whether filename of specified easyconfigs matches with contents (default: False) +``--wait-on-lock=WAIT-ON-LOCK`` Wait interval (in seconds) to use when waiting for existing lock to be removed (0: implies no waiting, but exiting with an error) (type ; default: 0) ``--zip-logs=ZIP-LOGS`` Zip logs that are copied to install directory, using specified command (default: gzip) ========================================================================= ================================================================================================================================================================================== @@ -354,6 +361,7 @@ Option flag Option description ``--try-toolchain=NAME,VERSION`` Try to search and build with given toolchain (name and version) (USE WITH CARE!) (type comma-separated list) ``--try-toolchain-name=NAME`` Try to search and build with given toolchain name (USE WITH CARE!) ``--try-toolchain-version=VERSION`` Try to search and build with given toolchain version (USE WITH CARE!) +``--try-update-deps`` Try to update versions of the dependencies of an easyconfig based on what is available in the robot path (default: False) =================================== =================================================================================================================================================================== From 862efe8202a35801b7053a65e25de6c5197d9de5 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 14 Apr 2020 18:40:46 +0800 Subject: [PATCH 025/286] update release notes for EasyBuild v4.2.0 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 252 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 252 insertions(+), 5 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 967c3f0a..1741bd0f 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20200414.01** (`Apr 14th 2020`): update release notes for EasyBuild v4.2.0 (see :ref:`release_notes_eb420`) * **release 20200316.01** (`Mar 16th 2020`): update release notes for EasyBuild v4.1.2 (see :ref:`release_notes_eb412`) * **release 20200116.01** (`Jan 16th 2020`): update release notes for EasyBuild v4.1.1 (see :ref:`release_notes_eb411`) * **release 20191204.01** (`Dec 4th 2019`): update release notes for EasyBuild v4.1.0 (see :ref:`release_notes_eb410`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index bd584692..377f331b 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,258 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **1,798** different software packages, -including 31 different (compiler) toolchains. It contains 212 software-specific easyblocks and 36 generic easyblocks, -alongside 8,964 easyconfig files. +The latest version of EasyBuild provides support for building and installing **1,912** different software packages, +including 31 different (compiler) toolchains. It contains 219 software-specific easyblocks and 36 generic easyblocks, +alongside 9462 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb420: + +EasyBuild v4.2.0 (April 14th 2020) +---------------------------------- + +feature release + +**framework** + +* add support for --try-update-deps (experimental feature), to upgrade dependencies based on available easyconfigs (`#2599 `_) +* adding locking to prevent two parallel builds of the same installation directory (`#3009 `_) + + * for more information, see https://easybuild.readthedocs.io/en/latest/Locks.html + +* significantly speed up -D/--dry-run by avoiding useless 'module show' (`#3203 `_) +* add support for creating an index & using it when searching for easyconfigs (`#3210 `_) + + * for more information, see https://easybuild.readthedocs.io/en/latest/Easyconfigs_index.html + +* additional GitHub integration features: + + * add support for targeting easyblocks and framework repositories in --new-pr (`#1876 `_, `#3189 `_) + * add support for --include-easyblocks-from-pr (`#3206 `_) + * for more information, https://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html + +* various other enhancements, including: + + * add a contrib/hooks dir with some examples of hooks used (`#2777 `_) + * also mention working directory + input passed via stdin (if any) in trace output of run_cmd (`#3168 `_) + * probe external modules for missing metadata that is not provided via extermal module metadata file (`#3174 `_) + * also update $CMAKE_PREFIX_PATH and $CMAKE_LIBRARY_PATH in generated module file (`#3176 `_) + * optionally call log.warning in print_warning (`#3195 `_) + * add an option to git_config to retain the .git directory (`#3197 `_) + * allow use of SYSTEM as --try-toolchain option (`#3213 `_) + * mention CPU arch name in comment for uploaded test report, if it's known by archspec (`#3227 `_) + * make --merge-pr take into account --pr-target-branch (`#3236 `_) + * make --check-contrib print a warning when None is used for checksums (`#3244 `_) + * update install-EasyBuild-develop.sh script and create script for 2020a merge sprint (`#3245 `_) + * add template for mpi_cmd_prefix (`#3264 `_) + * update copy_dir to include option to merge directories (`#3270 `_) + * support template name for CUDA version (`#3274 `_) + +* various bug fixes, including: + + * use correct module for errors_found_in_log (`#3119 `_) + * fix EasyConfig.update code to handle both strings and lists as input (`#3170 `_) + * fix removing temporary branch on --check-github (`#3182 `_) + * fix shebang even if first line doesn't start with '#!' (`#3183 `_) + * make boostrap script work with Python 3 (`#3186 `_) + * read patch files as bytestring to avoid UnicodeDecodeError for patches that include funky characters (`#3191 `_) + * fix online check in --check-github: try repeatedly and with different URLs to cater for HTTP issues (`#3194 `_) + * don't crash when GitPython is not installed when using Python 3 (`#3198 `_) + * fix os_name_map for RHEL8 (`#3201 `_) + * don't add shebang to binary files (`#3208 `_) + * use checkout@v2 in GitHub Actions to fix broken re-triggered tests (`#3219 `_) + * don't filter out None values in to_checksums, leave them in place (`#3225 `_) + * fix defining of $MPI_INC_* and $MPI_LIB_* environment variables for impi version 2019 and later (`#3229 `_) + * use correct target account/repo when creating test report & posting comment in PR (`#3234 `_) + * reorganize EasyBlock.extensions_step to ensure correct filtering of extensions (`#3235 `_) + * also support %(installdir)s and %(builddir)s templates for extensions (`#3237 `_) + * unset $GITHUB_TOKEN in Travis after installing token, to avoid failing test_from_pr_token_log (`#3252 `_) + * fix reporting when skipping extensions (`#3254 `_) + * avoid API rate limit errors on online check in --check-github (`#3257 `_) + * show easyconfig filenames for parallel build (`#3258 `_) + * make EasyConfig.dump aware of toolchain hierarchy, to avoid hardcoded subtoolchains in dependencies easyconfig parameters (`#3261 `_) + * fix use of --copy-ec with a single argument, assume copy to current working directory (`#3262 `_) + * fix posting of comment in PR with --upload-test-report (`#3272 `_) + * take into account dependencies marked as external modules when composing template values like %(pyver)s (`#3273 `_) + +* other changes: + + * increase timeout & use api.github.com for connectivity check in check_github (`#3192 `_) + * restore flake8 default ignores (`#3193 `_) + * enable tracking of test suite coverage using coveralls (`#3204 `_) + * make tests use easybuilders/testrepository rather than hpcugent/testrepository after it was moved (`#3238 `_) + * improve raised error in remove_dir and deprecate rmtree2 (`#3228 `_) + +**easyblocks** + +* 7 new software-specific easyblocks: + + * BerkeleyGW (`#1951 `_), CMake (`#1936 `_), ELSI (`#1883 `_), LAMMPS (`#1964 `_, `#1975 `_, `#1978 `_, `#1982 `_, `#1997 `_), libdrm (`#1983 `_), Mesa (`#1892 `_, `#2006 `_), SEPP (`#1998 `_) + +* minor enhancements, including: + + * make ParMETIS easyblock compatible with custom configopts (`#1774 `_) + * update Trinity easyblock for v2.9.0 (`#1906 `_) + * disable ROCM and Android workspace explicitely in TensorFlow easyblock (`#1944 `_) + * update QuantumESPRESSO easyblock for version 6.5 (`#1947 `_) + * update Siesta easyblock to support MaX-1.0 release (`#1954 `_) + * update Ferret easyblock for versions >= 7.5.0 (`#1956 `_) + * update XCrySDen easyblock to support Togl dependency (`#1959 `_) + * pass value for TARGET specified in buildopts to testopts and installopts in OpenBLAS easyblock (`#1960 `_) + * fix netCDF(-Fortran) support in Siesta easyblock (`#1967 `_, 1971) + * add NCDF_PARALLEL and METIS support to Siesta easyblock (`#1973 `_) + * add support for 'use_pip_extras' custom easyconfig parameter in PythonPackage easyblock (`#1980 `_) + * update Open Babel easyblock for version 3.0.0 (`#1992 `_) + * allow differing names for TensorFlow wheel (`#1995 `_) + * make MATLAB runtime available from MATLAB (`#2008 `_) + +* various bug fixes, including: + + * fix linking of Hypre to external BLAS/LAPACK + support building (only) static/shared library (`#1885 `_) + * fix MPI-CXX dependency of PETSc (`#1917 `_) + * limit amount of parallelism in TensorFlow easyblock (`#1934 `_) + * support GCCcore and gcc4.8 (if that dir exists) in function get_tbb_gccprefix in tbb easyblock (`#1943 `_) + * restore default flake8 warnings (`#1950 `_) + * remove tests from build_step and raise error on failed tests in OpenBLAS easyblock (`#1952 `_, `#1955 `_, `#1962 `_) + * add optional runtest to the catch for FATAL ERRORS to OpenBLAS easyblock (`#1958 `_) + * ensure right 'python' command is used to determine Python lib dir when system Python is used with PythonBundle easyblock (`#1961 `_) + * make sure lib/python*/lib-dynload exists in Python installation (`#1966 `_) + * in version 6.0 of TensorRT, libnvinfer.a is renamed libnvinfer_static.a (`#1970 `_) + * handle configopts without configure args in CMake easyblock (`#1974 `_) + * use checkout@v2 in GitHub Actions to fix broken re-triggered tests (`#1976 `_) + * don't insist that pylibdir always exists in OpenCV easyblock (`#1977 `_) + * also set $TRINITY_HOME environment variable in Trinity easyblock (`#1979 `_) + * fix sanity check for OpenFOAM-Extend >= 4.1 (`#1981 `_) + * fix pattern matching in regex subst for I_MPI_ROOT in impi easyblock (`#1986 `_) + * use remove_dir instead of deprecated rmtree2 in various easyblocks (`#1993 `_) + * fix "AttributeError: module 'git' has no attribute 'Git'" that may occur when using Python 3 (`#1994 `_) + * don't sanity check for QtWebEngine in Qt easyblock when building for POWER (`#2000 `_) + * fix installation of TensorFlow in some environments, by setting $PYTHONNOUSERSITE (& more) (`#2002 `_, `#2020 `_) + * make sure libxml2 is built with XZ provided as dependency (`#2005 `_) + * look for Python version directories with suffixes in ROOT easyblock (`#2010 `_) + * enable TK, FLTK and OPENGL configure options in VMD easyblock (`#2013 `_) + * update the contributing docs (`#2014 `_) + * fix numexpr easyblock to allow (correctly) installing it as extension (`#2022 `_) + +* other changes: + + * simplify various CMakeMake-based easyblocks by enhancing CMakeMake (w.r.t. CMAKE_BUILD_TYPE, shared vs static libs, fPIC) (`#1929 `_) + * enable out of tree build by default in CMakeMake easyblock (`#1933 `_) + * force building Clang without CUDA when it is not found as a proper dependency (`#1968 `_) + +**easyconfigs** + +* added example easyconfig files for 114 new software packages: + + * ABRA2 (`#10272 `_, ABRicate (`#10310 `_, ADIOS (`#10036 `_, aNCI (`#9929 `_, any2fasta (`#10310 `_, apex (`#10269 `_, + archspec (`#9898 `_, ArviZ (`#10366 `_, autopep8 (`#9626 `_, BAMSurgeon (`#10330 `_, BatMeth2 (`#10323 `_, + BiG-SCAPE (`#10352 `_, BinSanity (`#10001 `_, Bonito (`#10269 `_, BSMAPz (`#10283 `_, BSseeker2 (`#10039 `_, + BUStools (`#9838 `_, Cbc (`#10052 `_, Cgl (`#10048 `_, CGmapTools (`#10288 `_, Clp (`#10033 `_, CoinUtils (`#9937 `_, + dtcwt (`#9695 `_, ELSI (`#9857 `_, EnsEMBLCoreAPI (`#8734 `_, fastq-pair (`#9894 `_, FigureGen (`#10076 `_, Fiona (`#10321 `_, + FuSeq (`#10004 `_, GenomeTools (`#9797 `_, GraphMap2 (`#10299 `_, GRASP (`#9896 `_, Groovy (`#9809 `_, gsport (`#9821 `_, + gubbins (`#9689 `_, igv-reports (`#9977 `_, inferCNV (`#9686 `_, iVar (`#10291 `_, joypy (`#10212 `_, JupyterLab (`#9752 `_, + kma (`#10259 `_, LAMMPS (`#10371 `_, lancet (`#10271 `_, libBigWig (`#10006 `_, libGridXC (`#9858 `_, libPSML (`#5859 `_, + LtrDetector (`#10343 `_, manta (`#5104 `_, medImgProc (`#10228 `_, MedPy (`#9748 `_, Mini-XML (`#10036 `_, mkl_fft (`#9887 `_, + Monocle3 (`#9825 `_, MoreRONN (`#10255 `_, motionSegmentation (`#10228 `_, NanoComp (`#10212 `_, NanoFilt (`#10212 `_, + nanoget (`#10212 `_, nanomath (`#10212 `_, NanoPlot (`#10212 `_, ngspice (`#9922 `_, ntEdit (`#9836 `_, ntHits (`#9833 `_, + occt (`#9939 `_, OCNet (`#9955 `_, OpenAI-Gym (`#10347 `_, OpenPIV (`#9959 `_, OpenPyXL (`#10115 `_, orca (`#9518 `_, + Osi (`#10361 `_, PartitionFinder (`#9983 `_, pauvre (`#10212 `_, polymake (`#9904 `_, pretty-yaml (`#10041 `_), + PRSice (`#9988 `_, pycodestyle (`#9626 `_, pydot (`#9899 `_, pygraphviz (`#9969 `_, pylift (`#10051 `_, PyMC3 (`#10279 `_, + pyparsing (`#9983 `_, PyRe (`#10095 `_, python-weka-wrapper3 (`#9704 `_, PyTorch-Geometric (`#9995 `_, qcat (`#10244 `_, + RAxML-NG (`#9990 `_, Ray (`#10302 `_, rclone (`#7934 `_, Red (`#9856 `_, rstanarm (`#9964 `_, scikit-build (`#9762 `_, + scVelo (`#9805 `_, SECAPR (`#9721 `_, segmentation-models (`#10211 `_, SentencePiece (`#10192 `_, SEPP (`#10047 `_, + Shapely (`#10309 `_, Singular (`#10030 `_, SLATEC (`#7529 `_, spatialreg (`#9767 `_, split-seq (`#9749 `_, spoa (`#9705 `_, + SSN (`#9955 `_, STEAK (`#10337 `_, stpipeline (`#9736 `_, SVG (`#9905 `_, Togl (`#9868 `_, torchtext (`#10193 `_, + units (`#9682 `_, UQTk (`#10279 `_, WildMagic (`#10044 `_, Winnowmap (`#10005 `_, xtb (`#9993 `_, Zip (`#9972 `_ + +* added additional easyconfigs for various supported software packages, including: + + * ABySS 2.1.5, Arrow 0.16.0, BCFtools 1.10.2, BEDTools 2.29.2, BUSCO 4.0.5, BerkeleyGW 2.1.0, binutils 2.34, + CVXPY 1.0.28, CharLS 2.1.0, CheckM 1.1.2, Clang 10.0.0, CppUnit 1.15.1, canu 1.9, cutadapt 2.8, + DIAMOND 0.9.30, davix 0.7.5, ELPA 2019.11.001, FastANI 1.3, FastQC 0.11.9, Ferret 7.5.0, GATK 4.1.4.1, + GCCcore 9.3.0, GDB 9.1, GMAP-GSNAP-2019-09-12, GObject-Introspection 1.63.1, GPAW 20.1.0, GROMACS 2020, + GTDB-Tk 1.0.2, GTK+ 3.24.13, Go 1.14.1, Gradle 6.1.1, GraphicsMagick 1.3.34, Graphviz 2.42.2, Gurobi 9.0.1, + gSOAP 2.8.100, gnuplot 5.2.8, gtest 1.10.0, HDDM 0.7.5, HTSlib 1.10.2, HarfBuzz 2.6.4, Horovod 0.19.1, + Hypre 2.18.2, IGV 2.8.0, IQ-TREE 1.6.12, IRkernel 1.1, iccifort 2020.0.166, igraph 0.8.0, impi 2019.6.166, + ispc 1.12.0, Java 13(.0.2), Julia 1.4.0, Keras 2.3.1, Kraken2 2.0.8-beta, kim-api 2.1.3, LAST 1045, + LASTZ 1.04.03, LLVM 9.0.1 + 10.0.0, LMfit 0.9.14, LS-PrePost 4.7.8, likwid 5.0.1, MAFFT 7.453, + MATLAB 2019b, MMseqs2 10, Maven 3.6.3, Meson 0.53.1, MethylDackel 0.5.0, Mono 6.8.0.105, medaka 0.12.0, + Nextflow 20.01.0, ncdf4 1.17, netcdf4-python 1.5.3, nodejs 12.16.1, numba 0.47.0, numexpr 2.7.1, + Octave 5.1.0, OpenBLAS 0.3.8, OpenBabel 3.0.0, OpenCV 4.2.0, OpenFOAM-Extend 4.1-20191120, OrthoFinder 2.3.11, + PETSc 3.12.4, PGI 19.10, PMIx 2.2.1, Pango 1.44.7, PyTables 3.6.1, PyTorch 1.4.0, parasail 2.4.1, + pydicom 1.4.2, pyproj 2.4.2, Qhull 2019.1, QuantumESPRESSO 6.5, R-bundle-Bioconductor 3.10, RDKit 2019.09.3 + Racon 1.4.10, ReFrame 2.21, Ruby 2.7.1, rjags 4-9, rpy2 3.2.6, SLEPc 3.12.2, SPAdes 3.14.0, + SPAdes 3.14.0, STAR-Fusion 1.8.1, STAR 2.7.3a, Seaborn 0.10.0, SeqAn 1.4.2, Seurat 3.1.2, SimpleElastix 1.1.0, + SimpleITK 1.2.4, Stacks 2.5, Stata 16, StringTie 2.1.0, scikit-optimize 0.7.4, statsmodels 0.11.0, + TensorFlow 1.15.2 + 2.0.1, Tkinter 2.7.16, Trim_Galore 0.6.5, Trimmomatic 0.39, Trinity 2.10.0, tbb 2020.2, + tqdm 4.41.1, XCrySDen 1.6.2, XGBoost 0.90, xarray 0.15.1, xmlf90 1.5.4 + +* minor enhancements, including: + + * add easyconfig for Java 11.0.6 on ppc64le and alter the Java 11 wrapper to support both x86_64 and ppc64le (`#9371 `_ + * add additional extensions for R: HiddenMarkov (`#9685 `_, lmerTest (`#9853 `_, VSURF + Rborist (`#10355 `_ + * change Mesa 19.1.7 + 19.2.1 easyconfigs to use custom easyblock for Mesa (`#9764 `_ + * build shared libs and install header files for Ghostscript (`#9785 `_ + * add MUMPS as dependency in PETSc 3.12.4 easyconfigs (#9880, `#9891 `_ + * add Perl extensions: Term::ReadLine::Gnu (`#9901 `_, URI::Escape and Set::IntervalTree (`#10049 `_ + * add dat directory to aNCI (`#9929 `_ + * add patch to create a symlink from libsvm.so.$(SHVER) to libsvm.so in LIBSVM easyconfigs (`#10045 `_ + * build SUNDIALS with 'pic' (`#10278 `_ + * add BSgenome.Hsapiens.UCSC.hg38 + MEDIPS extensions to R-bundle-Bioconductor v3.10 (`#10298 `_ + * fix checksums for mkl-dnn and tbb extensions (moved to oneAPI repo) in PyTorch easyconfigs (`#10367 `_ + * update Java/1.8 wrapper to Java/1.8.0_241.eb (`#10305 `_ + +* various bug fixes, including: + + * use CMake for building double-conversion (`#9659 `_ + * update recent libdrm easyconfigs to use custom easyblock & avoid hardcoded x86-specific sanity check (`#9694 `_ + * add alternate checksum for OpenMolcas 18.09 (`#9701 `_ + * use Github to download releases for MariaDB-connector-c (`#9702 `_ + * add -DOMPI_SKIP_MPICXX in configopts for MathGL, to avoid using mpicxx during build (`#9703 `_ + * make installing independent of build folder in pybind11 easyconfig (`#9738 `_ + * add Lua as a dependency to gnuplot (`#9773 `_ + * stick to http:// source URLS for ISL in GCCcore easyconfigs, since https:// doesn't work (`#9784 `_ + * add alternative checksums for farver/fracdiff/pkgmaker/rngtools/doRNG/cobs extensions in R 3.6.2 easyconfigs (`#9789 `_ + * add patch for OpenBLAS 0.3.4 w/ GCC/8.2.0-2.31.1 to fix broken tests (`#9865 `_ + * revert removal of AVX512 vmovd with 64-bit operands in binutils 2.32 easyconfigs (`#9866 `_ + * fix inline asm in dscal: mark x, x1 as clobbered, in OpenBLAS 0.3.8 (`#9867 `_ + * add missing sanity_check_commands to cutadapt v1.18 and v2.7 easyconfigs (`#9869 `_ + * don't overwrite configopts in BLAST+ easyconfigs, append to it (`#9875 `_ + * add alternate checksum for LaplacesDemon in R 3.6.x easyconfigs (#9879, `#10382 `_ + * fix redefining of preconfigopts in OpenCV easyconfigs (`#9895 `_ + * use symlinks for terminfo files instead of hard links in ncurses 6.1 easyconfigs (`#9912 `_ + * fix NCIPLOT build flags (`#9915 `_ + * add missing patch to iccifort libxc easyconfigs (`#9918 `_ + * use checkout@v2 in GitHub Actions to fix broken re-triggered tests (`#9925 `_ + * re-enable building utils in Siesta 4.1-MaX-1.0 release (`#9936 `_ + * fix homepage and source URLs in SLEPc easyconfigs by using https (`#9943 `_ + * fix source URLs for rgeos after source tarball was moved to CRAN archive (`#9954 `_ + * add dependencies on Python 3 and SciPy-bundle in Trinity v2.9.1 easyconfig (`#9957 `_ + * patch GCC lisanitizer for glibc 2.31 (`#9966 `_ + * add Zip as build dependency for recent Bazel versions (`#9972 `_ + * fix checksums in Jellyfish v2.3.0 easyconfigs (`#9997 `_ + * fix source URLs for ParMGridGen easyconfigs (`#10019 `_ + * disable unintended Octave support in all libsndfile easyconfigs (`#10027 `_ + * fix sources for LS-PrePost 4.6 (`#10236 `_ + * security update for vsc-mympirun 4.1.9 (`#10185 `_ + * configure libwebp to also install libwebpmux (`#10274 `_ + * ensure that CVS easyconfigs are included in source tarball produced by 'python setup.py sdist' (`#10326 `_ + * fix undefined reference error due to libxc 4.3.4 built with CMake (`#10356 `_ + * fix source_urls for tbb: use (new) official 'oneapi-src' GitHub repository (`#10361 `_ + * add missing build dependency on pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (`#10380 `_ + * update checksums and homepage in tbb easyconfigs (`#10285 `_ + +* other changes: + + * use new custom easyblock in recent CMake easyconfigs (#9871, `#9923 `_ + * add check for redefined easyconfig parameters in easyconfig tests (`#9876 `_ + * use M4-1.4.18.eb for test installation in easyconfigs test suite (`#9926 `_ + * use https in homepage/source_urls of zlib-1.2.11.eb (`#10018 `_ + * add -GCCcore-9.2.0 versionsuffix for intel/2020.00 components (`#10083 `_ + * add checksum of new tbb 2019_U9 source tarball, next to original one + update homepage (`#10237 `_ + * add comment informing about manually setting Gallium drivers in easyconfigs for Mesa v19.1.7 and v19.2.1 (`#10276 `_ + .. _release_notes_eb412: EasyBuild v4.1.2 (March 16th 2020) diff --git a/docs/conf.py b/docs/conf.py index 1ed64c26..b2f8f013 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.1.2' # this is meant to reference the version of EasyBuild +version = '4.2.0' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20200316.0' # this is meant to reference the version of the documentation itself +release = '20200414.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From dd956565f29de3b81c824c7d811fb9c750e715eb Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 14 Apr 2020 19:08:00 +0800 Subject: [PATCH 026/286] tweak release notes for EasyBuild v4.2.0 --- docs/Release_notes.rst | 248 +++++++++++++++++++++-------------------- 1 file changed, 125 insertions(+), 123 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 377f331b..411c50b9 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -18,73 +18,75 @@ feature release **framework** -* add support for --try-update-deps (experimental feature), to upgrade dependencies based on available easyconfigs (`#2599 `_) +* add support for ``--try-update-deps`` (experimental feature), to upgrade dependencies based on available easyconfigs (`#2599 `_) + * adding locking to prevent two parallel builds of the same installation directory (`#3009 `_) * for more information, see https://easybuild.readthedocs.io/en/latest/Locks.html -* significantly speed up -D/--dry-run by avoiding useless 'module show' (`#3203 `_) +* significantly speed up ``-D/--dry-run`` by avoiding useless 'module show' (`#3203 `_) + * add support for creating an index & using it when searching for easyconfigs (`#3210 `_) * for more information, see https://easybuild.readthedocs.io/en/latest/Easyconfigs_index.html * additional GitHub integration features: - * add support for targeting easyblocks and framework repositories in --new-pr (`#1876 `_, `#3189 `_) - * add support for --include-easyblocks-from-pr (`#3206 `_) - * for more information, https://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html + * add support for targeting easyblocks and framework repositories in ``--new-pr`` (`#1876 `_, `#3189 `_) + * add support for ``--include-easyblocks-from-pr`` (`#3206 `_) + * for more information, https://easybuild.readthedocs.io/en/latest/Integration_with_GitHub.html * various other enhancements, including: * add a contrib/hooks dir with some examples of hooks used (`#2777 `_) - * also mention working directory + input passed via stdin (if any) in trace output of run_cmd (`#3168 `_) + * also mention working directory + input passed via stdin (if any) in trace output of ``run_cmd`` (`#3168 `_) * probe external modules for missing metadata that is not provided via extermal module metadata file (`#3174 `_) - * also update $CMAKE_PREFIX_PATH and $CMAKE_LIBRARY_PATH in generated module file (`#3176 `_) - * optionally call log.warning in print_warning (`#3195 `_) - * add an option to git_config to retain the .git directory (`#3197 `_) - * allow use of SYSTEM as --try-toolchain option (`#3213 `_) + * also update ``$CMAKE_PREFIX_PATH`` and ``$CMAKE_LIBRARY_PATH`` in generated module file (`#3176 `_) + * optionally call log.warning in ``print_warning`` (`#3195 `_) + * add an option to ``git_config`` to retain the .git directory (`#3197 `_) + * allow use of ``SYSTEM`` as ``--try-toolchain`` option (`#3213 `_) * mention CPU arch name in comment for uploaded test report, if it's known by archspec (`#3227 `_) - * make --merge-pr take into account --pr-target-branch (`#3236 `_) - * make --check-contrib print a warning when None is used for checksums (`#3244 `_) - * update install-EasyBuild-develop.sh script and create script for 2020a merge sprint (`#3245 `_) - * add template for mpi_cmd_prefix (`#3264 `_) - * update copy_dir to include option to merge directories (`#3270 `_) + * make ``--merge-pr`` take into account ``--pr-target-branch`` (`#3236 `_) + * make ``--check-contrib`` print a warning when None is used for checksums (`#3244 `_) + * update ``install-EasyBuild-develop.sh`` script and create script for 2020a merge sprint (`#3245 `_) + * add template for ``mpi_cmd_prefix`` (`#3264 `_) + * update ``copy_dir`` to include option to merge directories (`#3270 `_) * support template name for CUDA version (`#3274 `_) * various bug fixes, including: - * use correct module for errors_found_in_log (`#3119 `_) - * fix EasyConfig.update code to handle both strings and lists as input (`#3170 `_) - * fix removing temporary branch on --check-github (`#3182 `_) + * use correct module for ``errors_found_in_log`` (`#3119 `_) + * fix ``EasyConfig.update`` code to handle both strings and lists as input (`#3170 `_) + * fix removing temporary branch on ``--check-github`` (`#3182 `_) * fix shebang even if first line doesn't start with '#!' (`#3183 `_) * make boostrap script work with Python 3 (`#3186 `_) * read patch files as bytestring to avoid UnicodeDecodeError for patches that include funky characters (`#3191 `_) - * fix online check in --check-github: try repeatedly and with different URLs to cater for HTTP issues (`#3194 `_) + * fix online check in ``--check-github``: try repeatedly and with different URLs to cater for HTTP issues (`#3194 `_) * don't crash when GitPython is not installed when using Python 3 (`#3198 `_) - * fix os_name_map for RHEL8 (`#3201 `_) + * fix ``os_name_map`` for RHEL8 (`#3201 `_) * don't add shebang to binary files (`#3208 `_) - * use checkout@v2 in GitHub Actions to fix broken re-triggered tests (`#3219 `_) - * don't filter out None values in to_checksums, leave them in place (`#3225 `_) - * fix defining of $MPI_INC_* and $MPI_LIB_* environment variables for impi version 2019 and later (`#3229 `_) + * use ``checkout@v2`` in GitHub Actions to fix broken re-triggered tests (`#3219 `_) + * don't filter out ``None`` values in to_checksums, leave them in place (`#3225 `_) + * fix defining of ``$MPI_INC_*`` and ``$MPI_LIB_*`` environment variables for impi version 2019 and later (`#3229 `_) * use correct target account/repo when creating test report & posting comment in PR (`#3234 `_) - * reorganize EasyBlock.extensions_step to ensure correct filtering of extensions (`#3235 `_) - * also support %(installdir)s and %(builddir)s templates for extensions (`#3237 `_) - * unset $GITHUB_TOKEN in Travis after installing token, to avoid failing test_from_pr_token_log (`#3252 `_) + * reorganize ``EasyBlock.extensions_step`` to ensure correct filtering of extensions (`#3235 `_) + * also support ``%(installdir)s`` and ``%(builddir)s`` templates for extensions (`#3237 `_) + * unset ``$GITHUB_TOKEN`` in Travis after installing token, to avoid failing ``test_from_pr_token_log`` (`#3252 `_) * fix reporting when skipping extensions (`#3254 `_) - * avoid API rate limit errors on online check in --check-github (`#3257 `_) + * avoid API rate limit errors on online check in ``--check-github`` (`#3257 `_) * show easyconfig filenames for parallel build (`#3258 `_) - * make EasyConfig.dump aware of toolchain hierarchy, to avoid hardcoded subtoolchains in dependencies easyconfig parameters (`#3261 `_) - * fix use of --copy-ec with a single argument, assume copy to current working directory (`#3262 `_) - * fix posting of comment in PR with --upload-test-report (`#3272 `_) - * take into account dependencies marked as external modules when composing template values like %(pyver)s (`#3273 `_) + * make ``EasyConfig.dump`` aware of toolchain hierarchy, to avoid hardcoded subtoolchains in dependencies easyconfig parameters (`#3261 `_) + * fix use of ``--copy-ec`` with a single argument, assume copy to current working directory (`#3262 `_) + * fix posting of comment in PR with ``--upload-test-report`` (`#3272 `_) + * take into account dependencies marked as external modules when composing template values like ``%(pyver)s`` (`#3273 `_) * other changes: - * increase timeout & use api.github.com for connectivity check in check_github (`#3192 `_) + * increase timeout & use ``api.github.com`` for connectivity check in ``check_github`` (`#3192 `_) * restore flake8 default ignores (`#3193 `_) * enable tracking of test suite coverage using coveralls (`#3204 `_) * make tests use easybuilders/testrepository rather than hpcugent/testrepository after it was moved (`#3238 `_) - * improve raised error in remove_dir and deprecate rmtree2 (`#3228 `_) + * improve raised error in ``remove_dir`` and deprecate ``rmtree2`` (`#3228 `_) **easyblocks** @@ -94,17 +96,17 @@ feature release * minor enhancements, including: - * make ParMETIS easyblock compatible with custom configopts (`#1774 `_) + * make ParMETIS easyblock compatible with custom ``configopts`` (`#1774 `_) * update Trinity easyblock for v2.9.0 (`#1906 `_) * disable ROCM and Android workspace explicitely in TensorFlow easyblock (`#1944 `_) * update QuantumESPRESSO easyblock for version 6.5 (`#1947 `_) * update Siesta easyblock to support MaX-1.0 release (`#1954 `_) * update Ferret easyblock for versions >= 7.5.0 (`#1956 `_) * update XCrySDen easyblock to support Togl dependency (`#1959 `_) - * pass value for TARGET specified in buildopts to testopts and installopts in OpenBLAS easyblock (`#1960 `_) + * pass value for ``TARGET`` specified in buildopts to testopts and installopts in OpenBLAS easyblock (`#1960 `_) * fix netCDF(-Fortran) support in Siesta easyblock (`#1967 `_, 1971) - * add NCDF_PARALLEL and METIS support to Siesta easyblock (`#1973 `_) - * add support for 'use_pip_extras' custom easyconfig parameter in PythonPackage easyblock (`#1980 `_) + * add ``NCDF_PARALLEL`` and METIS support to Siesta easyblock (`#1973 `_) + * add support for ``use_pip_extras`` custom easyconfig parameter in PythonPackage easyblock (`#1980 `_) * update Open Babel easyblock for version 3.0.0 (`#1992 `_) * allow differing names for TensorFlow wheel (`#1995 `_) * make MATLAB runtime available from MATLAB (`#2008 `_) @@ -114,23 +116,23 @@ feature release * fix linking of Hypre to external BLAS/LAPACK + support building (only) static/shared library (`#1885 `_) * fix MPI-CXX dependency of PETSc (`#1917 `_) * limit amount of parallelism in TensorFlow easyblock (`#1934 `_) - * support GCCcore and gcc4.8 (if that dir exists) in function get_tbb_gccprefix in tbb easyblock (`#1943 `_) + * support GCCcore and gcc4.8 (if that dir exists) in function ``get_tbb_gccprefix`` in tbb easyblock (`#1943 `_) * restore default flake8 warnings (`#1950 `_) * remove tests from build_step and raise error on failed tests in OpenBLAS easyblock (`#1952 `_, `#1955 `_, `#1962 `_) * add optional runtest to the catch for FATAL ERRORS to OpenBLAS easyblock (`#1958 `_) * ensure right 'python' command is used to determine Python lib dir when system Python is used with PythonBundle easyblock (`#1961 `_) * make sure lib/python*/lib-dynload exists in Python installation (`#1966 `_) * in version 6.0 of TensorRT, libnvinfer.a is renamed libnvinfer_static.a (`#1970 `_) - * handle configopts without configure args in CMake easyblock (`#1974 `_) - * use checkout@v2 in GitHub Actions to fix broken re-triggered tests (`#1976 `_) + * handle ``configopts`` without configure args in CMake easyblock (`#1974 `_) + * use ``checkout@v2`` in GitHub Actions to fix broken re-triggered tests (`#1976 `_) * don't insist that pylibdir always exists in OpenCV easyblock (`#1977 `_) - * also set $TRINITY_HOME environment variable in Trinity easyblock (`#1979 `_) + * also set ``$TRINITY_HOME`` environment variable in Trinity easyblock (`#1979 `_) * fix sanity check for OpenFOAM-Extend >= 4.1 (`#1981 `_) - * fix pattern matching in regex subst for I_MPI_ROOT in impi easyblock (`#1986 `_) - * use remove_dir instead of deprecated rmtree2 in various easyblocks (`#1993 `_) + * fix pattern matching in regex subst for ``I_MPI_ROOT`` in impi easyblock (`#1986 `_) + * use ``remove_dir`` instead of deprecated ``rmtree2`` in various easyblocks (`#1993 `_) * fix "AttributeError: module 'git' has no attribute 'Git'" that may occur when using Python 3 (`#1994 `_) * don't sanity check for QtWebEngine in Qt easyblock when building for POWER (`#2000 `_) - * fix installation of TensorFlow in some environments, by setting $PYTHONNOUSERSITE (& more) (`#2002 `_, `#2020 `_) + * fix installation of TensorFlow in some environments, by setting ``$PYTHONNOUSERSITE`` (& more) (`#2002 `_, `#2020 `_) * make sure libxml2 is built with XZ provided as dependency (`#2005 `_) * look for Python version directories with suffixes in ROOT easyblock (`#2010 `_) * enable TK, FLTK and OPENGL configure options in VMD easyblock (`#2013 `_) @@ -147,26 +149,26 @@ feature release * added example easyconfig files for 114 new software packages: - * ABRA2 (`#10272 `_, ABRicate (`#10310 `_, ADIOS (`#10036 `_, aNCI (`#9929 `_, any2fasta (`#10310 `_, apex (`#10269 `_, - archspec (`#9898 `_, ArviZ (`#10366 `_, autopep8 (`#9626 `_, BAMSurgeon (`#10330 `_, BatMeth2 (`#10323 `_, - BiG-SCAPE (`#10352 `_, BinSanity (`#10001 `_, Bonito (`#10269 `_, BSMAPz (`#10283 `_, BSseeker2 (`#10039 `_, - BUStools (`#9838 `_, Cbc (`#10052 `_, Cgl (`#10048 `_, CGmapTools (`#10288 `_, Clp (`#10033 `_, CoinUtils (`#9937 `_, - dtcwt (`#9695 `_, ELSI (`#9857 `_, EnsEMBLCoreAPI (`#8734 `_, fastq-pair (`#9894 `_, FigureGen (`#10076 `_, Fiona (`#10321 `_, - FuSeq (`#10004 `_, GenomeTools (`#9797 `_, GraphMap2 (`#10299 `_, GRASP (`#9896 `_, Groovy (`#9809 `_, gsport (`#9821 `_, - gubbins (`#9689 `_, igv-reports (`#9977 `_, inferCNV (`#9686 `_, iVar (`#10291 `_, joypy (`#10212 `_, JupyterLab (`#9752 `_, - kma (`#10259 `_, LAMMPS (`#10371 `_, lancet (`#10271 `_, libBigWig (`#10006 `_, libGridXC (`#9858 `_, libPSML (`#5859 `_, - LtrDetector (`#10343 `_, manta (`#5104 `_, medImgProc (`#10228 `_, MedPy (`#9748 `_, Mini-XML (`#10036 `_, mkl_fft (`#9887 `_, - Monocle3 (`#9825 `_, MoreRONN (`#10255 `_, motionSegmentation (`#10228 `_, NanoComp (`#10212 `_, NanoFilt (`#10212 `_, - nanoget (`#10212 `_, nanomath (`#10212 `_, NanoPlot (`#10212 `_, ngspice (`#9922 `_, ntEdit (`#9836 `_, ntHits (`#9833 `_, - occt (`#9939 `_, OCNet (`#9955 `_, OpenAI-Gym (`#10347 `_, OpenPIV (`#9959 `_, OpenPyXL (`#10115 `_, orca (`#9518 `_, - Osi (`#10361 `_, PartitionFinder (`#9983 `_, pauvre (`#10212 `_, polymake (`#9904 `_, pretty-yaml (`#10041 `_), - PRSice (`#9988 `_, pycodestyle (`#9626 `_, pydot (`#9899 `_, pygraphviz (`#9969 `_, pylift (`#10051 `_, PyMC3 (`#10279 `_, - pyparsing (`#9983 `_, PyRe (`#10095 `_, python-weka-wrapper3 (`#9704 `_, PyTorch-Geometric (`#9995 `_, qcat (`#10244 `_, - RAxML-NG (`#9990 `_, Ray (`#10302 `_, rclone (`#7934 `_, Red (`#9856 `_, rstanarm (`#9964 `_, scikit-build (`#9762 `_, - scVelo (`#9805 `_, SECAPR (`#9721 `_, segmentation-models (`#10211 `_, SentencePiece (`#10192 `_, SEPP (`#10047 `_, - Shapely (`#10309 `_, Singular (`#10030 `_, SLATEC (`#7529 `_, spatialreg (`#9767 `_, split-seq (`#9749 `_, spoa (`#9705 `_, - SSN (`#9955 `_, STEAK (`#10337 `_, stpipeline (`#9736 `_, SVG (`#9905 `_, Togl (`#9868 `_, torchtext (`#10193 `_, - units (`#9682 `_, UQTk (`#10279 `_, WildMagic (`#10044 `_, Winnowmap (`#10005 `_, xtb (`#9993 `_, Zip (`#9972 `_ + * ABRA2 (`#10272 `_), ABRicate (`#10310 `_), ADIOS (`#10036 `_), aNCI (`#9929 `_), any2fasta (`#10310 `_), apex (`#10269 `_), + archspec (`#9898 `_), ArviZ (`#10366 `_), autopep8 (`#9626 `_), BAMSurgeon (`#10330 `_), BatMeth2 (`#10323 `_), + BiG-SCAPE (`#10352 `_), BinSanity (`#10001 `_), Bonito (`#10269 `_), BSMAPz (`#10283 `_), BSseeker2 (`#10039 `_), + BUStools (`#9838 `_), Cbc (`#10052 `_), Cgl (`#10048 `_), CGmapTools (`#10288 `_), Clp (`#10033 `_), CoinUtils (`#9937 `_), + dtcwt (`#9695 `_), ELSI (`#9857 `_), EnsEMBLCoreAPI (`#8734 `_), fastq-pair (`#9894 `_), FigureGen (`#10076 `_), Fiona (`#10321 `_), + FuSeq (`#10004 `_), GenomeTools (`#9797 `_), GraphMap2 (`#10299 `_), GRASP (`#9896 `_), Groovy (`#9809 `_), gsport (`#9821 `_), + gubbins (`#9689 `_), igv-reports (`#9977 `_), inferCNV (`#9686 `_), iVar (`#10291 `_), joypy (`#10212 `_), JupyterLab (`#9752 `_), + kma (`#10259 `_), LAMMPS (`#10371 `_), lancet (`#10271 `_), libBigWig (`#10006 `_), libGridXC (`#9858 `_), libPSML (`#5859 `_), + LtrDetector (`#10343 `_), manta (`#5104 `_), medImgProc (`#10228 `_), MedPy (`#9748 `_), Mini-XML (`#10036 `_), mkl_fft (`#9887 `_), + Monocle3 (`#9825 `_), MoreRONN (`#10255 `_), motionSegmentation (`#10228 `_), NanoComp (`#10212 `_), NanoFilt (`#10212 `_), + nanoget (`#10212 `_), nanomath (`#10212 `_), NanoPlot (`#10212 `_), ngspice (`#9922 `_), ntEdit (`#9836 `_), ntHits (`#9833 `_), + occt (`#9939 `_), OCNet (`#9955 `_), OpenAI-Gym (`#10347 `_), OpenPIV (`#9959 `_), OpenPyXL (`#10115 `_), orca (`#9518 `_), + Osi (`#10361 `_), PartitionFinder (`#9983 `_), pauvre (`#10212 `_), polymake (`#9904 `_), pretty-yaml (`#10041 `_)), + PRSice (`#9988 `_), pycodestyle (`#9626 `_), pydot (`#9899 `_), pygraphviz (`#9969 `_), pylift (`#10051 `_), PyMC3 (`#10279 `_), + pyparsing (`#9983 `_), PyRe (`#10095 `_), python-weka-wrapper3 (`#9704 `_), PyTorch-Geometric (`#9995 `_), qcat (`#10244 `_), + RAxML-NG (`#9990 `_), Ray (`#10302 `_), rclone (`#7934 `_), Red (`#9856 `_), rstanarm (`#9964 `_), scikit-build (`#9762 `_), + scVelo (`#9805 `_), SECAPR (`#9721 `_), segmentation-models (`#10211 `_), SentencePiece (`#10192 `_), SEPP (`#10047 `_), + Shapely (`#10309 `_), Singular (`#10030 `_), SLATEC (`#7529 `_), spatialreg (`#9767 `_), split-seq (`#9749 `_), spoa (`#9705 `_), + SSN (`#9955 `_), STEAK (`#10337 `_), stpipeline (`#9736 `_), SVG (`#9905 `_), Togl (`#9868 `_), torchtext (`#10193 `_), + units (`#9682 `_), UQTk (`#10279 `_), WildMagic (`#10044 `_), Winnowmap (`#10005 `_), xtb (`#9993 `_), Zip (`#9972 `_) * added additional easyconfigs for various supported software packages, including: @@ -192,68 +194,68 @@ feature release * minor enhancements, including: - * add easyconfig for Java 11.0.6 on ppc64le and alter the Java 11 wrapper to support both x86_64 and ppc64le (`#9371 `_ - * add additional extensions for R: HiddenMarkov (`#9685 `_, lmerTest (`#9853 `_, VSURF + Rborist (`#10355 `_ - * change Mesa 19.1.7 + 19.2.1 easyconfigs to use custom easyblock for Mesa (`#9764 `_ - * build shared libs and install header files for Ghostscript (`#9785 `_ - * add MUMPS as dependency in PETSc 3.12.4 easyconfigs (#9880, `#9891 `_ - * add Perl extensions: Term::ReadLine::Gnu (`#9901 `_, URI::Escape and Set::IntervalTree (`#10049 `_ - * add dat directory to aNCI (`#9929 `_ - * add patch to create a symlink from libsvm.so.$(SHVER) to libsvm.so in LIBSVM easyconfigs (`#10045 `_ - * build SUNDIALS with 'pic' (`#10278 `_ - * add BSgenome.Hsapiens.UCSC.hg38 + MEDIPS extensions to R-bundle-Bioconductor v3.10 (`#10298 `_ - * fix checksums for mkl-dnn and tbb extensions (moved to oneAPI repo) in PyTorch easyconfigs (`#10367 `_ - * update Java/1.8 wrapper to Java/1.8.0_241.eb (`#10305 `_ - -* various bug fixes, including: - - * use CMake for building double-conversion (`#9659 `_ - * update recent libdrm easyconfigs to use custom easyblock & avoid hardcoded x86-specific sanity check (`#9694 `_ - * add alternate checksum for OpenMolcas 18.09 (`#9701 `_ - * use Github to download releases for MariaDB-connector-c (`#9702 `_ - * add -DOMPI_SKIP_MPICXX in configopts for MathGL, to avoid using mpicxx during build (`#9703 `_ - * make installing independent of build folder in pybind11 easyconfig (`#9738 `_ - * add Lua as a dependency to gnuplot (`#9773 `_ - * stick to http:// source URLS for ISL in GCCcore easyconfigs, since https:// doesn't work (`#9784 `_ - * add alternative checksums for farver/fracdiff/pkgmaker/rngtools/doRNG/cobs extensions in R 3.6.2 easyconfigs (`#9789 `_ - * add patch for OpenBLAS 0.3.4 w/ GCC/8.2.0-2.31.1 to fix broken tests (`#9865 `_ - * revert removal of AVX512 vmovd with 64-bit operands in binutils 2.32 easyconfigs (`#9866 `_ - * fix inline asm in dscal: mark x, x1 as clobbered, in OpenBLAS 0.3.8 (`#9867 `_ - * add missing sanity_check_commands to cutadapt v1.18 and v2.7 easyconfigs (`#9869 `_ - * don't overwrite configopts in BLAST+ easyconfigs, append to it (`#9875 `_ - * add alternate checksum for LaplacesDemon in R 3.6.x easyconfigs (#9879, `#10382 `_ - * fix redefining of preconfigopts in OpenCV easyconfigs (`#9895 `_ - * use symlinks for terminfo files instead of hard links in ncurses 6.1 easyconfigs (`#9912 `_ - * fix NCIPLOT build flags (`#9915 `_ - * add missing patch to iccifort libxc easyconfigs (`#9918 `_ - * use checkout@v2 in GitHub Actions to fix broken re-triggered tests (`#9925 `_ - * re-enable building utils in Siesta 4.1-MaX-1.0 release (`#9936 `_ - * fix homepage and source URLs in SLEPc easyconfigs by using https (`#9943 `_ - * fix source URLs for rgeos after source tarball was moved to CRAN archive (`#9954 `_ - * add dependencies on Python 3 and SciPy-bundle in Trinity v2.9.1 easyconfig (`#9957 `_ - * patch GCC lisanitizer for glibc 2.31 (`#9966 `_ - * add Zip as build dependency for recent Bazel versions (`#9972 `_ - * fix checksums in Jellyfish v2.3.0 easyconfigs (`#9997 `_ - * fix source URLs for ParMGridGen easyconfigs (`#10019 `_ - * disable unintended Octave support in all libsndfile easyconfigs (`#10027 `_ - * fix sources for LS-PrePost 4.6 (`#10236 `_ - * security update for vsc-mympirun 4.1.9 (`#10185 `_ - * configure libwebp to also install libwebpmux (`#10274 `_ - * ensure that CVS easyconfigs are included in source tarball produced by 'python setup.py sdist' (`#10326 `_ - * fix undefined reference error due to libxc 4.3.4 built with CMake (`#10356 `_ - * fix source_urls for tbb: use (new) official 'oneapi-src' GitHub repository (`#10361 `_ - * add missing build dependency on pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (`#10380 `_ - * update checksums and homepage in tbb easyconfigs (`#10285 `_ + * add easyconfig for Java 11.0.6 on ppc64le and alter the Java 11 wrapper to support both x86_64 and ppc64le (`#9371 `_) + * add additional extensions for R: HiddenMarkov (`#9685 `_), lmerTest (`#9853 `_), VSURF + Rborist (`#10355 `_) + * change Mesa 19.1.7 + 19.2.1 easyconfigs to use custom easyblock for Mesa (`#9764 `_) + * build shared libs and install header files for Ghostscript (`#9785 `_) + * add MUMPS as dependency in PETSc 3.12.4 easyconfigs (#9880, `#9891 `_) + * add Perl extensions: Term::ReadLine::Gnu (`#9901 `_), URI::Escape and Set::IntervalTree (`#10049 `_) + * add dat directory to aNCI (`#9929 `_) + * add patch to create a symlink from libsvm.so.$(SHVER) to libsvm.so in LIBSVM easyconfigs (`#10045 `_) + * build SUNDIALS with 'pic' (`#10278 `_) + * add BSgenome.Hsapiens.UCSC.hg38 + MEDIPS extensions to R-bundle-Bioconductor v3.10 (`#10298 `_) + * fix checksums for mkl-dnn and tbb extensions (moved to oneAPI repo) in PyTorch easyconfigs (`#10367 `_) + * update Java/1.8 wrapper to Java/1.8.0_241.eb (`#10305 `_) + +* various bug fixes, including: + + * use CMake for building double-conversion (`#9659 `_) + * update recent libdrm easyconfigs to use custom easyblock & avoid hardcoded x86-specific sanity check (`#9694 `_) + * add alternate checksum for OpenMolcas 18.09 (`#9701 `_) + * use Github to download releases for MariaDB-connector-c (`#9702 `_) + * add ``-DOMPI_SKIP_MPICXX`` in ``configopts`` for MathGL, to avoid using mpicxx during build (`#9703 `_) + * make installing independent of build folder in pybind11 easyconfig (`#9738 `_) + * add Lua as a dependency to gnuplot (`#9773 `_) + * stick to ``http://`` source URLS for ISL in GCCcore easyconfigs, since ``https://`` doesn't work (`#9784 `_) + * add alternative checksums for farver/fracdiff/pkgmaker/rngtools/doRNG/cobs extensions in R 3.6.2 easyconfigs (`#9789 `_) + * add patch for OpenBLAS 0.3.4 w/ GCC/8.2.0-2.31.1 to fix broken tests (`#9865 `_) + * revert removal of AVX512 vmovd with 64-bit operands in binutils 2.32 easyconfigs (`#9866 `_) + * fix inline asm in dscal: mark x, x1 as clobbered, in OpenBLAS 0.3.8 (`#9867 `_) + * add missing ``sanity_check_commands`` to cutadapt v1.18 and v2.7 easyconfigs (`#9869 `_) + * don't overwrite ``configopts`` in BLAST+ easyconfigs, append to it (`#9875 `_) + * add alternate checksum for LaplacesDemon in R 3.6.x easyconfigs (#9879, `#10382 `_) + * fix redefining of preconfigopts in OpenCV easyconfigs (`#9895 `_) + * use symlinks for terminfo files instead of hard links in ncurses 6.1 easyconfigs (`#9912 `_) + * fix NCIPLOT build flags (`#9915 `_) + * add missing patch to iccifort libxc easyconfigs (`#9918 `_) + * use ``checkout@v2`` in GitHub Actions to fix broken re-triggered tests (`#9925 `_) + * re-enable building utils in Siesta 4.1-MaX-1.0 release (`#9936 `_) + * fix homepage and source URLs in SLEPc easyconfigs by using https (`#9943 `_) + * fix source URLs for rgeos after source tarball was moved to CRAN archive (`#9954 `_) + * add dependencies on Python 3 and SciPy-bundle in Trinity v2.9.1 easyconfig (`#9957 `_) + * patch GCC lisanitizer for glibc 2.31 (`#9966 `_) + * add Zip as build dependency for recent Bazel versions (`#9972 `_) + * fix checksums in Jellyfish v2.3.0 easyconfigs (`#9997 `_) + * fix source URLs for ParMGridGen easyconfigs (`#10019 `_) + * disable unintended Octave support in all libsndfile easyconfigs (`#10027 `_) + * fix sources for LS-PrePost 4.6 (`#10236 `_) + * security update for vsc-mympirun 4.1.9 (`#10185 `_) + * configure libwebp to also install libwebpmux (`#10274 `_) + * ensure that CVS easyconfigs are included in source tarball produced by 'python setup.py sdist' (`#10326 `_) + * fix undefined reference error due to libxc 4.3.4 built with CMake (`#10356 `_) + * fix source_urls for tbb: use (new) official 'oneapi-src' GitHub repository (`#10361 `_) + * add missing build dependency on pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (`#10380 `_) + * update checksums and homepage in tbb easyconfigs (`#10285 `_) * other changes: - * use new custom easyblock in recent CMake easyconfigs (#9871, `#9923 `_ - * add check for redefined easyconfig parameters in easyconfig tests (`#9876 `_ - * use M4-1.4.18.eb for test installation in easyconfigs test suite (`#9926 `_ - * use https in homepage/source_urls of zlib-1.2.11.eb (`#10018 `_ - * add -GCCcore-9.2.0 versionsuffix for intel/2020.00 components (`#10083 `_ - * add checksum of new tbb 2019_U9 source tarball, next to original one + update homepage (`#10237 `_ - * add comment informing about manually setting Gallium drivers in easyconfigs for Mesa v19.1.7 and v19.2.1 (`#10276 `_ + * use new custom easyblock in recent CMake easyconfigs (#9871, `#9923 `_) + * add check for redefined easyconfig parameters in easyconfig tests (`#9876 `_) + * use M4-1.4.18.eb for test installation in easyconfigs test suite (`#9926 `_) + * use https in homepage/source_urls of zlib-1.2.11.eb (`#10018 `_) + * add -GCCcore-9.2.0 versionsuffix for intel/2020.00 components (`#10083 `_) + * add checksum of new tbb 2019_U9 source tarball, next to original one + update homepage (`#10237 `_) + * add comment informing about manually setting Gallium drivers in easyconfigs for Mesa v19.1.7 and v19.2.1 (`#10276 `_) .. _release_notes_eb412: From f62712ef90a895bccea6254ce7e02f5979b01d2a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 15:58:04 +0200 Subject: [PATCH 027/286] minor tweaks to v4.2.0 release notes --- docs/Release_notes.rst | 81 +++++++++++++++++++++--------------------- 1 file changed, 41 insertions(+), 40 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 411c50b9..b1decf3a 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -5,7 +5,7 @@ EasyBuild release notes The latest version of EasyBuild provides support for building and installing **1,912** different software packages, including 31 different (compiler) toolchains. It contains 219 software-specific easyblocks and 36 generic easyblocks, -alongside 9462 easyconfig files. +alongside 9,462 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. @@ -24,7 +24,7 @@ feature release * for more information, see https://easybuild.readthedocs.io/en/latest/Locks.html -* significantly speed up ``-D/--dry-run`` by avoiding useless 'module show' (`#3203 `_) +* significantly speed up ``-D/--dry-run`` by avoiding useless '``module show``' (`#3203 `_) * add support for creating an index & using it when searching for easyconfigs (`#3210 `_) @@ -42,12 +42,12 @@ feature release * also mention working directory + input passed via stdin (if any) in trace output of ``run_cmd`` (`#3168 `_) * probe external modules for missing metadata that is not provided via extermal module metadata file (`#3174 `_) * also update ``$CMAKE_PREFIX_PATH`` and ``$CMAKE_LIBRARY_PATH`` in generated module file (`#3176 `_) - * optionally call log.warning in ``print_warning`` (`#3195 `_) - * add an option to ``git_config`` to retain the .git directory (`#3197 `_) + * optionally call ``log.warning`` in ``print_warning`` (`#3195 `_) + * add an option to ``git_config`` to retain the ``.git`` directory (`#3197 `_) * allow use of ``SYSTEM`` as ``--try-toolchain`` option (`#3213 `_) - * mention CPU arch name in comment for uploaded test report, if it's known by archspec (`#3227 `_) + * mention CPU arch name in comment for uploaded test report, if it's known by ``archspec`` (`#3227 `_) * make ``--merge-pr`` take into account ``--pr-target-branch`` (`#3236 `_) - * make ``--check-contrib`` print a warning when None is used for checksums (`#3244 `_) + * make ``--check-contrib`` print a warning when ``None`` is used for checksums (`#3244 `_) * update ``install-EasyBuild-develop.sh`` script and create script for 2020a merge sprint (`#3245 `_) * add template for ``mpi_cmd_prefix`` (`#3264 `_) * update ``copy_dir`` to include option to merge directories (`#3270 `_) @@ -58,9 +58,9 @@ feature release * use correct module for ``errors_found_in_log`` (`#3119 `_) * fix ``EasyConfig.update`` code to handle both strings and lists as input (`#3170 `_) * fix removing temporary branch on ``--check-github`` (`#3182 `_) - * fix shebang even if first line doesn't start with '#!' (`#3183 `_) - * make boostrap script work with Python 3 (`#3186 `_) - * read patch files as bytestring to avoid UnicodeDecodeError for patches that include funky characters (`#3191 `_) + * fix shebang even if first line doesn't start with '``#!``' (`#3183 `_) + * make bootstrap script work with Python 3 (`#3186 `_) + * read patch files as bytestring to avoid ``UnicodeDecodeError`` for patches that include funky characters (`#3191 `_) * fix online check in ``--check-github``: try repeatedly and with different URLs to cater for HTTP issues (`#3194 `_) * don't crash when GitPython is not installed when using Python 3 (`#3198 `_) * fix ``os_name_map`` for RHEL8 (`#3201 `_) @@ -83,9 +83,9 @@ feature release * other changes: * increase timeout & use ``api.github.com`` for connectivity check in ``check_github`` (`#3192 `_) - * restore flake8 default ignores (`#3193 `_) + * restore ``flake8`` default ignores (`#3193 `_) * enable tracking of test suite coverage using coveralls (`#3204 `_) - * make tests use easybuilders/testrepository rather than hpcugent/testrepository after it was moved (`#3238 `_) + * make tests use ``easybuilders/testrepository`` rather than ``hpcugent/testrepository`` after it was moved (`#3238 `_) * improve raised error in ``remove_dir`` and deprecate ``rmtree2`` (`#3228 `_) **easyblocks** @@ -98,15 +98,15 @@ feature release * make ParMETIS easyblock compatible with custom ``configopts`` (`#1774 `_) * update Trinity easyblock for v2.9.0 (`#1906 `_) - * disable ROCM and Android workspace explicitely in TensorFlow easyblock (`#1944 `_) + * disable ROCM and Android workspace explicitly in TensorFlow easyblock (`#1944 `_) * update QuantumESPRESSO easyblock for version 6.5 (`#1947 `_) * update Siesta easyblock to support MaX-1.0 release (`#1954 `_) * update Ferret easyblock for versions >= 7.5.0 (`#1956 `_) * update XCrySDen easyblock to support Togl dependency (`#1959 `_) - * pass value for ``TARGET`` specified in buildopts to testopts and installopts in OpenBLAS easyblock (`#1960 `_) + * pass value for ``TARGET`` specified in ``buildopts`` to ``testopts`` and ``installopts`` in OpenBLAS easyblock (`#1960 `_) * fix netCDF(-Fortran) support in Siesta easyblock (`#1967 `_, 1971) * add ``NCDF_PARALLEL`` and METIS support to Siesta easyblock (`#1973 `_) - * add support for ``use_pip_extras`` custom easyconfig parameter in PythonPackage easyblock (`#1980 `_) + * add support for ``use_pip_extras`` custom easyconfig parameter in ``PythonPackage`` easyblock (`#1980 `_) * update Open Babel easyblock for version 3.0.0 (`#1992 `_) * allow differing names for TensorFlow wheel (`#1995 `_) * make MATLAB runtime available from MATLAB (`#2008 `_) @@ -117,12 +117,12 @@ feature release * fix MPI-CXX dependency of PETSc (`#1917 `_) * limit amount of parallelism in TensorFlow easyblock (`#1934 `_) * support GCCcore and gcc4.8 (if that dir exists) in function ``get_tbb_gccprefix`` in tbb easyblock (`#1943 `_) - * restore default flake8 warnings (`#1950 `_) - * remove tests from build_step and raise error on failed tests in OpenBLAS easyblock (`#1952 `_, `#1955 `_, `#1962 `_) - * add optional runtest to the catch for FATAL ERRORS to OpenBLAS easyblock (`#1958 `_) - * ensure right 'python' command is used to determine Python lib dir when system Python is used with PythonBundle easyblock (`#1961 `_) - * make sure lib/python*/lib-dynload exists in Python installation (`#1966 `_) - * in version 6.0 of TensorRT, libnvinfer.a is renamed libnvinfer_static.a (`#1970 `_) + * restore default ``flake8`` warnings (`#1950 `_) + * remove tests from ``build_step`` and raise error on failed tests in OpenBLAS easyblock (`#1952 `_, `#1955 `_, `#1962 `_) + * add optional ``runtest`` to the catch for ``FATAL ERRORS`` to OpenBLAS easyblock (`#1958 `_) + * ensure right '``python``' command is used to determine Python lib dir when system Python is used with PythonBundle easyblock (`#1961 `_) + * make sure ``lib/python*/lib-dynload`` exists in Python installation (`#1966 `_) + * in version 6.0 of TensorRT, ``libnvinfer.a`` is renamed ``libnvinfer_static.a`` (`#1970 `_) * handle ``configopts`` without configure args in CMake easyblock (`#1974 `_) * use ``checkout@v2`` in GitHub Actions to fix broken re-triggered tests (`#1976 `_) * don't insist that pylibdir always exists in OpenCV easyblock (`#1977 `_) @@ -130,8 +130,8 @@ feature release * fix sanity check for OpenFOAM-Extend >= 4.1 (`#1981 `_) * fix pattern matching in regex subst for ``I_MPI_ROOT`` in impi easyblock (`#1986 `_) * use ``remove_dir`` instead of deprecated ``rmtree2`` in various easyblocks (`#1993 `_) - * fix "AttributeError: module 'git' has no attribute 'Git'" that may occur when using Python 3 (`#1994 `_) - * don't sanity check for QtWebEngine in Qt easyblock when building for POWER (`#2000 `_) + * fix "``AttributeError: module 'git' has no attribute 'Git'``" that may occur when using Python 3 (`#1994 `_) + * don't sanity check for ``QtWebEngine`` in Qt easyblock when building for POWER (`#2000 `_) * fix installation of TensorFlow in some environments, by setting ``$PYTHONNOUSERSITE`` (& more) (`#2002 `_, `#2020 `_) * make sure libxml2 is built with XZ provided as dependency (`#2005 `_) * look for Python version directories with suffixes in ROOT easyblock (`#2010 `_) @@ -141,8 +141,8 @@ feature release * other changes: - * simplify various CMakeMake-based easyblocks by enhancing CMakeMake (w.r.t. CMAKE_BUILD_TYPE, shared vs static libs, fPIC) (`#1929 `_) - * enable out of tree build by default in CMakeMake easyblock (`#1933 `_) + * simplify various CMakeMake-based easyblocks by enhancing ``CMakeMake`` (w.r.t. ``CMAKE_BUILD_TYPE``, shared vs static libs, ``-fPIC``) (`#1929 `_) + * enable out of tree build by default in ``CMakeMake`` easyblock (`#1933 `_) * force building Clang without CUDA when it is not found as a proper dependency (`#1968 `_) **easyconfigs** @@ -194,18 +194,18 @@ feature release * minor enhancements, including: - * add easyconfig for Java 11.0.6 on ppc64le and alter the Java 11 wrapper to support both x86_64 and ppc64le (`#9371 `_) - * add additional extensions for R: HiddenMarkov (`#9685 `_), lmerTest (`#9853 `_), VSURF + Rborist (`#10355 `_) + * add easyconfig for Java 11.0.6 on ``ppc64le`` and alter the Java 11 wrapper to support both x86_64 and ppc64le (`#9371 `_) + * add additional extensions for R: ``HiddenMarkov`` (`#9685 `_), ``lmerTest`` (`#9853 `_), ``VSURF`` + ``Rborist`` (`#10355 `_) * change Mesa 19.1.7 + 19.2.1 easyconfigs to use custom easyblock for Mesa (`#9764 `_) * build shared libs and install header files for Ghostscript (`#9785 `_) * add MUMPS as dependency in PETSc 3.12.4 easyconfigs (#9880, `#9891 `_) - * add Perl extensions: Term::ReadLine::Gnu (`#9901 `_), URI::Escape and Set::IntervalTree (`#10049 `_) + * add Perl extensions: ``Term::ReadLine::Gnu`` (`#9901 `_), ``URI::Escape`` and ``Set::IntervalTree`` (`#10049 `_) * add dat directory to aNCI (`#9929 `_) - * add patch to create a symlink from libsvm.so.$(SHVER) to libsvm.so in LIBSVM easyconfigs (`#10045 `_) - * build SUNDIALS with 'pic' (`#10278 `_) - * add BSgenome.Hsapiens.UCSC.hg38 + MEDIPS extensions to R-bundle-Bioconductor v3.10 (`#10298 `_) - * fix checksums for mkl-dnn and tbb extensions (moved to oneAPI repo) in PyTorch easyconfigs (`#10367 `_) - * update Java/1.8 wrapper to Java/1.8.0_241.eb (`#10305 `_) + * add patch to create a symlink from ``libsvm.so.$(SHVER)`` to ``libsvm.so`` in LIBSVM easyconfigs (`#10045 `_) + * build SUNDIALS with '``pic``' (`#10278 `_) + * add ``BSgenome.Hsapiens.UCSC.hg38`` + ``MEDIPS`` extensions to R-bundle-Bioconductor v3.10 (`#10298 `_) + * fix checksums for ``mkl-dnn`` and ``tbb`` extensions (moved to oneAPI repo) in PyTorch easyconfigs (`#10367 `_) + * update ``Java/1.8`` wrapper to ``Java/1.8.0_241.eb`` (`#10305 `_) * various bug fixes, including: @@ -217,13 +217,13 @@ feature release * make installing independent of build folder in pybind11 easyconfig (`#9738 `_) * add Lua as a dependency to gnuplot (`#9773 `_) * stick to ``http://`` source URLS for ISL in GCCcore easyconfigs, since ``https://`` doesn't work (`#9784 `_) - * add alternative checksums for farver/fracdiff/pkgmaker/rngtools/doRNG/cobs extensions in R 3.6.2 easyconfigs (`#9789 `_) + * add alternative checksums for ``farver``/``fracdiff``/``pkgmaker``/``rngtools``/``doRNG``/``cobs`` extensions in R 3.6.2 easyconfigs (`#9789 `_) * add patch for OpenBLAS 0.3.4 w/ GCC/8.2.0-2.31.1 to fix broken tests (`#9865 `_) * revert removal of AVX512 vmovd with 64-bit operands in binutils 2.32 easyconfigs (`#9866 `_) * fix inline asm in dscal: mark x, x1 as clobbered, in OpenBLAS 0.3.8 (`#9867 `_) * add missing ``sanity_check_commands`` to cutadapt v1.18 and v2.7 easyconfigs (`#9869 `_) * don't overwrite ``configopts`` in BLAST+ easyconfigs, append to it (`#9875 `_) - * add alternate checksum for LaplacesDemon in R 3.6.x easyconfigs (#9879, `#10382 `_) + * add alternate checksum for ``LaplacesDemon`` in R 3.6.x easyconfigs (#9879, `#10382 `_) * fix redefining of preconfigopts in OpenCV easyconfigs (`#9895 `_) * use symlinks for terminfo files instead of hard links in ncurses 6.1 easyconfigs (`#9912 `_) * fix NCIPLOT build flags (`#9915 `_) @@ -233,17 +233,17 @@ feature release * fix homepage and source URLs in SLEPc easyconfigs by using https (`#9943 `_) * fix source URLs for rgeos after source tarball was moved to CRAN archive (`#9954 `_) * add dependencies on Python 3 and SciPy-bundle in Trinity v2.9.1 easyconfig (`#9957 `_) - * patch GCC lisanitizer for glibc 2.31 (`#9966 `_) + * patch GCC ``lisanitizer`` for glibc 2.31 (`#9966 `_) * add Zip as build dependency for recent Bazel versions (`#9972 `_) * fix checksums in Jellyfish v2.3.0 easyconfigs (`#9997 `_) * fix source URLs for ParMGridGen easyconfigs (`#10019 `_) * disable unintended Octave support in all libsndfile easyconfigs (`#10027 `_) * fix sources for LS-PrePost 4.6 (`#10236 `_) * security update for vsc-mympirun 4.1.9 (`#10185 `_) - * configure libwebp to also install libwebpmux (`#10274 `_) - * ensure that CVS easyconfigs are included in source tarball produced by 'python setup.py sdist' (`#10326 `_) + * configure libwebp to also install ``libwebpmux`` (`#10274 `_) + * ensure that CVS easyconfigs are included in source tarball produced by '``python setup.py sdist``' (`#10326 `_) * fix undefined reference error due to libxc 4.3.4 built with CMake (`#10356 `_) - * fix source_urls for tbb: use (new) official 'oneapi-src' GitHub repository (`#10361 `_) + * fix source_urls for tbb: use (new) official '``oneapi-src``' GitHub repository (`#10361 `_) * add missing build dependency on pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (`#10380 `_) * update checksums and homepage in tbb easyconfigs (`#10285 `_) @@ -252,11 +252,12 @@ feature release * use new custom easyblock in recent CMake easyconfigs (#9871, `#9923 `_) * add check for redefined easyconfig parameters in easyconfig tests (`#9876 `_) * use M4-1.4.18.eb for test installation in easyconfigs test suite (`#9926 `_) - * use https in homepage/source_urls of zlib-1.2.11.eb (`#10018 `_) - * add -GCCcore-9.2.0 versionsuffix for intel/2020.00 components (`#10083 `_) + * use ``https://`` in ``homepage``/``source_urls`` of ``zlib-1.2.11.eb`` (`#10018 `_) + * add ``-GCCcore-9.2.0`` versionsuffix for ``intel/2020.00`` components (`#10083 `_) * add checksum of new tbb 2019_U9 source tarball, next to original one + update homepage (`#10237 `_) * add comment informing about manually setting Gallium drivers in easyconfigs for Mesa v19.1.7 and v19.2.1 (`#10276 `_) + .. _release_notes_eb412: EasyBuild v4.1.2 (March 16th 2020) From 19daf04888e5d24f297e80983aa6e91ad35ac311 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 16:02:40 +0200 Subject: [PATCH 028/286] mention new docs in changelog --- docs/Changelog.rst | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 1741bd0f..5873e559 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,7 +5,11 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) -* **release 20200414.01** (`Apr 14th 2020`): update release notes for EasyBuild v4.2.0 (see :ref:`release_notes_eb420`) +* **release 20200414.01** (`Apr 14th 2020`): + + * document new EasyBuild locking mechanism (see :ref:`locks`) + * document support for creating index files (see :ref:`easyconfigs_index`) + * update release notes for EasyBuild v4.2.0 (see :ref:`release_notes_eb420`) * **release 20200316.01** (`Mar 16th 2020`): update release notes for EasyBuild v4.1.2 (see :ref:`release_notes_eb412`) * **release 20200116.01** (`Jan 16th 2020`): update release notes for EasyBuild v4.1.1 (see :ref:`release_notes_eb411`) * **release 20191204.01** (`Dec 4th 2019`): update release notes for EasyBuild v4.1.0 (see :ref:`release_notes_eb410`) From 80c981c210b929271294f490d3ac4eded45e6a56 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 14 Apr 2020 22:34:35 +0800 Subject: [PATCH 029/286] release EasyBuild v4.2.0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 92eb5c04..587ca5c3 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.1.2' +VERSION = '4.2.0' # Utility function to read README file From 3a8c81b1baaff93d3dc94b9b0cadc9bdf43d8fae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 17:25:33 +0200 Subject: [PATCH 030/286] fix versions for easyblocks & easyconfigs in easybuild v4.2.0 --- setup.py | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/setup.py b/setup.py index 587ca5c3..7c93b627 100644 --- a/setup.py +++ b/setup.py @@ -81,17 +81,13 @@ def read(fname): # for distutils requires=[ 'easybuild_framework(==%s)' % VERSION, - # there is no 4.1.2 release for easyblocks/easyconfigs, - # only for framework (which includes an important security-related bug fix) - 'easybuild_easyblocks(==4.1.1)', - 'easybuild_easyconfigs(==4.1.1)', + 'easybuild_easyblocks(==%s)' % VERSION, + 'easybuild_easyconfigs(==%s)' % VERSION, ], # for setuptools/pip install_requires=[ 'easybuild-framework == %s' % VERSION, - # there is no 4.1.2 release for easyblocks/easyconfigs, - # only for framework (which includes an important security-related bug fix) - 'easybuild-easyblocks == 4.1.1', - 'easybuild-easyconfigs == 4.1.1' + 'easybuild-easyblocks == %s' % VERSION, + 'easybuild-easyconfigs == %s' % VERSION, ], ) From 7f8f08f612dcf2ddfde89f6de1454d4cc0ce55bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 17:41:55 +0200 Subject: [PATCH 031/286] use 4.2.0.post0 as version for re-release of EasyBuild v4.2.0 package on PyPI after correcting packaging mistake (see 3a8c81b) --- setup.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 7c93b627..cb2ece20 100644 --- a/setup.py +++ b/setup.py @@ -36,6 +36,12 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware + +# note: using '4.2.0.post0' as version for EasyBuild v4.2.0 because of +# mistake in easybuild-4.2.0 package that was pushed to PyPI; +# the version of easyblocks/easyconfigs was accidentally still locked to '==4.1.1', +# see https://github.com/easybuilders/easybuild/pull/615/commits/3a8c81b1baaff93d3dc94b9b0cadc9bdf43d8fae +PYPI_VERSION = '4.2.0.post0' VERSION = '4.2.0' @@ -51,7 +57,7 @@ def read(fname): setup( name="easybuild", - version=str(VERSION), + version=PYPI_VERSION, author="EasyBuild community", author_email="easybuild@lists.ugent.be", description="""EasyBuild is a software build \ From e2c41c2a1bfbadd60fa0b97c90a5d8577eb8d769 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 18:28:10 +0200 Subject: [PATCH 032/286] remove https://github.com/easybuilders/easybuild-easyconfigs/pull/10380 from EasyBuild v4.2.0 release notes (was merged into 'develop' branch after forking off '4.2.x' branch) --- docs/Release_notes.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index b1decf3a..1720e9e1 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -244,7 +244,6 @@ feature release * ensure that CVS easyconfigs are included in source tarball produced by '``python setup.py sdist``' (`#10326 `_) * fix undefined reference error due to libxc 4.3.4 built with CMake (`#10356 `_) * fix source_urls for tbb: use (new) official '``oneapi-src``' GitHub repository (`#10361 `_) - * add missing build dependency on pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (`#10380 `_) * update checksums and homepage in tbb easyconfigs (`#10285 `_) * other changes: From 099c21013819a5f4e63200d91321fb0150f36a02 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Apr 2020 19:24:22 +0200 Subject: [PATCH 033/286] document of use 'keep_git_dir' in 'git_config' spec for sources --- docs/Writing_easyconfig_files.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index edd0aff4..6439d832 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -405,6 +405,9 @@ In addition, either of the following keys *must* also be defined: If a recursive checkout should be made of the repository, the ``recursive`` key can be set to ``True``. +To also retain the ``.git`` directory (which holds the Git metadata for the repository), +you can set the ``keep_git_dir`` to ``True`` (supported since EasyBuild v4.2.0). + Examples: * creating a source tarball named ``example-master.tar.gz`` of the ``master`` branch of a (fictional) @@ -433,6 +436,7 @@ Examples: 'repo_name': 'test', 'commit': 'abcdef12', 'recursive': True, + 'keep_git_dir': True, }, }] From 9898944e0eaf6e535dc2c936e7c721c7891314b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Apr 2020 20:05:18 +0200 Subject: [PATCH 034/286] tweak command to extract version so we'll get the correct version for easybuild 4.2.0.post0 special case... --- scripts/create_source_tarball.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/scripts/create_source_tarball.sh b/scripts/create_source_tarball.sh index d998e2b9..f8ba68ca 100755 --- a/scripts/create_source_tarball.sh +++ b/scripts/create_source_tarball.sh @@ -109,7 +109,8 @@ elif [[ "$repo" == "easybuild-easyblocks" ]]; then else curr_version_file='setup.py' fi -curr_version=$(grep '^VERSION' $curr_version_file | sed 's/[^0-9]*\([0-9a-zA-Z.]*\).*/\1/g') +# grab version from file, usually a line like "VERSION = '...'", but could slightly diverge +curr_version=$(grep '^[A-Z_]*VERSION\s*=' $curr_version_file | head -1 | sed 's/[^0-9]*\([0-9a-zA-Z.]*\).*/\1/g') if [[ "$curr_version" == "$version" ]]; then ok else From 26c47f53b88ed0ead5e66339a83678ad3237f85f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Apr 2020 20:35:15 +0200 Subject: [PATCH 035/286] add check to ensure that 'requires' in setup.py of easybuild package are as expected, print warning if they're not --- scripts/create_source_tarball.sh | 35 +++++++++++++++++++++++++++++++- 1 file changed, 34 insertions(+), 1 deletion(-) diff --git a/scripts/create_source_tarball.sh b/scripts/create_source_tarball.sh index f8ba68ca..79e03797 100755 --- a/scripts/create_source_tarball.sh +++ b/scripts/create_source_tarball.sh @@ -21,6 +21,11 @@ function success() { echo -e "\033[32mSUCCESS!\033[0m" } +function warning() { + echo -e "\033[31mWARNING: $1\033[0m" >&2 + warnings="$warnings$1 " +} + # ================================================================================================= if [ $# -ne 2 ]; then @@ -37,6 +42,8 @@ echo ">> creating source tarball for $repo $version..." # create temporary directory tmpdir=`mktemp -d` +warnings="" + # we need to create an index file when composing the source tarball for easybuild-easyconfigs, # which requires running 'eb --create-index' if [[ "$repo" == "easybuild-easyconfigs" ]]; then @@ -117,6 +124,27 @@ else error "Found version '$curr_version'" fi +if [[ "$repo" == "easybuild" ]]; then + # check whether 'requires' statements are what we expect + # if not, print a clear warning, since it may actually be fine if the version for some of the required easybuild-* + # packages diverges from the version of the 'easybuid' package... + # examples: + # - easybuild-4.1.2 which requires easybuild-easyblocks and easybuild-easyconfigs v4.1.1 + # - easybuild-4.2.0.post0 which requires easybuild-{framework,easyblocks,easyconfigs} v4.2.0 + echo ">> checking whether required packages for 'easybuild' are what's expected ... " + python setup.py --requires 2> /dev/null | grep '^easybuild' | tee $tmpdir/easybuild_requires.txt + for dep in framework easyblocks easyconfigs; do + echo -n ">>>> $dep ... " + pattern="^easybuild_${dep}(==${curr_version})" + grep $pattern $tmpdir/easybuild_requires.txt > /dev/null + if [ $? -eq 0 ]; then + ok + else + warning "expected pattern '$pattern' in 'requires' in setup.py not found" + fi + done +fi + if [[ "$repo" == "easybuild-easyconfigs" ]]; then # create index file @@ -235,7 +263,12 @@ fi # all done checking, if no checks failed up until now, we're done! echo -success +if [ -z "$warnings" ]; then + success +else + warning "One or more warnings were raised, proceed with caution!" +fi + echo "Source tarball for $repo $version is ready for publishing with:" echo " twine upload $sdist_tar_gz" echo From e30b6e166f2c909d7e5d7c467df754a51e4bfd75 Mon Sep 17 00:00:00 2001 From: Michael H Kelsey Date: Thu, 16 Apr 2020 23:08:16 -0500 Subject: [PATCH 036/286] Add paragraph explaining exts_list options. --- docs/version-specific/easyconfig_parameters.rst | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/docs/version-specific/easyconfig_parameters.rst b/docs/version-specific/easyconfig_parameters.rst index b57e93ac..5a108cb0 100644 --- a/docs/version-specific/easyconfig_parameters.rst +++ b/docs/version-specific/easyconfig_parameters.rst @@ -34,6 +34,7 @@ toolchain parameters ``toolchainopts`` Extra options for compilers None ================== ================================================================================================================================================================================================================================= ================= +.. _easyconfig_parameters_build_parameters: build parameters ---------------- @@ -137,6 +138,12 @@ extensions parameters ``exts_list`` List with extensions added to the base installation [] ========================== ========================================================================================================== ================= +Each entry in ``exts_list`` is a tuple with the extension name +(``ext_name``), version string (``ext_version``), and a dictionary of +source options. Any of the +:ref:`easyconfig_parameters_build_parameters` can be specified within +the options dictionary. + modules parameters ------------------ From b9df5b10e14eaf4ac629a15693367e40c40cc39a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Apr 2020 10:31:12 +0200 Subject: [PATCH 037/286] flesh out tests for scripts into separate .yml in .github/workflows --- .github/workflows/doc_build.yml | 115 ------------------------------- .github/workflows/scripts.yml | 118 ++++++++++++++++++++++++++++++++ 2 files changed, 118 insertions(+), 115 deletions(-) create mode 100644 .github/workflows/scripts.yml diff --git a/.github/workflows/doc_build.yml b/.github/workflows/doc_build.yml index 118d5378..9b4d04f1 100644 --- a/.github/workflows/doc_build.yml +++ b/.github/workflows/doc_build.yml @@ -37,118 +37,3 @@ jobs: # test installation too (using options that don't require to have a modules tool installed) eb --list-easyblocks | grep EB_bzip2 eb --fetch bzip2-1.0.6.eb - scripts: - runs-on: ubuntu-latest - strategy: - matrix: - repo: [easybuild-framework, easybuild-easyblocks, easybuild-easyconfigs, easybuild] - fail-fast: false - steps: - - uses: actions/checkout@v2 - - name: Set up Python 3.8 - uses: actions/setup-python@v1 - with: - python-version: 3.8 - - name: install EasyBuild (framework-only) - run: | - pip install easybuild-framework - eb --version - - name: clone repo - run: | - cd $HOME - git clone https://github.com/easybuilders/${{matrix.repo}}.git - - name: test create_source_tarball.sh script - run: | - cd $HOME/${{matrix.repo}} - git checkout master - - # file to figure out the version from depends on repo - if [[ ${{matrix.repo}} == "easybuild-framework" ]]; then - version_file=easybuild/tools/version.py - elif [[ ${{matrix.repo}} == "easybuild-easyblocks" ]]; then - version_file=easybuild/easyblocks/__init__.py - else - version_file=setup.py - fi - version=$(grep '^VERSION' $version_file | sed 's/[^0-9]*\([0-9a-zA-Z.]*\).*/\1/g') - echo "${{matrix.repo}} version: $version" - - echo "testing with '$GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version'" - - out=$HOME/out.txt - - echo "================================================================================================" - - # check use of script outside correct directory - cd $HOME - ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true - grep "ERROR: Expected to be in ${{matrix.repo}} directory" $out - echo "Expected error found in output: OK!" - - echo "================================================================================================" - - cd ${{matrix.repo}} - - # script should make sure we're on master branch - git checkout develop &> /dev/null - ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true - grep "ERROR: Not on master branch" $out - echo "Expected error found in output: OK!" - git checkout master &> /dev/null - - echo "================================================================================================" - - # specified version should match with current version - ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} 0.0.0 2>&1 | tee $out) || true - grep "ERROR: Found version '${version}'" $out - echo "Expected error found in output: OK!" - - echo "================================================================================================" - - # existing source tarball in dist should result in an error - mkdir -p dist - touch dist/${{matrix.repo}}-${version}.tar.gz - ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true - grep "ERROR: Found dist/${{matrix.repo}}-${version}.tar.gz" $out - echo "Expected error found in output: OK!" - rm dist/${{matrix.repo}}-${version}.tar.gz - - echo "================================================================================================" - - # check for error when script is run in a dirty working copy - touch dirty.txt - ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true - grep "ERROR: Working directory not clean" $out - echo "Expected error found in output: OK!" - rm dirty.txt - - echo "================================================================================================" - - # script should fail if expected source tarball did not get created in dist/ - mkdir -p /tmp/$USER/bin - echo '#!/bin/bash' > /tmp/$USER/bin/python - chmod u+x /tmp/$USER/bin/python - export PATH=/tmp/$USER/bin:$PATH - ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true - grep "ERROR: Expected file dist/${{matrix.repo}}-${version}.tar.gz not found!" $out - echo "Expected error found in output: OK!" - - echo "================================================================================================" - - # script should deal well with failing 'python setup.py sdist' - echo 'exit 1' >> /tmp/$USER/bin/python - ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true - grep "ERROR: Creating source tarball failed" $out - echo "Expected error found in output: OK!" - rm /tmp/$USER/bin/python - - echo "================================================================================================" - - # check use of script in correct way, should yield "SUCCESS" in output - $GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out - grep SUCCESS $out - # no errors in output - errors=$(grep ERROR $out || true) - if [ ! -z $errors ]; then "Errors found: $errors"; fi - - echo "Correct run of script OK!" diff --git a/.github/workflows/scripts.yml b/.github/workflows/scripts.yml new file mode 100644 index 00000000..2d70007f --- /dev/null +++ b/.github/workflows/scripts.yml @@ -0,0 +1,118 @@ +name: Tests for scripts +on: [push, pull_request] +jobs: + scripts: + runs-on: ubuntu-latest + strategy: + matrix: + repo: [easybuild-framework, easybuild-easyblocks, easybuild-easyconfigs, easybuild] + fail-fast: false + steps: + - uses: actions/checkout@v2 + - name: Set up Python 3.8 + uses: actions/setup-python@v1 + with: + python-version: 3.8 + - name: install EasyBuild (framework-only) + run: | + pip install easybuild-framework + eb --version + - name: clone repo + run: | + cd $HOME + git clone https://github.com/easybuilders/${{matrix.repo}}.git + - name: test create_source_tarball.sh script + run: | + cd $HOME/${{matrix.repo}} + git checkout master + + # file to figure out the version from depends on repo + if [[ ${{matrix.repo}} == "easybuild-framework" ]]; then + version_file=easybuild/tools/version.py + elif [[ ${{matrix.repo}} == "easybuild-easyblocks" ]]; then + version_file=easybuild/easyblocks/__init__.py + else + version_file=setup.py + fi + version=$(grep '^VERSION' $version_file | sed 's/[^0-9]*\([0-9a-zA-Z.]*\).*/\1/g') + echo "${{matrix.repo}} version: $version" + + echo "testing with '$GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version'" + + out=$HOME/out.txt + + echo "================================================================================================" + + # check use of script outside correct directory + cd $HOME + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true + grep "ERROR: Expected to be in ${{matrix.repo}} directory" $out + echo "Expected error found in output: OK!" + + echo "================================================================================================" + + cd ${{matrix.repo}} + + # script should make sure we're on master branch + git checkout develop &> /dev/null + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true + grep "ERROR: Not on master branch" $out + echo "Expected error found in output: OK!" + git checkout master &> /dev/null + + echo "================================================================================================" + + # specified version should match with current version + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} 0.0.0 2>&1 | tee $out) || true + grep "ERROR: Found version '${version}'" $out + echo "Expected error found in output: OK!" + + echo "================================================================================================" + + # existing source tarball in dist should result in an error + mkdir -p dist + touch dist/${{matrix.repo}}-${version}.tar.gz + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true + grep "ERROR: Found dist/${{matrix.repo}}-${version}.tar.gz" $out + echo "Expected error found in output: OK!" + rm dist/${{matrix.repo}}-${version}.tar.gz + + echo "================================================================================================" + + # check for error when script is run in a dirty working copy + touch dirty.txt + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true + grep "ERROR: Working directory not clean" $out + echo "Expected error found in output: OK!" + rm dirty.txt + + echo "================================================================================================" + + # script should fail if expected source tarball did not get created in dist/ + mkdir -p /tmp/$USER/bin + echo '#!/bin/bash' > /tmp/$USER/bin/python + chmod u+x /tmp/$USER/bin/python + export PATH=/tmp/$USER/bin:$PATH + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true + grep "ERROR: Expected file dist/${{matrix.repo}}-${version}.tar.gz not found!" $out + echo "Expected error found in output: OK!" + + echo "================================================================================================" + + # script should deal well with failing 'python setup.py sdist' + echo 'exit 1' >> /tmp/$USER/bin/python + ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true + grep "ERROR: Creating source tarball failed" $out + echo "Expected error found in output: OK!" + rm /tmp/$USER/bin/python + + echo "================================================================================================" + + # check use of script in correct way, should yield "SUCCESS" in output + $GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out + grep SUCCESS $out + # no errors in output + errors=$(grep ERROR $out || true) + if [ ! -z $errors ]; then "Errors found: $errors"; fi + + echo "Correct run of script OK!" From 4aa88a5679c49e4eeef6fd4256c7dd9fc6e58bae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Apr 2020 10:32:22 +0200 Subject: [PATCH 038/286] extract correct version for easybuild repo in tests for create_source_tarball.sh script --- .github/workflows/scripts.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/scripts.yml b/.github/workflows/scripts.yml index 2d70007f..60be73a2 100644 --- a/.github/workflows/scripts.yml +++ b/.github/workflows/scripts.yml @@ -34,7 +34,7 @@ jobs: else version_file=setup.py fi - version=$(grep '^VERSION' $version_file | sed 's/[^0-9]*\([0-9a-zA-Z.]*\).*/\1/g') + version=$(grep '^.*VERSION[ ]*=' $version_file | head -1 |sed 's/[^0-9]*\([0-9a-zA-Z.]*\).*/\1/g') echo "${{matrix.repo}} version: $version" echo "testing with '$GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version'" From 99903126dee245f6d8eead4fbd521f2bd894d3d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Apr 2020 14:20:35 +0200 Subject: [PATCH 039/286] loosen check whether create_source_tarball.sh completes correctly + also install modules tool when testing scripts --- .github/workflows/scripts.yml | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/.github/workflows/scripts.yml b/.github/workflows/scripts.yml index 60be73a2..c3e4c3f0 100644 --- a/.github/workflows/scripts.yml +++ b/.github/workflows/scripts.yml @@ -17,12 +17,24 @@ jobs: run: | pip install easybuild-framework eb --version + - name: install modules tool + run: | + sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl-dev + # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082 + sudo ln -s /usr/lib/x86_64-linux-gnu/lua/5.2/posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so + # use script provided by easybuild-framework to install recent Lmod + source install_eb_dep.sh Lmod-8.3.8 $HOME + echo $MOD_INIT > $HOME/mod_init + echo $PATH > $HOME/path - name: clone repo run: | cd $HOME git clone https://github.com/easybuilders/${{matrix.repo}}.git - name: test create_source_tarball.sh script run: | + source $(cat $HOME/mod_init); type module + export PATH=$(cat $HOME/path) + cd $HOME/${{matrix.repo}} git checkout master @@ -110,7 +122,7 @@ jobs: # check use of script in correct way, should yield "SUCCESS" in output $GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out - grep SUCCESS $out + egrep "SUCCESS|Source tarball for ${{matrix.repo}} ${version} is ready for publishing with" $out # no errors in output errors=$(grep ERROR $out || true) if [ ! -z $errors ]; then "Errors found: $errors"; fi From e10aa82a7d88211be41a6b5d10994fe1cdb33688 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Apr 2020 15:52:55 +0200 Subject: [PATCH 040/286] only make 'python setup.py' commands fail in checks for create_source_tarball.sh script --- .github/workflows/scripts.yml | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/.github/workflows/scripts.yml b/.github/workflows/scripts.yml index c3e4c3f0..cb735b6f 100644 --- a/.github/workflows/scripts.yml +++ b/.github/workflows/scripts.yml @@ -100,23 +100,36 @@ jobs: echo "================================================================================================" - # script should fail if expected source tarball did not get created in dist/ + # create fake 'python' command: + # just exits when 1st argument is setup.py, but calls out to origin Python command otherwise; + # this is important w.r.t. the Python version checks run by the 'eb' script mkdir -p /tmp/$USER/bin + export PATH=/tmp/$USER/bin:$PATH echo '#!/bin/bash' > /tmp/$USER/bin/python chmod u+x /tmp/$USER/bin/python - export PATH=/tmp/$USER/bin:$PATH + echo 'orig_python=$(which -a python | head -2 | tail -1)' >> /tmp/$USER/bin/python + echo 'if [[ "$1" == "setup.py" ]]; then exit 0; else $orig_python "$@"; fi' >> /tmp/$USER/bin/python + + # script should fail if expected source tarball did not get created in dist/ ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true grep "ERROR: Expected file dist/${{matrix.repo}}-${version}.tar.gz not found!" $out echo "Expected error found in output: OK!" + + # clean up index file, to avoid check for dirty working directory failing + rm -f easybuild/easyconfigs/.eb-path-index echo "================================================================================================" + # make fake python command fail if 1st argument is setup.py + sed -i 's/exit 0/exit 1/g' /tmp/$USER/bin/python + # script should deal well with failing 'python setup.py sdist' - echo 'exit 1' >> /tmp/$USER/bin/python ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true grep "ERROR: Creating source tarball failed" $out echo "Expected error found in output: OK!" - rm /tmp/$USER/bin/python + + # cleanup + rm -f /tmp/$USER/bin/python easybuild/easyconfigs/.eb-path-index echo "================================================================================================" From ad027b1456039e591f12ccd3846472203a0e63a5 Mon Sep 17 00:00:00 2001 From: Michael H Kelsey Date: Tue, 21 Apr 2020 12:05:04 -0500 Subject: [PATCH 041/286] Remove modifications under version-specific. Start adding section on Extensions in Writing_easyconfig_fils. --- docs/Writing_easyconfig_files.rst | 9 +++++++++ docs/version-specific/easyconfig_parameters.rst | 7 ------- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index edd0aff4..a64f475b 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -506,12 +506,21 @@ which is equivalent to:: dependencies = [('PnMPI', '1.2.0', '', True)] + Using external modules as dependencies ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Since EasyBuild v2.1, specifying modules that are not provided via EasyBuild as dependencies is also supported. See :ref:`using_external_modules` for more information. + +Module Extensions +~~~~~~~~~~~~~~~~~ + +Besides dependencies, which are found outside the package being built but are part of the site's EasyBuild +installation, it is also possible to incorporate "dependencies" into the package build itself. This is typically used as part of a PythonPackage or PythonBundle, ... This is done via the `exts_list` array. + + .. _configure_build_install_command_options: Configure/build/install command options diff --git a/docs/version-specific/easyconfig_parameters.rst b/docs/version-specific/easyconfig_parameters.rst index 5a108cb0..b57e93ac 100644 --- a/docs/version-specific/easyconfig_parameters.rst +++ b/docs/version-specific/easyconfig_parameters.rst @@ -34,7 +34,6 @@ toolchain parameters ``toolchainopts`` Extra options for compilers None ================== ================================================================================================================================================================================================================================= ================= -.. _easyconfig_parameters_build_parameters: build parameters ---------------- @@ -138,12 +137,6 @@ extensions parameters ``exts_list`` List with extensions added to the base installation [] ========================== ========================================================================================================== ================= -Each entry in ``exts_list`` is a tuple with the extension name -(``ext_name``), version string (``ext_version``), and a dictionary of -source options. Any of the -:ref:`easyconfig_parameters_build_parameters` can be specified within -the options dictionary. - modules parameters ------------------ From 85a105f91a28c02df832c81105ec0dc4f51b898e Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Tue, 21 Apr 2020 21:36:47 -0700 Subject: [PATCH 042/286] Expand new 'Module extensions' section with example code and cross-refernences to sources dictionary and git_config. --- docs/Writing_easyconfig_files.rst | 33 +++++++++++++++++++++++++++++-- 1 file changed, 31 insertions(+), 2 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index a64f475b..a5d6d111 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -517,8 +517,37 @@ See :ref:`using_external_modules` for more information. Module Extensions ~~~~~~~~~~~~~~~~~ -Besides dependencies, which are found outside the package being built but are part of the site's EasyBuild -installation, it is also possible to incorporate "dependencies" into the package build itself. This is typically used as part of a PythonPackage or PythonBundle, ... This is done via the `exts_list` array. +Besides dependencies, which are found outside the module being built but are part of the site's EasyBuild installation, +it is also possible to incorporate extensions to the module within the build. This is typically used as part of a +PythonPackage or PythonBundle, and done via the `exts_list` array:: + +.. code:: python + + exts_list = [ + ('llvmlite', '0.26.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'patches': ['llvmlite-0.26.0_fix-ffi-Makefile.patch'], + 'checksums': [ + '13e84fe6ebb0667233074b429fd44955f309dead3161ec89d9169145dbad2ebf', # llvmlite-0.26.0.tar.gz + '40e6fe6de48709b45daebf8082f65ac26f73a4afdf58fc1e8099b97c575fecae', # llvmlite-0.26.0_fix-ffi-Makefile.patch + ], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + 'checksums': ['c62121b2d384d8b4d244ef26c1cf8bb5cb819278a80b893bf41918ad6d391258'], + }), + ] + +Each entry in `exts_list` is a three-component tuple, with the name and version number, and a dictionary of source +information. The latter is essentially the same as the the dictionary structure of `sources`; see +:ref:`_common_easyconfig_param_sources_alt` for details. + +Since EasyBuild v4.2.1, the `git_config` dictionary (see :ref:`downloading-from-a-git-repository`) may be included in +the `exts_list` source definition. .. _configure_build_install_command_options: From fdd50c39b5ed40e637e960435ed05071512e664b Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Wed, 22 Apr 2020 23:03:24 -0700 Subject: [PATCH 043/286] Clean up formatting of new 'Module extensions' Fix my various RST mistakes in the new 'Module extensions' section of Writing_easyconfig_files. Remove spurious double-colon, improve indentation in `exts_list` example, add specific example for using `git_config` here (coming as part of Framework PR #3294. --- docs/Writing_easyconfig_files.rst | 22 ++++++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index a5d6d111..c5e0c50c 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -519,7 +519,7 @@ Module Extensions Besides dependencies, which are found outside the module being built but are part of the site's EasyBuild installation, it is also possible to incorporate extensions to the module within the build. This is typically used as part of a -PythonPackage or PythonBundle, and done via the `exts_list` array:: +PythonPackage or PythonBundle, and done via the `exts_list` array: .. code:: python @@ -528,8 +528,8 @@ PythonPackage or PythonBundle, and done via the `exts_list` array:: 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], 'patches': ['llvmlite-0.26.0_fix-ffi-Makefile.patch'], 'checksums': [ - '13e84fe6ebb0667233074b429fd44955f309dead3161ec89d9169145dbad2ebf', # llvmlite-0.26.0.tar.gz - '40e6fe6de48709b45daebf8082f65ac26f73a4afdf58fc1e8099b97c575fecae', # llvmlite-0.26.0_fix-ffi-Makefile.patch + '13e84fe6ebb0667233074b429fd44955f309dead3161ec89d9169145dbad2ebf', # llvmlite-0.26.0.tar.gz + '40e6fe6de48709b45daebf8082f65ac26f73a4afdf58fc1e8099b97c575fecae', # llvmlite-0.26.0_fix-ffi-Makefile.patch ], }), ('singledispatch', '3.4.0.3', { @@ -547,7 +547,21 @@ information. The latter is essentially the same as the the dictionary structure :ref:`_common_easyconfig_param_sources_alt` for details. Since EasyBuild v4.2.1, the `git_config` dictionary (see :ref:`downloading-from-a-git-repository`) may be included in -the `exts_list` source definition. +the `exts_list` source definition. For example, to download Git sources from a private repository and convert them to a tar-ball for installation: + +.. code:: python + + exts_defaultclass = 'PythonPackage' + exts_list = [ + ('pyCAP', 'master', { + 'filename': 'pyCAP-master.tar.gz', + 'git_config': { + 'url': 'ssh://nero.stanford.edu/data/git/Analysis', + 'repo_name': 'pyCAP', + 'tag': 'master', + } + }), + ] .. _configure_build_install_command_options: From 544c236393b197c62b689a905a2b9cedebb2c5cf Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Fri, 24 Apr 2020 22:56:27 -0700 Subject: [PATCH 044/286] Update exts_list to be explicit about options. --- docs/Writing_easyconfig_files.rst | 28 +++++++++++++++++++--------- 1 file changed, 19 insertions(+), 9 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index c5e0c50c..04cbc24e 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -197,7 +197,7 @@ Using the ``--inject-checksums`` command line option, you can let EasyBuild add in one or more easyconfig files (which is significantly more convenient than doing it manually). With ``--inject-checksums``, checksums are injected for all sources and patches (if any), -as well as for all sources & patches of every extension listed in ``exts_list`` (if any). +as well as for all sources & patches of every extension listed in ``exts_list`` (if any, see :ref:`module_extensions`). If the sources (& patches) are not available yet, EasyBuild will try to download them first; i.e., the ``fetch`` step is run prior to computing & injecting the checksums. @@ -518,8 +518,18 @@ Module Extensions ~~~~~~~~~~~~~~~~~ Besides dependencies, which are found outside the module being built but are part of the site's EasyBuild installation, -it is also possible to incorporate extensions to the module within the build. This is typically used as part of a -PythonPackage or PythonBundle, and done via the `exts_list` array: +it is also possible to incorporate extensions to the module within the build. This is done via the `exts_list` array. + +Each entry in `exts_list` is a three-component tuple, with the name and version number, and a dictionary of source +information. The latter consist of most of the allowed keys as in the dictionary structure of `sources` (see +:ref:`_common_easyconfig_param_sources_alt`): + +* **nosource**: If specified, no download will be done +* **source_tmpl**: Template string for the file to be downloaded + * default is `'%(name)s-%(version)s.tar.gz'` + * `%(name)s` and `%(version)s` come from the `exts_list` entry (above) +* **source_urls**, **patches**, **checksums**, **force_download**: as in `sources` +* **git_config**: Dictionary specifying download from a Git repository .. code:: python @@ -542,19 +552,16 @@ PythonPackage or PythonBundle, and done via the `exts_list` array: }), ] -Each entry in `exts_list` is a three-component tuple, with the name and version number, and a dictionary of source -information. The latter is essentially the same as the the dictionary structure of `sources`; see -:ref:`_common_easyconfig_param_sources_alt` for details. - Since EasyBuild v4.2.1, the `git_config` dictionary (see :ref:`downloading-from-a-git-repository`) may be included in -the `exts_list` source definition. For example, to download Git sources from a private repository and convert them to a tar-ball for installation: +the `exts_list` source definition. For example, to download Git sources from a private repository and convert them to a +tar-ball for installation: .. code:: python exts_defaultclass = 'PythonPackage' exts_list = [ ('pyCAP', 'master', { - 'filename': 'pyCAP-master.tar.gz', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'git_config': { 'url': 'ssh://nero.stanford.edu/data/git/Analysis', 'repo_name': 'pyCAP', @@ -563,6 +570,9 @@ the `exts_list` source definition. For example, to download Git sources from a }), ] +Here, the template strings `%(name)s` and `%(version)s` will be substituted from the `exts_list` entry elements ("pyCAP" +and "master", respectively), not from the EasyConfigs values. + .. _configure_build_install_command_options: From 0a97a7d3a2213cc9c4163d72aeb1280f30bd59df Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Sat, 25 Apr 2020 14:23:37 -0700 Subject: [PATCH 045/286] Improve description of exts_list options, and how they differ from main sources options. --- docs/Writing_easyconfig_files.rst | 26 ++++++++++++++++++-------- 1 file changed, 18 insertions(+), 8 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index 04cbc24e..624fd116 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -520,16 +520,26 @@ Module Extensions Besides dependencies, which are found outside the module being built but are part of the site's EasyBuild installation, it is also possible to incorporate extensions to the module within the build. This is done via the `exts_list` array. -Each entry in `exts_list` is a three-component tuple, with the name and version number, and a dictionary of source -information. The latter consist of most of the allowed keys as in the dictionary structure of `sources` (see -:ref:`_common_easyconfig_param_sources_alt`): +Each entry in `exts_list` is a three-component tuple, with the name and +version number, and a dictionary of source options:: -* **nosource**: If specified, no download will be done +.. code:: python + + exts_list = [ + ('name', 'version', { 'option':'value', 'option':'value' }) + ] + +The latter consist of most of the allowed keys as in the dictionary structure of `sources` (see +:ref:`_common_easyconfig_param_sources_alt`). Among those options, the following exceptions and +special cases should be noted: + +* **nosource**: If set `True`, no download will be done +* **filename** and **download_filename** are ignored; use `'source_tmpl'` * **source_tmpl**: Template string for the file to be downloaded * default is `'%(name)s-%(version)s.tar.gz'` * `%(name)s` and `%(version)s` come from the `exts_list` entry (above) -* **source_urls**, **patches**, **checksums**, **force_download**: as in `sources` * **git_config**: Dictionary specifying download from a Git repository +* **start_dir**: If not set, will be derived; the EasyConfigs value will not be used .. code:: python @@ -552,9 +562,9 @@ information. The latter consist of most of the allowed keys as in the dictionar }), ] -Since EasyBuild v4.2.1, the `git_config` dictionary (see :ref:`downloading-from-a-git-repository`) may be included in -the `exts_list` source definition. For example, to download Git sources from a private repository and convert them to a -tar-ball for installation: +Since EasyBuild v4.2.1, the `git_config` dictionary (see :ref:`downloading-from-a-git-repository`) +may be included in the `exts_list` source definition. For example, to download Git sources from a +private repository and convert them to a tar-ball for installation: .. code:: python From 3a4d12cb2065d9fb2b3594d40345e724db1bdb4e Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Sat, 25 Apr 2020 14:29:07 -0700 Subject: [PATCH 046/286] Fix literal quoting in Module Extensions section. --- docs/Writing_easyconfig_files.rst | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index 624fd116..c481e855 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -518,10 +518,10 @@ Module Extensions ~~~~~~~~~~~~~~~~~ Besides dependencies, which are found outside the module being built but are part of the site's EasyBuild installation, -it is also possible to incorporate extensions to the module within the build. This is done via the `exts_list` array. +it is also possible to incorporate extensions to the module within the build. This is done via the ``exts_list`` array. -Each entry in `exts_list` is a three-component tuple, with the name and -version number, and a dictionary of source options:: +Each entry in ``exts_list`` is a three-component tuple, with the name and +version number, and a dictionary of source options: .. code:: python @@ -529,15 +529,15 @@ version number, and a dictionary of source options:: ('name', 'version', { 'option':'value', 'option':'value' }) ] -The latter consist of most of the allowed keys as in the dictionary structure of `sources` (see +The latter consist of most of the allowed keys as in the dictionary structure of ``sources`` (see :ref:`_common_easyconfig_param_sources_alt`). Among those options, the following exceptions and special cases should be noted: -* **nosource**: If set `True`, no download will be done -* **filename** and **download_filename** are ignored; use `'source_tmpl'` +* **nosource**: If set ``True``, no download will be done +* **filename** and **download_filename** are ignored; use ``'source_tmpl'`` * **source_tmpl**: Template string for the file to be downloaded - * default is `'%(name)s-%(version)s.tar.gz'` - * `%(name)s` and `%(version)s` come from the `exts_list` entry (above) + * default is ``'%(name)s-%(version)s.tar.gz'`` + * ``%(name)s`` and ``%(version)s`` come from the ``exts_list`` entry (above) * **git_config**: Dictionary specifying download from a Git repository * **start_dir**: If not set, will be derived; the EasyConfigs value will not be used @@ -562,8 +562,10 @@ special cases should be noted: }), ] -Since EasyBuild v4.2.1, the `git_config` dictionary (see :ref:`downloading-from-a-git-repository`) -may be included in the `exts_list` source definition. For example, to download Git sources from a +That third instance uses the ``name`` and ``version`` variables defined in the EasyConfigs file. + +Since EasyBuild v4.2.1, the ``git_config`` dictionary (see :ref:`downloading-from-a-git-repository`) +may be included in the ``exts_list`` source definition. For example, to download Git sources from a private repository and convert them to a tar-ball for installation: .. code:: python @@ -580,8 +582,8 @@ private repository and convert them to a tar-ball for installation: }), ] -Here, the template strings `%(name)s` and `%(version)s` will be substituted from the `exts_list` entry elements ("pyCAP" -and "master", respectively), not from the EasyConfigs values. +Here, the template strings ``%(name)s`` and ``%(version)s`` will be substituted from the +``exts_list`` entry elements ("pyCAP" and "master", respectively), not from the EasyConfigs values. .. _configure_build_install_command_options: From b9701ae42ed4cbd0ee9f569589a108759aab1fcd Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Sat, 25 Apr 2020 14:54:56 -0700 Subject: [PATCH 047/286] Add section explaining how to use self.cfg in an EasyBlock, for issue #618. --- docs/Implementing-easyblocks.rst | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/docs/Implementing-easyblocks.rst b/docs/Implementing-easyblocks.rst index 82cccc66..0484753e 100644 --- a/docs/Implementing-easyblocks.rst +++ b/docs/Implementing-easyblocks.rst @@ -254,6 +254,37 @@ redefining it entirely, since we call out to the original ``configure_step`` met Specific aspects of easyblocks ------------------------------ +.. _implementing_easyblocks_default_parameters: + +Default easyconfig parameters +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +All of the parameters which are "set" in an easyconfig file (see :ref:`vsd_avail_easyconfig_params`) +become key-value pairs in the ``self.cfg`` dictionary. For instance, where the easyconfig file might +specify + +.. code:: python + + name = 'example' + version = '2.5.3' + versionsuffix = '-Python-3.7.4' + +you could access these within an easyblock via + +.. code:: python + + ec_name = self.cfg['name'] + ec_ver = self.cfg['version'] + ec_suffix = self.cfg['versionsuffix'] + +For these particular "universal" arguments, this mapping is done for you in the ``EasyBlock`` base +class and generic subclasses, so most easyconfig parameters are directly available as local Python +variables (``name``, ``version``, etc.). + +Some variables, and in particular :ref:`custom parameters +` which you define for your own easyblock, will not be +automatically mapped. You will need to use ``self.cfg`` to access them in your code. + .. _implementing_easyblocks_custom_parameters: From 53e4aec5e7b2d30943d98bb15b0b369820a29fbc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 3 May 2020 09:37:23 +0200 Subject: [PATCH 048/286] add readthedocs configuration file (fixes #587) --- .readthedocs.yml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 .readthedocs.yml diff --git a/.readthedocs.yml b/.readthedocs.yml new file mode 100644 index 00000000..10836de1 --- /dev/null +++ b/.readthedocs.yml @@ -0,0 +1,20 @@ +# .readthedocs.yml +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# version of configuration file (required) +version: 2 + +# Build documentation in the docs/ directory with Sphinx +sphinx: + configuration: docs/conf.py + +# also build docs in PDF format +formats: [pdf] + +# Optionally set the version of Python and requirements required to build your docs +python: + version: 3.7 + install: + - method: pip + path: . From 91b9697a78fae0ea3f1664bb85ef47a1b151cc4f Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Fri, 8 May 2020 07:11:27 -0700 Subject: [PATCH 049/286] Expand explanation of self.cfg[] vs. local self.variable usage. --- docs/Implementing-easyblocks.rst | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/docs/Implementing-easyblocks.rst b/docs/Implementing-easyblocks.rst index 0484753e..37f30ee4 100644 --- a/docs/Implementing-easyblocks.rst +++ b/docs/Implementing-easyblocks.rst @@ -269,21 +269,23 @@ specify version = '2.5.3' versionsuffix = '-Python-3.7.4' -you could access these within an easyblock via +these are accessible within an easyblock via .. code:: python - ec_name = self.cfg['name'] - ec_ver = self.cfg['version'] - ec_suffix = self.cfg['versionsuffix'] + longform = ''.join(self.cfg['name'],'/',self.cfg['version'],self.cfg['versionsuffix']) -For these particular "universal" arguments, this mapping is done for you in the ``EasyBlock`` base -class and generic subclasses, so most easyconfig parameters are directly available as local Python -variables (``name``, ``version``, etc.). +For these "universal" arguments, this mapping is done for you in the ``EasyBlock`` base class, so +they are also available as local Python variables (``self.name``, ``self.version``, etc.): -Some variables, and in particular :ref:`custom parameters -` which you define for your own easyblock, will not be -automatically mapped. You will need to use ``self.cfg`` to access them in your code. +.. code:: python + + longform = ''.join(self.name,'/',self.version,self.versionsuffix) + +This is true for the variables listed in :ref:`vsd_avail_easyconfig_params`. Any additional +:ref:`custom parameters ` which you define for your own +easyblock, will not be automatically mapped. You will need to use ``self.cfg`` to access them in +your code. .. _implementing_easyblocks_custom_parameters: From bf4df40795a73f62e47330363ca69153abbb2730 Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Fri, 8 May 2020 08:05:05 -0700 Subject: [PATCH 050/286] Use proper version number in 'pyCAP' example of downloading extension sources. --- docs/Writing_easyconfig_files.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index c481e855..5cd90579 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -572,7 +572,7 @@ private repository and convert them to a tar-ball for installation: exts_defaultclass = 'PythonPackage' exts_list = [ - ('pyCAP', 'master', { + ('pyCAP', '0.1', { 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'git_config': { 'url': 'ssh://nero.stanford.edu/data/git/Analysis', @@ -583,7 +583,7 @@ private repository and convert them to a tar-ball for installation: ] Here, the template strings ``%(name)s`` and ``%(version)s`` will be substituted from the -``exts_list`` entry elements ("pyCAP" and "master", respectively), not from the EasyConfigs values. +``exts_list`` entry elements ("pyCAP" and "0.1", respectively), not from the EasyConfigs values. .. _configure_build_install_command_options: From 89f29aaa73d764ae42d4b117547e75c126c46a24 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 May 2020 17:08:20 +0200 Subject: [PATCH 051/286] update list of known toolchains, using improved output of 'eb --list-toolchains --output-format=rst' --- docs/eb_list_toolchains.rst | 2 +- docs/scripts/update-all-docs.sh | 4 +- docs/version-specific/eb_list_toolchains.txt | 42 ----- docs/version-specific/toolchains.rst | 162 +++++++++---------- 4 files changed, 84 insertions(+), 126 deletions(-) delete mode 100644 docs/version-specific/eb_list_toolchains.txt diff --git a/docs/eb_list_toolchains.rst b/docs/eb_list_toolchains.rst index 23cc3658..7726c1eb 100644 --- a/docs/eb_list_toolchains.rst +++ b/docs/eb_list_toolchains.rst @@ -10,6 +10,6 @@ The list of known toolchains can easily be obtained with:: List of known toolchains (toolchainname: module[,module...]): [...] -.. include:: version-specific/eb_list_toolchains.txt +An up-to-date overview of known toolchains is available at :ref:`vsd_list_toolchains`. .. note:: The `system` toolchain is a special case, see :ref:`system_toolchain`. diff --git a/docs/scripts/update-all-docs.sh b/docs/scripts/update-all-docs.sh index 813739d0..72b4ba61 100755 --- a/docs/scripts/update-all-docs.sh +++ b/docs/scripts/update-all-docs.sh @@ -181,9 +181,9 @@ echo "* :ref:\`List of available toolchain options \`" >> # list-toolchain doc echo ".. _vsd_list_toolchains:" > $VERSION_SPECIFIC_DIR/toolchains.rst echo >> $VERSION_SPECIFIC_DIR/toolchains.rst -echo "*(see also* \`\`eb --list-toolchains\`\` *)*" >> $VERSION_SPECIFIC_DIR/toolchains.rst -echo >> $VERSION_SPECIFIC_DIR/toolchains.rst eb --list-toolchains --output-format rst >> $VERSION_SPECIFIC_DIR/toolchains.rst +echo >> $VERSION_SPECIFIC_DIR/toolchains.rst +echo "*(see also* \`\`eb --list-toolchains\`\` *)*" >> $VERSION_SPECIFIC_DIR/toolchains.rst echo "* :ref:\`List of known toolchains \`" >> $overview diff --git a/docs/version-specific/eb_list_toolchains.txt b/docs/version-specific/eb_list_toolchains.txt deleted file mode 100644 index 669a7e2f..00000000 --- a/docs/version-specific/eb_list_toolchains.txt +++ /dev/null @@ -1,42 +0,0 @@ - -.. table: List of toolchains - -================== ============== =========== ========================================= -Toolchain Components that comprise the toolchain ------------------- -------------------------------------------------------------------- -Name Compilers MPI stack Included Libraries -================== ============== =========== ========================================= -ClangGCC Clang/GCC -GCC GCC -cgmpich Clang/GCC MPICH -cgmpolf Clang/GCC MPICH OpenBLAS/LAPACK, ScaLAPACK(/BLACS), FFTW -cgmvapich2 Clang/GCC MVAPICH2 -cgmvolf Clang/GCC MVAPICH2 OpenBLAS/LAPACK, ScaLAPACK(/BLACS), FFTW -cgompi Clang/GCC OpenMPI -cgoolf Clang/GCC OpenMPI OpenBLAS/LAPACK, ScaLAPACK(/BLACS), FFTW -dummy -foss GCC OpenMPI OpenBLAS/LAPACK, ScaLAPACK(/BLACS), FFTW -gcccuda GCC, CUDA -gimkl GCC impi imkl -gmacml GCC MVAPICH2 ACML, ScaLAPACK(/BLACS), FFTW -gmpich2 GCC MPICH2 -gmpolf GCC MPICH2 OpenBLAS/LAPACK, ScaLAPACK(/BLACS), FFTW -gmvapich2 GCC MVAPICH2 -gmvolf GCC MVAPICH2 OpenBLAS/LAPACK, ScaLAPACK(/BLACS), FFTW -goalf GCC OpenMPI ATLAS, ScaLAPACK(/BLACS), FFTW -gompi GCC OpenMPI -gompic GCC, CUDA OpenMPI -goolf GCC OpenMPI OpenBLAS/LAPACK, ScaLAPACK(/BLACS), FFTW -goolfc GCC, CUDA OpenMPI OpenBLAS/LAPACK, ScaLAPACK(/BLACS), FFTW -gqacml GCC QLogicMPI ACML, ScaLAPACK(/BLACS), FFTW -iccifort icc, ifort -ictce icc, ifort impi imkl -iimpi icc, ifort impi -iiqmpi icc, ifort QLogicMPI -impmkl icc, ifort MPICH2 imkl -intel icc, ifort impi imkl -iomkl icc, ifort OpenMPI imkl -iqacml icc, ifort QLogicMPI ACML, ScaLAPACK(/BLACS), FFTW -ismkl icc, ifort MPICH2 imkl -================== ============== =========== ========================================= - diff --git a/docs/version-specific/toolchains.rst b/docs/version-specific/toolchains.rst index add5ddcb..1a7b6ced 100644 --- a/docs/version-specific/toolchains.rst +++ b/docs/version-specific/toolchains.rst @@ -1,87 +1,87 @@ .. _vsd_list_toolchains: -*(see also* ``eb --list-toolchains`` *)* - List of known toolchains ------------------------ -================ ================ =========== ================ ======== ========= ======== ==== ===== ============= -name compiler MPI COMPILER LAPACK ScaLAPACK BLAS FFT BLACS CUDA compiler -================ ================ =========== ================ ======== ========= ======== ==== ===== ============= -**system** -**ismkl** icc, ifort MPICH2 icc, ifort imkl imkl imkl imkl imkl -**gompic** GCC, CUDA OpenMPI GCC, CUDA CUDA -**cgoolf** Clang, GCC OpenMPI Clang, GCC OpenBLAS ScaLAPACK OpenBLAS FFTW BLACS -**gmacml** GCC MVAPICH2 GCC ACML ScaLAPACK ACML FFTW BLACS -**GNU** GCC GCC -**iimpic** icc, ifort, CUDA impi icc, ifort, CUDA CUDA -**gpsolf** GCC psmpi GCC OpenBLAS ScaLAPACK OpenBLAS FFTW BLACS -**xlompi** xlc, xlf OpenMPI xlc, xlf -**gimpic** GCC, CUDA impi GCC, CUDA CUDA -**gmpich2** GCC MPICH2 GCC -**cgmvolf** Clang, GCC MVAPICH2 Clang, GCC OpenBLAS ScaLAPACK OpenBLAS FFTW BLACS -**CrayIntel** PrgEnv-intel PrgEnv-intel -**gcccuda** GCC, CUDA GCC, CUDA CUDA -**iompi** icc, ifort OpenMPI icc, ifort -**golf** GCC GCC OpenBLAS OpenBLAS FFTW -**foss** GCC OpenMPI GCC OpenBLAS ScaLAPACK OpenBLAS FFTW BLACS -**CrayGNU** PrgEnv-gnu PrgEnv-gnu -**gpsmpi** GCC psmpi GCC -**CrayCCE** PrgEnv-cray PrgEnv-cray -**cgmpolf** Clang, GCC MPICH Clang, GCC OpenBLAS ScaLAPACK OpenBLAS FFTW BLACS -**gmvapich2** GCC MVAPICH2 GCC -**gompi** GCC OpenMPI GCC -**pompi** PGI OpenMPI PGI -**gsolf** GCC SpectrumMPI GCC OpenBLAS ScaLAPACK OpenBLAS FFTW BLACS -**PGI** PGI PGI -**fosscuda** GCC, CUDA OpenMPI GCC, CUDA OpenBLAS ScaLAPACK OpenBLAS FFTW BLACS CUDA -**gqacml** GCC QLogicMPI GCC ACML ScaLAPACK ACML FFTW BLACS -**xlmvapich2** xlc, xlf MVAPICH2 xlc, xlf -**xlmpich2** xlc, xlf MPICH2 xlc, xlf -**pomkl** PGI OpenMPI PGI imkl imkl imkl imkl imkl -**impich** icc, ifort MPICH icc, ifort -**gomklc** GCC, CUDA OpenMPI GCC, CUDA imkl imkl imkl imkl imkl CUDA -**CrayPGI** PrgEnv-pgi PrgEnv-pgi -**iqacml** icc, ifort QLogicMPI icc, ifort ACML ScaLAPACK ACML FFTW BLACS -**GCCcore** GCCcore GCCcore -**goalf** GCC OpenMPI GCC ATLAS ScaLAPACK ATLAS FFTW BLACS -**gmkl** GCC GCC imkl imkl imkl imkl imkl -**GCC** GCC GCC -**gsmpi** GCC SpectrumMPI GCC -**goolfc** GCC, CUDA OpenMPI GCC, CUDA OpenBLAS ScaLAPACK OpenBLAS FFTW BLACS CUDA -**iompic** icc, ifort, CUDA OpenMPI icc, ifort, CUDA CUDA -**iimkl** icc, ifort icc, ifort imkl imkl imkl imkl imkl -**iomklc** icc, ifort, CUDA OpenMPI icc, ifort, CUDA imkl imkl imkl imkl imkl CUDA -**gmpolf** GCC MPICH GCC OpenBLAS ScaLAPACK OpenBLAS FFTW BLACS -**ipsmpi** icc, ifort psmpi icc, ifort -**gomkl** GCC OpenMPI GCC imkl imkl imkl imkl imkl -**gmpich** GCC MPICH GCC -**iimpi** icc, ifort impi icc, ifort -**iimklc** icc, ifort, CUDA icc, ifort, CUDA imkl imkl imkl imkl imkl CUDA -**goolf** GCC OpenMPI GCC OpenBLAS ScaLAPACK OpenBLAS FFTW BLACS -**xlmpich** xlc, xlf MPICH xlc, xlf -**intelcuda** icc, ifort, CUDA impi icc, ifort, CUDA imkl imkl imkl imkl imkl CUDA -**gmvolf** GCC MVAPICH2 GCC OpenBLAS ScaLAPACK OpenBLAS FFTW BLACS -**goblf** GCC OpenMPI GCC LAPACK ScaLAPACK BLIS FFTW BLACS -**pmkl** PGI PGI imkl imkl imkl imkl imkl -**ictce** icc, ifort impi icc, ifort imkl imkl imkl imkl imkl -**iomkl** icc, ifort OpenMPI icc, ifort imkl imkl imkl imkl imkl -**iccifort** icc, ifort icc, ifort -**impmkl** icc, ifort MPICH icc, ifort imkl imkl imkl imkl imkl -**intel** icc, ifort impi icc, ifort imkl imkl imkl imkl imkl -**golfc** GCC, CUDA GCC, CUDA OpenBLAS OpenBLAS FFTW CUDA -**gimkl** GCC impi GCC imkl imkl imkl imkl imkl -**iiqmpi** icc, ifort QLogicMPI icc, ifort -**cgompi** Clang, GCC OpenMPI Clang, GCC -**cgmvapich2** Clang, GCC MVAPICH2 Clang, GCC -**intel-para** icc, ifort psmpi icc, ifort imkl imkl imkl imkl imkl -**iccifortcuda** icc, ifort, CUDA icc, ifort, CUDA CUDA -**giolf** GCC impi GCC OpenBLAS ScaLAPACK OpenBLAS FFTW BLACS -**giolfc** GCC, CUDA impi GCC, CUDA OpenBLAS ScaLAPACK OpenBLAS FFTW BLACS CUDA -**gmklc** GCC, CUDA GCC, CUDA imkl imkl imkl imkl imkl CUDA -**ClangGCC** Clang, GCC Clang, GCC -**xlcxlf** xlc, xlf xlc, xlf -**cgmpich** Clang, GCC MPICH Clang, GCC -**gimpi** GCC impi GCC -================ ================ =========== ================ ======== ========= ======== ==== ===== ============= +================ ================ =========== ======================= ======== +Name Compiler(s) MPI Linear algebra FFT +================ ================ =========== ======================= ======== +**cgmpich** Clang, GCC MPICH *(none)* *(none)* +**cgmpolf** Clang, GCC MPICH OpenBLAS, ScaLAPACK FFTW +**cgmvapich2** Clang, GCC MVAPICH2 *(none)* *(none)* +**cgmvolf** Clang, GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW +**cgompi** Clang, GCC OpenMPI *(none)* *(none)* +**cgoolf** Clang, GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**ClangGCC** Clang, GCC *(none)* *(none)* *(none)* +**CrayCCE** PrgEnv-cray cray-mpich cray-libsci *(none)* +**CrayGNU** PrgEnv-gnu cray-mpich cray-libsci *(none)* +**CrayIntel** PrgEnv-intel cray-mpich cray-libsci *(none)* +**CrayPGI** PrgEnv-pgi cray-mpich cray-libsci *(none)* +**foss** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**fosscuda** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW +**GCC** GCC *(none)* *(none)* *(none)* +**GCCcore** GCCcore *(none)* *(none)* *(none)* +**gcccuda** GCC, CUDA *(none)* *(none)* *(none)* +**gimkl** GCC impi imkl imkl +**gimpi** GCC impi *(none)* *(none)* +**gimpic** GCC, CUDA impi *(none)* *(none)* +**giolf** GCC impi OpenBLAS, ScaLAPACK FFTW +**giolfc** GCC, CUDA impi OpenBLAS, ScaLAPACK FFTW +**gmacml** GCC MVAPICH2 ACML, ScaLAPACK FFTW +**gmkl** GCC *(none)* imkl imkl +**gmklc** GCC, CUDA *(none)* imkl imkl +**gmpich** GCC MPICH *(none)* *(none)* +**gmpich2** GCC MPICH2 *(none)* *(none)* +**gmpolf** GCC MPICH OpenBLAS, ScaLAPACK FFTW +**gmvapich2** GCC MVAPICH2 *(none)* *(none)* +**gmvolf** GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW +**GNU** GCC *(none)* *(none)* *(none)* +**goalf** GCC OpenMPI ATLAS, ScaLAPACK FFTW +**goblf** GCC OpenMPI BLIS, LAPACK, ScaLAPACK FFTW +**golf** GCC *(none)* OpenBLAS FFTW +**golfc** GCC, CUDA *(none)* OpenBLAS FFTW +**gomkl** GCC OpenMPI imkl imkl +**gomklc** GCC, CUDA OpenMPI imkl imkl +**gompi** GCC OpenMPI *(none)* *(none)* +**gompic** GCC, CUDA OpenMPI *(none)* *(none)* +**goolf** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**goolfc** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW +**gpsmpi** GCC psmpi *(none)* *(none)* +**gpsolf** GCC psmpi OpenBLAS, ScaLAPACK FFTW +**gqacml** GCC QLogicMPI ACML, ScaLAPACK FFTW +**gsmpi** GCC SpectrumMPI *(none)* *(none)* +**gsolf** GCC SpectrumMPI OpenBLAS, ScaLAPACK FFTW +**iccifort** icc, ifort *(none)* *(none)* *(none)* +**iccifortcuda** icc, ifort, CUDA *(none)* *(none)* *(none)* +**ictce** icc, ifort impi imkl imkl +**iimkl** icc, ifort *(none)* imkl imkl +**iimklc** icc, ifort, CUDA *(none)* imkl imkl +**iimpi** icc, ifort impi *(none)* *(none)* +**iimpic** icc, ifort, CUDA impi *(none)* *(none)* +**iiqmpi** icc, ifort QLogicMPI *(none)* *(none)* +**impich** icc, ifort MPICH *(none)* *(none)* +**impmkl** icc, ifort MPICH imkl imkl +**intel** icc, ifort impi imkl imkl +**intel-para** icc, ifort psmpi imkl imkl +**intelcuda** icc, ifort, CUDA impi imkl imkl +**iomkl** icc, ifort OpenMPI imkl imkl +**iomklc** icc, ifort, CUDA OpenMPI imkl imkl +**iompi** icc, ifort OpenMPI *(none)* *(none)* +**iompic** icc, ifort, CUDA OpenMPI *(none)* *(none)* +**ipsmpi** icc, ifort psmpi *(none)* *(none)* +**iqacml** icc, ifort QLogicMPI ACML, ScaLAPACK FFTW +**ismkl** icc, ifort MPICH2 imkl imkl +**PGI** PGI *(none)* *(none)* *(none)* +**pmkl** PGI *(none)* imkl imkl +**pomkl** PGI OpenMPI imkl imkl +**pompi** PGI OpenMPI *(none)* *(none)* +**system** *(none)* *(none)* *(none)* *(none)* +**xlcxlf** xlc, xlf *(none)* *(none)* *(none)* +**xlmpich** xlc, xlf MPICH *(none)* *(none)* +**xlmpich2** xlc, xlf MPICH2 *(none)* *(none)* +**xlmvapich2** xlc, xlf MVAPICH2 *(none)* *(none)* +**xlompi** xlc, xlf OpenMPI *(none)* *(none)* +================ ================ =========== ======================= ======== + +*(see also* ``eb --list-toolchains`` *)* From 06b015e410b882dfdf49544f5a46c91ab0c2f37c Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Fri, 8 May 2020 14:23:54 -0700 Subject: [PATCH 052/286] Use version-number with exaple of exts_list git_config. --- docs/Writing_easyconfig_files.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index 5cd90579..a97521ee 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -577,7 +577,7 @@ private repository and convert them to a tar-ball for installation: 'git_config': { 'url': 'ssh://nero.stanford.edu/data/git/Analysis', 'repo_name': 'pyCAP', - 'tag': 'master', + 'tag': '%(version)s', } }), ] From 3a437df491f7996e00e7c06d71c5794e34d29a08 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 May 2020 16:46:51 +0800 Subject: [PATCH 053/286] update release notes for EasyBuild v4.2.1 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 172 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 172 insertions(+), 5 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 5873e559..bcfbcd39 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20200520.01** (`May 20th 2020`): update release notes for EasyBuild v4.2.1 (see :ref:`release_notes_eb421`) * **release 20200414.01** (`Apr 14th 2020`): * document new EasyBuild locking mechanism (see :ref:`locks`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 1720e9e1..f97b2234 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,178 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **1,912** different software packages, -including 31 different (compiler) toolchains. It contains 219 software-specific easyblocks and 36 generic easyblocks, -alongside 9,462 easyconfig files. +The latest version of EasyBuild provides support for building and installing **1,978** different software packages, +including 31 different (compiler) toolchains. It contains 219 software-specific easyblocks and 37 generic easyblocks, +alongside 9,894 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb421: + +EasyBuild v4.2.1 (May 20th 2020) +-------------------------------- + +bugfix/update release + +**framework** + +* various enhancements, including: + + * also mention CPU architecture (x86_64, POWER) in comment for test reports (`#3281 `_) + * add support for enhancing existing sanity check in easyconfigs, as opposed to overwriting paths/commands (`#3288 `_) + * clean up locks when EasyBuild session is cancelled with a signal like ``SIGTERM`` (`#3291 `_, `#3321 `_) + * add ``find_glob_pattern`` function to ``filetools`` module (`#3297 `_) + * add constants for common OS dependencies (``OS_PKG_IBVERBS_DEV``, ``OS_PKG_OPENSSL_DEV``, ...) (`#3309 `_, `#3334 `_) + * flesh out ``get_mpi_cmd_template`` function from ``Mpi.mpi_cmd_for`` method (`#3312 `_) + * add variable ``moddependpaths`` to specify extra ``$MODULEPATH`` entry to consider for loading dependency modules (`#3324 `_) + * allow copying of tweaked easyconfigs when using ``--try-*`` with ``--copy-ec`` (`#3332 `_) + +* various bug fixes, including: + + * make ``ModulesTool.exist`` more robust w.r.t. module wrappers, aliases, defaults, etc. (`#3216 `_, `#3337 `_) + * clean up rst output of ``--list-toolchains`` (`#3246 `_) + * cast CPU arch name provided by archspec to a regular string (`#3286 `_) + * get ``pr_title`` and ``pr_descr`` build_options in ``new_pr_from_branch`` instead of ``new_pr`` (and commit_msg in both) (`#3298 `_) + * make ``pypi_source_urls`` more robust by using ``HTMLParser`` rather than ``xml.etree.ElementTree`` (`#3303 `_, `#3329 `_) + * fix broken test for ``--include-easyblocks-from-pr`` (`#3304 `_) + * don't use ``distutils.dir_util`` in ``copy_dir`` (`#3310 `_) + * print trace message for sanity check command before running it (`#3316 `_) + * fix problems with processing of easyconfigs using a Cray* toolchain when there are no actual external modules (`#3319 `_) + * make ``test_find_eb_script`` more robust in case ``$EB_SCRIPT_PATH`` is already set (`#3320 `_) + * fix several small problems with ``--try-update-deps`` (experimental feature) (`#3325 `_, `#3326 `_, `#3330 `_) + * add ``--disable-job`` in ``eb`` command used in jobs, to prevent infinite job cycle (`#3328 `_) + * avoid empty entries in ``$LD_LIBRARY_PATH`` and other path-like environment variables (`#3333 `_) + +* other changes: + + * fix code style issues in ``easybuild.tools`` + add ``flake8`` linting test (`#3282 `_) + * introduce ``contextmanager`` for disabling templating and reduce resolving errors (`#3287 `_) + * add ``change_into_dir`` named argument to ``extract_file`` + print deprecation warning if it's not specified (`#3292 `_) + * improve ``install_eb_dep.sh`` script to install EasyBuild dependencies in CI environment (`#3314 `_) + +**easyblocks** + +* add generic easyblock for installing Go packages: ``GoPackage`` (`#2042 `_) + +* minor enhancements, including: + + * update ``config.guess`` for all R packages, required installing R + extensions on Linux/POWER systems (`#1949 `_) + * add support for ``preinstallopts`` and install in subdirectory to ``Tarball`` generic easyblock (`#1989 `_, `#2049 `_) + * rewrite ``GROMACS`` easyblock to install all four variations (single/double precision, with/without MPI) in the same directory (`#1991 `_) + * add custom ``subdir_version`` easyconfig parameter for FLUENT (`#2021 `_) + * use updated ``config.guess`` in ``GCC`` easyblock (`#2033 `_, `#2059 `_) + * add extra question pattern to support installing CPLEX 12.10 (`#2038 `_) + * add support for building NWChem on top of external GlobalArrays + also define ``$LAPACK_LIB`` (required for NWChem 7.x) (`#2043 `_) + * execute minimal test in sanity check commands in ``impi`` easyblock (`#2045 `_) + * update for ``MotionCor2`` easyblock for v1.3.1 (`#2046 `_) + * fixes + enhancements for ``PETSc`` easyblock (`#2048 `_) + +* various bug fixes, including: + + * use correct version in ``ELPA`` preprocessor flag used for QuantumESPRESSO v6.x (`#2027 `_) + * generically find the arch folder and add top-level bin/lib symlinks in ``PDT`` & ``TAU`` easyblocks (`#2029 `_) + * fix typo in ``LAMMPS`` easyblock preventing disabling the ``USER-INTEL`` package via ``configopts`` (`#2031 `_) + * let ``CMakeMake`` remove ``easybuild_obj`` build directory if it already exists (`#2032 `_) + * include own lib dir in ``RPATH`` before system lib dirs in ``binutils`` easyblock (`#2044 `_) + * clean ``$CPATH`` before building ROOT to avoid clash between external LLVM loaded as a dependency and internal LLVM used by ROOT (`#2047 `_) + * don't let ``extract_file`` change directory in various easyblocks (`#2051 `_) + * make ``postinstallcmds`` available to Mathematica easyconfigs + add bin/Executables to ``$PATH`` (`#2052 `_) + * fix the extra dirs added to PATH in ``FreeSurfer`` easyblock (`#2053 `_) + * correct download url for test data in ``WPS`` easyblock (`#2055 `_) + * fix typo in warning in ``TensorFlow`` easyblock (`#2057 `_) + * fix failing sanity check under ``--module-only`` in ``GCC`` easyblock (`#2059 `_) + +* other changes: + + * add configure options for CubeLib/CubeWriter dependencies in ``Score-P`` easyblock (`#2030 `_) + * remove local ``find_glob_pattern`` in ``Blender`` & ``ROOT`` easyblocks, use function provided by ``filetools`` instead (`#2037 `_) + +**easyconfigs** + +* added easyconfigs for new common toolchains: foss/2020a (`#10483 `_, `#10492 `_), intel/2020a (`#10494 `_) + +* added example easyconfig files for 66 new software packages: + + * Alpha (`#9994 `_), antiSMASH (`#10589 `_), Arlequin (`#10620 `_), artic-ncov2019 (`#10459 `_), augur (`#10405 `_), AutoMap (`#10419 `_), + Bio-EUtilities (`#10037 `_), CaSpER (`#10593 `_), cdbfasta (`#10547 `_), cddlib (`#10429 `_), CoCoALib (`#10429 `_) + dftd3-lib (`#10351 `_), DoubletFinder (`#10603 `_), E-ANTIC (`#10429 `_), FastViromeExplorer (`#10571 `_), FIX (`#8870 `_), + FusionCatcher (`#10134 `_), geopandas (`#10322 `_), goalign (`#10469 `_), gotree (`#10459 `_), gretl (`#10413 `_), harmony (`#10604 `_), + HDF-EOS (`#10534 `_), HDF-EOS5 (`#10536 `_), HMMER2 (`#10588 `_), HyPo (`#10642 `_), king (`#10365 `_), libdeflate (`#10459 `_), + libfabric (`#10616 `_), libgit2 (`#10453 `_), libuv (`#10444 `_), mbuffer (`#10524 `_), MDAnalysis (`#10545 `_), MEM (`#10605 `_), + MESS (`#10597 `_), metaerg (`#10037 `_), MinCED (`#10037 `_), MitoZ (`#7735 `_), nauty (`#10429 `_), nifti2dicom (`#10598 `_), + NLMpy (`#10029 `_), ntCard (`#10502 `_), NTL (`#10431 `_), pIRS (`#10508 `_), popscle (`#10550 `_), ProtHint (`#10549 `_), + protozero (`#10495 `_), pysndfx (`#10452 `_), PyVCF (`#10564 `_), PyWavelets (`#10501 `_), rampart (`#10459 `_), rickflow (`#10641 `_), + RNA-Bloom (`#10502 `_), root_numpy (`#10424 `_), rstudio (`#10619 `_), ScaFaCoS (`#10537 `_), Scythe (`#10524 `_), SDSL (`#10642 `_), + SHAP (`#10379 `_), SNPomatic (`#10524 `_), SoX (`#10452 `_), swissknife (`#10037 `_),) Taiyaki (`#10573 `_), TCLAP (`#10598 `_), + torchaudio (`#10516 `_), wtdbg2 (`#10524 `_) + +* added additional easyconfigs for various supported software packages, including: + + * ADF 2019.303, BRAKER 2.1.5, Bazel 2.0.0, Bonito 0.1.4, Boost.Python 1.72.0, Bowtie2 2.4.1, CMake 3.16.4, + CPLEX 12.10, CVXOPT 1.2.4, Coreutils 8.32, cURL 7.69.1, DFTB+ 19.1, ecCodes 2.17.0, expat 2.2.9, FFmpeg 4.2.2, + FriBidi 1.0.9, GATK 4.1.5.0, GCC(core) 10.1.0, GDAL 3.0.4, GEOS 3.8.1, GLib 2.64.1, GMP 6.2.0, GROMACS 2020.1, + GTK+ 3.24.17, GenomeThreader 1.7.3, GffCompare 0.11.6, Ghostscript 9.52, GlimmerHMM 3.0.4c, GlobalArrays 5.7.2, + gmpy2 2.1.0b4, gmsh 4.5.6, gpustat 0.6.0, gradunwarp 1.2.0, HDF5 1.10.6, hwloc 2.2.0, hypothesis 5.6.0, ICU 66.1, + IPython 7.13.0, ImageMagick 7.0.10, Julia 1.4.1, KMC 3.1.2rc1, Kraken2 2.0.9, LMfit 1.0.0, Longshot 0.4.1, + libarchive 3.4.2, libffcall 2.2, libffi 3.3, libgd 2.3.0, libjpeg-turbo 2.0.4, librsvg 2.48.4, libsigsegv 2.12, + lrslib 7.0a, MEME 5.1.1, MPC 1.1.0, Mako 1.1.2, Mesa 20.0.2, Meson 0.53.2, MotionCor2 1.3.1, MultiQC 1.8, + matplotlib 3.2.1, NGS-Python-2.10.4, NGS 2.10.4, NSPR 4.25, NSS 3.51, NWChem 7.0.0, Nextflow 20.04.1, + Ninja 1.10.0, Normaliz 3.7.4, nanopolish 0.13.1, ncbi-vdb 2.10.4 netCDF 4.7.4, OpenBLAS 0.3.9, OpenEXR 2.4.1, + OpenMPI 4.0.3, OpenSSL 1.1.1e, openpyxl 3.0.3, PAPI 6.0.0, PCRE 8.44, PCRE2 10.34, PLUMED 2.6.0, PMIx 3.1.5, + PROJ 7.0.0, Perl 5.30.2, Pillow 7.0.0, PyYAML 5.3, Python 2.7.18 + 3.8.2, parallel 20200422, Qt5 5.14.1, + R-bundle-Bioconductor 3.11, R 3.6.3 + 4.0.0, RMBlast 2.9.0, Racon 1.4.13, Ray 0.8.4, Rust 1.42.0, re2c 1.3, + rioxarray 0.0.24, rootpy 1.0.1, rstudio 1.2.5042, SCons 3.1.2, SDL2 2.0.10, SIONlib 1.7.6, SQLite 3.31.1, + SRA-Toolkit 2.10.4, Salmon 1.2.0, ScaLAPACK 2.1.0, SciPy-bundle 2020.03, Stacks 2.53, StringTie 2.1.1, + SuiteSparse 5.7.1, snappy 1.1.8, spaln 2.4.03, sympy 1.5.1, Tcl 8.6.10, TensorFlow 2.2.0, Tk 8.6.10, Tkinter 3.8.2, + tbl2asn 20200302, torchvision 0.5.0, UCX 1.8.0, UMI-tools 1.0.1, utf8proc 2.5.0, util-linux 2.35, worker 1.6.12, + wxWidgets 3.1.3, X11 20200222, XZ 5.2.5, x264 20191217, x265 3.3, zsh 5.8, zstd 1.4.4 + +* minor enhancements, including: + + * add additional extensions for recent versions of R (`#10359 `_, `#10585 `_, `#10586 `_, `#10621 `_) and R-bundle-Bioconductor (`#10585 `_, `#10596 `_, `#10621 `_) + * add additional extensions for recent versions of Perl (`#10412 `_, `#10546 `_, `#10623 `_) + * include LLVM linker in Clang 7.0.1 on GCC 7.3.0-2.30(`#10458 `_) + * include static lib and header in nimimap2 easyconfigs for foss-2018b and GCC-8.2.0* (`#10464 `_) + * add alternate checksum for EMBOSS (`#10607 `_) + +* various bug fixes, including: + + * fix incorrect checksums for Amber patches (`#8870 `_) + * add patches to fix installation of R 3.6.2 on POWER (`#9830 `_) + * add missing build dep. pkg-config in GObject-Introspection 1.63.1 w/ Python 3.7.4 easyconfig (`#10380 `_) + * add Perl as a build dependency for recent Autoconf/Automake easyconfigs (`#10408 `_, `#10426 `_) + * fix source_urls in ICU easyconfigs (`#10417 `_) + * disable ``USER-INTEL`` package in LAMMPS easyconfigs using intel/2019b, since it results in an installation that produces incorrect results (`#10418 `_) + * fix undefined reference to ``qfloat16::mantissatable`` in Qt5-5.13.1-GCCcore-8.3.0 (`#10425 `_) + * get rid of double '-' in versionsuffix of torchtext easyconfig (`#10472 `_) + * fix broken Mako easyconfigs (`#10480 `_, `#10627 `_) + * move builddependencies to dependencies in OTF2 and Score-P easyconfigs (`#10496 `_) + * add missing cURL dep for LAMMPS (`#10527 `_) + * add Python 2 build dependency for OpenPGM (`#10539 `_) + * use ``OS_PKG_IBVERBS_DEV`` constant for OS dependency in PyTorch 1.4.0 easyconfigs (`#10540 `_) + * add missing Bison build dep in Graphviz easyconfigs (`#10541 `_) + * use https in homepage for Mathematica 12.0.0 + clean up sanity check commands (now done by easyblock) (`#10559 `_) + * add missing PyVCF dependency for BAMSurgeon (`#10564 `_) + * remove FFTW dependencies from LAMMPS easyconfigs, no longer needed (MKL can be used too now) (`#10565 `_) + * fix ITK v5.0.1 easyconfig w.r.t. locale and location of libjpeg-turbo library (`#10592 `_) + * add patch to fix missing ``const`` qualifiers for ncurses (`#10606 `_) + * fix OS dependency for rstudio for Debian-based systems (`#10608 `_) + * fix Rmath paths in easyconfig for FastQTL v2.184 (`#10612 `_) + * add symlink for Arlequin commands + fix sanity check commands (`#10620 `_) + * fix recent binutils easyconfigs using system toolchain for Fedora 32 / GCC 10 (`#10633 `_) + * replace '/path/to' with actual installation prefix in FuSeq scripts (`#10640 `_) + +* other changes: + + * check sdist with different Python versions in CI (`#10388 `_) + * use Bison 3.3.2 as build dep for flex 2.6.4 (`#10403 `_) + * mention ``http://`` Pfam website rather than ``ftp://`` in load message of BiG-SCAPE easyconfig (`#10439 `_) + * archive old Singularity configs (`#10591 `_) + * Singularity is not well suited to install via EasyBuild because it requires admin privileges to enable setuid + * stop using old hpcugent URL for cloning framework/easyblocks repos in CI (`#10635 `_) + * use ``SYSTEM`` constant for toolchain in easyconfigs already use ``system`` toolchain (`#10638 `_) + + .. _release_notes_eb420: EasyBuild v4.2.0 (April 14th 2020) diff --git a/docs/conf.py b/docs/conf.py index b2f8f013..6de1da7d 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.2.0' # this is meant to reference the version of EasyBuild +version = '4.2.1' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20200414.0' # this is meant to reference the version of the documentation itself +release = '20200520.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From b2776fe2ad264fc9170b30519813e0635d18abc9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2020 12:00:48 +0200 Subject: [PATCH 054/286] auto-update docs for EasyBuild v4.2.1 --- docs/version-specific/Supported_software.rst | 2971 ++++++++++++----- docs/version-specific/easyblocks.rst | 1 + .../version-specific/easyconfig_constants.rst | 27 +- .../easyconfig_parameters.rst | 24 +- docs/version-specific/generic_easyblocks.rst | 47 +- docs/version-specific/help.rst | 146 +- 6 files changed, 2264 insertions(+), 952 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 0e08fd78..46a21ceb 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 1912 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 1978 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -52,11 +52,11 @@ A software package for algebraic, geometric and combinatorial problems on linear *homepage*: https://4ti2.github.io/ -========= =============== -version toolchain -========= =============== -``1.6.9`` ``intel/2018b`` -========= =============== +========= ===================================== +version toolchain +========= ===================================== +``1.6.9`` ``GCC/8.2.0-2.31.1``, ``intel/2018b`` +========= ===================================== .. _list_software_letter_a: @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_ALPS_304` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_ART_231` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -273,16 +273,17 @@ version toolchain ADF is an accurate, parallelized, powerful computational chemistry program to understand and predict chemical structure and reactivity with density functional theory (DFT). -*homepage*: http://www.scm.com/ADF/ +*homepage*: https://www.scm.com/ADF/ -================================ =============== -version toolchain -================================ =============== -``2009.01a.pc64_linux.intelmpi`` ``system`` -``2014.02`` ``system`` -``2014.11.r48287`` ``intel/2016a`` -``2016.101`` ``system`` -================================ =============== +================================ ============= =============== +version versionsuffix toolchain +================================ ============= =============== +``2009.01a.pc64_linux.intelmpi`` ``system`` +``2014.02`` ``system`` +``2014.11.r48287`` ``intel/2016a`` +``2016.101`` ``system`` +``2019.303`` ``-intelmpi`` ``system`` +================================ ============= =============== .. _list_software_ADIOS_368: @@ -520,6 +521,22 @@ version toolchain ========= ============== +.. _list_software_Alpha_486: + +*Alpha* ++++++++ + +Alpha is a tool designed for detailed comparative study of bacteriophage genomes. + +*homepage*: https://www.lirmm.fr/~swenson/alpha/alpha.htm + +============ ================== ============== +version versionsuffix toolchain +============ ================== ============== +``20200430`` ``-Python-2.7.16`` ``foss/2019b`` +============ ================== ============== + + .. _list_software_ALPS_304: *ALPS* @@ -753,6 +770,7 @@ version toolchain ``2019.03`` ``system`` ``2019.07`` ``system`` ``2019.10`` ``system`` +``2020.02`` ``system`` =========== ========== @@ -781,13 +799,14 @@ Program for analysing NGS data. *homepage*: http://www.popgen.dk/angsd -========= ============== -version toolchain -========= ============== -``0.910`` ``foss/2016a`` -``0.921`` ``foss/2018a`` -``0.925`` ``foss/2018b`` -========= ============== +========= ====================================== +version toolchain +========= ====================================== +``0.910`` ``foss/2016a`` +``0.921`` ``foss/2018a`` +``0.925`` ``foss/2018b`` +``0.933`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +========= ====================================== .. _list_software_Annif_492: @@ -892,6 +911,22 @@ version versionsuffix toolchain ========== =================== ========== +.. _list_software_antiSMASH_808: + +*antiSMASH* ++++++++++++ + +antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. + +*homepage*: https://github.com/antismash/antismash + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``5.1.2`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_ANTLR_385: *ANTLR* @@ -1038,11 +1073,11 @@ a program to detect tRNA genes and tmRNA genes in nucleotide sequences *homepage*: http://mbio-serv2.mbioekol.lu.se/ARAGORN/ -========== ============== -version toolchain -========== ============== -``1.2.38`` ``foss/2016b`` -========== ============== +========== ======================================= +version toolchain +========== ======================================= +``1.2.38`` ``foss/2016b``, ``iccifort/2019.5.281`` +========== ======================================= .. _list_software_Arb_277: @@ -1054,11 +1089,11 @@ Arb is a C library for arbitrary-precision interval arithmetic. It has full sup *homepage*: http://arblib.org -========== ========================================================== -version toolchain -========== ========================================================== -``2.16.0`` ``GCC/7.3.0-2.30``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` -========== ========================================================== +========== ================================================================================ +version toolchain +========== ================================================================================ +``2.16.0`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` +========== ================================================================================ .. _list_software_ARCH_286: @@ -1090,6 +1125,7 @@ A library for detecting, labeling, and reasoning about microarchitectures version versionsuffix toolchain ========= ================= ================= ``0.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.1.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ================= ================= @@ -1125,6 +1161,22 @@ version toolchain ======== ====================================================================================================== +.. _list_software_Arlequin_833: + +*Arlequin* +++++++++++ + +Arlequin: An Integrated Software for Population Genetics Data Analysis + +*homepage*: http://cmpg.unibe.ch/software/arlequin35/Arlequin35.html + +=========== ============== +version toolchain +=========== ============== +``3.5.2.2`` ``foss/2019b`` +=========== ============== + + .. _list_software_Armadillo_917: *Armadillo* @@ -1250,6 +1302,22 @@ version toolchain ============== ================================== +.. _list_software_artic-ncov2019_1218: + +*artic-ncov2019* +++++++++++++++++ + +Initial implementation of an ARTIC bioinformatics platform for nanopore sequencing of nCoV2019 novel coronavirus. + +*homepage*: https://github.com/artic-network/artic-ncov2019 + +============== ================= ============== +version versionsuffix toolchain +============== ================= ============== +``2020.04.13`` ``-Python-3.6.6`` ``foss/2018b`` +============== ================= ============== + + .. _list_software_ArviZ_492: *ArviZ* @@ -1259,11 +1327,11 @@ Exploratory analysis of Bayesian models with Python *homepage*: https://github.com/arviz-devs/arviz -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``0.7.0`` ``-Python-3.7.4`` ``intel/2019b`` -========= ================= =============== +========= ================= =============================== +version versionsuffix toolchain +========= ================= =============================== +``0.7.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +========= ================= =============================== .. _list_software_ARWEN_381: @@ -1441,7 +1509,7 @@ version versionsuffix toolchain *at-spi2-atk* +++++++++++++ -AT-SPI 2 toolkit bridge +AT-SPI 2 toolkit bridge *homepage*: https://wiki.gnome.org/Accessibility @@ -1451,6 +1519,7 @@ version toolchain ``2.26.3`` ``fosscuda/2018b`` ``2.32.0`` ``GCCcore/8.2.0`` ``2.34.1`` ``GCCcore/8.3.0`` +``2.34.2`` ``GCCcore/9.3.0`` ========== ================== @@ -1469,6 +1538,7 @@ version toolchain ``2.26.3`` ``fosscuda/2018b`` ``2.32.0`` ``GCCcore/8.2.0`` ``2.34.0`` ``GCCcore/8.3.0`` +``2.36.0`` ``GCCcore/9.3.0`` ========== ================== @@ -1493,6 +1563,7 @@ version toolchain ``2.28.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a`` ``2.32.0`` ``GCCcore/8.2.0`` ``2.34.1`` ``GCCcore/8.3.0`` +``2.36.0`` ``GCCcore/9.3.0`` ========== =================================================================== @@ -1593,9 +1664,26 @@ Commands for Manipulating Filesystem Extended Attributes version toolchain ========== ================= ``2.4.47`` ``GCCcore/8.2.0`` +``2.4.48`` ``GCCcore/9.3.0`` ========== ================= +.. _list_software_augur_548: + +*augur* ++++++++ + +Pipeline components for real-time phylodynamic analysis + +*homepage*: https://github.com/nextstrain/augur + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``7.0.2`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + .. _list_software_AUGUSTUS_641: *AUGUSTUS* @@ -1614,7 +1702,7 @@ version versionsuffix toolchain ``3.3.2`` ``-Python-2.7.13`` ``intel/2017a`` ``3.3.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``3.3.2`` ``-Python-2.7.15`` ``intel/2018b`` -``3.3.3`` ``foss/2019b`` +``3.3.3`` ``foss/2019b``, ``intel/2019b`` ========= ================== =============================== @@ -1627,12 +1715,12 @@ Autoconf is an extensible package of M4 macros that produce shell scripts to au *homepage*: http://www.gnu.org/software/autoconf/ -======== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain -======== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``2.68`` ``foss/2016b`` -``2.69`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -======== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +======== ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +version toolchain +======== ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +``2.68`` ``foss/2016b`` +``2.69`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +======== ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= .. _list_software_Autoconf-archive_1614: @@ -1716,10 +1804,26 @@ version toolchain ``1.14.1`` ``GCC/4.8.2`` ``1.15`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.15.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` -``1.16.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` +``1.16.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +.. _list_software_AutoMap_695: + +*AutoMap* ++++++++++ + +Tool to find regions of homozygosity (ROHs) from sequencing data. + +*homepage*: https://github.com/mquinodo/AutoMap + +======= ============= ============== +version versionsuffix toolchain +======= ============= ============== +``1.0`` ``-20200324`` ``foss/2019b`` +======= ============= ============== + + .. _list_software_autopep8_822: *autopep8* @@ -1743,7 +1847,7 @@ version versionsuffix toolchain This bundle collect the standard GNU build tools: Autoconf, Automake and libtool -*homepage*: http://autotools.io +*homepage*: https://autotools.io ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain @@ -1751,7 +1855,7 @@ version toolchain ``20150119`` ``GCC/4.9.2`` ``20150215`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``20170619`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` -``20180311`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` +``20180311`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -1780,7 +1884,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_Biopython_956` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` +:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_Biopython_956` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` .. _list_software_Bader_478: @@ -2107,6 +2211,7 @@ version toolchain ``0.26.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``0.29.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``1.1.0`` ``GCCcore/8.3.0`` +``2.0.0`` ``GCCcore/8.3.0`` ========== ==================================== @@ -2159,6 +2264,7 @@ version versionsuffix toolchain ``38.26`` ``foss/2018b`` ``38.50b`` ``GCC/8.2.0-2.31.1`` ``38.76`` ``GCC/8.2.0-2.31.1`` +``38.79`` ``GCC/8.3.0`` ========== =================== =============================== @@ -2225,7 +2331,7 @@ version toolchain ``1.3`` ``foss/2016a``, ``intel/2016a`` ``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` ``1.9`` ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``1.10.2`` ``GCC/8.3.0`` +``1.10.2`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ========== ========================================================================================= @@ -2254,14 +2360,14 @@ bcl2fastq Conversion Software both demultiplexes data and converts BCL files gen *homepage*: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html -========== ================== =============================== -version versionsuffix toolchain -========== ================== =============================== -``2.19.1`` ``-Python-2.7.12`` ``foss/2016b`` -``2.20.0`` ``foss/2018b``, ``intel/2019a`` -``2.20.0`` ``-Python-2.7.12`` ``foss/2016b`` -``2.20.0`` ``-Python-2.7.14`` ``intel/2017b`` -========== ================== =============================== +========== ================== ============================================== +version versionsuffix toolchain +========== ================== ============================================== +``2.19.1`` ``-Python-2.7.12`` ``foss/2016b`` +``2.20.0`` ``GCC/8.3.0``, ``foss/2018b``, ``intel/2019a`` +``2.20.0`` ``-Python-2.7.12`` ``foss/2016b`` +``2.20.0`` ``-Python-2.7.14`` ``intel/2017b`` +========== ================== ============================================== .. _list_software_bcolz_538: @@ -2538,7 +2644,7 @@ version toolchain ``2.30`` ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``system`` ``2.31.1`` ``GCCcore/7.4.0``, ``GCCcore/8.2.0``, ``system`` ``2.32`` ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` -``2.34`` ``GCCcore/9.3.0``, ``system`` +``2.34`` ``GCCcore/10.1.0``, ``GCCcore/9.3.0``, ``system`` ========== ======================================================================================================================================================================================== @@ -2561,6 +2667,22 @@ version versionsuffix toolchain ======== ================ =============================== +.. _list_software_Bio-EUtilities_1352: + +*Bio-EUtilities* +++++++++++++++++ + +BioPerl low-level API for retrieving and storing data from NCBI eUtils + +*homepage*: https://github.com/bioperl/bio-eutilities + +======== ================= +version toolchain +======== ================= +``1.76`` ``GCCcore/8.3.0`` +======== ================= + + .. _list_software_Bio-SamTools_1145: *Bio-SamTools* @@ -2677,7 +2799,7 @@ version versionsuffix toolchain ``1.73`` ``-Python-3.6.6`` ``foss/2018b`` ``1.74`` ``foss/2019a`` ``1.75`` ``-Python-2.7.16`` ``foss/2019b`` -``1.75`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.75`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ======== ================== =================================================== @@ -2719,7 +2841,7 @@ version toolchain *Bison* +++++++ -Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. +Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. *homepage*: https://www.gnu.org/software/bison @@ -2735,6 +2857,7 @@ version toolchain ``3.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` ``3.5.2`` ``system`` ``3.5.3`` ``GCCcore/9.3.0``, ``system`` +``3.6.1`` ``GCCcore/10.1.0`` ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -2950,7 +3073,7 @@ version toolchain ``1.14.2`` ``GCCcore/6.4.0``, ``foss/2016a`` ``1.14.4`` ``GCCcore/7.3.0`` ``1.17.0`` ``GCCcore/8.2.0`` -``1.17.1`` ``GCCcore/8.3.0`` +``1.17.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ================================================================== @@ -3052,6 +3175,7 @@ Convolution Basecaller for Oxford Nanopore Reads version versionsuffix toolchain ========= ================= ================================== ``0.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``0.1.4`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ================= ================================== @@ -3139,6 +3263,7 @@ version versionsuffix toolchain ``1.69.0`` ``intel/2019.01`` ``1.70.0`` ``gompi/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` ``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b`` +``1.72.0`` ``gompi/2020a``, ``iimpi/2020a`` ========== ================== ==================================================================== @@ -3162,6 +3287,7 @@ version versionsuffix toolchain ``1.67.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.70.0`` ``gompi/2019a``, ``iimpi/2019a`` ``1.71.0`` ``gompi/2019b`` +``1.72.0`` ``gompi/2020a``, ``iimpi/2020a`` ========== ================== =================================================== @@ -3190,14 +3316,14 @@ Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DN *homepage*: http://bowtie-bio.sourceforge.net/index.shtml -=========== ====================================================================================================================== -version toolchain -=========== ====================================================================================================================== -``1.1.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a`` -``1.2.1.1`` ``foss/2016b``, ``intel/2017b`` -``1.2.2`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` -``1.2.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` -=========== ====================================================================================================================== +=========== ===================================================================================================================================== +version toolchain +=========== ===================================================================================================================================== +``1.1.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a`` +``1.2.1.1`` ``foss/2016b``, ``intel/2017b`` +``1.2.2`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` +``1.2.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` +=========== ===================================================================================================================================== .. _list_software_Bowtie2_668: @@ -3221,6 +3347,7 @@ version toolchain ``2.3.4.2`` ``foss/2018b``, ``intel/2018b`` ``2.3.4.3`` ``foss/2017b`` ``2.3.5.1`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` +``2.4.1`` ``GCC/9.3.0`` =========== ====================================================================================================== @@ -3297,11 +3424,12 @@ BRAKER is a pipeline for fully automated prediction of protein coding genes with *homepage*: https://github.com/Gaius-Augustus/BRAKER -========= =============== -version toolchain -========= =============== -``2.1.2`` ``intel/2019a`` -========= =============== +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``2.1.2`` ``intel/2019a`` +``2.1.5`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== .. _list_software_BreakDancer_1074: @@ -3461,15 +3589,15 @@ Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively sh *homepage*: http://bio-bwa.sourceforge.net/ -=========== ========================================================================================================================================================================================================= -version toolchain -=========== ========================================================================================================================================================================================================= -``0.7.12`` ``foss/2016b`` -``0.7.13`` ``foss/2016a``, ``intel/2016a`` -``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``0.7.16a`` ``foss/2016b``, ``intel/2017a`` -``0.7.17`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -=========== ========================================================================================================================================================================================================= +=========== ======================================================================================================================================================================================================================== +version toolchain +=========== ======================================================================================================================================================================================================================== +``0.7.12`` ``foss/2016b`` +``0.7.13`` ``foss/2016a``, ``intel/2016a`` +``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``0.7.16a`` ``foss/2016b``, ``intel/2017a`` +``0.7.17`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +=========== ======================================================================================================================================================================================================================== .. _list_software_bwa-meth_789: @@ -3604,7 +3732,7 @@ bzip2 is a freely available, patent free, high-quality data compressor. It typi version toolchain ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.0.6`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.0.8`` ``GCCcore/8.3.0`` +``1.0.8`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -3614,7 +3742,7 @@ version toolchain --- -:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_charmm_632` - :ref:`list_software_CHARMM_440` - :ref:`list_software_CHASE_356` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_charmm_632` - :ref:`list_software_CHARMM_440` - :ref:`list_software_CHASE_356` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_C3D_186: @@ -3685,7 +3813,7 @@ version versionsuffix toolchain ``1.14.8`` ``intel/2017a`` ``1.14.10`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017b`` ``1.14.12`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.16.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.16.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` =========== ================ ================================================================ @@ -3831,6 +3959,22 @@ version toolchain ========== ============== +.. _list_software_CaSpER_510: + +*CaSpER* +++++++++ + +CaSpER is a signal processing approach for identification, visualization, and integrative analysis of focal and large-scale CNV events in multiscale resolution using either bulk or single-cell RNA sequencing data. + +*homepage*: https://github.com/akdess/CaSpER + +======= ============== +version toolchain +======= ============== +``2.0`` ``foss/2019b`` +======= ============== + + .. _list_software_CastXML_636: *CastXML* @@ -4015,6 +4159,38 @@ version versionsuffix toolchain ========= ============== ================================================ +.. _list_software_cdbfasta_824: + +*cdbfasta* +++++++++++ + +Fasta file indexing and retrival tool + +*homepage*: https://sourceforge.net/projects/cdbfasta + +======== ================================================================================ +version toolchain +======== ================================================================================ +``0.99`` ``GCC/8.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` +======== ================================================================================ + + +.. _list_software_cddlib_610: + +*cddlib* +++++++++ + +An efficient implementation of the Double Description Method + +*homepage*: https://github.com/cddlib/cddlib + +========= ================= +version toolchain +========= ================= +``0.94i`` ``GCCcore/8.2.0`` +========= ================= + + .. _list_software_cDNA_Cupcake_1105: *cDNA_Cupcake* @@ -4536,6 +4712,7 @@ A python package that allows to count antibody TAGS from a CITE-seq and/or cell version versionsuffix toolchain ========= ================= ============== ``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` +``1.4.3`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -4635,13 +4812,13 @@ version toolchain Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language. -*homepage*: http://www.clisp.org/ +*homepage*: https://clisp.sourceforge.io/ -======== ================= -version toolchain -======== ================= -``2.49`` ``GCCcore/6.4.0`` -======== ================= +======== ==================================== +version toolchain +======== ==================================== +``2.49`` ``GCCcore/6.4.0``, ``GCCcore/9.3.0`` +======== ==================================== .. _list_software_ClonalFrameML_1245: @@ -4801,6 +4978,7 @@ version toolchain ``3.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``system`` ``3.13.3`` ``GCCcore/8.2.0`` ``3.15.3`` ``GCCcore/8.3.0`` +``3.16.4`` ``GCCcore/9.3.0`` ========== ================================================================================================================================================= @@ -4853,6 +5031,22 @@ version toolchain ========= ============== +.. _list_software_CoCoALib_700: + +*CoCoALib* +++++++++++ + +CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebra. + +*homepage*: http://cocoa.dima.unige.it/cocoalib + +=========== ==================== +version toolchain +=========== ==================== +``0.99601`` ``GCC/8.2.0-2.31.1`` +=========== ==================== + + .. _list_software_CODEX2_421: *CODEX2* @@ -5060,7 +5254,7 @@ version toolchain The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system. -*homepage*: http://www.gnu.org/software/coreutils/ +*homepage*: https://www.gnu.org/software/coreutils/ ======== ================= version toolchain @@ -5068,6 +5262,7 @@ version toolchain ``8.23`` ``GCC/4.9.2`` ``8.27`` ``GCCcore/5.4.0`` ``8.29`` ``GCCcore/6.4.0`` +``8.32`` ``GCCcore/8.3.0`` ======== ================= @@ -5166,11 +5361,12 @@ IBM ILOG CPLEX Optimizer's mathematical programming technology enables analytic *homepage*: https://www.ibm.com/analytics/cplex-optimizer -======== ================= -version toolchain -======== ================= -``12.9`` ``GCCcore/8.2.0`` -======== ================= +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``12.9`` ``GCCcore/8.2.0`` +``12.10`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= .. _list_software_CppUnit_707: @@ -5425,11 +5621,12 @@ csvkit is a suite of command-line tools for converting to and working with CSV, *homepage*: https://github.com/wireservice/csvkit -========= ================= -version toolchain -========= ================= -``1.0.4`` ``GCCcore/8.2.0`` -========= ================= +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``1.0.4`` ``GCCcore/8.2.0`` +``1.0.5`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= .. _list_software_ctags_530: @@ -5457,11 +5654,11 @@ Program for finding CTFs of electron micrographs. *homepage*: https://grigoriefflab.umassmed.edu/ctffind4 -========== ================================== -version toolchain -========== ================================== -``4.1.13`` ``foss/2019a``, ``fosscuda/2019a`` -========== ================================== +========== ====================================================== +version toolchain +========== ====================================================== +``4.1.13`` ``foss/2019a``, ``fosscuda/2019a``, ``fosscuda/2019b`` +========== ====================================================== .. _list_software_Cube_383: @@ -5505,11 +5702,11 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is *homepage*: https://www.scalasca.org/software/cube-4.x/download.html -========= ================= -version toolchain -========= ================= -``4.4.4`` ``GCCcore/8.2.0`` -========= ================= +========= ==================================== +version toolchain +========= ==================================== +``4.4.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ==================================== .. _list_software_CubeWriter_1020: @@ -5521,11 +5718,11 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is *homepage*: https://www.scalasca.org/software/cube-4.x/download.html -========= ================= -version toolchain -========= ================= -``4.4.3`` ``GCCcore/8.2.0`` -========= ================= +========= ==================================== +version toolchain +========= ==================================== +``4.4.3`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ==================================== .. _list_software_CUDA_285: @@ -5651,6 +5848,7 @@ version toolchain ``7.60.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``7.63.0`` ``GCCcore/8.2.0`` ``7.66.0`` ``GCCcore/8.3.0`` +``7.69.1`` ``GCCcore/9.3.0`` ========== =================================================================================== @@ -5721,7 +5919,7 @@ version toolchain CVXOPT is a free software package for convex optimization based on the Python programming language. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Python's extensive standard library and on the strengths of Python as a high-level programming language. -*homepage*: http://cvxopt.org +*homepage*: https://cvxopt.org ========= ================== =============== version versionsuffix toolchain @@ -5729,6 +5927,7 @@ version versionsuffix toolchain ``1.1.9`` ``-Python-2.7.13`` ``intel/2017a`` ``1.2.1`` ``-Python-3.6.4`` ``intel/2018a`` ``1.2.3`` ``foss/2019a`` +``1.2.4`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================== =============== @@ -5843,7 +6042,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` .. _list_software_dadi_402: @@ -6016,15 +6215,15 @@ Berkeley DB enables the development of custom data management solutions, withou *homepage*: http://www.oracle.com/technetwork/products/berkeleydb -=========== ==================================== -version toolchain -=========== ==================================== -``4.8.30`` ``intel/2016a`` -``6.2.23`` ``foss/2016a`` -``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` -``18.1.25`` ``GCCcore/7.3.0`` -``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -=========== ==================================== +=========== ======================================================= +version toolchain +=========== ======================================================= +``4.8.30`` ``intel/2016a`` +``6.2.23`` ``foss/2016a`` +``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` +``18.1.25`` ``GCCcore/7.3.0`` +``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +=========== ======================================================= .. _list_software_DB_File_613: @@ -6102,7 +6301,7 @@ version toolchain ``1.13.0`` ``intel/2017b`` ``1.13.6`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.13.8`` ``GCCcore/8.2.0`` -``1.13.12`` ``GCCcore/8.3.0`` +``1.13.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` =========== ==================================== @@ -6150,12 +6349,12 @@ DCMTK is a collection of libraries and applications implementing large parts the *homepage*: https://dicom.offis.de/dcmtk -========= ================= -version toolchain -========= ================= -``3.6.3`` ``GCCcore/7.3.0`` -``3.6.5`` ``GCCcore/8.2.0`` -========= ================= +========= ==================================== +version toolchain +========= ==================================== +``3.6.3`` ``GCCcore/7.3.0`` +``3.6.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ==================================== .. _list_software_deal.II_598: @@ -6376,16 +6575,34 @@ version toolchain *DFTB+* +++++++ -DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed. +DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed. *homepage*: https://www.dftb-plus.info -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``1.3.1`` ``intel/2017a`` -``17.1`` ``-Python-2.7.14`` ``intel/2017b`` -========= ================== =============== +========= ====================== =============== +version versionsuffix toolchain +========= ====================== =============== +``1.3.1`` ``intel/2017a`` +``17.1`` ``-Python-2.7.14`` ``intel/2017b`` +``19.1`` ``-Python-2.7.16`` ``foss/2019b`` +``19.1`` ``-Python-2.7.16-mpi`` ``foss/2019b`` +========= ====================== =============== + + +.. _list_software_dftd3-lib_825: + +*dftd3-lib* ++++++++++++ + +This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules. + +*homepage*: https://github.com/dftbplus/dftd3-lib + +======= ============= +version toolchain +======= ============= +``0.9`` ``GCC/8.3.0`` +======= ============= .. _list_software_DIAL_282: @@ -6589,9 +6806,26 @@ version toolchain ========= ==================================== ``3.0.3`` ``foss/2018a`` ``3.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.1.5`` ``GCCcore/9.3.0`` ========= ==================================== +.. _list_software_DoubletFinder_1319: + +*DoubletFinder* ++++++++++++++++ + +R package for detecting doublets in single-cell RNA sequencing data + +*homepage*: https://github.com/chris-mcginnis-ucsf/DoubletFinder + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``2.0.3`` ``-R-4.0.0`` ``foss/2020a`` +========= ============= ============== + + .. _list_software_Doxygen_734: *Doxygen* @@ -6611,6 +6845,7 @@ version toolchain ``1.8.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``1.8.15`` ``GCCcore/8.2.0`` ``1.8.16`` ``GCCcore/8.3.0`` +``1.8.17`` ``GCCcore/9.3.0`` =========== ======================================================================================================================================================= @@ -6749,7 +6984,23 @@ version versionsuffix toolchain --- -:ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` + + +.. _list_software_E-ANTIC_481: + +*E-ANTIC* ++++++++++ + +E-ANTIC is a C/C++ library to deal with real embedded number fields built on top of ANTIC (https://github.com/wbhart/antic). Its aim is to have as fast as possible exact arithmetic operations and comparisons. + +*homepage*: https://github.com/videlec/e-antic + +========= ==================== +version toolchain +========= ==================== +``0.1.2`` ``GCC/8.2.0-2.31.1`` +========= ==================== .. _list_software_ea-utils_804: @@ -6869,6 +7120,7 @@ version toolchain ``4.1.0`` ``system`` ``4.1.1`` ``system`` ``4.1.2`` ``system`` +``4.2.0`` ``system`` ========== ========== @@ -6897,15 +7149,17 @@ ecCodes is a package developed by ECMWF which provides an application programmin *homepage*: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home -========== ================================ -version toolchain -========== ================================ -``2.7.3`` ``intel/2018a`` -``2.8.2`` ``intel/2018a`` -``2.9.2`` ``intel/2018b``, ``iomkl/2018b`` -``2.12.5`` ``gompi/2019a`` -``2.15.0`` ``iimpi/2019b`` -========== ================================ +========== ================= ================================ +version versionsuffix toolchain +========== ================= ================================ +``2.7.3`` ``intel/2018a`` +``2.8.2`` ``intel/2018a`` +``2.9.2`` ``intel/2018b``, ``iomkl/2018b`` +``2.12.5`` ``gompi/2019a`` +``2.15.0`` ``iimpi/2019b`` +``2.17.0`` ``-Python-3.6.6`` ``foss/2018b`` +``2.17.0`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ================================ .. _list_software_ED2_187: @@ -6980,7 +7234,7 @@ version toolchain ``3.3.3`` ``GCCcore/6.3.0``, ``intel/2016b`` ``3.3.4`` ``system`` ``3.3.5`` ``system`` -``3.3.7`` ``system`` +``3.3.7`` ``GCCcore/9.3.0``, ``system`` ========== =========================================== @@ -7331,6 +7585,7 @@ A Python framework for the analysis and visualization of trees version versionsuffix toolchain ============ ================== =============== ``3.0.0b36`` ``-Python-2.7.12`` ``intel/2016b`` +``3.1.1`` ``-Python-3.6.6`` ``foss/2018b`` ============ ================== =============== @@ -7425,11 +7680,11 @@ Exonerate is a generic tool for pairwise sequence comparison. It allows you to *homepage*: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate -========= ==================================================================================================================================================================== -version toolchain -========= ==================================================================================================================================================================== -``2.4.0`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a`` -========= ==================================================================================================================================================================== +========= ============================================================================================================================================================================================= +version toolchain +========= ============================================================================================================================================================================================= +``2.4.0`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a`` +========= ============================================================================================================================================================================================= .. _list_software_expat_546: @@ -7451,6 +7706,7 @@ version toolchain ``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.2.6`` ``GCCcore/8.2.0`` ``2.2.7`` ``GCCcore/8.3.0`` +``2.2.9`` ``GCCcore/9.3.0`` ========= ========================================================================================================================= @@ -7509,7 +7765,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FIAT_292` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FIAT_292` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -7871,6 +8127,22 @@ version toolchain ========== ================================================================= +.. _list_software_FastViromeExplorer_1873: + +*FastViromeExplorer* +++++++++++++++++++++ + +Identify the viruses/phages and their abundance in the viral metagenomics data. + +*homepage*: https://code.vt.edu/saima5/FastViromeExplorer + +============ ============== +version toolchain +============ ============== +``20180422`` ``foss/2019b`` +============ ============== + + .. _list_software_FASTX-Toolkit_1177: *FASTX-Toolkit* @@ -8084,6 +8356,7 @@ version toolchain ``4.1`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``4.1.3`` ``GCCcore/8.2.0`` ``4.2.1`` ``GCCcore/8.3.0`` +``4.2.2`` ``GCCcore/9.3.0`` =========== =================================================== @@ -8112,17 +8385,17 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: http://www.fftw.org -========= ============= ============================================================================================================================================================================================== -version versionsuffix toolchain -========= ============= ============================================================================================================================================================================================== -``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` -``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` -``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` -``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` -``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` -``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` -``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``iomkl/2018b`` -========= ============= ============================================================================================================================================================================================== +========= ============= ================================================================================================================================================================================================================================ +version versionsuffix toolchain +========= ============= ================================================================================================================================================================================================================================ +``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` +``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` +``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` +``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` +``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` +``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` +``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``iomkl/2018b`` +========= ============= ================================================================================================================================================================================================================================ .. _list_software_FGSL_300: @@ -8198,7 +8471,7 @@ version toolchain The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains. -*homepage*: http://www.darwinsys.com/file/ +*homepage*: https://www.darwinsys.com/file/ ======== ================= version toolchain @@ -8209,6 +8482,7 @@ version toolchain ``5.30`` ``intel/2017a`` ``5.33`` ``GCCcore/6.4.0`` ``5.35`` ``GCCcore/7.3.0`` +``5.38`` ``GCCcore/8.3.0`` ======== ================= @@ -8356,6 +8630,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_FIX_231: + +*FIX* ++++++ + +FIX attempts to auto-classify ICA components into "good" vs "bad" components, so that the bad components can be removed from the 4D FMRI data. + +*homepage*: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX + +=========== ======================== ============== +version versionsuffix toolchain +=========== ======================== ============== +``1.06.12`` ``-Octave-Python-3.7.2`` ``foss/2019a`` +=========== ======================== ============== + + .. _list_software_fixesproto_1107: *fixesproto* @@ -8398,12 +8688,12 @@ FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate softwa *homepage*: https://ccb.jhu.edu/software/FLASH/ -========== ============================================== -version toolchain -========== ============================================== -``1.2.11`` ``foss/2016a``, ``foss/2018a``, ``foss/2018b`` -``2.2.00`` ``foss/2018b`` -========== ============================================== +========== ============================================================= +version toolchain +========== ============================================================= +``1.2.11`` ``GCC/8.3.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b`` +``2.2.00`` ``foss/2018b`` +========== ============================================================= .. _list_software_Flask_497: @@ -8456,7 +8746,7 @@ version toolchain ``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``2.6.2`` ``intel/2016b`` ``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` -``2.6.4`` ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` +``2.6.4`` ``GCCcore/10.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` ========== ==================================================================================================================================================================================================================================================================================================================================================================== @@ -8485,11 +8775,11 @@ FLINT (Fast Library for Number Theory) is a C library in support of computations *homepage*: http://www.flintlib.org -========= ========================================================== -version toolchain -========= ========================================================== -``2.5.2`` ``GCC/7.3.0-2.30``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` -========= ========================================================== +========= ================================================================================ +version toolchain +========= ================================================================================ +``2.5.2`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` +========= ================================================================================ .. _list_software_FLTK_305: @@ -8638,6 +8928,7 @@ version versionsuffix toolchain ``2.12.6`` ``GCCcore/6.4.0`` ``2.13.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.13.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.13.92`` ``GCCcore/9.3.0`` =========== ================== ====================================================================================== @@ -8682,6 +8973,7 @@ version toolchain ``2018b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` +``2020a`` ``system`` =========== ========== @@ -8895,7 +9187,7 @@ version versionsuffix toolchain ``2.8.1`` ``GCCcore/6.4.0`` ``2.9`` ``GCCcore/6.4.0`` ``2.9.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``2.10.1`` ``GCCcore/8.3.0`` +``2.10.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ================== ====================================================================== @@ -8932,6 +9224,7 @@ version toolchain ``1.0.1`` ``foss/2018a``, ``intel/2018a`` ``1.0.2`` ``GCCcore/6.4.0`` ``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.0.9`` ``GCCcore/9.3.0`` ========= ======================================================= @@ -8955,8 +9248,9 @@ version versionsuffix toolchain ``5.0.11`` ``-Python-3.6.6`` ``foss/2018b`` ``6.0.1`` ``-Python-2.7.15`` ``foss/2019a`` ``6.0.1`` ``-Python-3.7.2`` ``foss/2019a`` -``6.0.2`` ``-Python-2.7.15`` ``foss/2018b`` +``6.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` ``6.0.2`` ``-Python-2.7.15-CUDA-9.2.88`` ``foss/2018b`` +``6.0.2`` ``-Python-3.7.2`` ``foss/2019a`` ``6.0.3`` ``-Python-3.7.4`` ``foss/2019b`` ========== ============================== ================================================ @@ -9059,6 +9353,22 @@ version toolchain ========= =============== +.. _list_software_FusionCatcher_1326: + +*FusionCatcher* ++++++++++++++++ + +FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end or single-end reads from Illumina NGS platforms like Solexa/HiSeq/NextSeq/MiSeq/MiniSeq) from diseased samples. + +*homepage*: https://github.com/ndaniel/fusioncatcher + +======== ================== ============== +version versionsuffix toolchain +======== ================== ============== +``1.20`` ``-Python-2.7.16`` ``foss/2019b`` +======== ================== ============== + + .. _list_software_future_667: *future* @@ -9100,7 +9410,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gblocks_709` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_gtest_551` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gblocks_709` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_gtest_551` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -9197,11 +9507,12 @@ GAP is a system for computational discrete algebra, with particular emphasis on *homepage*: https://www.gap-system.org -========= =============== -version toolchain -========= =============== -``4.9.3`` ``intel/2018b`` -========= =============== +========== =============== +version toolchain +========== =============== +``4.9.3`` ``intel/2018b`` +``4.11.0`` ``foss/2019a`` +========== =============== .. _list_software_GapCloser_896: @@ -9332,6 +9643,7 @@ version versionsuffix toolchain ``4.1.2.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` ``4.1.3.0`` ``-Java-1.8`` ``GCCcore/8.3.0`` ``4.1.4.1`` ``-Java-11`` ``GCCcore/8.3.0`` +``4.1.5.0`` ``-Java-11`` ``GCCcore/9.3.0`` ============ =================== ================= @@ -9376,15 +9688,15 @@ The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage *homepage*: http://hboehm.info/gc/ -========== ================================== -version toolchain -========== ================================== -``7.4.4`` ``GCC/4.9.3-2.25``, ``foss/2016a`` -``7.6.0`` ``GCCcore/6.4.0`` -``7.6.4`` ``GCCcore/7.3.0`` -``7.6.10`` ``GCCcore/8.2.0`` -``7.6.12`` ``GCCcore/8.3.0`` -========== ================================== +========== ==================================== +version toolchain +========== ==================================== +``7.4.4`` ``GCC/4.9.3-2.25``, ``foss/2016a`` +``7.6.0`` ``GCCcore/6.4.0`` +``7.6.4`` ``GCCcore/7.3.0`` +``7.6.10`` ``GCCcore/8.2.0`` +``7.6.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ==================================== .. _list_software_GC3Pie_475: @@ -9466,6 +9778,8 @@ version versionsuffix toolchain ``9.1.0`` ``-2.32`` ``system`` ``9.2.0`` ``system`` ``9.2.0`` ``-2.32`` ``system`` +``9.3.0`` ``system`` +``10.1.0`` ``system`` ``system`` ``system`` ``system`` ``-2.29`` ``system`` ========== =================== ========== @@ -9504,6 +9818,7 @@ version toolchain ``9.1.0`` ``system`` ``9.2.0`` ``system`` ``9.3.0`` ``system`` +``10.1.0`` ``system`` ``system`` ``system`` ========== ========== @@ -9612,6 +9927,7 @@ version versionsuffix toolchain ``3.0.0`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ``3.0.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``3.0.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.0.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========= ============================== ================================================================ @@ -9706,6 +10022,7 @@ version toolchain ``2.8.8`` ``GCCcore/6.4.0`` ``2.8.9`` ``GCCcore/7.3.0`` ``3.0.4`` ``GCCcore/8.2.0`` +``3.0.5`` ``GCCcore/8.3.0`` ========= ================= @@ -9763,6 +10080,7 @@ version toolchain ``2.36.12`` ``foss/2018b``, ``fosscuda/2018b`` ``2.38.1`` ``GCCcore/8.2.0`` ``2.38.2`` ``GCCcore/8.3.0`` +``2.40.0`` ``GCCcore/9.3.0`` =========== ==================================================================================== @@ -9866,6 +10184,7 @@ Eukaryotic gene prediction suite with automatic training version toolchain ======== ================= ``4.38`` ``GCCcore/8.2.0`` +``4.57`` ``GCCcore/8.3.0`` ======== ================= @@ -9914,6 +10233,7 @@ GenomeThreader is a software tool to compute gene structure predictions. version versionsuffix toolchain ========= ======================= ========== ``1.7.1`` ``-Linux_x86_64-64bit`` ``system`` +``1.7.3`` ``-Linux_x86_64-64bit`` ``system`` ========= ======================= ========== @@ -9968,6 +10288,22 @@ version versionsuffix toolchain ========== ================== ============== +.. _list_software_geopandas_946: + +*geopandas* ++++++++++++ + +GeoPandas is a project to add support for geographic data to pandas objects. It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and perform geometric operations. + +*homepage*: https://github.com/geopandas/geopandas + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.7.0`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_geopy_548: *geopy* @@ -10010,6 +10346,7 @@ version versionsuffix toolchain ``3.7.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ``3.7.2`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``3.8.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``3.8.1`` ``-Python-3.8.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` ========= ================== ================================================================ @@ -10064,7 +10401,7 @@ version versionsuffix toolchain ``0.19.8`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016.04``, ``foss/2016b``, ``intel/2016b``, ``system`` ``0.19.8.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` ``0.19.8.1`` ``-libxml2-2.9.7`` ``GCCcore/6.4.0`` -``0.20.1`` ``GCCcore/8.3.0``, ``system`` +``0.20.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ============ ================== =================================================================================================== @@ -10082,6 +10419,7 @@ version toolchain ========== ================= ``0.10.1`` ``foss/2016b`` ``0.10.6`` ``GCCcore/7.3.0`` +``0.11.6`` ``GCCcore/8.3.0`` ========== ================= @@ -10112,13 +10450,13 @@ The gflags package contains a C++ library that implements commandline flags proc *homepage*: https://github.com/gflags/gflags -========= =================================================== -version toolchain -========= =================================================== -``2.1.2`` ``foss/2016a`` -``2.2.1`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` -``2.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= =================================================== +========= ======================================================= +version toolchain +========= ======================================================= +``2.1.2`` ``foss/2016a`` +``2.2.1`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` +``2.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================= .. _list_software_GFOLD_364: @@ -10174,6 +10512,7 @@ version versionsuffix toolchain ``9.23`` ``-cairo-1.14.12`` ``GCCcore/6.4.0`` ``9.27`` ``GCCcore/8.2.0`` ``9.50`` ``GCCcore/8.3.0`` +``9.52`` ``GCCcore/9.3.0`` ======== ================== ================================================== @@ -10389,6 +10728,7 @@ version versionsuffix toolchain ========== ================= =============================== ``2.1.11`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.0.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``3.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========== ================= =============================== @@ -10470,11 +10810,11 @@ The OpenGL Extension Wrangler Library The OpenGL Extension Wrangler Library (GL *homepage*: http://glew.sourceforge.net/ -========= ================================= -version toolchain -========= ================================= -``2.1.0`` ``GCCcore/8.2.0``, ``foss/2018b`` -========= ================================= +========= ======================================================================= +version toolchain +========= ======================================================================= +``2.1.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b`` +========= ======================================================================= .. _list_software_GLib_350: @@ -10500,6 +10840,7 @@ version toolchain ``2.54.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.60.1`` ``GCCcore/8.2.0`` ``2.62.0`` ``GCCcore/8.3.0`` +``2.64.1`` ``GCCcore/9.3.0`` ========== ================================================= @@ -10562,11 +10903,12 @@ GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. Alt *homepage*: https://ccb.jhu.edu/software/glimmerhmm -========= ============================== -version toolchain -========= ============================== -``3.0.4`` ``foss/2016b``, ``foss/2018b`` -========= ============================== +========== ============================== +version toolchain +========== ============================== +``3.0.4`` ``foss/2016b``, ``foss/2018b`` +``3.0.4c`` ``GCC/8.3.0`` +========== ============================== .. _list_software_GLM_224: @@ -10596,12 +10938,14 @@ Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming mode *homepage*: https://hpc.pnl.gov/globalarrays -======= ============= =============== -version versionsuffix toolchain -======= ============= =============== -``5.7`` ``intel/2018b`` -``5.7`` ``-peigs`` ``intel/2019a`` -======= ============= =============== +========= ============= =============== +version versionsuffix toolchain +========= ============= =============== +``5.7`` ``intel/2018b`` +``5.7`` ``-peigs`` ``intel/2019a`` +``5.7.2`` ``intel/2019b`` +``5.7.2`` ``-peigs`` ``intel/2019b`` +========= ============= =============== .. _list_software_Globus-CLI_881: @@ -10645,13 +10989,13 @@ A C++ implementation of the Google logging module. *homepage*: https://github.com/google/glog -========= =================================================== -version toolchain -========= =================================================== -``0.3.4`` ``foss/2016a`` -``0.3.5`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` -``0.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= =================================================== +========= ======================================================= +version toolchain +========= ======================================================= +``0.3.4`` ``foss/2016a`` +``0.3.5`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` +``0.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================= .. _list_software_GLPK_302: @@ -10663,14 +11007,14 @@ The GLPK (GNU Linear Programming Kit) package is intended for solving large-sca *homepage*: https://www.gnu.org/software/glpk/ -======== ========================================================================== -version toolchain -======== ========================================================================== -``4.58`` ``foss/2016a``, ``intel/2016a`` -``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` -``4.61`` ``intel/2017a`` -``4.65`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -======== ========================================================================== +======== ============================================================================================= +version toolchain +======== ============================================================================================= +``4.58`` ``foss/2016a``, ``intel/2016a`` +``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` +``4.61`` ``intel/2017a`` +``4.65`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======== ============================================================================================= .. _list_software_glproto_775: @@ -10715,9 +11059,9 @@ version toolchain *GMP* +++++ -GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. +GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. -*homepage*: http://gmplib.org/ +*homepage*: https://gmplib.org/ ========== ===================================================================================================================================================== version toolchain @@ -10729,6 +11073,7 @@ version toolchain ``6.1.0`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``6.1.1`` ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``6.1.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b`` +``6.2.0`` ``GCCcore/9.3.0`` ========== ===================================================================================================================================================== @@ -10783,6 +11128,7 @@ version versionsuffix toolchain ``2.0.8`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b4`` ``GCC/8.3.0`` =========== ================== =============================== @@ -10793,7 +11139,7 @@ version versionsuffix toolchain Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. -*homepage*: http://geuz.org/gmsh +*homepage*: https://gmsh.info/ ========= ================== ============== version versionsuffix toolchain @@ -10801,6 +11147,7 @@ version versionsuffix toolchain ``3.0.6`` ``-Python-2.7.14`` ``foss/2017b`` ``3.0.6`` ``-Python-3.6.6`` ``foss/2018b`` ``4.2.2`` ``-Python-3.6.6`` ``foss/2018b`` +``4.5.6`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== ============== @@ -10893,7 +11240,7 @@ version toolchain ``5.2.2`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``5.2.5`` ``foss/2018b`` ``5.2.6`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b`` -``5.2.8`` ``GCCcore/8.3.0`` +``5.2.8`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ================================================================ @@ -10940,6 +11287,22 @@ version toolchain ========== ================= +.. _list_software_goalign_737: + +*goalign* ++++++++++ + +Goalign is a set of command line tools to manipulate multiple alignments. + +*homepage*: https://github.com/evolbioinfo/goalign + +========= ========== +version toolchain +========= ========== +``0.3.2`` ``system`` +========= ========== + + .. _list_software_GObject-Introspection_2108: *GObject-Introspection* @@ -10947,7 +11310,7 @@ version toolchain GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library. -*homepage*: https://wiki.gnome.org/GObjectIntrospection/ +*homepage*: https://gi.readthedocs.io/en/latest/ ========== ================== ================================== version versionsuffix toolchain @@ -10965,6 +11328,7 @@ version versionsuffix toolchain ``1.58.3`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` ``1.60.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``1.63.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``1.64.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========== ================== ================================== @@ -11026,6 +11390,7 @@ version versionsuffix toolchain ``2018b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` +``2020a`` ``system`` ``system`` ``-2.29`` ``system`` =========== ============= ========== @@ -11082,6 +11447,22 @@ version toolchain ========= ===================================================================== +.. _list_software_gotree_646: + +*gotree* +++++++++ + +GoTree is a set of command line tools to manipulate phylogenetic trees. + +*homepage*: https://github.com/evolbioinfo/gotree + +========= ========== +version toolchain +========= ========== +``0.4.0`` ``system`` +========= ========== + + .. _list_software_GP2C_268: *GP2C* @@ -11149,7 +11530,7 @@ GNU gperf is a perfect hash function generator. For a given list of strings, it version toolchain ========= ========================================================================================================================= ``3.0.4`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``3.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ========================================================================================================================= @@ -11184,6 +11565,7 @@ dstat-like utilization monitor for NVIDIA GPUs version versionsuffix toolchain ========= ================== ================== ``0.5.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``0.6.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ================== ================== @@ -11249,6 +11631,8 @@ Gradient Unwarping. This is the Human Connectome Project fork of the no longer m version versionsuffix toolchain ========= ====================== ============== ``1.1.0`` ``-HCP-Python-2.7.15`` ``foss/2019a`` +``1.2.0`` ``-HCP-Python-2.7.15`` ``foss/2019a`` +``1.2.0`` ``-HCP-Python-3.7.2`` ``foss/2019a`` ========= ====================== ============== @@ -11426,6 +11810,22 @@ version toolchain ======== ============= +.. _list_software_gretl_542: + +*gretl* ++++++++ + +A cross-platform software package for econometric analysis + +*homepage*: http://gretl.sourceforge.net + +========= ============== +version toolchain +========= ============== +``2020a`` ``foss/2019a`` +========= ============== + + .. _list_software_grib_api_829: *grib_api* @@ -11527,6 +11927,7 @@ version versionsuffix toolchain ``2019.3`` ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019a``, ``fosscuda/2019b`` ``2019.4`` ``foss/2019b`` ``2020`` ``foss/2019b``, ``fosscuda/2019b`` +``2020.1`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================= ============================================================================================================ @@ -11612,7 +12013,7 @@ version toolchain ``2.3`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b``, ``intel/2017a`` ``2.4`` ``GCCcore/6.4.0`` ``2.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2.6`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``2.6`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217`` ========= ============================================================================================================================ @@ -11665,6 +12066,7 @@ version toolchain ``1.6.4`` ``foss/2016a`` ``1.8.3`` ``foss/2016a`` ``1.16.0`` ``GCC/8.2.0-2.31.1`` +``1.16.2`` ``GCC/8.3.0`` =========== ================================================================================================================== @@ -11685,6 +12087,7 @@ version toolchain ``1.8.3`` ``foss/2016a`` ``1.15.1`` ``fosscuda/2018b`` ``1.16.0`` ``GCC/8.2.0-2.31.1`` +``1.16.2`` ``GCC/8.3.0`` =========== ================================================================================================================== @@ -11743,6 +12146,7 @@ version toolchain ``3.22.30`` ``fosscuda/2018b`` ``3.24.8`` ``GCCcore/8.2.0`` ``3.24.13`` ``GCCcore/8.3.0`` +``3.24.17`` ``GCCcore/9.3.0`` =========== ================================================================================ @@ -11837,14 +12241,14 @@ Guile is a programming language, designed to help programmers create flexible a *homepage*: https://www.gnu.org/software/guile/ -========== =================================================================================================================================================================================================== -version toolchain -========== =================================================================================================================================================================================================== -``1.8.8`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b`` -``2.0.11`` ``GCC/4.9.3-2.25``, ``foss/2016a`` -``2.2.2`` ``GCCcore/6.4.0`` -``2.2.4`` ``GCCcore/7.3.0`` -========== =================================================================================================================================================================================================== +========== ====================================================================================================================================================================================================================== +version toolchain +========== ====================================================================================================================================================================================================================== +``1.8.8`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b`` +``2.0.11`` ``GCC/4.9.3-2.25``, ``foss/2016a`` +``2.2.2`` ``GCCcore/6.4.0`` +``2.2.4`` ``GCCcore/7.3.0`` +========== ====================================================================================================================================================================================================================== .. _list_software_GULP_312: @@ -11902,7 +12306,7 @@ version toolchain ======== ======================================================= ``1.8`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.9`` ``GCCcore/7.3.0`` -``1.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ======== ======================================================= @@ -11912,7 +12316,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -11988,6 +12392,7 @@ version versionsuffix toolchain ``2.8.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.9.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` ``2.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2.10.0`` ``-Python-3.8.2`` ``foss/2020a`` ========== ===================================== ==================================================================================== @@ -12084,7 +12489,7 @@ version toolchain ``1.9.0`` ``fosscuda/2018b`` ``2.2.0`` ``foss/2018b``, ``fosscuda/2018b`` ``2.4.0`` ``GCCcore/8.2.0`` -``2.6.4`` ``GCCcore/8.3.0`` +``2.6.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ================================================ @@ -12104,6 +12509,22 @@ version toolchain ======= ============== +.. _list_software_harmony_766: + +*harmony* ++++++++++ + +Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. + +*homepage*: https://portals.broadinstitute.org/harmony + +================== ============= ============== +version versionsuffix toolchain +================== ============= ============== +``1.0.0-20200224`` ``-R-4.0.0`` ``foss/2020a`` +================== ============= ============== + + .. _list_software_HBase_451: *HBase* @@ -12125,7 +12546,7 @@ version toolchain *HDDM* ++++++ -HDDM is a Puthon toolbox for hierarchical Bayesian parameter estimation of the Drift Diffusion Model (via PyMC). +HDDM is a Python toolbox for hierarchical Bayesian parameter estimation of the Drift Diffusion Model (via PyMC). *homepage*: http://ski.clps.brown.edu/hddm_docs @@ -12134,6 +12555,7 @@ version versionsuffix toolchain ========= ================== =============== ``0.6.1`` ``-Python-3.6.6`` ``intel/2018b`` ``0.7.5`` ``-Python-2.7.16`` ``intel/2019b`` +``0.7.5`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================== =============== @@ -12157,6 +12579,38 @@ version versionsuffix toolchain ========== ============== ========================================================================== +.. _list_software_HDF-EOS_486: + +*HDF-EOS* ++++++++++ + +HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath. + +*homepage*: https://hdfeos.org/ + +======== ================= +version toolchain +======== ================= +``2.20`` ``GCCcore/7.3.0`` +======== ================= + + +.. _list_software_HDF-EOS5_539: + +*HDF-EOS5* +++++++++++ + +HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath. + +*homepage*: https://hdfeos.org/ + +======== ============== +version toolchain +======== ============== +``1.16`` ``foss/2018b`` +======== ============== + + .. _list_software_HDF5_263: *HDF5* @@ -12185,6 +12639,7 @@ version versionsuffix toolchain ``1.10.1`` ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2017b``, ``iomkl/2018a`` ``1.10.2`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``1.10.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompic/2019a``, ``gompic/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpic/2019a``, ``iimpic/2019b`` +``1.10.6`` ``gompi/2020a``, ``iimpi/2020a`` ================= ============= ================================================================================================================================================================================================================== @@ -12288,6 +12743,7 @@ version toolchain ``1.47.8`` ``GCCcore/7.4.0``, ``GCCcore/8.3.0`` ``1.47.10`` ``GCCcore/9.1.0``, ``GCCcore/9.2.0`` ``1.47.12`` ``GCCcore/9.3.0`` +``1.47.15`` ``GCCcore/10.1.0`` =========== ================================================================================================================================================================================== @@ -12408,6 +12864,22 @@ version toolchain ========= ============================================================================================================================================ +.. _list_software_HMMER2_427: + +*HMMER2* +++++++++ + +HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. + +*homepage*: http://hmmer.org + +========= ============= +version toolchain +========= ============= +``2.3.2`` ``GCC/8.3.0`` +========= ============= + + .. _list_software_hmmlearn_852: *hmmlearn* @@ -12540,7 +13012,7 @@ version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019b``, ``gomkl/2019a``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intelcuda/2019b``, ``iomkl/2019.01`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``fosscuda/2019b``, ``gomkl/2019a``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020a``, ``intelcuda/2019b``, ``iomkl/2019.01`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= @@ -12608,7 +13080,7 @@ version versionsuffix toolchain ``1.7`` ``intel/2018a`` ``1.8`` ``foss/2018a``, ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``1.10.2`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ``20160107`` ``-PacBio`` ``intel/2017a`` ============ ============= =========================================================================================================================================================== @@ -12678,6 +13150,7 @@ version toolchain ``2.0.2`` ``GCCcore/8.2.0`` ``2.0.3`` ``GCCcore/8.3.0`` ``2.1.0`` ``GCCcore/9.2.0`` +``2.2.0`` ``GCCcore/9.3.0`` =========== ===================================================================================================================================================================================================================================================== @@ -12730,6 +13203,22 @@ version toolchain ========= =============== +.. _list_software_HyPo_384: + +*HyPo* +++++++ + +HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies + +*homepage*: https://github.com/kensung-lab/hypo + +========= ================= ============= +version versionsuffix toolchain +========= ================= ============= +``1.0.3`` ``-Python-3.7.4`` ``GCC/8.3.0`` +========= ================= ============= + + .. _list_software_hypothesis_1104: *hypothesis* @@ -12745,6 +13234,7 @@ version versionsuffix toolchain ``4.5.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``4.23.4`` ``GCCcore/8.2.0`` ``4.44.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``5.6.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========== ================= ================================== @@ -12757,14 +13247,14 @@ Hypre is a library for solving large, sparse linear systems of equations on mass *homepage*: https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods -========== =============================== -version toolchain -========== =============================== -``2.11.1`` ``foss/2016a``, ``intel/2016a`` -``2.14.0`` ``foss/2018a``, ``intel/2018a`` -``2.15.1`` ``foss/2019a``, ``intel/2019a`` -``2.18.2`` ``foss/2019b``, ``intel/2019b`` -========== =============================== +========== ================================================================ +version toolchain +========== ================================================================ +``2.11.1`` ``foss/2016a``, ``intel/2016a`` +``2.14.0`` ``foss/2018a``, ``intel/2018a`` +``2.15.1`` ``foss/2019a``, ``intel/2019a`` +``2.18.2`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` +========== ================================================================ .. _list_software_letter_i: @@ -12922,6 +13412,7 @@ version versionsuffix toolchain ``2019.5.281`` ``system`` ``2020.0.166`` ``system`` ``2020.0.166`` ``-GCC-9.2.0`` ``system`` +``2020.1.217`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ============== ===================== ========== @@ -12984,7 +13475,7 @@ version versionsuffix toolchain ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. -*homepage*: https://site.icu-project.org/home +*homepage*: https://icu-project.org/ ======== ==================================== version toolchain @@ -12992,6 +13483,7 @@ version toolchain ``61.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``64.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``65.1`` ``GCCcore/8.3.0`` +``66.1`` ``GCCcore/9.3.0`` ======== ==================================== @@ -13195,6 +13687,7 @@ version versionsuffix toolchain ``2019a`` ``system`` ``2019b`` ``system`` ``2020.00`` ``system`` +``2020a`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` =========== ==================== ========== @@ -13315,6 +13808,7 @@ version versionsuffix toolchain ``7.0.8-11`` ``GCCcore/7.3.0`` ``7.0.8-46`` ``GCCcore/8.2.0`` ``7.0.9-5`` ``GCCcore/8.3.0`` +``7.0.10-1`` ``GCCcore/9.3.0`` ============ =================================== =============================== @@ -13420,6 +13914,7 @@ version toolchain ``2019.3.199`` ``iimpi/2019.03`` ``2019.5.281`` ``iimpi/2019b``, ``iimpic/2019b`` ``2020.0.166`` ``iimpi/2020.00`` +``2020.1.217`` ``iimpi/2020a`` ============== ====================================================================================================================================================================================================================================================================== @@ -13497,6 +13992,7 @@ version versionsuffix toolchain ``2019.2.187`` ``iccifort/2019.2.187-GCC-8.2.0-2.31.1`` ``2019.3.199`` ``iccifort/2019.3.199-GCC-8.3.0-2.32`` ``2019.6.166`` ``iccifort/2020.0.166-GCC-9.2.0`` +``2019.7.217`` ``iccifort/2020.1.217`` ``system`` ``iccifort/system-GCC-system-2.29`` ============== ============= ================================================================================================================================================================================================================================ @@ -13714,6 +14210,7 @@ version versionsuffix toolchain ``2019a`` ``system`` ``2019b`` ``system`` ``2020.00`` ``system`` +``2020a`` ``system`` =========== ============= ========== @@ -13799,7 +14296,7 @@ intltool is a set of tools to centralize translation of many different file for ========== ================ ====================================================================================== version versionsuffix toolchain ========== ================ ====================================================================================== -``0.51.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.51.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.51.0`` ``-Perl-5.20.3`` ``intel/2016a`` ``0.51.0`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` ``0.51.0`` ``-Perl-5.24.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` @@ -14002,28 +14499,29 @@ IPython provides a rich architecture for interactive computing with: Powerful i *homepage*: https://ipython.org/index.html -========= ================== ======================================================================================= -version versionsuffix toolchain -========= ================== ======================================================================================= -``3.2.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``4.2.0`` ``-Python-2.7.11`` ``intel/2016a`` -``5.0.0`` ``-Python-2.7.11`` ``foss/2016a`` -``5.0.0`` ``-Python-3.5.1`` ``foss/2016a`` -``5.1.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``5.1.0`` ``-Python-3.5.2`` ``intel/2016b`` -``5.2.2`` ``-Python-2.7.12`` ``intel/2016b`` -``5.3.0`` ``-Python-2.7.13`` ``intel/2017a`` -``5.7.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``5.8.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``5.8.0`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``fosscuda/2018b``, ``fosscuda/2019a``, ``intel/2018b`` -``5.8.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``6.2.1`` ``-Python-3.6.4`` ``foss/2017a`` -``6.3.1`` ``-Python-3.6.4`` ``intel/2018a`` -``6.4.0`` ``-Python-3.6.4`` ``foss/2018a`` -``7.2.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``7.7.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` -``7.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -========= ================== ======================================================================================= +========== ================== ======================================================================================= +version versionsuffix toolchain +========== ================== ======================================================================================= +``3.2.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``4.2.0`` ``-Python-2.7.11`` ``intel/2016a`` +``5.0.0`` ``-Python-2.7.11`` ``foss/2016a`` +``5.0.0`` ``-Python-3.5.1`` ``foss/2016a`` +``5.1.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``5.1.0`` ``-Python-3.5.2`` ``intel/2016b`` +``5.2.2`` ``-Python-2.7.12`` ``intel/2016b`` +``5.3.0`` ``-Python-2.7.13`` ``intel/2017a`` +``5.7.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``5.8.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``5.8.0`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``fosscuda/2018b``, ``fosscuda/2019a``, ``intel/2018b`` +``5.8.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``6.2.1`` ``-Python-3.6.4`` ``foss/2017a`` +``6.3.1`` ``-Python-3.6.4`` ``intel/2018a`` +``6.4.0`` ``-Python-3.6.4`` ``foss/2018a`` +``7.2.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``7.7.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` +``7.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``7.13.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +========== ================== ======================================================================================= .. _list_software_IQ-TREE_503: @@ -14035,13 +14533,13 @@ Efficient phylogenomic software by maximum likelihood *homepage*: http://www.iqtree.org/ -========== ============= =============== -version versionsuffix toolchain -========== ============= =============== -``1.5.5`` ``-omp-mpi`` ``foss/2016a`` -``1.6.6`` ``intel/2018a`` -``1.6.12`` ``intel/2019b`` -========== ============= =============== +========== ============= =============================== +version versionsuffix toolchain +========== ============= =============================== +``1.5.5`` ``-omp-mpi`` ``foss/2016a`` +``1.6.6`` ``intel/2018a`` +``1.6.12`` ``foss/2018b``, ``intel/2019b`` +========== ============= =============================== .. _list_software_IRkernel_796: @@ -14252,7 +14750,7 @@ version toolchain ``1.900.1`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``2.0.10`` ``intel/2016b`` ``2.0.12`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` -``2.0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` =========== ========================================================================================================================================================== @@ -14342,11 +14840,11 @@ JBIG-KIT is a software implementation of the JBIG1 data compression standard (I *homepage*: -======= ==================================== -version toolchain -======= ==================================== -``2.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -======= ==================================== +======= ======================================================= +version toolchain +======= ======================================================= +``2.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +======= ======================================================= .. _list_software_Jellyfish_938: @@ -14539,6 +15037,7 @@ version versionsuffix toolchain ``1.2.0`` ``-linux-x86_64`` ``system`` ``1.3.1`` ``-linux-x86_64`` ``system`` ``1.4.0`` ``-linux-x86_64`` ``system`` +``1.4.1`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -14630,7 +15129,7 @@ version toolchain --- -:ref:`list_software_Kaiju_500` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_kma_313` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` +:ref:`list_software_Kaiju_500` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_king_425` - :ref:`list_software_kma_313` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` .. _list_software_Kaiju_500: @@ -14786,12 +15285,28 @@ Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collec *homepage*: https://openkim.org/ -========= =============================== -version toolchain -========= =============================== -``2.1.2`` ``foss/2019a``, ``intel/2019a`` -``2.1.3`` ``foss/2019b``, ``intel/2019b`` -========= =============================== +========= ================================================================ +version toolchain +========= ================================================================ +``2.1.2`` ``foss/2019a``, ``intel/2019a`` +``2.1.3`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` +========= ================================================================ + + +.. _list_software_king_425: + +*king* +++++++ + +KING is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequencing project. Applications of KING include family relationship inference and pedigree error checking, quality control, population substructure identification, forensics, gene mapping, etc. + +*homepage*: https://people.virginia.edu/~wc9c/KING/ + +========= ========== +version toolchain +========= ========== +``2.2.4`` ``system`` +========= ========== .. _list_software_kma_313: @@ -14819,12 +15334,13 @@ KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/F *homepage*: http://sun.aei.polsl.pl/kmc -========= ================= ============================== -version versionsuffix toolchain -========= ================= ============================== -``3.1.0`` ``foss/2018a``, ``foss/2018b`` -``3.1.1`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` -========= ================= ============================== +============ ================= ============================== +version versionsuffix toolchain +============ ================= ============================== +``3.1.0`` ``foss/2018a``, ``foss/2018b`` +``3.1.1`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` +``3.1.2rc1`` ``-Python-3.7.4`` ``GCC/8.3.0`` +============ ================= ============================== .. _list_software_KmerGenie_887: @@ -14911,6 +15427,7 @@ version versionsuffix toolchain ``2.0.6-beta`` ``-Perl-5.26.1`` ``foss/2018a`` ``2.0.7-beta`` ``-Perl-5.28.0`` ``foss/2018b`` ``2.0.8-beta`` ``-Perl-5.30.0`` ``gompi/2019b`` +``2.0.9-beta`` ``-Perl-5.28.0`` ``foss/2018b`` ============== ================ =============== @@ -15017,7 +15534,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libpsml_755` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libpsml_755` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -15045,12 +15562,12 @@ LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGP *homepage*: http://lame.sourceforge.net/ -========== =========================================================================================== -version toolchain -========== =========================================================================================== -``3.99.5`` ``foss/2016b``, ``intel/2017a`` -``3.100`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b`` -========== =========================================================================================== +========== ============================================================================================================== +version toolchain +========== ============================================================================================================== +``3.99.5`` ``foss/2016b``, ``intel/2017a`` +``3.100`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` +========== ============================================================================================================== .. _list_software_LAMMPS_458: @@ -15066,6 +15583,7 @@ LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale At version versionsuffix toolchain ============ ======================== =============================== ``3Mar2020`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` +``3Mar2020`` ``-Python-3.8.2-kokkos`` ``foss/2020a`` ``7Aug2019`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` ============ ======================== =============================== @@ -15282,6 +15800,7 @@ Multi-format archive and compression library version toolchain ========= ================= ``3.4.0`` ``GCCcore/8.2.0`` +``3.4.2`` ``GCCcore/9.3.0`` ========= ================= @@ -15333,7 +15852,7 @@ version toolchain ``1.5`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``1.7`` ``GCCcore/7.3.0`` ``1.11`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.13`` ``GCCcore/8.3.0`` +``1.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ======== ========================================================================================================= @@ -15416,6 +15935,7 @@ Libcroco is a standalone css2 parsing and manipulation library. version toolchain ========== =============== ``0.6.11`` ``intel/2016a`` +``0.6.13`` ``foss/2019a`` ========== =============== @@ -15455,6 +15975,22 @@ version versionsuffix toolchain ========== ================== ================================================== +.. _list_software_libdeflate_1036: + +*libdeflate* +++++++++++++ + +Generic PCI access library. + +*homepage*: https://github.com/ebiggers/libdeflate + +======= ================= +version toolchain +======= ================= +``1.5`` ``GCCcore/7.3.0`` +======= ================= + + .. _list_software_libdrm_634: *libdrm* @@ -15464,19 +16000,20 @@ Direct Rendering Manager runtime library. *homepage*: https://dri.freedesktop.org -========== ================================================== -version toolchain -========== ================================================== -``2.4.67`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``2.4.68`` ``foss/2016a``, ``intel/2016a`` -``2.4.70`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` -``2.4.76`` ``GCCcore/6.3.0``, ``intel/2017a`` -``2.4.88`` ``GCCcore/6.4.0`` -``2.4.91`` ``GCCcore/6.4.0`` -``2.4.92`` ``GCCcore/7.3.0`` -``2.4.97`` ``GCCcore/8.2.0`` -``2.4.99`` ``GCCcore/8.3.0`` -========== ================================================== +=========== ================================================== +version toolchain +=========== ================================================== +``2.4.67`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``2.4.68`` ``foss/2016a``, ``intel/2016a`` +``2.4.70`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` +``2.4.76`` ``GCCcore/6.3.0``, ``intel/2017a`` +``2.4.88`` ``GCCcore/6.4.0`` +``2.4.91`` ``GCCcore/6.4.0`` +``2.4.92`` ``GCCcore/7.3.0`` +``2.4.97`` ``GCCcore/8.2.0`` +``2.4.99`` ``GCCcore/8.3.0`` +``2.4.100`` ``GCCcore/9.3.0`` +=========== ================================================== .. _list_software_libdwarf_843: @@ -15543,7 +16080,7 @@ Epoxy is a library for handling OpenGL function pointer management for you version toolchain ========= ===================================== ``1.5.3`` ``GCCcore/8.2.0``, ``fosscuda/2018b`` -``1.5.4`` ``GCCcore/8.3.0`` +``1.5.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ===================================== @@ -15561,10 +16098,27 @@ version toolchain ========== ====================================================================================== ``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` ``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` -``2.1.11`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +``2.1.11`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ====================================================================================== +.. _list_software_libfabric_926: + +*libfabric* ++++++++++++ + +Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric. + +*homepage*: https://ofiwg.github.io/libfabric/ + +========== ================= +version toolchain +========== ================= +``1.9.1`` ``GCCcore/9.3.0`` +``1.10.1`` ``GCCcore/9.3.0`` +========== ================= + + .. _list_software_libffcall_927: *libffcall* @@ -15574,11 +16128,12 @@ GNU Libffcall is a collection of four libraries which can be used to build fore *homepage*: https://www.gnu.org/software/libffcall/ -======== ================= -version toolchain -======== ================= -``1.13`` ``GCCcore/6.4.0`` -======== ================= +======== ==================================== +version toolchain +======== ==================================== +``1.13`` ``GCCcore/6.4.0`` +``2.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======== ==================================== .. _list_software_libffi_620: @@ -15586,14 +16141,15 @@ version toolchain *libffi* ++++++++ -The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. +The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. -*homepage*: http://sourceware.org/libffi/ +*homepage*: https://sourceware.org/libffi/ ========= ============================================================================================================================================================================================================================================================================================================= version toolchain ========= ============================================================================================================================================================================================================================================================================================================= ``3.2.1`` ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``system`` +``3.3`` ``GCCcore/9.3.0`` ========= ============================================================================================================================================================================================================================================================================================================= @@ -15662,6 +16218,7 @@ version toolchain ``2.2.3`` ``foss/2016b``, ``intel/2016b`` ``2.2.4`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` ``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b``, ``intel/2018a`` +``2.3.0`` ``GCCcore/9.3.0`` ========= ============================================================================================================ @@ -15674,12 +16231,28 @@ Library for reading and writing coordinate system information from/to GeoTIFF fi *homepage*: https://directory.fsf.org/wiki/Libgeotiff -========= =============================================== -version toolchain -========= =============================================== -``1.4.2`` ``foss/2018a``, ``foss/2018b``, ``intel/2018b`` -``1.5.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= =============================================== +========= ======================================================= +version toolchain +========= ======================================================= +``1.4.2`` ``foss/2018a``, ``foss/2018b``, ``intel/2018b`` +``1.5.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================= + + +.. _list_software_libgit2_685: + +*libgit2* ++++++++++ + +libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings. + +*homepage*: https://libgit2.org/ + +========= ================= +version toolchain +========= ================= +``1.0.0`` ``GCCcore/8.3.0`` +========= ================= .. _list_software_libglade_820: @@ -15712,7 +16285,7 @@ version versionsuffix toolchain ========= ================ =========================================================================================================================================================================================================================================================================================================================================== ``9.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b``, ``iomkl/2018a`` ``9.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` -``9.0.1`` ``GCCcore/8.3.0`` +``9.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ================ =========================================================================================================================================================================================================================================================================================================================================== @@ -15725,11 +16298,11 @@ libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls bet *homepage*: https://github.com/NVIDIA/libglvnd -========= ==================================== -version toolchain -========= ==================================== -``1.2.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= ==================================== +========= ======================================================= +version toolchain +========= ======================================================= +``1.2.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================= .. _list_software_libgpg-error_1228: @@ -15944,6 +16517,7 @@ version versionsuffix toolchain ``2.0.0`` ``GCCcore/7.3.0`` ``2.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.0.3`` ``GCCcore/8.3.0`` +``2.0.4`` ``GCCcore/9.3.0`` ========= ================= ================================================================== @@ -15956,11 +16530,11 @@ GNU libmatheval is a library (callable from C and Fortran) to parse and evaluat *homepage*: http://www.gnu.org/software/libmatheval/ -========== ============================================================================================================================================ -version toolchain -========== ============================================================================================================================================ -``1.1.11`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b`` -========== ============================================================================================================================================ +========== =============================================================================================================================================================== +version toolchain +========== =============================================================================================================================================================== +``1.1.11`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b`` +========== =============================================================================================================================================================== .. _list_software_libmaus2_799: @@ -16009,7 +16583,7 @@ version toolchain ========== ============================================================================================= ``0.13.4`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.16`` ``GCCcore/9.2.0`` +``0.16`` ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ========== ============================================================================================= @@ -16037,7 +16611,7 @@ version toolchain ``1.6.32`` ``GCCcore/6.4.0`` ``1.6.34`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.6.36`` ``GCCcore/8.2.0`` -``1.6.37`` ``GCCcore/8.3.0`` +``1.6.37`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ===================================================================== @@ -16156,7 +16730,7 @@ version toolchain ======= =================================================================================================================================================================================================================================================================================================================================================================================== ``6.3`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``7.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``8.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` +``8.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ======= =================================================================================================================================================================================================================================================================================================================================================================================== @@ -16189,6 +16763,7 @@ librsvg is a library to render SVG files using cairo. version toolchain =========== =============== ``2.40.15`` ``intel/2016a`` +``2.48.4`` ``foss/2019a`` =========== =============== @@ -16239,6 +16814,7 @@ GNU libsigsegv is a library for handling page faults in user mode. version toolchain ======== ================= ``2.11`` ``GCCcore/6.4.0`` +``2.12`` ``GCCcore/9.3.0`` ======== ================= @@ -16267,11 +16843,11 @@ Libsndfile is a C library for reading and writing files containing sampled sound *homepage*: http://www.mega-nerd.com/libsndfile -========== =========================================================================================== -version toolchain -========== =========================================================================================== -``1.0.28`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a`` -========== =========================================================================================== +========== ============================================================================================================== +version toolchain +========== ============================================================================================================== +``1.0.28`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a`` +========== ============================================================================================================== .. _list_software_libsodium_968: @@ -16293,7 +16869,7 @@ version toolchain ``1.0.13`` ``GCCcore/6.4.0``, ``foss/2017a`` ``1.0.16`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.0.17`` ``GCCcore/8.2.0`` -``1.0.18`` ``GCCcore/8.3.0`` +``1.0.18`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ==================================== @@ -16430,7 +17006,7 @@ version toolchain ``4.0.8`` ``intel/2017a``, ``intel/2017b`` ``4.0.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018b`` ``4.0.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``4.1.0`` ``GCCcore/8.3.0`` +``4.1.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ========================================================================================================= @@ -16459,13 +17035,13 @@ GNU libtool is a generic library support script. Libtool hides the complexity of *homepage*: http://www.gnu.org/software/libtool -========= ======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= -version toolchain -========= ======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= -``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` -``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` -``2.4.6`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -========= ======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +version toolchain +========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` +``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``2.4.6`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_libunistring_1306: @@ -16477,14 +17053,14 @@ This library provides functions for manipulating Unicode strings and for manipu *homepage*: http://www.gnu.org/software/libunistring/ -========== ======================================================================= -version toolchain -========== ======================================================================= -``0.9.3`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` -``0.9.6`` ``GCCcore/5.4.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016b`` -``0.9.7`` ``GCCcore/6.4.0`` -``0.9.10`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========== ======================================================================= +========== ========================================================================== +version toolchain +========== ========================================================================== +``0.9.3`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` +``0.9.6`` ``GCCcore/5.4.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016b`` +``0.9.7`` ``GCCcore/6.4.0`` +``0.9.10`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ========================================================================== .. _list_software_libunwind_972: @@ -16501,7 +17077,7 @@ version toolchain ========= ======================================================================= ``1.1`` ``GCC/4.9.2``, ``foss/2016a``, ``intel/2016b`` ``1.2.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016b`` -``1.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ======================================================================= @@ -16537,6 +17113,22 @@ version toolchain ========= ========================================================================================================= +.. _list_software_libuv_546: + +*libuv* ++++++++ + +libuv is a multi-platform support library with a focus on asynchronous I/O. + +*homepage*: https://libuv.org + +========== ================= +version toolchain +========== ================= +``1.37.0`` ``GCCcore/8.3.0`` +========== ================= + + .. _list_software_libvdwxc_867: *libvdwxc* @@ -16622,7 +17214,7 @@ version toolchain ``4.0.1`` ``foss/2017b``, ``intel/2017b`` ``4.0.3`` ``foss/2016b``, ``foss/2017a`` ``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` -``4.3.4`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` +``4.3.4`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` ========= ======================================================================================================================================= @@ -16845,7 +17437,7 @@ version versionsuffix toolchain ``2.9.7`` ``GCCcore/6.4.0`` ``2.9.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.9.9`` ``GCCcore/8.3.0`` -``2.9.10`` ``GCCcore/9.2.0`` +``2.9.10`` ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ========== ================== ================================================================================================================================================================================== @@ -17037,7 +17629,7 @@ version toolchain ``0.1.6`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``0.1.7`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``system`` ``0.2.1`` ``GCCcore/7.3.0``, ``system`` -``0.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= =================================================================== @@ -17135,13 +17727,13 @@ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, *homepage*: http://www.littlecms.com/ -======= =========================================================================================================================== -version toolchain -======= =========================================================================================================================== -``2.7`` ``intel/2016a`` -``2.8`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``2.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` -======= =========================================================================================================================== +======= ============================================================================================================================================== +version toolchain +======= ============================================================================================================================================== +``2.7`` ``intel/2016a`` +``2.8`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``2.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` +======= ============================================================================================================================================== .. _list_software_LLVM_315: @@ -17170,7 +17762,7 @@ version toolchain ``7.0.1`` ``GCCcore/8.2.0`` ``8.0.1`` ``GCCcore/8.3.0`` ``9.0.0`` ``GCCcore/8.3.0`` -``9.0.1`` ``GCCcore/8.3.0`` +``9.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``10.0.0`` ``GCCcore/8.3.0`` ========== ======================================================================== @@ -17184,15 +17776,15 @@ LMDB is a fast, memory-efficient database. With memory-mapped files, it has the *homepage*: https://symas.com/lmdb -========== ================================== -version toolchain -========== ================================== -``0.9.18`` ``foss/2016a`` -``0.9.21`` ``GCCcore/6.4.0``, ``intel/2017a`` -``0.9.22`` ``GCCcore/7.3.0`` -``0.9.23`` ``GCCcore/8.2.0`` -``0.9.24`` ``GCCcore/8.3.0`` -========== ================================== +========== ==================================== +version toolchain +========== ==================================== +``0.9.18`` ``foss/2016a`` +``0.9.21`` ``GCCcore/6.4.0``, ``intel/2017a`` +``0.9.22`` ``GCCcore/7.3.0`` +``0.9.23`` ``GCCcore/8.2.0`` +``0.9.24`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ==================================== .. _list_software_LMfit_476: @@ -17209,6 +17801,7 @@ version versionsuffix toolchain ========== ================== =============== ``0.9.9`` ``-Python-3.6.4`` ``intel/2018a`` ``0.9.14`` ``-Python-2.7.15`` ``intel/2018b`` +``1.0.0`` ``-Python-3.7.4`` ``intel/2019b`` ========== ================== =============== @@ -17332,11 +17925,12 @@ Longshot is a variant calling tool for diploid genomes using long error prone re *homepage*: https://github.com/pjedge/longshot -========= ================= -version toolchain -========= ================= -``0.3.4`` ``GCCcore/8.2.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``0.3.4`` ``GCCcore/8.2.0`` +``0.4.1`` ``GCC/7.3.0-2.30`` +========= ================== .. _list_software_lpsolve_773: @@ -17348,11 +17942,11 @@ Mixed Integer Linear Programming (MILP) solver *homepage*: https://sourceforge.net/projects/lpsolve/ -=========== ===================================================================================================================================================================== -version toolchain -=========== ===================================================================================================================================================================== -``5.5.2.5`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` -=========== ===================================================================================================================================================================== +=========== ============================================================================================================================================================================================== +version toolchain +=========== ============================================================================================================================================================================================== +``5.5.2.5`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a``, ``intel/2018b`` +=========== ============================================================================================================================================================================================== .. _list_software_lrslib_648: @@ -17364,11 +17958,12 @@ lrslib is a self-contained ANSI C implementation of the reverse search algorithm *homepage*: http://cgm.cs.mcgill.ca/~avis/C/lrs.html -======= =============== -version toolchain -======= =============== -``6.2`` ``intel/2018b`` -======= =============== +======== =============== +version toolchain +======== =============== +``6.2`` ``intel/2018b`` +``7.0a`` ``gompi/2019a`` +======== =============== .. _list_software_LS-PrePost_921: @@ -17430,16 +18025,16 @@ Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combin *homepage*: http://www.lua.org/ -=========== ================================================ -version toolchain -=========== ================================================ -``5.1.4-5`` ``GCC/4.8.2`` -``5.1.4-8`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``system`` -``5.1.5`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` -``5.2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``5.3.4`` ``GCCcore/7.2.0``, ``system`` -``5.3.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` -=========== ================================================ +=========== =================================================================== +version toolchain +=========== =================================================================== +``5.1.4-5`` ``GCC/4.8.2`` +``5.1.4-8`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``system`` +``5.1.5`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +``5.2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``5.3.4`` ``GCCcore/7.2.0``, ``system`` +``5.3.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +=========== =================================================================== .. _list_software_LuaJIT_521: @@ -17579,7 +18174,7 @@ version toolchain ``1.8.2`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0`` ``1.9.0`` ``GCCcore/7.3.0`` ``1.9.1`` ``GCCcore/8.2.0`` -``1.9.2`` ``GCCcore/8.3.0`` +``1.9.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ==================================== @@ -17592,12 +18187,12 @@ Portable lossless data compression library *homepage*: http://www.oberhumer.com/opensource/lzo/ -======== ============================================================================================================================================================================ -version toolchain -======== ============================================================================================================================================================================ -``2.09`` ``intel/2016b``, ``intel/2017b`` -``2.10`` ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` -======== ============================================================================================================================================================================ +======== ================================================================================================================================================================================================================== +version toolchain +======== ================================================================================================================================================================================================================== +``2.09`` ``intel/2016b``, ``intel/2017b`` +``2.10`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` +======== ================================================================================================================================================================================================================== .. _list_software_letter_m: @@ -17606,7 +18201,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_magma_515` - :ref:`list_software_MAGMA_355` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_magma_515` - :ref:`list_software_MAGMA_355` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -17623,7 +18218,7 @@ version toolchain ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.4.16`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.4.18`` ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` +``1.4.18`` ``GCCcore/10.1.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -17692,7 +18287,7 @@ version versionsuffix toolchain ========= ==================== ====================================== ``7.305`` ``-with-extensions`` ``foss/2016b`` ``7.397`` ``-with-extensions`` ``intel/2018a`` -``7.427`` ``-with-extensions`` ``intel/2018b`` +``7.427`` ``-with-extensions`` ``foss/2018b``, ``intel/2018b`` ``7.429`` ``-with-extensions`` ``GCC/8.2.0-2.31.1`` ``7.453`` ``-with-extensions`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ========= ==================== ====================================== @@ -17856,7 +18451,7 @@ version toolchain A super-fast templating language that borrows the best ideas from the existing templating languages -*homepage*: http://www.makotemplates.org +*homepage*: https://www.makotemplates.org ========= ================== ================================================================================================================================================================= version versionsuffix toolchain @@ -17869,6 +18464,7 @@ version versionsuffix toolchain ``1.0.7`` ``-Python-3.6.6`` ``fosscuda/2018b`` ``1.0.8`` ``GCCcore/8.2.0`` ``1.1.0`` ``GCCcore/8.3.0`` +``1.1.2`` ``GCCcore/9.3.0`` ========= ================== ================================================================================================================================================================= @@ -17978,6 +18574,7 @@ version toolchain ``2.3.4`` ``foss/2017b``, ``intel/2017b`` ``2.3.5`` ``intel/2018a``, ``iomkl/2018a`` ``2.3.7`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` +``3.1.7`` ``GCCcore/9.3.0`` ========= ==================================================== @@ -18160,6 +18757,7 @@ version versionsuffix toolchain ``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` ``3.0.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` ``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``3.2.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========= ================================= ======================================================================== @@ -18269,6 +18867,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_mbuffer_743: + +*mbuffer* ++++++++++ + +mbuffer is a tool for buffering data streams with a large set of unique features. + +*homepage*: https://www.maier-komor.de/mbuffer.html + +============ ================= +version toolchain +============ ================= +``20191016`` ``GCCcore/9.3.0`` +============ ================= + + .. _list_software_mc_208: *mc* @@ -18330,6 +18944,22 @@ version toolchain ========== ========== +.. _list_software_MDAnalysis_981: + +*MDAnalysis* +++++++++++++ + +MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. + +*homepage*: https://www.mdanalysis.org/ + +========== ================= =============================== +version versionsuffix toolchain +========== ================= =============================== +``0.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +========== ================= =============================== + + .. _list_software_MDBM_288: *MDBM* @@ -18388,13 +19018,13 @@ Read, write and analyze MD trajectories with only a few lines of Python code. *homepage*: http://mdtraj.org -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``1.9.1`` ``-Python-3.6.3`` ``intel/2017b`` -``1.9.2`` ``-Python-3.6.6`` ``intel/2018b`` -``1.9.3`` ``-Python-3.7.4`` ``intel/2019b`` -========= ================= =============== +========= ================= =============================== +version versionsuffix toolchain +========= ================= =============================== +``1.9.1`` ``-Python-3.6.3`` ``intel/2017b`` +``1.9.2`` ``-Python-3.6.6`` ``intel/2018b`` +``1.9.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +========= ================= =============================== .. _list_software_medaka_611: @@ -18532,6 +19162,23 @@ version versionsuffix toolchain ========== ================= ================= +.. _list_software_MEM_223: + +*MEM* ++++++ + +Marker Enrichment Modeling (MEM) is a tool designed to calculate enrichment scores. + +*homepage*: https://github.com/cytolab/mem + +============ ============= ============== +version versionsuffix toolchain +============ ============= ============== +``20191023`` ``foss/2019b`` +``20191023`` ``-R-4.0.0`` ``foss/2020a`` +============ ============= ============== + + .. _list_software_MEME_292: *MEME* @@ -18546,6 +19193,7 @@ version versionsuffix toolchain ========= ============================== =============================== ``5.0.4`` ``-Perl-5.26.0-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``5.0.4`` ``-Perl-5.26.0-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``5.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========= ============================== =============================== @@ -18652,6 +19300,7 @@ version toolchain ``19.0.1`` ``GCCcore/8.2.0`` ``19.1.7`` ``GCCcore/8.3.0`` ``19.2.1`` ``GCCcore/8.3.0`` +``20.0.2`` ``GCCcore/9.3.0`` ========== ==================================================================== @@ -18692,6 +19341,7 @@ version versionsuffix toolchain ``0.50.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``0.51.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``0.53.1`` ``-Python-3.6.3`` ``intel/2017b`` +``0.53.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========== ================= ================================== @@ -18711,6 +19361,22 @@ version toolchain ========= ======================================================================================== +.. _list_software_MESS_312: + +*MESS* +++++++ + +Master Equation System Solver (MESS) + +*homepage*: https://github.com/PACChem/MESS + +========= ============== +version toolchain +========= ============== +``0.1.6`` ``foss/2019b`` +========= ============== + + .. _list_software_MetaBAT_606: *MetaBAT* @@ -18744,6 +19410,22 @@ version versionsuffix toolchain ================== ============= ============== +.. _list_software_metaerg_741: + +*metaerg* ++++++++++ + +MetaErg is a stand-alone and fully automated metagenomic and metaproteomic data annotation pipeline. + +*homepage*: https://github.com/xiaoli-dong/metaerg + +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``1.2.3`` ``-Python-2.7.16`` ``intel/2019b`` +========= ================== =============== + + .. _list_software_MetaGeneAnnotator_1724: *MetaGeneAnnotator* @@ -18868,13 +19550,13 @@ METIS is a set of serial programs for partitioning graphs, partitioning finite e *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview -========= ============= =============================================================================================================================================================================================================== -version versionsuffix toolchain -========= ============= =============================================================================================================================================================================================================== -``5.0.2`` ``gimkl/2.11.5`` -``5.1.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``5.1.0`` ``-32bitIDX`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -========= ============= =============================================================================================================================================================================================================== +========= ============= ================================================================================================================================================================================================================================== +version versionsuffix toolchain +========= ============= ================================================================================================================================================================================================================================== +``5.0.2`` ``gimkl/2.11.5`` +``5.1.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``5.1.0`` ``-32bitIDX`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +========= ============= ================================================================================================================================================================================================================================== .. _list_software_mhcflurry_988: @@ -18942,6 +19624,22 @@ version toolchain ========== =============================================== +.. _list_software_MinCED_496: + +*MinCED* +++++++++ + +Mining CRISPRs in Environmental Datasets + +*homepage*: https://github.com/ctSkennerton/minced + +========= ============= ================= +version versionsuffix toolchain +========= ============= ================= +``0.4.2`` ``-Java-11`` ``GCCcore/8.3.0`` +========= ============= ================= + + .. _list_software_Mini-XML_683: *Mini-XML* @@ -19039,16 +19737,16 @@ Minimap2 is a fast sequence mapping and alignment program that can find overlaps *homepage*: https://github.com/lh3/minimap2 -========== ==================== -version toolchain -========== ==================== -``2.0rc1`` ``foss/2016b`` -``2.10`` ``foss/2018a`` -``2.11`` ``intel/2018a`` -``2.12`` ``foss/2018a`` -``2.13`` ``foss/2018b`` -``2.17`` ``GCC/8.2.0-2.31.1`` -========== ==================== +========== ====================================================== +version toolchain +========== ====================================================== +``2.0rc1`` ``foss/2016b`` +``2.10`` ``foss/2018a`` +``2.11`` ``intel/2018a`` +``2.12`` ``foss/2018a`` +``2.13`` ``foss/2018b`` +``2.17`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/9.3.0`` +========== ====================================================== .. _list_software_MinPath_689: @@ -19058,12 +19756,13 @@ version toolchain MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset. -*homepage*: http://omics.informatics.indiana.edu/MinPath +*homepage*: https://omics.informatics.indiana.edu/MinPath ======= ================== =============================== version versionsuffix toolchain ======= ================== =============================== ``1.4`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``1.4`` ``-Python-2.7.16`` ``intel/2019b`` ======= ================== =============================== @@ -19102,6 +19801,22 @@ version versionsuffix toolchain =========== ================= =============== +.. _list_software_MitoZ_499: + +*MitoZ* ++++++++ + +MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization. + +*homepage*: https://github.com/linzhi2013/MitoZ + +======= ================= ============== +version versionsuffix toolchain +======= ================= ============== +``2.3`` ``-Python-3.6.6`` ``foss/2018b`` +======= ================= ============== + + .. _list_software_MiXCR_419: *MiXCR* @@ -19327,6 +20042,7 @@ version versionsuffix toolchain ``1.4.4`` ``-Python-2.7.15`` ``intel/2018b`` ``1.4.4`` ``-Python-3.7.2`` ``intel/2019a`` ``1.4.5`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.4.5`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========= ================== =============================== @@ -19487,6 +20203,7 @@ MotionCor2 correct anisotropic image motion at the single pixel level across the version toolchain ========= ================= ``1.2.6`` ``GCCcore/8.2.0`` +``1.3.1`` ``GCCcore/8.3.0`` ========= ================= @@ -19536,6 +20253,7 @@ version versionsuffix toolchain ========= =============== =============================== ``1.0.3`` ``intel/2017a`` ``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` +``1.1.0`` ``GCC/8.3.0`` ========= =============== =============================== @@ -19556,7 +20274,7 @@ version toolchain ``3.1.5`` ``GCCcore/6.4.0``, ``intel/2017a`` ``3.1.6`` ``GCCcore/6.4.0`` ``4.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``4.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``4.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ================================================================ @@ -19825,7 +20543,7 @@ version toolchain Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. -*homepage*: http://multiqc.info +*homepage*: https://multiqc.info ======= ================== =============================== version versionsuffix toolchain @@ -19837,6 +20555,8 @@ version versionsuffix toolchain ``1.6`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.7`` ``-Python-2.7.15`` ``intel/2018b`` ``1.7`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.8`` ``-Python-2.7.16`` ``intel/2019b`` +``1.8`` ``-Python-3.7.4`` ``intel/2019b`` ======= ================== =============================== @@ -19849,12 +20569,12 @@ Multiwfn is an extremely powerful program for realizingi electronic wavefunctio *homepage*: http://sobereva.com/multiwfn/ -========= =============== -version toolchain -========= =============== -``3.4.1`` ``intel/2017b`` -``3.6`` ``intel/2019a`` -========= =============== +========= ================================ +version toolchain +========= ================================ +``3.4.1`` ``intel/2017b`` +``3.6`` ``intel/2019a``, ``intel/2019b`` +========= ================================ .. _list_software_MUMmer_563: @@ -19881,15 +20601,15 @@ version toolchain A parallel sparse direct solver -*homepage*: http://graal.ens-lyon.fr/MUMPS/ +*homepage*: https://graal.ens-lyon.fr/MUMPS/ -========= ============== ================================================================================ -version versionsuffix toolchain -========= ============== ================================================================================ -``5.1.2`` ``-metis`` ``foss/2017b`` -``5.2.1`` ``-metis`` ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``intel/2019a``, ``intel/2019b`` -``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` -========= ============== ================================================================================ +========= ============== ================================================================================================================= +version versionsuffix toolchain +========= ============== ================================================================================================================= +``5.1.2`` ``-metis`` ``foss/2017b`` +``5.2.1`` ``-metis`` ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a`` +``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` +========= ============== ================================================================================================================= .. _list_software_muParser_847: @@ -19933,13 +20653,13 @@ MUSCLE is one of the best-performing multiple alignment programs according to *homepage*: http://drive5.com/muscle/ -============ =============== ================================================================================================================== -version versionsuffix toolchain -============ =============== ================================================================================================================== -``3.8.31`` ``foss/2016a``, ``foss/2017b``, ``foss/2018a``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``3.8.31`` ``-i86linux64`` ``system`` -``3.8.1551`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` -============ =============== ================================================================================================================== +============ =============== ====================================================================================================================================== +version versionsuffix toolchain +============ =============== ====================================================================================================================================== +``3.8.31`` ``GCC/7.3.0-2.30``, ``foss/2016a``, ``foss/2017b``, ``foss/2018a``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``3.8.31`` ``-i86linux64`` ``system`` +``3.8.1551`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` +============ =============== ====================================================================================================================================== .. _list_software_MuSiC_449: @@ -20152,7 +20872,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -20333,6 +21053,7 @@ version versionsuffix toolchain ========== ================== =============================== ``0.9.2`` ``intel/2018a`` ``0.10.2`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.13.1`` ``-Python-3.6.6`` ``foss/2018b`` ========== ================== =============================== @@ -20353,10 +21074,27 @@ version toolchain ``2.12.02`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a``, ``system`` ``2.13.01`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``2.13.03`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.14.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.14.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` =========== ==================================================================================== +.. _list_software_nauty_561: + +*nauty* ++++++++ + +nauty and Traces are programs for computing automorphism groups of graphs and digraphs. They can also produce a canonical label. + +*homepage*: http://pallini.di.uniroma1.it/ + +========== ==================== +version toolchain +========== ==================== +``2.6r12`` ``GCC/8.2.0-2.31.1`` +``2.7rc2`` ``GCC/8.2.0-2.31.1`` +========== ==================== + + .. _list_software_NBO_223: *NBO* @@ -20407,6 +21145,7 @@ version toolchain ``2.8.2`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``2.9.1-1`` ``foss/2018a``, ``intel/2018a`` ``2.9.3`` ``foss/2018b`` +``2.10.4`` ``gompi/2019b`` =========== ================================================ @@ -20448,6 +21187,7 @@ version versionsuffix toolchain ``1.16.1`` ``-R-3.5.1`` ``foss/2018b``, ``intel/2018b`` ``1.16.1`` ``-R-3.6.0`` ``foss/2019a`` ``1.17`` ``foss/2019b`` +``1.17`` ``-R-4.0.0`` ``foss/2020a`` ========== ============= =============================== @@ -20481,6 +21221,7 @@ NCIPLOT is a program for revealing non covalent interactions based on the reduc version toolchain ================ ======================= ``4.0-20190718`` ``iccifort/2019.5.281`` +``4.0-20200106`` ``iccifort/2019.5.281`` ================ ======================= @@ -20562,7 +21303,7 @@ version toolchain *ncurses* +++++++++ -The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. +The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. *homepage*: https://www.gnu.org/software/ncurses/ @@ -20572,6 +21313,7 @@ version toolchain ``5.9`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25``, ``gimkl/2.11.5``, ``system`` ``6.0`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``6.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` +``6.2`` ``GCCcore/9.3.0`` ======= ============================================================================================================================================================================================================================================================================================================================================================================= @@ -20662,7 +21404,7 @@ version toolchain *netCDF* ++++++++ -NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. +NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. *homepage*: https://www.unidata.ucar.edu/software/netcdf/ @@ -20681,6 +21423,7 @@ version versionsuffix toolchain ``4.6.1`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``4.6.2`` ``gompi/2019a``, ``iimpi/2019a`` ``4.7.1`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` +``4.7.4`` ``gompi/2020a``, ``iimpi/2020a`` =========== ================ ========================================================================================================================== @@ -20715,7 +21458,7 @@ version versionsuffix toolchain ``4.3.0`` ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``4.3.0`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.3.0`` ``-HDF5-1.8.19`` ``intel/2017b`` -``4.3.1`` ``iimpi/2019b`` +``4.3.1`` ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a`` ========= ================ ====================================================================================================================================================== @@ -20738,7 +21481,7 @@ version versionsuffix toolchain ``4.4.4`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.4.4`` ``-HDF5-1.8.19`` ``foss/2017b``, ``intel/2017b`` ``4.4.5`` ``gompi/2019a``, ``iimpi/2019a`` -``4.5.2`` ``gompi/2019b``, ``iimpi/2019b`` +``4.5.2`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a`` ========= ================ ==================================================================================================================================================================================================================================================================================================================================== @@ -20751,21 +21494,21 @@ Python/numpy interface to netCDF. *homepage*: https://unidata.github.io/netcdf4-python/ -========= ============================= =============== -version versionsuffix toolchain -========= ============================= =============== -``1.2.9`` ``-Python-2.7.13`` ``intel/2017a`` -``1.3.1`` ``-Python-3.6.3`` ``intel/2017b`` -``1.3.1`` ``-Python-3.6.3-HDF5-1.8.19`` ``intel/2017b`` -``1.4.0`` ``-Python-3.6.2-HDF5-1.8.19`` ``foss/2017b`` -``1.4.0`` ``-Python-3.6.4`` ``intel/2018a`` -``1.4.1`` ``-Python-2.7.15`` ``intel/2018b`` -``1.4.1`` ``-Python-3.6.6`` ``intel/2018b`` -``1.4.2`` ``-Python-3.6.4`` ``foss/2018a`` -``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` -``1.5.2`` ``intel/2019a`` -``1.5.3`` ``-Python-3.7.4`` ``intel/2019b`` -========= ============================= =============== +========= ============================= =============================== +version versionsuffix toolchain +========= ============================= =============================== +``1.2.9`` ``-Python-2.7.13`` ``intel/2017a`` +``1.3.1`` ``-Python-3.6.3`` ``intel/2017b`` +``1.3.1`` ``-Python-3.6.3-HDF5-1.8.19`` ``intel/2017b`` +``1.4.0`` ``-Python-3.6.2-HDF5-1.8.19`` ``foss/2017b`` +``1.4.0`` ``-Python-3.6.4`` ``intel/2018a`` +``1.4.1`` ``-Python-2.7.15`` ``intel/2018b`` +``1.4.1`` ``-Python-3.6.6`` ``intel/2018b`` +``1.4.2`` ``-Python-3.6.4`` ``foss/2018a`` +``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` +``1.5.2`` ``intel/2019a`` +``1.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +========= ============================= =============================== .. _list_software_netloc_645: @@ -20822,15 +21565,15 @@ version toolchain *netMHCIIpan* +++++++++++++ -The NetMHCIIpan software predicts binding of peptides to MHC class II molecules. The predictions are available for the three human MHC class II isotypes HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules (H-2). +NetMHCIIpan 3.2 server predicts binding of peptides to MHC class II molecules. The predictions are available for the three human MHC class II isotypes HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules (H-2). -*homepage*: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCIIpan +*homepage*: https://www.cbs.dtu.dk/services/NetMHCIIpan/ -======= ================= -version toolchain -======= ================= -``3.2`` ``GCCcore/7.3.0`` -======= ================= +======= ==================================== +version toolchain +======= ==================================== +``3.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +======= ==================================== .. _list_software_netMHCpan_862: @@ -20905,10 +21648,12 @@ version versionsuffix toolchain ``2.0`` ``-Python-2.7.14`` ``intel/2017b`` ``2.1`` ``-Python-2.7.14`` ``intel/2017b`` ``2.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b`` +``2.2`` ``-Python-2.7.16`` ``foss/2019b`` ``2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``2.4`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``2.4`` ``-Python-3.8.2`` ``foss/2020a`` ======== ================== =============================================== @@ -20961,6 +21706,7 @@ version toolchain ``19.07.0`` ``system`` ``19.12.0`` ``system`` ``20.01.0`` ``system`` +``20.04.1`` ``system`` =========== ========== @@ -21031,6 +21777,7 @@ version versionsuffix toolchain ``2.9.3`` ``-Java-1.8`` ``foss/2018b`` ``2.10.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` ``2.10.0`` ``-Java-11`` ``GCCcore/8.2.0`` +``2.10.4`` ``-Java-11`` ``GCCcore/8.3.0`` ========== =================== ================================== @@ -21039,15 +21786,16 @@ version versionsuffix toolchain *NGS-Python* ++++++++++++ -NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. +NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. *homepage*: https://github.com/ncbi/ngs -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``1.2.3`` ``-Python-2.7.11`` ``intel/2016a`` -========= ================== =============== +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``1.2.3`` ``-Python-2.7.11`` ``intel/2016a`` +``2.10.4`` ``-Python-2.7.16`` ``gompi/2019b`` +========== ================== =============== .. _list_software_NGSadmix_763: @@ -21122,6 +21870,22 @@ version toolchain ========= ================= +.. _list_software_nifti2dicom_1112: + +*nifti2dicom* ++++++++++++++ + +Nifti2Dicom is a conversion tool that converts 3D NIfTI files (and other formats supported by ITK, including Analyze, MetaImage Nrrd and VTK) to DICOM. Unlike other conversion tools, it can import a DICOM file that is used to import the patient and study DICOM tags, and allows you to edit the accession number and other DICOM tags, in order to create a valid DICOM that can be imported in a PACS. + +*homepage*: https://github.com/biolab-unige/nifti2dicom + +========== ============== +version toolchain +========== ============== +``0.4.11`` ``foss/2019b`` +========== ============== + + .. _list_software_Nilearn_713: *Nilearn* @@ -21183,12 +21947,13 @@ Ninja is a small build system with a focus on speed. *homepage*: https://ninja-build.org/ -========= ==================================================================================== -version toolchain -========= ==================================================================================== -``1.8.2`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017b``, ``intel/2018a`` -``1.9.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` -========= ==================================================================================== +========== ==================================================================================== +version toolchain +========== ==================================================================================== +``1.8.2`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017b``, ``intel/2018a`` +``1.9.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` +``1.10.0`` ``GCCcore/9.3.0`` +========== ==================================================================================== .. _list_software_Nipype_629: @@ -21208,6 +21973,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_NLMpy_464: + +*NLMpy* ++++++++ + +NLMpy is a Python package for the creation of neutral landscape models that are widely used in the modelling of ecological patterns and processes across landscapes. + +*homepage*: https://pypi.org/project/nlmpy + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.1.5`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + .. _list_software_NLopt_493: *NLopt* @@ -21221,7 +22002,7 @@ NLopt is a free/open-source library for nonlinear optimization, providing a com version toolchain ========= =================================================================================================================================================================================================================================================== ``2.4.2`` ``GCC/5.4.0-2.26``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``iomkl/2018a`` -``2.6.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.6.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= =================================================================================================================================================================================================================================================== @@ -21267,16 +22048,16 @@ Node.js is a platform built on Chrome's JavaScript runtime for easily building *homepage*: http://nodejs.org -=========== ================= -version toolchain -=========== ================= -``4.4.7`` ``foss/2016a`` -``6.10.3`` ``foss/2017a`` -``8.9.4`` ``foss/2017a`` -``10.15.1`` ``foss/2018b`` -``10.15.3`` ``GCCcore/8.2.0`` -``12.16.1`` ``GCCcore/8.3.0`` -=========== ================= +=========== ==================================== +version toolchain +=========== ==================================== +``4.4.7`` ``foss/2016a`` +``6.10.3`` ``foss/2017a`` +``8.9.4`` ``foss/2017a`` +``10.15.1`` ``foss/2018b`` +``10.15.3`` ``GCCcore/8.2.0`` +``12.16.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +=========== ==================================== .. _list_software_Normaliz_844: @@ -21284,7 +22065,7 @@ version toolchain *Normaliz* ++++++++++ -Normaliz is an open source tool for computations in affine monoids, vector configurations, lattice polytopes, and rational cones. +Normaliz is a open source tool for computations in affine monoids, vector configurations, rational polyhedra and rational cones. Normaliz now computes rational and algebraic polyhedra, i.e., polyhedra defined over real algebraic extensions of QQ. *homepage*: https://www.normaliz.uni-osnabrueck.de/ @@ -21292,6 +22073,7 @@ Normaliz is an open source tool for computations in affine monoids, vector confi version toolchain ========= =============== ``3.6.3`` ``intel/2018b`` +``3.7.4`` ``gompi/2019a`` ========= =============== @@ -21393,6 +22175,7 @@ version toolchain ======== ==================================== ``4.20`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``4.21`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``4.25`` ``GCCcore/9.3.0`` ======== ==================================== @@ -21411,9 +22194,26 @@ version toolchain ``3.39`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``3.42.1`` ``GCCcore/8.2.0`` ``3.45`` ``GCCcore/8.3.0`` +``3.51`` ``GCCcore/9.3.0`` ========== ==================================== +.. _list_software_ntCard_604: + +*ntCard* +++++++++ + +ntCard is a streaming algorithm for estimating the frequencies of k-mers in genomics datasets. + +*homepage*: https://www.bcgsc.ca/resources/software/ntcard + +========= ============= +version toolchain +========= ============= +``1.2.1`` ``GCC/8.3.0`` +========= ============= + + .. _list_software_ntEdit_616: *ntEdit* @@ -21446,6 +22246,22 @@ version toolchain ========= ====================================== +.. _list_software_NTL_238: + +*NTL* ++++++ + +NTL is a high-performance, portable C++ library providing data structures and algorithms for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the integers and over finite fields. + +*homepage*: https://shoup.net/ntl/ + +========== ==================== +version toolchain +========== ==================== +``11.3.4`` ``GCC/8.2.0-2.31.1`` +========== ==================== + + .. _list_software_numactl_756: *numactl* @@ -21462,7 +22278,7 @@ version toolchain ``2.0.10`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25`` ``2.0.11`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.3.0-2.26``, ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``GCC/6.2.0-2.27``, ``GCC/6.3.0-2.27``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` ``2.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2.0.13`` ``GCCcore/9.2.0`` +``2.0.13`` ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ========== ============================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -21499,24 +22315,25 @@ The numexpr package evaluates multiple-operator array expressions many times fas *homepage*: https://numexpr.readthedocs.io/en/latest/ -========= ================== ================================== -version versionsuffix toolchain -========= ================== ================================== -``2.5.2`` ``-Python-2.7.11`` ``intel/2016a`` -``2.6.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.6.1`` ``-Python-3.5.2`` ``intel/2016b`` -``2.6.4`` ``-Python-2.7.13`` ``foss/2017a`` -``2.6.4`` ``-Python-2.7.14`` ``intel/2018a`` -``2.6.4`` ``-Python-3.5.1`` ``foss/2016a`` -``2.6.4`` ``-Python-3.6.1`` ``intel/2017a`` -``2.6.4`` ``-Python-3.6.3`` ``intel/2017b`` -``2.6.4`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``2.6.5`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``2.6.5`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``2.7.0`` ``intel/2019a`` -``2.7.1`` ``-Python-2.7.16`` ``intel/2019b`` -``2.7.1`` ``-Python-3.7.4`` ``foss/2019b`` -========= ================== ================================== +========= ================== =================================================== +version versionsuffix toolchain +========= ================== =================================================== +``2.5.2`` ``-Python-2.7.11`` ``intel/2016a`` +``2.6.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``2.6.1`` ``-Python-3.5.2`` ``intel/2016b`` +``2.6.4`` ``-Python-2.7.13`` ``foss/2017a`` +``2.6.4`` ``-Python-2.7.14`` ``intel/2018a`` +``2.6.4`` ``-Python-3.5.1`` ``foss/2016a`` +``2.6.4`` ``-Python-3.6.1`` ``intel/2017a`` +``2.6.4`` ``-Python-3.6.3`` ``intel/2017b`` +``2.6.4`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``2.6.5`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``2.6.5`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``2.7.0`` ``intel/2019a`` +``2.7.1`` ``-Python-2.7.16`` ``intel/2019b`` +``2.7.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.7.1`` ``-Python-3.8.2`` ``intel/2020a`` +========= ================== =================================================== .. _list_software_numpy_569: @@ -21572,6 +22389,7 @@ version versionsuffix toolc ``6.6.revision27746`` ``-2015-10-20-Python-2.7.12`` ``iomkl/2017a`` ``6.6.revision27746`` ``-2015-10-20-patches-20170814-Python-2.7.13`` ``intel/2017a`` ``6.8.revision47`` ``-2017-12-14-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` +``7.0.0`` ``-Python-3.7.4`` ``intel/2019b`` ===================== ============================================== ================================ @@ -21745,12 +22563,12 @@ OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-sour *homepage*: https://www.score-p.org -========= ================= -version toolchain -========= ================= -``2.0`` ``foss/2016a`` -``2.0.5`` ``GCCcore/8.2.0`` -========= ================= +========= ==================================== +version toolchain +========= ==================================== +``2.0`` ``foss/2016a`` +``2.0.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ==================================== .. _list_software_OpenAI-Gym_886: @@ -21820,6 +22638,7 @@ version versionsuffix toolchain ``0.3.6`` ``GCC/8.3.0-2.32`` ``0.3.7`` ``GCC/8.3.0`` ``0.3.8`` ``GCC/9.2.0`` +``0.3.9`` ``GCC/9.3.0`` ========== ================= ========================================================== @@ -21917,6 +22736,7 @@ version toolchain ``2.2.0`` ``intel/2016b``, ``intel/2017a`` ``2.3.0`` ``foss/2018b``, ``intel/2018b`` ``2.4.0`` ``GCCcore/8.3.0`` +``2.4.1`` ``GCCcore/9.3.0`` ========= ================================ @@ -22120,6 +22940,7 @@ version versionsuffix toolchain ``4.0.0`` ``-hpcx`` ``GCC/8.2.0-2.31.1`` ``4.0.1`` ``GCC/8.3.0-2.32`` ``4.0.2`` ``GCC/9.2.0-2.32`` +``4.0.3`` ``GCC/9.3.0`` ``system`` ``GCC/system-2.29`` ========== ============= ==================================================================================================================== @@ -22149,11 +22970,11 @@ OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM *homepage*: http://code.google.com/p/openpgm/ -=========== ============================================================================================================================================================================= -version toolchain -=========== ============================================================================================================================================================================= -``5.2.122`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -=========== ============================================================================================================================================================================= +=========== ================================================================================================================================================================================================ +version toolchain +=========== ================================================================================================================================================================================================ +``5.2.122`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +=========== ================================================================================================================================================================================================ .. _list_software_OpenPIV_641: @@ -22181,11 +23002,12 @@ A Python library to read/write Excel 2010 xlsx/xlsm files *homepage*: https://openpyxl.readthedocs.io -========= ================= -version toolchain -========= ================= -``2.6.2`` ``GCCcore/8.2.0`` -========= ================= +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``2.6.2`` ``GCCcore/8.2.0`` +``3.0.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= .. _list_software_OpenPyXL_767: @@ -22259,7 +23081,7 @@ version toolchain The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. -*homepage*: http://www.openssl.org/ +*homepage*: https://www.openssl.org/ ========== ===================================================================== version toolchain @@ -22274,6 +23096,7 @@ version toolchain ``1.1.0h`` ``GCCcore/7.3.0`` ``1.1.1b`` ``GCCcore/8.2.0`` ``1.1.1d`` ``GCCcore/8.3.0`` +``1.1.1e`` ``GCCcore/9.3.0`` ========== ===================================================================== @@ -22475,12 +23298,12 @@ The Open Trace Format 2 is a highly scalable, memory efficient event trace data *homepage*: https://www.score-p.org -======= ============================== -version toolchain -======= ============================== -``2.0`` ``foss/2016a``, ``foss/2017a`` -``2.2`` ``GCCcore/8.2.0`` -======= ============================== +======= ==================================== +version toolchain +======= ==================================== +``2.0`` ``foss/2016a``, ``foss/2017a`` +``2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +======= ==================================== .. _list_software_ownCloud_843: @@ -22522,7 +23345,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_pip_329` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_pip_329` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-mpi_1052` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -22710,21 +23533,21 @@ Pango is a library for laying out and rendering of text, with an emphasis on int *homepage*: https://www.pango.org/ -=========== ================================== -version toolchain -=========== ================================== -``1.39.0`` ``foss/2016a``, ``intel/2016a`` -``1.40.1`` ``foss/2016a``, ``intel/2016a`` -``1.40.3`` ``foss/2016b``, ``intel/2016b`` -``1.40.5`` ``intel/2017a`` -``1.40.12`` ``intel/2017a`` -``1.40.14`` ``foss/2017b``, ``intel/2017b`` -``1.41.0`` ``foss/2017b``, ``intel/2017b`` -``1.41.1`` ``foss/2018a``, ``intel/2018a`` -``1.42.4`` ``foss/2018b``, ``fosscuda/2018b`` -``1.43.0`` ``GCCcore/8.2.0`` -``1.44.7`` ``GCCcore/8.3.0`` -=========== ================================== +=========== ==================================== +version toolchain +=========== ==================================== +``1.39.0`` ``foss/2016a``, ``intel/2016a`` +``1.40.1`` ``foss/2016a``, ``intel/2016a`` +``1.40.3`` ``foss/2016b``, ``intel/2016b`` +``1.40.5`` ``intel/2017a`` +``1.40.12`` ``intel/2017a`` +``1.40.14`` ``foss/2017b``, ``intel/2017b`` +``1.41.0`` ``foss/2017b``, ``intel/2017b`` +``1.41.1`` ``foss/2018a``, ``intel/2018a`` +``1.42.4`` ``foss/2018b``, ``fosscuda/2018b`` +``1.43.0`` ``GCCcore/8.2.0`` +``1.44.7`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +=========== ==================================== .. _list_software_PAPI_298: @@ -22734,7 +23557,7 @@ version toolchain PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. -*homepage*: http://icl.cs.utk.edu/projects/papi/ +*homepage*: https://icl.cs.utk.edu/projects/papi/ ========= ==================================== version toolchain @@ -22743,6 +23566,7 @@ version toolchain ``5.5.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``5.6.0`` ``GCCcore/6.4.0`` ``5.7.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``6.0.0`` ``GCCcore/8.3.0`` ========= ==================================== @@ -22771,6 +23595,7 @@ version toolchain ``20190222`` ``GCCcore/7.3.0`` ``20190622`` ``GCCcore/8.2.0`` ``20190922`` ``GCCcore/8.3.0`` +``20200422`` ``GCCcore/9.3.0`` ============ =============================== @@ -22984,13 +23809,13 @@ PatchELF is a small utility to modify the dynamic linker and RPATH of ELF execut *homepage*: http://nixos.org/patchelf.html -======== ================================= -version toolchain -======== ================================= -``0.8`` ``GNU/4.9.3-2.25`` -``0.9`` ``GCCcore/6.4.0``, ``foss/2016a`` -``0.10`` ``GCCcore/7.2.0`` -======== ================================= +======== ==================================== +version toolchain +======== ==================================== +``0.8`` ``GNU/4.9.3-2.25`` +``0.9`` ``GCCcore/6.4.0``, ``foss/2016a`` +``0.10`` ``GCCcore/7.2.0``, ``GCCcore/8.3.0`` +======== ==================================== .. _list_software_path.py_708: @@ -23229,6 +24054,7 @@ version toolchain ``8.40`` ``GCCcore/6.3.0``, ``gimkl/2017a``, ``intel/2016b``, ``intel/2017a`` ``8.41`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``8.43`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``8.44`` ``GCCcore/9.3.0`` ======== ================================================================================== @@ -23247,6 +24073,7 @@ version toolchain ``10.21`` ``foss/2016a`` ``10.31`` ``foss/2018b`` ``10.33`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``10.34`` ``GCCcore/9.3.0`` ========= ==================================== @@ -23257,14 +24084,14 @@ version toolchain Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations. -*homepage*: http://www.cs.uoregon.edu/research/pdt/ +*homepage*: https://www.cs.uoregon.edu/research/pdt/ -======== ================= -version toolchain -======== ================= -``3.22`` ``foss/2016a`` -``3.25`` ``GCCcore/8.2.0`` -======== ================= +======== ==================================== +version toolchain +======== ==================================== +``3.22`` ``foss/2016a`` +``3.25`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +======== ==================================== .. _list_software_PEAR_296: @@ -23313,6 +24140,7 @@ version versionsuffix toolchain ``5.28.0`` ``GCCcore/7.3.0`` ``5.28.1`` ``GCCcore/8.2.0`` ``5.30.0`` ``GCCcore/8.3.0`` +``5.30.2`` ``GCCcore/9.3.0`` ========== ============= ========================================================================================= @@ -23370,6 +24198,7 @@ version versionsuffix toolchain ``3.11.1`` ``foss/2019a``, ``intel/2019a`` ``3.12.3`` ``foss/2019b`` ``3.12.4`` ``foss/2019b``, ``intel/2019b`` +``3.12.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ==================== =============================== @@ -23811,6 +24640,7 @@ version versionsuffix toolchain ``5.3.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``6.0.0`` ``GCCcore/8.2.0`` ``6.2.1`` ``GCCcore/8.3.0`` +``7.0.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ================================= =================================================== @@ -23902,6 +24732,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_pIRS_350: + +*pIRS* +++++++ + +pIRS (profile based Illumina pair-end Reads Simulator) is a program for simulating paired-end reads from a reference genome. It is optimized for simulating reads similar to those generated from the Illumina platform. + +*homepage*: https://github.com/galaxy001/pirs + +========= =============== +version toolchain +========= =============== +``2.0.2`` ``gompi/2019b`` +========= =============== + + .. _list_software_Pisces_615: *Pisces* @@ -23964,7 +24810,7 @@ version toolchain ========== ============================================================================================================================================ ``0.34.0`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``0.38.0`` ``GCCcore/8.2.0`` -``0.38.4`` ``GCCcore/8.3.0`` +``0.38.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ============================================================================================================================================ @@ -23999,7 +24845,7 @@ version toolchain ``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` ``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``0.29.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``system`` +``0.29.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a``, ``system`` ========== =========================================================================================================================================================================== @@ -24028,6 +24874,7 @@ version versionsuffix toolchain ``1.3.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.3.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``1.5.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``1.5.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``1.5.1`` ``-python`` ``GCCcore/8.2.0`` ========= ================== =================================================== @@ -24131,6 +24978,7 @@ version toolchain ``2.00-alpha1-x86_64`` ``system`` ``2.00-alpha2-x86_64`` ``system`` ``2.00-alpha2-x86_64_avx2`` ``system`` +``2.00a2.3_x86_64`` ``system`` =========================== ============================== @@ -24224,7 +25072,7 @@ version versionsuffix toolchain PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. -*homepage*: http://www.plumed-code.org +*homepage*: https://www.plumed.org ========= ================== ================================================ version versionsuffix toolchain @@ -24244,6 +25092,7 @@ version versionsuffix toolchain ``2.5.2`` ``-Python-3.7.2`` ``intel/2019a`` ``2.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``2.5b`` ``-Python-2.7.14`` ``intel/2018a`` +``2.6.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========= ================== ================================================ @@ -24283,6 +25132,7 @@ version toolchain ``3.0.2`` ``GCCcore/8.2.0`` ``3.1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``3.1.4`` ``GCCcore/8.3.0`` +``3.1.5`` ``GCCcore/9.3.0`` ========= ======================================================= @@ -24390,6 +25240,22 @@ version toolchain ========== ============== +.. _list_software_popscle_758: + +*popscle* ++++++++++ + +A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools + +*homepage*: https://github.com/statgen/popscle + +============ ============== +version toolchain +============ ============== +``0.1-beta`` ``foss/2019b`` +============ ============== + + .. _list_software_popt_451: *popt* @@ -24759,6 +25625,7 @@ version toolchain ``5.0.0`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018a`` ``6.0.0`` ``GCCcore/8.2.0`` ``6.2.1`` ``GCCcore/8.3.0`` +``7.0.0`` ``GCCcore/9.3.0`` ========= ================================================================================= @@ -24866,6 +25733,23 @@ version versionsuffix toolchain ========= ============================= ============== +.. _list_software_ProtHint_824: + +*ProtHint* +++++++++++ + +ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences. + +*homepage*: https://github.com/gatech-genemark/ProtHint + +========= ================= ======================================== +version versionsuffix toolchain +========= ================= ======================================== +``2.4.0`` ``-Python-3.7.2`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.4.0`` ``-Python-3.7.4`` ``iccifort/2019.5.281`` +========= ================= ======================================== + + .. _list_software_protobuf_881: *protobuf* @@ -24902,23 +25786,40 @@ Python Protocol Buffers runtime library. *homepage*: https://github.com/google/protobuf/ -========= ================== ================================== -version versionsuffix toolchain -========= ================== ================================== -``3.0.2`` ``-Python-2.7.11`` ``foss/2016a`` -``3.0.2`` ``-Python-3.5.1`` ``foss/2016a`` -``3.2.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.2.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``3.3.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.3.0`` ``-Python-3.5.2`` ``foss/2016b`` -``3.3.0`` ``-Python-3.6.1`` ``intel/2017a`` -``3.4.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.4.0`` ``-Python-2.7.14`` ``intel/2017b`` -``3.4.0`` ``-Python-3.6.1`` ``intel/2017a`` -``3.4.0`` ``-Python-3.6.3`` ``intel/2017b`` -``3.6.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``3.6.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -========= ================== ================================== +========== ================== ================================== +version versionsuffix toolchain +========== ================== ================================== +``3.0.2`` ``-Python-2.7.11`` ``foss/2016a`` +``3.0.2`` ``-Python-3.5.1`` ``foss/2016a`` +``3.2.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.2.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``3.3.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.3.0`` ``-Python-3.5.2`` ``foss/2016b`` +``3.3.0`` ``-Python-3.6.1`` ``intel/2017a`` +``3.4.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.4.0`` ``-Python-2.7.14`` ``intel/2017b`` +``3.4.0`` ``-Python-3.6.1`` ``intel/2017a`` +``3.4.0`` ``-Python-3.6.3`` ``intel/2017b`` +``3.6.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``3.6.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``3.10.0`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================== ================================== + + +.. _list_software_protozero_1012: + +*protozero* ++++++++++++ + +Minimalistic protocol buffer decoder and encoder in C++. + +*homepage*: https://github.com/mapbox/protozero + +========= ================= +version toolchain +========= ================= +``1.6.8`` ``GCCcore/7.3.0`` +========= ================= .. _list_software_PRSice_550: @@ -25326,6 +26227,7 @@ version versionsuffix toolchain ``2.2.4`` ``-Python-3.6.4`` ``foss/2018a`` ``2.2.4`` ``-Python-3.6.6`` ``intel/2018b`` ``2.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ================= ================= @@ -25922,11 +26824,11 @@ Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machin *homepage*: https://docs.pymc.io/ -======= ================= =============== -version versionsuffix toolchain -======= ================= =============== -``3.8`` ``-Python-3.7.4`` ``intel/2019b`` -======= ================= =============== +======= ================= =============================== +version versionsuffix toolchain +======= ================= =============================== +``3.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +======= ================= =============================== .. _list_software_pymemcache_1052: @@ -26272,6 +27174,22 @@ version versionsuffix toolchain ========== ================= ============== +.. _list_software_pysndfx_780: + +*pysndfx* ++++++++++ + +A lightweight Python wrapper for SoX - Sound eXchange. Supported effects range from EQ and compression to phasers, reverb and pitch shifters. + +*homepage*: https://github.com/carlthome/python-audio-effects + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.3.6`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_Pysolar_746: *Pysolar* @@ -26348,25 +27266,26 @@ PyTables is a package for managing hierarchical datasets and designed to efficie *homepage*: https://www.pytables.org -=========== ================== ================================== -version versionsuffix toolchain -=========== ================== ================================== -``3.2.2`` ``-Python-2.7.12`` ``foss/2016b`` -``3.2.3.1`` ``-Python-2.7.12`` ``intel/2016b`` -``3.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.3.0`` ``-Python-3.5.2`` ``intel/2016b`` -``3.4.2`` ``-Python-2.7.13`` ``foss/2017a`` -``3.4.2`` ``-Python-3.6.1`` ``intel/2017a`` -``3.4.2`` ``-Python-3.6.3`` ``intel/2017b`` -``3.4.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``3.4.4`` ``-Python-2.7.15`` ``foss/2018b`` -``3.4.4`` ``-Python-3.5.1`` ``foss/2016a`` -``3.4.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``3.5.2`` ``intel/2019a`` -``3.5.2`` ``-Python-2.7.14`` ``intel/2018a`` -``3.5.2`` ``-Python-2.7.16`` ``intel/2019b`` -``3.6.1`` ``-Python-3.7.4`` ``foss/2019b`` -=========== ================== ================================== +=========== ================== =================================================== +version versionsuffix toolchain +=========== ================== =================================================== +``3.2.2`` ``-Python-2.7.12`` ``foss/2016b`` +``3.2.3.1`` ``-Python-2.7.12`` ``intel/2016b`` +``3.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.3.0`` ``-Python-3.5.2`` ``intel/2016b`` +``3.4.2`` ``-Python-2.7.13`` ``foss/2017a`` +``3.4.2`` ``-Python-3.6.1`` ``intel/2017a`` +``3.4.2`` ``-Python-3.6.3`` ``intel/2017b`` +``3.4.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``3.4.4`` ``-Python-2.7.15`` ``foss/2018b`` +``3.4.4`` ``-Python-3.5.1`` ``foss/2016a`` +``3.4.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``3.5.2`` ``intel/2019a`` +``3.5.2`` ``-Python-2.7.14`` ``intel/2018a`` +``3.5.2`` ``-Python-2.7.16`` ``intel/2019b`` +``3.6.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``3.6.1`` ``-Python-3.8.2`` ``intel/2020a`` +=========== ================== =================================================== .. _list_software_pytest_681: @@ -26394,6 +27313,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_pytest-mpi_1052: + +*pytest-mpi* +++++++++++++ + +pytest_mpi is a plugin for pytest providing some useful tools when running tests under MPI, and testing MPI-related code. + +*homepage*: https://pytest-mpi.readthedocs.io + +======= ================= ================= +version versionsuffix toolchain +======= ================= ================= +``0.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +======= ================= ================= + + .. _list_software_PYTHIA_463: *PYTHIA* @@ -26437,6 +27372,7 @@ version versionsuffix toolchain ``2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``2.7.15`` ``-bare`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``2.7.16`` ``GCCcore/8.3.0`` +``2.7.18`` ``GCCcore/9.3.0`` ``3.5.1`` ``foss/2016a``, ``intel/2016a`` ``3.5.2`` ``foss/2016.04``, ``foss/2016b``, ``intel/2016b`` ``3.5.2`` ``-bare`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` @@ -26448,6 +27384,7 @@ version versionsuffix toolchain ``3.7.0`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.7.2`` ``GCCcore/8.2.0`` ``3.7.4`` ``GCCcore/8.3.0`` +``3.8.2`` ``GCCcore/9.3.0`` ========== ================= ================================================================================================================================================================= @@ -26482,6 +27419,7 @@ Python extension for computing string edit distances and similarities. version versionsuffix toolchain ========== ================= ============== ``0.12.0`` ``-Python-3.6.6`` ``foss/2018b`` +``0.12.0`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================= ============== @@ -26577,6 +27515,38 @@ version versionsuffix toolchain ========= =============================== ============== +.. _list_software_PyVCF_424: + +*PyVCF* ++++++++ + +A Variant Call Format reader for Python. + +*homepage*: https://github.com/jamescasbon/PyVCF + +========= ============= +version toolchain +========= ============= +``0.6.8`` ``GCC/8.3.0`` +========= ============= + + +.. _list_software_PyWavelets_1044: + +*PyWavelets* +++++++++++++ + +PyWavelets is open source wavelet transform software for Python. + +*homepage*: https://pywavelets.readthedocs.io + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``1.1.1`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + .. _list_software_PyYAML_508: *PyYAML* @@ -26603,6 +27573,7 @@ version versionsuffix toolchain ``3.13`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``5.1`` ``GCCcore/8.2.0`` ``5.1.2`` ``GCCcore/8.3.0`` +``5.3`` ``GCCcore/9.3.0`` ========= ================== ==================================================================================== @@ -26949,6 +27920,7 @@ version toolchain ``5.11.2`` ``foss/2018b`` ``5.12.3`` ``GCCcore/8.2.0`` ``5.13.1`` ``GCCcore/8.3.0`` +``5.14.1`` ``GCCcore/9.3.0`` ========== ==================================================================================== @@ -27058,20 +28030,20 @@ Quantum ESPRESSO is an integrated suite of computer codes for electronic-struc *homepage*: https://www.quantum-espresso.org -========= ============= =============================== -version versionsuffix toolchain -========= ============= =============================== -``5.3.0`` ``intel/2016.02-GCC-4.9`` -``5.4.0`` ``intel/2016.02-GCC-4.9`` -``5.4.0`` ``-hybrid`` ``foss/2016b`` -``6.0`` ``intel/2016b`` -``6.1`` ``intel/2017a`` -``6.2`` ``intel/2017b`` -``6.2.1`` ``iomkl/2017b`` -``6.3`` ``foss/2018b``, ``intel/2018b`` -``6.4.1`` ``intel/2019a`` -``6.5`` ``intel/2019a`` -========= ============= =============================== +========= ============= ================================ +version versionsuffix toolchain +========= ============= ================================ +``5.3.0`` ``intel/2016.02-GCC-4.9`` +``5.4.0`` ``intel/2016.02-GCC-4.9`` +``5.4.0`` ``-hybrid`` ``foss/2016b`` +``6.0`` ``intel/2016b`` +``6.1`` ``intel/2017a`` +``6.2`` ``intel/2017b`` +``6.2.1`` ``iomkl/2017b`` +``6.3`` ``foss/2018b``, ``intel/2018b`` +``6.4.1`` ``intel/2019a`` +``6.5`` ``intel/2019a``, ``intel/2019b`` +========= ============= ================================ .. _list_software_QUAST_398: @@ -27216,7 +28188,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray_300` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray_300` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_rstudio_778` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -27246,6 +28218,8 @@ version versionsuffix toolchain ``3.5.1`` ``-Python-2.7.15`` ``foss/2018b`` ``3.6.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``3.6.2`` ``foss/2019b``, ``fosscuda/2019b`` +``3.6.3`` ``foss/2020a`` +``4.0.0`` ``foss/2020a`` ========= ================== =================================================== @@ -27271,6 +28245,7 @@ version versionsuffix toolchain ``3.8`` ``-R-3.5.1`` ``foss/2018b`` ``3.9`` ``-R-3.6.0`` ``foss/2019a`` ``3.10`` ``foss/2019b`` +``3.11`` ``-R-4.0.0`` ``foss/2020a`` ======== ============= =============================== @@ -27323,6 +28298,7 @@ version toolchain ``1.3.2`` ``GCCcore/8.2.0`` ``1.4.7`` ``GCCcore/8.2.0``, ``gcccuda/2019b`` ``1.4.10`` ``GCC/7.3.0-2.30`` +``1.4.13`` ``GCCcore/8.3.0`` ========== ==================================== @@ -27342,6 +28318,22 @@ version versionsuffix toolchain ======= ================== ============== +.. _list_software_rampart_759: + +*rampart* ++++++++++ + +Read Assignment, Mapping, and Phylogenetic Analysis in Real Time. + +*homepage*: https://github.com/artic-network/rampart/ + +============ ================= ============== +version versionsuffix toolchain +============ ================= ============== +``1.2.0rc3`` ``-Python-3.6.6`` ``foss/2018b`` +============ ================= ============== + + .. _list_software_randfold_842: *randfold* @@ -27485,11 +28477,12 @@ Parallel genome assemblies for parallel DNA sequencing *homepage*: http://denovoassembler.sourceforge.net/ -========= =============== -version toolchain -========= =============== -``2.3.1`` ``iimpi/2019a`` -========= =============== +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.8.4`` ``-Python-3.7.4`` ``foss/2019b`` +``2.3.1`` ``iimpi/2019a`` +========= ================= =============== .. _list_software_RBFOpt_525: @@ -27622,6 +28615,7 @@ version toolchain ========= ================= ``1.1.1`` ``GCCcore/8.2.0`` ``1.2.1`` ``GCCcore/8.3.0`` +``1.3`` ``GCCcore/9.3.0`` ========= ================= @@ -27869,6 +28863,22 @@ version versionsuffix toolchain ========== ============= =============== +.. _list_software_rickflow_865: + +*rickflow* +++++++++++ + +Running and Analyzing OpenMM Jobs + +*homepage*: https://gitlab.com/Olllom/rickflow + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.7.0`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + .. _list_software_rioxarray_993: *rioxarray* @@ -27882,6 +28892,7 @@ geospatial xarray extension powered by rasterio version versionsuffix toolchain ========== ================= =============== ``0.0.12`` ``-Python-3.7.2`` ``intel/2019a`` +``0.0.24`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================= =============== @@ -27925,15 +28936,32 @@ version toolchain *RMBlast* +++++++++ -RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. +RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. *homepage*: http://www.repeatmasker.org/RMBlast.html -========== ================== ============== -version versionsuffix toolchain -========== ================== ============== -``2.2.28`` ``-Python-2.7.11`` ``foss/2016a`` -========== ================== ============== +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``2.2.28`` ``-Python-2.7.11`` ``foss/2016a`` +``2.9.0`` ``gompi/2019b`` +========== ================== =============== + + +.. _list_software_RNA-Bloom_775: + +*RNA-Bloom* ++++++++++++ + +RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. + +*homepage*: https://github.com/bcgsc/RNA-Bloom + +========= ============= +version toolchain +========= ============= +``1.2.3`` ``GCC/8.3.0`` +========= ============= .. _list_software_RNA-SeQC_602: @@ -28108,12 +29136,28 @@ version versionsuffix toolchain ============ ================== =============================== +.. _list_software_root_numpy_1116: + +*root_numpy* +++++++++++++ + +root_numpy is a Python extension module that provides an efficient interface between ROOT and NumPy. root_numpy’s internals are compiled C++ and can therefore handle large amounts of data much faster than equivalent pure Python implementations. + +*homepage*: https://scikit-hep.org/root_numpy/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``4.8.0`` ``-Python-3.6.6`` ``foss/2018b`` +========= ================= ============== + + .. _list_software_rootpy_685: *rootpy* ++++++++ -The rootpy project is a community-driven initiative aiming to provide a more pythonic interface with ROOT on top of the existing PyROOT bindings. Given Python’s reflective and dynamic nature, rootpy also aims to improve ROOT design flaws and supplement existing ROOT functionality. The scientific Python community also offers a multitude of powerful packages such as SciPy, NumPy, matplotlib, scikit-learn, and PyTables, but a suitable interface between them and ROOT has been lacking. rootpy provides the interfaces and conversion mechanisms required to liberate your data and to take advantage of these alternatives if needed. +The rootpy project is a community-driven initiative aiming to provide a more pythonic interface with ROOT on top of the existing PyROOT bindings. Given Python’s reflective and dynamic nature, rootpy also aims to improve ROOT design flaws and supplement existing ROOT functionality. The scientific Python community also offers a multitude of powerful packages such as SciPy, NumPy, matplotlib, scikit-learn, and PyTables, but a suitable interface between them and ROOT has been lacking. rootpy provides the interfaces and conversion mechanisms required to liberate your data and to take advantage of these alternatives if needed. *homepage*: http://www.rootpy.org/ @@ -28121,6 +29165,7 @@ The rootpy project is a community-driven initiative aiming to provide a more pyt version versionsuffix toolchain ========= ================== ============== ``0.8.0`` ``-Python-2.7.11`` ``foss/2016a`` +``1.0.1`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================== ============== @@ -28263,6 +29308,23 @@ version versionsuffix toolchain ========== ============= ============== +.. _list_software_rstudio_778: + +*rstudio* ++++++++++ + +This RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) + +*homepage*: https://www.rstudio.com/ + +============ ============= ================== +version versionsuffix toolchain +============ ============= ================== +``1.2.5033`` ``-Java-11`` ``fosscuda/2019b`` +``1.2.5042`` ``-Java-11`` ``foss/2019b`` +============ ============= ================== + + .. _list_software_RTG-Tools_811: *RTG-Tools* @@ -28329,20 +29391,21 @@ Rust is a systems programming language that runs blazingly fast, prevents segfau *homepage*: https://www.rust-lang.org -========== ================= -version toolchain -========== ================= -``1.8.0`` ``foss/2016a`` -``1.12.0`` ``foss/2016b`` -``1.12.1`` ``foss/2016b`` -``1.18.0`` ``foss/2017a`` -``1.21.0`` ``foss/2017b`` -``1.22.1`` ``GCCcore/6.4.0`` -``1.29.2`` ``GCCcore/7.3.0`` -``1.30.1`` ``GCCcore/6.4.0`` -``1.35.0`` ``GCCcore/8.2.0`` -``1.37.0`` ``GCCcore/8.3.0`` -========== ================= +========== ======================================================= +version toolchain +========== ======================================================= +``1.8.0`` ``foss/2016a`` +``1.12.0`` ``foss/2016b`` +``1.12.1`` ``foss/2016b`` +``1.18.0`` ``foss/2017a`` +``1.21.0`` ``foss/2017b`` +``1.22.1`` ``GCCcore/6.4.0`` +``1.29.2`` ``GCCcore/7.3.0`` +``1.30.1`` ``GCCcore/6.4.0`` +``1.35.0`` ``GCCcore/8.2.0`` +``1.37.0`` ``GCCcore/8.3.0`` +``1.42.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +========== ======================================================= .. _list_software_letter_s: @@ -28351,7 +29414,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL2_277` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_Shannon_725` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_Singularity_1179` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_Stata_509` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_SymEngine_911` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_Stata_509` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -28441,9 +29504,9 @@ version versionsuffix toolchain *Salmon* ++++++++ -Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. +Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves its accuracy and speed via a number of different innovations, including the use of selective-alignment, and massively-parallel stochastic collapsed variational inference. -*homepage*: https://github.com/COMBINE-lab/salmon +*homepage*: https://salmon.readthedocs.io ========== ================== ================================ version versionsuffix toolchain @@ -28456,6 +29519,7 @@ version versionsuffix toolchain ``0.14.2`` ``gompi/2019a`` ``1.0.0`` ``gompi/2019a``, ``gompi/2019b`` ``1.1.0`` ``gompi/2019b`` +``1.2.0`` ``gompi/2019b`` ========== ================== ================================ @@ -28550,7 +29614,7 @@ version versionsuffix toolchain ``1.7`` ``foss/2018a``, ``intel/2018a`` ``1.8`` ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``1.10`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``1.10`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ========== ================= ======================================================================================================================================= @@ -28619,6 +29683,22 @@ version versionsuffix toolchain ========= =================== ========== +.. _list_software_ScaFaCoS_707: + +*ScaFaCoS* +++++++++++ + +ScaFaCoS is a library of scalable fast coulomb solvers. + +*homepage*: http://www.scafacos.de/ + +========= =============================== +version toolchain +========= =============================== +``1.0.1`` ``foss/2020a``, ``intel/2020a`` +========= =============================== + + .. _list_software_ScaLAPACK_707: *ScaLAPACK* @@ -28642,6 +29722,7 @@ version versionsuffix toolchain ``2.0.2`` ``-OpenBLAS-0.3.1`` ``gompi/2018b``, ``gompic/2018b`` ``2.0.2`` ``-OpenBLAS-0.3.3`` ``gompi/2018.08`` ``2.0.2`` ``-OpenBLAS-0.3.5`` ``gompi/2019a``, ``gompic/2019a`` +``2.1.0`` ``gompi/2020a`` ========= ================================= ============================================================================================================================================ @@ -28739,6 +29820,7 @@ Scikit-Build, or skbuild, is an improved build system generator for CPython C/C version versionsuffix toolchain ========== ================= =============================== ``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.10.0`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================= =============================== @@ -28891,6 +29973,7 @@ version versionsuffix toolchain ``2019.03`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` ``2019.10`` ``-Python-2.7.16`` ``foss/2019b``, ``intel/2019b`` ``2019.10`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2020.03`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` =========== ================== ======================================================================== @@ -28953,6 +30036,7 @@ version versionsuffix toolchain ``3.0.5`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``3.0.5`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``3.1.1`` ``GCCcore/8.3.0`` +``3.1.2`` ``GCCcore/9.3.0`` ========= ======================= ================================================================================= @@ -28985,12 +30069,12 @@ The Score-P measurement infrastructure is a highly scalable and easy-to-use too *homepage*: https://www.score-p.org -========= =============== -version toolchain -========= =============== -``2.0.1`` ``foss/2016a`` -``6.0`` ``gompi/2019a`` -========= =============== +========= ================================= +version toolchain +========= ================================= +``2.0.1`` ``foss/2016a`` +``6.0`` ``gompi/2019a``, ``gompic/2019b`` +========= ================================= .. _list_software_SCOTCH_452: @@ -29009,7 +30093,7 @@ version versionsuffix toolchain ``6.0.4`` ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``6.0.4`` ``-64bitint`` ``foss/2017b`` ``6.0.6`` ``foss/2018a``, ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2018a`` -``6.0.9`` ``gompi/2019b``, ``iimpi/2019b`` +``6.0.9`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a`` =================== ============= ===================================================================================================================================================== @@ -29063,6 +30147,22 @@ version versionsuffix toolchain ========== ================= ============== +.. _list_software_Scythe_624: + +*Scythe* +++++++++ + +Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases. + +*homepage*: https://github.com/ucdavis-bioinformatics/scythe + +========= ================= +version toolchain +========= ================= +``0.994`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_SDCC_285: *SDCC* @@ -29088,13 +30188,30 @@ SDL: Simple DirectMedia Layer, a cross-platform multimedia library *homepage*: http://www.libsdl.org/ -========= ====================================================================== -version toolchain -========= ====================================================================== -``2.0.4`` ``intel/2016b`` -``2.0.8`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``2.0.9`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -========= ====================================================================== +========== ====================================================================== +version toolchain +========== ====================================================================== +``2.0.4`` ``intel/2016b`` +``2.0.8`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``2.0.9`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``2.0.10`` ``GCCcore/8.3.0`` +========== ====================================================================== + + +.. _list_software_SDSL_310: + +*SDSL* +++++++ + +The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. + +*homepage*: https://github.com/simongog/sdsl-lite + +================== ============= +version toolchain +================== ============= +``2.1.1-20191211`` ``GCC/8.3.0`` +================== ============= .. _list_software_Seaborn_714: @@ -29293,13 +30410,13 @@ SeqAn is an open source C++ library of efficient algorithms and data structures *homepage*: https://www.seqan.de/ -========= ============= ===================================================== -version versionsuffix toolchain -========= ============= ===================================================== -``1.4.2`` ``-library`` ``system`` -``2.3.2`` ``foss/2016b`` -``2.4.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` -========= ============= ===================================================== +========= ============= ======================================================================== +version versionsuffix toolchain +========= ============= ======================================================================== +``1.4.2`` ``-library`` ``system`` +``2.3.2`` ``foss/2016b`` +``2.4.0`` ``GCC/8.2.0-2.31.1``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2018b`` +========= ============= ======================================================================== .. _list_software_SeqAn3_523: @@ -29436,6 +30553,22 @@ version versionsuffix toolchain ============ ================== =============== +.. _list_software_SHAP_300: + +*SHAP* +++++++ + +SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions. + +*homepage*: https://github.com/slundberg/shap + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.35.0`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_shapAAR_640: *shapAAR* @@ -29764,30 +30897,11 @@ Singular is a computer algebra system for polynomial computations, with special *homepage*: https://www.singular.uni-kl.de/ -========= ========== -version toolchain -========= ========== -``4.1.2`` ``system`` -========= ========== - - -.. _list_software_Singularity_1179: - -*Singularity* -+++++++++++++ - -Singularity is a portable application stack packaging and runtime utility. - -*homepage*: http://singularity.lbl.gov - -========= ================== -version toolchain -========= ================== -``1.0`` ``GCC/4.9.3-2.25`` -``2.2.1`` ``GCC/6.3.0-2.27`` -``2.3.1`` ``GCC/5.4.0-2.26`` -``2.4.2`` ``GCC/5.4.0-2.26`` -========= ================== +========= ================================ +version toolchain +========= ================================ +``4.1.2`` ``GCC/8.2.0-2.31.1``, ``system`` +========= ================================ .. _list_software_SIONlib_624: @@ -29797,7 +30911,7 @@ version toolchain SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. -*homepage*: http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html +*homepage*: https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html ========= ============= ================= version versionsuffix toolchain @@ -29807,6 +30921,7 @@ version versionsuffix toolchain ``1.7.1`` ``foss/2017a`` ``1.7.1`` ``-tools`` ``foss/2017a`` ``1.7.4`` ``-tools`` ``GCCcore/8.2.0`` +``1.7.6`` ``-tools`` ``GCCcore/8.3.0`` ========= ============= ================= @@ -29891,11 +31006,11 @@ SLATEC Common Mathematical Library, a comprehensive software library containing *homepage*: https://www.netlib.org/slatec/ -======= ========================================================== -version toolchain -======= ========================================================== -``4.1`` ``GCC/6.4.0-2.28``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` -======= ========================================================== +======= ========================================================================= +version toolchain +======= ========================================================================= +``4.1`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` +======= ========================================================================= .. _list_software_SLEPc_407: @@ -30131,6 +31246,7 @@ version toolchain ``1.1.3`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25`` ``1.1.6`` ``system`` ``1.1.7`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``intel/2017b`` +``1.1.8`` ``GCCcore/9.3.0`` ========= ============================================================================================================ @@ -30184,6 +31300,22 @@ version versionsuffix toolchain ============ ========================== =============================== +.. _list_software_SNPomatic_878: + +*SNPomatic* ++++++++++++ + +High throughput sequencing technologies generate large amounts of short reads. Mapping these to a reference sequence consumes large amounts of processing time and memory, and read mapping errors can lead to noisy or incorrect alignments. SNP-o-matic is a fast, memory-efficient, and stringent read mapping tool offering a variety of analytical output functions, with an emphasis on genotyping. + +*homepage*: https://github.com/magnusmanske/snpomatic + +======= ================= +version toolchain +======= ================= +``1.0`` ``GCCcore/9.3.0`` +======= ================= + + .. _list_software_SOAPaligner_1045: *SOAPaligner* @@ -30298,6 +31430,22 @@ version toolchain ======= ============== +.. _list_software_SoX_282: + +*SoX* ++++++ + +SoX is the Swiss Army Knife of sound processing utilities. It can convert audio files to other popular audio file types and also apply sound effects and filters during the conversion. + +*homepage*: https://sourceforge.net/projects/sox + +========== ============= +version toolchain +========== ============= +``14.4.2`` ``GCC/8.3.0`` +========== ============= + + .. _list_software_Spack_498: *Spack* @@ -30352,6 +31500,7 @@ Spaln (space-efficient spliced alignment) is a stand-alone program that maps an version toolchain ========== ======================================== ``2.3.3c`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.4.03`` ``iccifort/2019.5.281`` ========== ======================================== @@ -30671,6 +31820,7 @@ version toolchain ``3.26.0`` ``GCCcore/8.2.0`` ``3.27.2`` ``GCCcore/8.2.0`` ``3.29.0`` ``GCCcore/8.3.0`` +``3.31.1`` ``GCCcore/9.3.0`` ============ ==================================================================================================================================================================== @@ -30699,18 +31849,20 @@ The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will all *homepage*: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software -=========== =================== ========== -version versionsuffix toolchain -=========== =================== ========== -``2.3.5`` ``-centos_linux64`` ``system`` -``2.5.4-1`` ``-centos_linux64`` ``system`` -``2.5.7`` ``-centos_linux64`` ``system`` -``2.8.2-1`` ``-centos_linux64`` ``system`` -``2.9.0`` ``-centos_linux64`` ``system`` -``2.9.2`` ``-ubuntu64`` ``system`` -``2.9.4`` ``-centos_linux64`` ``system`` -``2.9.6-1`` ``-centos_linux64`` ``system`` -=========== =================== ========== +=========== =================== =============== +version versionsuffix toolchain +=========== =================== =============== +``2.3.5`` ``-centos_linux64`` ``system`` +``2.5.4-1`` ``-centos_linux64`` ``system`` +``2.5.7`` ``-centos_linux64`` ``system`` +``2.8.2-1`` ``-centos_linux64`` ``system`` +``2.9.0`` ``-centos_linux64`` ``system`` +``2.9.2`` ``-ubuntu64`` ``system`` +``2.9.4`` ``-centos_linux64`` ``system`` +``2.9.6-1`` ``-centos_linux64`` ``system`` +``2.10.4`` ``gompi/2019b`` +``2.10.5`` ``-centos_linux64`` ``system`` +=========== =================== =============== .. _list_software_SRPRISM_560: @@ -30787,7 +31939,7 @@ version versionsuffix toolchain Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. -*homepage*: http://catchenlab.life.illinois.edu/stacks +*homepage*: https://catchenlab.life.illinois.edu/stacks/ ============== ============================================================================== version toolchain @@ -30809,6 +31961,7 @@ version toolchain ``2.3e`` ``foss/2018b`` ``2.5`` ``iccifort/2019.5.281`` ``2.41`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.53`` ``foss/2019b`` ============== ============================================================================== @@ -31049,6 +32202,7 @@ version toolchain ``1.3.5`` ``GCCcore/8.2.0``, ``foss/2018b`` ``2.0.3`` ``GCCcore/7.3.0`` ``2.1.0`` ``foss/2018b`` +``2.1.1`` ``GCC/8.3.0`` ========== ================================== @@ -31145,6 +32299,7 @@ version versionsuffix toolchain ``5.1.2`` ``-ParMETIS-4.0.3`` ``foss/2017b``, ``intel/2017b`` ``5.4.0`` ``-METIS-5.1.0`` ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` ``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b``, ``intel/2019b`` +``5.7.1`` ``-METIS-5.1.0`` ``foss/2020a``, ``intel/2020a`` ========= =================== ================================================================================================= @@ -31356,10 +32511,26 @@ version versionsuffix toolchain ``3.0.12`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` ``3.0.12`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.0.12`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``4.0.1`` ``GCCcore/8.3.0`` +``4.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ============================ ================================================================ +.. _list_software_swissknife_1094: + +*swissknife* +++++++++++++ + +Perl module for reading and writing UniProtKB data in plain text format. + +*homepage*: https://sourceforge.net/projects/swissknife/ + +======== ================= +version toolchain +======== ================= +``1.80`` ``GCCcore/8.3.0`` +======== ================= + + .. _list_software_SymEngine_911: *SymEngine* @@ -31384,18 +32555,19 @@ version versionsuffix toolchain SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries. -*homepage*: http://sympy.org/ +*homepage*: https://sympy.org/ -======= ================== =============================== -version versionsuffix toolchain -======= ================== =============================== -``1.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``1.3`` ``-Python-2.7.14`` ``intel/2018a`` -``1.3`` ``-Python-2.7.15`` ``foss/2018b`` -``1.3`` ``-Python-3.6.4`` ``intel/2018a`` -``1.3`` ``-Python-3.6.6`` ``foss/2018b`` -``1.4`` ``foss/2019a``, ``intel/2019a`` -======= ================== =============================== +========= ================== =============================== +version versionsuffix toolchain +========= ================== =============================== +``1.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``1.3`` ``-Python-2.7.14`` ``intel/2018a`` +``1.3`` ``-Python-2.7.15`` ``foss/2018b`` +``1.3`` ``-Python-3.6.4`` ``intel/2018a`` +``1.3`` ``-Python-3.6.6`` ``foss/2018b`` +``1.4`` ``foss/2019a``, ``intel/2019a`` +``1.5.1`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================== =============================== .. _list_software_Szip_422: @@ -31411,7 +32583,7 @@ Szip compression software, providing lossless compression of scientific data version toolchain ========= ========================================================================================================================================================================================================================================================================= ``2.1`` ``GCC/4.8.1``, ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``2.1.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.1.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ========================================================================================================================================================================================================================================================================= @@ -31421,7 +32593,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_texinfo_765` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` +:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_texinfo_765` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` .. _list_software_tabix_536: @@ -31472,6 +32644,22 @@ version toolchain ========== ================= +.. _list_software_Taiyaki_716: + +*Taiyaki* ++++++++++ + +Taiyaki is research software for training models for basecalling Oxford Nanopore reads. + +*homepage*: https://github.com/nanoporetech/taiyaki + +================== ================= ================================== +version versionsuffix toolchain +================== ================= ================================== +``5.0.1-20200316`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +================== ================= ================================== + + .. _list_software_TAMkin_548: *TAMkin* @@ -31533,6 +32721,7 @@ version toolchain ``2018_U5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2019_U4`` ``GCCcore/8.2.0`` ``2019_U9`` ``GCCcore/8.3.0`` +``2020.1`` ``GCCcore/9.3.0`` ``2020.2`` ``GCCcore/8.3.0`` ============== ================================================== @@ -31551,6 +32740,7 @@ version versionsuffix toolchain ============ ============= ========== ``25.8`` ``-linux64`` ``system`` ``20180227`` ``-linux64`` ``system`` +``20200302`` ``-linux64`` ``system`` ============ ============= ========== @@ -31590,9 +32780,26 @@ version toolchain ``8.6.7`` ``GCCcore/6.4.0`` ``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``8.6.10`` ``GCCcore/9.3.0`` ========== ========================================================================================================================================================================= +.. _list_software_TCLAP_372: + +*TCLAP* ++++++++ + +TCLAP is a small, flexible library that provides a simple interface for defining and accessing command line arguments. It was intially inspired by the user friendly CLAP libary. + +*homepage*: http://tclap.sourceforge.net/ + +========= ================= +version toolchain +========= ================= +``1.2.2`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_tcsh_434: *tcsh* @@ -31677,6 +32884,7 @@ version versionsuffix toolchain ``2.0.1`` ``-Python-3.7.2`` ``foss/2019a`` ``2.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.2.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========== ============================= =================================================== @@ -31989,19 +33197,20 @@ Tk is an open source, cross-platform widget toolchain that provides a library of *homepage*: https://www.tcl.tk/ -========= ================= ================================================================================================================================================ -version versionsuffix toolchain -========= ================= ================================================================================================================================================ -``8.6.3`` ``-no-X11`` ``GCC/4.8.4``, ``GCC/4.9.2`` -``8.6.4`` ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``8.6.4`` ``-libX11-1.6.3`` ``intel/2016a`` -``8.6.4`` ``-no-X11`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a`` -``8.6.5`` ``GCC/5.4.0-2.26``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016b`` -``8.6.6`` ``foss/2017a``, ``intel/2017a`` -``8.6.7`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2018a``, ``iomkl/2018a`` -``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= ================= ================================================================================================================================================ +========== ================= ================================================================================================================================================ +version versionsuffix toolchain +========== ================= ================================================================================================================================================ +``8.6.3`` ``-no-X11`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``8.6.4`` ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` +``8.6.4`` ``-libX11-1.6.3`` ``intel/2016a`` +``8.6.4`` ``-no-X11`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a`` +``8.6.5`` ``GCC/5.4.0-2.26``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016b`` +``8.6.6`` ``foss/2017a``, ``intel/2017a`` +``8.6.7`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2018a``, ``iomkl/2018a`` +``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``8.6.10`` ``GCCcore/9.3.0`` +========== ================= ================================================================================================================================================ .. _list_software_Tkinter_737: @@ -32028,6 +33237,7 @@ version versionsuffix toolchain ``3.6.6`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.7.2`` ``GCCcore/8.2.0`` ``3.7.4`` ``GCCcore/8.3.0`` +``3.8.2`` ``GCCcore/9.3.0`` ========== ================== ========================================================================================================= @@ -32119,6 +33329,22 @@ version versionsuffix toolchain ========= ================== ================================================================================ +.. _list_software_torchaudio_1074: + +*torchaudio* +++++++++++++ + +Data manipulation and transformation for audio signal processing, powered by PyTorch + +*homepage*: https://github.com/pytorch/audio + +========= =============================== ================================== +version versionsuffix toolchain +========= =============================== ================================== +``0.5.0`` ``-Python-3.7.4-PyTorch-1.4.0`` ``foss/2019b``, ``fosscuda/2019b`` +========= =============================== ================================== + + .. _list_software_torchtext_997: *torchtext* @@ -32128,11 +33354,11 @@ Data loaders and abstractions for text and NLP *homepage*: https://github.com/pytorch/text -========= ================================ ================== -version versionsuffix toolchain -========= ================================ ================== -``0.5.0`` ``-PyTorch-1.4.0--Python-3.7.4`` ``fosscuda/2019b`` -========= ================================ ================== +========= =============================== ================== +version versionsuffix toolchain +========= =============================== ================== +``0.5.0`` ``-PyTorch-1.4.0-Python-3.7.4`` ``fosscuda/2019b`` +========= =============================== ================== .. _list_software_torchvision_1208: @@ -32144,15 +33370,16 @@ Datasets, Transforms and Models specific to Computer Vision *homepage*: https://github.com/pytorch/vision -========= ============================= ================================== -version versionsuffix toolchain -========= ============================= ================================== -``0.2.0`` ``-Python-3.6.4`` ``intel/2018a`` -``0.2.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` -``0.2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` -``0.4.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` -========= ============================= ================================== +========= =============================== ================================== +version versionsuffix toolchain +========= =============================== ================================== +``0.2.0`` ``-Python-3.6.4`` ``intel/2018a`` +``0.2.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` +``0.2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` +``0.4.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``0.5.0`` ``-Python-3.7.4-PyTorch-1.4.0`` ``fosscuda/2019b`` +========= =============================== ================================== .. _list_software_TotalView_927: @@ -32651,6 +33878,7 @@ version versionsuffix toolchain ``1.5.0rc1`` ``-hpcx`` ``GCCcore/8.2.0`` ``1.5.1`` ``GCCcore/8.2.0`` ``1.6.1`` ``GCCcore/8.3.0`` +``1.8.0`` ``GCCcore/9.3.0`` ============ ============= ======================================================= @@ -32680,14 +33908,14 @@ UDUNITS supports conversion of unit specifications between formatted and binary *homepage*: http://www.unidata.ucar.edu/software/udunits/ -========== ======================================================================================================================================== -version toolchain -========== ======================================================================================================================================== -``2.2.20`` ``foss/2016a``, ``intel/2016b`` -``2.2.24`` ``intel/2017a`` -``2.2.25`` ``foss/2017b``, ``intel/2017b`` -``2.2.26`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -========== ======================================================================================================================================== +========== =========================================================================================================================================================== +version toolchain +========== =========================================================================================================================================================== +``2.2.20`` ``foss/2016a``, ``intel/2016b`` +``2.2.24`` ``intel/2017a`` +``2.2.25`` ``foss/2017b``, ``intel/2017b`` +``2.2.26`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +========== =========================================================================================================================================================== .. _list_software_UFL_231: @@ -32719,6 +33947,7 @@ Tools for handling Unique Molecular Identifiers in NGS data sets version versionsuffix toolchain ========= ================= ============== ``1.0.0`` ``-Python-3.6.6`` ``foss/2018b`` +``1.0.1`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -32899,6 +34128,7 @@ version toolchain ========= ================= ``2.2.0`` ``GCCcore/6.4.0`` ``2.3.0`` ``GCCcore/8.2.0`` +``2.5.0`` ``GCCcore/8.3.0`` ========= ================= @@ -32927,6 +34157,7 @@ version toolchain ``2.32.1`` ``GCCcore/7.3.0`` ``2.33`` ``GCCcore/8.2.0`` ``2.34`` ``GCCcore/8.3.0`` +``2.35`` ``GCCcore/9.3.0`` ========== ==================================== @@ -33128,16 +34359,16 @@ The aim of VCFtools is to provide easily accessible methods for working with c *homepage*: https://vcftools.github.io -========== ================ =============================== -version versionsuffix toolchain -========== ================ =============================== -``0.1.14`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` -``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` -``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` -``0.1.16`` ``GCC/8.3.0`` -``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` -========== ================ =============================== +========== ================ ===================================================== +version versionsuffix toolchain +========== ================ ===================================================== +``0.1.14`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` +``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` +``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` +``0.1.16`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` +``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` +========== ================ ===================================================== .. _list_software_VEGAS_374: @@ -33323,11 +34554,11 @@ Voro++ is a software library for carrying out three-dimensional computations of *homepage*: http://math.lbl.gov/voro++/ -========= =================================================================================== -version toolchain -========= =================================================================================== -``0.4.6`` ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2019b``, ``intel/2016a``, ``intel/2019b`` -========= =================================================================================== +========= ====================================================================================================== +version toolchain +========= ====================================================================================================== +``0.4.6`` ``GCCcore/6.4.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2019b``, ``intel/2016a``, ``intel/2019b`` +========= ====================================================================================================== .. _list_software_vsc-base_788: @@ -33505,6 +34736,7 @@ version versionsuffix toolchain ``8.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ``8.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``8.2.0`` ``-Python-3.7.4`` ``foss/2019b`` +``8.2.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========= ================== ================================== @@ -33578,7 +34810,7 @@ version toolchain --- -:ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` +:ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` .. _list_software_Wannier90_829: @@ -33830,6 +35062,7 @@ version versionsuffix toolchain ``1.6.8`` ``-intel-2018a`` ``system`` ``1.6.8`` ``-intel-2018b`` ``system`` ``1.6.11`` ``-intel-2019b`` ``system`` +``1.6.12`` ``-foss-2019a`` ``system`` ========== ================ =============== @@ -33904,6 +35137,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_wtdbg2_586: + +*wtdbg2* +++++++++ + +Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. + +*homepage*: https://github.com/ruanjue/wtdbg2 + +======= ================= +version toolchain +======= ================= +``2.5`` ``GCCcore/9.3.0`` +======= ================= + + .. _list_software_wxPropertyGrid_1498: *wxPropertyGrid* @@ -33956,6 +35205,7 @@ version toolchain ========= ==================== ``3.0.3`` ``foss/2018a`` ``3.0.4`` ``GCC/8.2.0-2.31.1`` +``3.1.3`` ``GCC/8.3.0`` ========= ==================== @@ -33988,6 +35238,7 @@ version toolchain ``20180604`` ``GCCcore/7.3.0`` ``20190311`` ``GCCcore/8.2.0`` ``20190717`` ``GCCcore/8.3.0`` +``20200222`` ``GCCcore/9.3.0`` ============ ================================================== @@ -34015,6 +35266,7 @@ version toolchain ``20181203`` ``GCCcore/7.3.0`` ``20190413`` ``GCCcore/8.2.0`` ``20190925`` ``GCCcore/8.3.0`` +``20191217`` ``GCCcore/9.3.0`` ============ ================================= @@ -34037,6 +35289,7 @@ version toolchain ``2.9`` ``GCCcore/7.3.0`` ``3.0`` ``GCCcore/8.2.0`` ``3.2`` ``GCCcore/8.3.0`` +``3.3`` ``GCCcore/9.3.0`` ======= ================================== @@ -34482,13 +35735,13 @@ X.org macros utilities. *homepage*: https://cgit.freedesktop.org/xorg/util/macros -========== ============================================================================================= -version toolchain -========== ============================================================================================= -``1.19.0`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` -``1.19.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``1.19.2`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` -========== ============================================================================================= +========== ================================================================================================================ +version toolchain +========== ================================================================================================================ +``1.19.0`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` +``1.19.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``1.19.2`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +========== ================================================================================================================ .. _list_software_xprop_569: @@ -34611,6 +35864,7 @@ version versionsuffix toolchain ``5.2.2`` ``-gettext-0.19.7`` ``foss/2016a``, ``intel/2016a`` ``5.2.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``gimkl/2017a`` ``5.2.4`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` +``5.2.5`` ``GCCcore/9.3.0`` ========= =================== =========================================================================================================================================================== @@ -34664,6 +35918,7 @@ version versionsuffix toolchain ``1.5.0`` ``-Python-3.7.2`` ``intel/2019a`` ``1.6.0`` ``-Python-3.7.2`` ``intel/2019a`` ``1.6.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.6.0`` ``-Python-3.8.2`` ``foss/2020a`` ==================== ============================== ================================================ @@ -34709,11 +35964,11 @@ Yasm: Complete rewrite of the NASM assembler with BSD license *homepage*: http://www.tortall.net/projects/yasm/ -========= ================================================================================================================================================================================================================ -version toolchain -========= ================================================================================================================================================================================================================ -``1.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -========= ================================================================================================================================================================================================================ +========= =================================================================================================================================================================================================================================== +version toolchain +========= =================================================================================================================================================================================================================================== +``1.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +========= =================================================================================================================================================================================================================================== .. _list_software_YAXT_326: @@ -34730,7 +35985,7 @@ version toolchain ========= ================================================= ``0.5.1`` ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``0.6.0`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``0.6.2`` ``iimpi/2019b`` +``0.6.2`` ``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` ========= ================================================= @@ -34776,7 +36031,7 @@ version toolchain ``4.2.0`` ``foss/2016b``, ``intel/2016b`` ``4.2.2`` ``foss/2017a``, ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` ``4.2.5`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` -``4.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``4.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ========================================================================================================= @@ -34827,7 +36082,7 @@ version toolchain ``1.2.7`` ``GCC/4.8.1``, ``GCC/4.8.2`` ``1.2.8`` ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.2.10`` ``system`` -``1.2.11`` ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` +``1.2.11`` ``GCCcore/10.1.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -34871,13 +36126,14 @@ version toolchain Zsh is a shell designed for interactive use, although it is also a powerful scripting language. -*homepage*: http://www.zsh.org/ +*homepage*: https://www.zsh.org/ ========= ================== version toolchain ========= ================== ``5.1.1`` ``GNU/4.9.3-2.25`` ``5.2`` ``foss/2016b`` +``5.8`` ``GCC/8.3.0`` ========= ================== @@ -34895,5 +36151,6 @@ version toolchain ========= ================================= ``1.3.4`` ``foss/2016b`` ``1.4.0`` ``GCCcore/8.2.0``, ``foss/2018b`` +``1.4.4`` ``GCCcore/9.3.0`` ========= ================================= diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index 6505e118..d6a01d22 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -282,6 +282,7 @@ * RubyGem + * GoPackage * IntelBase * EB_Advisor diff --git a/docs/version-specific/easyconfig_constants.rst b/docs/version-specific/easyconfig_constants.rst index 0e6b7490..61682839 100644 --- a/docs/version-specific/easyconfig_constants.rst +++ b/docs/version-specific/easyconfig_constants.rst @@ -5,15 +5,20 @@ Constants that can be used in easyconfigs ----------------------------------------- -====================== =========================================== ================================================= -Constant name Constant value Description -====================== =========================================== ================================================= -``OS_NAME`` ``UNKNOWN`` System name (e.g. 'fedora' or 'RHEL') -``SYSTEM`` ``{'version': 'system', 'name': 'system'}`` System toolchain -``EXTERNAL_MODULE`` ``EXTERNAL_MODULE`` External module marker -``OS_VERSION`` ``UNKNOWN`` System version -``HOME`` ``/home/example`` Home directory ($HOME) -``OS_TYPE`` ``Darwin`` System type (e.g. 'Linux' or 'Darwin') -``SYS_PYTHON_VERSION`` ``2.7.16`` System Python version (platform.python_version()) -====================== =========================================== ================================================= +====================== ============================================================= ================================================================================ +Constant name Constant value Description +====================== ============================================================= ================================================================================ +``EXTERNAL_MODULE`` ``EXTERNAL_MODULE`` External module marker +``HOME`` ``/home/example`` Home directory ($HOME) +``OS_NAME`` ``UNKNOWN`` System name (e.g. 'fedora' or 'RHEL') +``OS_PKG_IBVERBS_DEV`` ``('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')`` OS packages providing ibverbs/infiniband development support +``OS_PKG_OPENSSL_BIN`` ``openssl`` OS packages providing the openSSL binary +``OS_PKG_OPENSSL_DEV`` ``('openssl-devel', 'libssl-dev', 'libopenssl-devel')`` OS packages providing openSSL developement support +``OS_PKG_OPENSSL_LIB`` ``('libssl', 'libopenssl')`` OS packages providing openSSL libraries +``OS_PKG_PAM_DEV`` ``('pam-devel', 'libpam0g-dev')`` OS packages providing Pluggable Authentication Module (PAM) developement support +``OS_TYPE`` ``Darwin`` System type (e.g. 'Linux' or 'Darwin') +``OS_VERSION`` ``UNKNOWN`` System version +``SYSTEM`` ``{'version': 'system', 'name': 'system'}`` System toolchain +``SYS_PYTHON_VERSION`` ``2.7.16`` System Python version (platform.python_version()) +====================== ============================================================= ================================================================================ diff --git a/docs/version-specific/easyconfig_parameters.rst b/docs/version-specific/easyconfig_parameters.rst index b57e93ac..bcb981c5 100644 --- a/docs/version-specific/easyconfig_parameters.rst +++ b/docs/version-specific/easyconfig_parameters.rst @@ -47,6 +47,7 @@ build parameters ``configopts`` Extra options passed to configure (default already has --prefix) "" ``easyblock`` EasyBlock to use for building; if set to None, an easyblock is selected based on the software name None ``easybuild_version`` EasyBuild-version this spec-file was written for None +``enhance_sanity_check`` Indicate that additional sanity check commands & paths should enhance the existin sanity check, not replace it False ``fix_perl_shebang_for`` List of files for which Perl shebang should be fixed to '#!/usr/bin/env perl' (glob patterns supported) None ``fix_python_shebang_for`` List of files for which Python shebang should be fixed to '#!/usr/bin/env python' (glob patterns supported) None ``github_account`` GitHub account name to be used to resolve template values in source URLs "%(namelower)s" @@ -96,17 +97,18 @@ file-management parameters dependencies parameters ----------------------- -=========================== ============================================================== ================= -**Parameter name** **Description** **Default value** -=========================== ============================================================== ================= -``allow_system_deps`` Allow listed system dependencies (format: (, )) [] -``builddependencies`` List of build dependencies [] -``dependencies`` List of dependencies [] -``hiddendependencies`` List of dependencies available as hidden modules [] -``multi_deps`` Dict of lists of dependency versions over which to iterate {} -``multi_deps_load_default`` Load module for first version listed in multi_deps by default True -``osdependencies`` OS dependencies that should be present on the system [] -=========================== ============================================================== ================= +=========================== ===================================================================== ================= +**Parameter name** **Description** **Default value** +=========================== ===================================================================== ================= +``allow_system_deps`` Allow listed system dependencies (format: (, )) [] +``builddependencies`` List of build dependencies [] +``dependencies`` List of dependencies [] +``hiddendependencies`` List of dependencies available as hidden modules [] +``moddependpaths`` Absolute path(s) to prepend to MODULEPATH before loading dependencies None +``multi_deps`` Dict of lists of dependency versions over which to iterate {} +``multi_deps_load_default`` Load module for first version listed in multi_deps by default True +``osdependencies`` OS dependencies that should be present on the system [] +=========================== ===================================================================== ================= license parameters diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index 478218ec..ff0d7f4f 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -10,7 +10,7 @@ Overview of generic easyblocks ============================== -:ref:`BinariesTarball` - :ref:`Binary` - :ref:`BuildEnv` - :ref:`Bundle` - :ref:`CMakeMake` - :ref:`CMakeMakeCp` - :ref:`CMakeNinja` - :ref:`CMakePythonPackage` - :ref:`CmdCp` - :ref:`Conda` - :ref:`ConfigureMake` - :ref:`ConfigureMakePythonPackage` - :ref:`CrayToolchain` - :ref:`FortranPythonPackage` - :ref:`IntelBase` - :ref:`JAR` - :ref:`MakeCp` - :ref:`MesonNinja` - :ref:`ModuleRC` - :ref:`OCamlPackage` - :ref:`OctavePackage` - :ref:`PackedBinary` - :ref:`PerlModule` - :ref:`PythonBundle` - :ref:`PythonPackage` - :ref:`RPackage` - :ref:`Rpm` - :ref:`RubyGem` - :ref:`SCons` - :ref:`SystemCompiler` - :ref:`SystemMPI` - :ref:`Tarball` - :ref:`Toolchain` - :ref:`VSCPythonPackage` - :ref:`VersionIndependentPythonPackage` - :ref:`Waf` +:ref:`BinariesTarball` - :ref:`Binary` - :ref:`BuildEnv` - :ref:`Bundle` - :ref:`CMakeMake` - :ref:`CMakeMakeCp` - :ref:`CMakeNinja` - :ref:`CMakePythonPackage` - :ref:`CmdCp` - :ref:`Conda` - :ref:`ConfigureMake` - :ref:`ConfigureMakePythonPackage` - :ref:`CrayToolchain` - :ref:`FortranPythonPackage` - :ref:`GoPackage` - :ref:`IntelBase` - :ref:`JAR` - :ref:`MakeCp` - :ref:`MesonNinja` - :ref:`ModuleRC` - :ref:`OCamlPackage` - :ref:`OctavePackage` - :ref:`PackedBinary` - :ref:`PerlModule` - :ref:`PythonBundle` - :ref:`PythonPackage` - :ref:`RPackage` - :ref:`Rpm` - :ref:`RubyGem` - :ref:`SCons` - :ref:`SystemCompiler` - :ref:`SystemMPI` - :ref:`Tarball` - :ref:`Toolchain` - :ref:`VSCPythonPackage` - :ref:`VersionIndependentPythonPackage` - :ref:`Waf` .. _BinariesTarball: @@ -21,6 +21,16 @@ Overview of generic easyblocks Support for installing a tarball of binaries +Extra easyconfig parameters specific to ``BinariesTarball`` easyblock +--------------------------------------------------------------------- + +==================== ============================================================================================================================================================= ============= +easyconfig parameter description default value +==================== ============================================================================================================================================================= ============= +``install_type`` Defaults to extract tarball into clean directory. Options: 'merge' merges tarball to existing directory, 'subdir' extracts tarball into its own sub-directory ``None`` +``preinstall_cmd`` Command to execute before installation ``None`` +==================== ============================================================================================================================================================= ============= + Customised steps in ``BinariesTarball`` easyblock ------------------------------------------------- * ``install_step`` - Install by copying unzipped binaries to 'bin' subdir of installation dir, and fixing permissions. @@ -653,6 +663,31 @@ Customised steps in ``FortranPythonPackage`` easyblock * ``configure_step`` - Customize the build step by adding compiler-specific flags to the build command. * ``install_step`` - Customize the build step by adding compiler-specific flags to the build command. +.. _GoPackage: + +``GoPackage`` +============= + +(derives from EasyBlock) + +Builds and installs a Go package, and provides a dedicated module file. + +Extra easyconfig parameters specific to ``GoPackage`` easyblock +--------------------------------------------------------------- + +==================== ===================================================================== ============= +easyconfig parameter description default value +==================== ===================================================================== ============= +``forced_deps`` Force specific version of Go package, when building non-native module ``None`` +``modulename`` Module name of the Go package, when building non-native module ``None`` +==================== ===================================================================== ============= + +Customised steps in ``GoPackage`` easyblock +------------------------------------------- +* ``build_step`` - If Go package is not native go module, lets try to make the module. +* ``configure_step`` - Configure Go package build/install. +* ``install_step`` - Install Go package to a custom path + .. _IntelBase: ``IntelBase`` @@ -1176,6 +1211,16 @@ easyconfig parameter description Precompiled software supplied as a tarball: - will unpack binary and copy it to the install dir +Extra easyconfig parameters specific to ``Tarball`` easyblock +------------------------------------------------------------- + +==================== ============================================================================================================================================================= ============= +easyconfig parameter description default value +==================== ============================================================================================================================================================= ============= +``install_type`` Defaults to extract tarball into clean directory. Options: 'merge' merges tarball to existing directory, 'subdir' extracts tarball into its own sub-directory ``None`` +``preinstall_cmd`` Command to execute before installation ``None`` +==================== ============================================================================================================================================================= ============= + Customised steps in ``Tarball`` easyblock ----------------------------------------- * ``build_step`` - Dummy build method: nothing to build diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index 0af240bb..f4a51094 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -242,78 +242,80 @@ Option flag Option description Override options ---------------- -========================================================================= ================================================================================================================================================================================== -Option flag Option description -========================================================================= ================================================================================================================================================================================== -``--add-dummy-to-minimal-toolchains`` Include dummy toolchain in minimal toolchain searches [DEPRECATED, use --add-system-to-minimal-toolchains instead!) (default: False) -``--add-system-to-minimal-toolchains`` Include system toolchain in minimal toolchain searches (default: False) -``--allow-loaded-modules=ALLOW-LOADED-MODULES`` List of software names for which to allow loaded modules in initial environment (type comma-separated list; default: EasyBuild) -``--allow-modules-tool-mismatch`` Allow mismatch of modules tool and definition of 'module' function (default: False) -``--allow-use-as-root-and-accept-consequences`` Allow using of EasyBuild as root (NOT RECOMMENDED!) (default: False) -``--backup-modules`` Back up an existing module file, if any. Only works when using --module-only -``--check-ebroot-env-vars=CHECK-EBROOT-ENV-VARS`` Action to take when defined $EBROOT* environment variables are found for which there is no matching loaded module; supported values: error, ignore, unset, warn (default: warn) -``--cleanup-builddir`` Cleanup build dir after successful installation. (default: True; disable with --disable-cleanup-builddir) -``--cleanup-tmpdir`` Cleanup tmp dir after successful run. (default: True; disable with --disable-cleanup-tmpdir) -``--color=WHEN`` Colorize output (type choice; default: auto) (choices: auto, always, never) -``--consider-archived-easyconfigs`` Also consider archived easyconfigs (default: False) -``-C, --containerize`` Generate container recipe/image (default: False) -``--copy-ec`` Copy specified easyconfig(s) to specified location (default: False) -``--cuda-compute-capabilities=CUDA-COMPUTE-CAPABILITIES`` List of CUDA compute capabilities to use when building GPU software (type comma-separated list) -``--debug-lmod`` Run Lmod modules tool commands in debug module (default: False) -``--default-opt-level=DEFAULT-OPT-LEVEL`` Specify default optimisation level (type choice; default: defaultopt) (choices: noopt, lowopt, defaultopt, opt) -``--deprecated=DEPRECATED`` Run pretending to be (future) version, to test removal of deprecated code. -``--detect-loaded-modules=DETECT-LOADED-MODULES`` Detect loaded EasyBuild-generated modules, act accordingly; supported values: error, ignore, purge, unload, warn (default: warn) -``--devel`` Enable including of development log messages (default: False) -``--download-timeout=DOWNLOAD-TIMEOUT`` Timeout for initiating downloads (in seconds) (type ) -``--dump-autopep8`` Reformat easyconfigs using autopep8 when dumping them (default: False) -``-e CLASS, --easyblock=CLASS`` easyblock to use for processing the spec file or dumping the options -``--enforce-checksums`` Enforce availability of checksums for all sources/patches, so they can be verified (default: False) -``--experimental`` Allow experimental code (with behaviour that can be changed/removed at any given time). (default: False) -``--extra-modules=EXTRA-MODULES`` List of extra modules to load after setting up the build environment (type comma-separated list) -``--fetch`` Allow downloading sources ignoring OS and modules tool dependencies, implies --stop=fetch, --ignore-osdeps and ignore modules tool (default: False) -``--filter-deps=FILTER-DEPS`` List of dependencies that you do *not* want to install with EasyBuild, because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses) (type comma-separated list) -``--filter-env-vars=FILTER-ENV-VARS`` List of names of environment variables that should *not* be defined/updated by module files generated by EasyBuild (type comma-separated list) -``--fixed-installdir-naming-scheme`` Use fixed naming scheme for installation directories (default: True; disable with --disable-fixed-installdir-naming-scheme) -``--force-download=FORCE-DOWNLOAD`` Force re-downloading of sources and/or patches, even if they are available already in source path (type choice; default: sources) (choices: all, patches, sources) -``--group=GROUP`` Group to be used for software installations (only verified, not set) -``--group-writable-installdir`` Enable group write permissions on installation directory after installation (default: False) -``--hidden`` Install 'hidden' module file(s) by prefixing their version with '.' (default: False) -``--hide-deps=HIDE-DEPS`` Comma separated list of dependencies that you want automatically hidden, (e.g. --hide-deps=zlib,ncurses) (type comma-separated list) -``--hide-toolchains=HIDE-TOOLCHAINS`` Comma separated list of toolchains that you want automatically hidden, (e.g. --hide-toolchains=GCCcore) (type comma-separated list) -``--ignore-checksums`` Ignore failing checksum verification (default: False) -``--ignore-osdeps`` Ignore any listed OS dependencies (default: False) -``--install-latest-eb-release`` Install latest known version of easybuild (default: False) -``--lib64-fallback-sanity-check`` Fallback in sanity check to lib64/ equivalent for missing libraries (default: True; disable with --disable-lib64-fallback-sanity-check) -``--max-fail-ratio-adjust-permissions=MAX-FAIL-RATIO-ADJUST-PERMISSIONS`` Maximum ratio for failures to allow when adjusting permissions (type float; default: 0.5) -``--minimal-toolchains`` Use minimal toolchain when resolving dependencies (default: False) -``--module-only`` Only generate module file(s); skip all steps except for module, prepare, ready, postiter, sanitycheck (default: False) -``--modules-tool-version-check`` Check version of modules tool being used (default: True; disable with --disable-modules-tool-version-check) -``--mpi-cmd-template=MPI-CMD-TEMPLATE`` Template for MPI commands (template keys: %(nr_ranks)s, %(cmd)s) -``--mpi-tests`` Run MPI tests (when relevant) (default: True; disable with --disable-mpi-tests) -``--optarch=OPTARCH`` Set architecture optimization, overriding native architecture optimizations -``--output-format=OUTPUT-FORMAT`` Set output format (type choice; default: txt) (choices: txt, rst) -``--parallel=PARALLEL`` Specify (maximum) level of parallellism used during build procedure (type int) -``--pre-create-installdir`` Create installation directory before submitting build jobs (default: True; disable with --disable-pre-create-installdir) -``-p, --pretend`` Does the build/installation in a test directory located in $HOME/easybuildinstall (default: False) -``--read-only-installdir`` Set read-only permissions on installation directory after installation (default: False) -``--remove-ghost-install-dirs`` Remove ghost installation directories when --force or --rebuild is used, rather than just warning about them (default: False) -``--rpath`` Enable use of RPATH for linking with libraries (default: False) -``--rpath-filter=RPATH-FILTER`` List of regex patterns to use for filtering out RPATH paths (type comma-separated list) -``--set-default-module`` Set the generated module as default (default: False) -``--set-gid-bit`` Set group ID bit on newly created directories (default: False) -``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` Silence specified deprecation warnings (type comma-separated list) -``-t, --skip-test-cases`` Skip running test cases (default: False) -``--sticky-bit`` Set sticky bit on newly created directories (default: False) -``-T, --trace`` Provide more information in output to stdout on progress (default: False) -``--umask=UMASK`` umask to use (e.g. '022'); non-user write permissions on install directories are removed -``--update-modules-tool-cache`` Update modules tool cache file(s) after generating module file (default: False) -``--use-ccache=PATH`` Enable use of ccache to speed up compilation, with specified cache dir (type ; default: False) -``--use-existing-modules`` Use existing modules when resolving dependencies with minimal toolchains (default: False) -``--use-f90cache=PATH`` Enable use of f90cache to speed up compilation, with specified cache dir (type ; default: False) -``--verify-easyconfig-filenames`` Verify whether filename of specified easyconfigs matches with contents (default: False) -``--wait-on-lock=WAIT-ON-LOCK`` Wait interval (in seconds) to use when waiting for existing lock to be removed (0: implies no waiting, but exiting with an error) (type ; default: 0) -``--zip-logs=ZIP-LOGS`` Zip logs that are copied to install directory, using specified command (default: gzip) -========================================================================= ================================================================================================================================================================================== +========================================================================= ============================================================================================================================================================================================================================================ +Option flag Option description +========================================================================= ============================================================================================================================================================================================================================================ +``--add-dummy-to-minimal-toolchains`` Include dummy toolchain in minimal toolchain searches [DEPRECATED, use --add-system-to-minimal-toolchains instead!) (default: False) +``--add-system-to-minimal-toolchains`` Include system toolchain in minimal toolchain searches (default: False) +``--allow-loaded-modules=ALLOW-LOADED-MODULES`` List of software names for which to allow loaded modules in initial environment (type comma-separated list; default: EasyBuild) +``--allow-modules-tool-mismatch`` Allow mismatch of modules tool and definition of 'module' function (default: False) +``--allow-use-as-root-and-accept-consequences`` Allow using of EasyBuild as root (NOT RECOMMENDED!) (default: False) +``--backup-modules`` Back up an existing module file, if any. Only works when using --module-only +``--check-ebroot-env-vars=CHECK-EBROOT-ENV-VARS`` Action to take when defined $EBROOT* environment variables are found for which there is no matching loaded module; supported values: error, ignore, unset, warn (default: warn) +``--cleanup-builddir`` Cleanup build dir after successful installation. (default: True; disable with --disable-cleanup-builddir) +``--cleanup-tmpdir`` Cleanup tmp dir after successful run. (default: True; disable with --disable-cleanup-tmpdir) +``--color=WHEN`` Colorize output (type choice; default: auto) (choices: auto, always, never) +``--consider-archived-easyconfigs`` Also consider archived easyconfigs (default: False) +``-C, --containerize`` Generate container recipe/image (default: False) +``--copy-ec`` Copy specified easyconfig(s) to specified location (default: False) +``--cuda-compute-capabilities=CUDA-COMPUTE-CAPABILITIES`` List of CUDA compute capabilities to use when building GPU software (type comma-separated list) +``--debug-lmod`` Run Lmod modules tool commands in debug module (default: False) +``--default-opt-level=DEFAULT-OPT-LEVEL`` Specify default optimisation level (type choice; default: defaultopt) (choices: noopt, lowopt, defaultopt, opt) +``--deprecated=DEPRECATED`` Run pretending to be (future) version, to test removal of deprecated code. +``--detect-loaded-modules=DETECT-LOADED-MODULES`` Detect loaded EasyBuild-generated modules, act accordingly; supported values: error, ignore, purge, unload, warn (default: warn) +``--devel`` Enable including of development log messages (default: False) +``--download-timeout=DOWNLOAD-TIMEOUT`` Timeout for initiating downloads (in seconds) (type ) +``--dump-autopep8`` Reformat easyconfigs using autopep8 when dumping them (default: False) +``-e CLASS, --easyblock=CLASS`` easyblock to use for processing the spec file or dumping the options +``--enforce-checksums`` Enforce availability of checksums for all sources/patches, so they can be verified (default: False) +``--experimental`` Allow experimental code (with behaviour that can be changed/removed at any given time). (default: False) +``--extra-modules=EXTRA-MODULES`` List of extra modules to load after setting up the build environment (type comma-separated list) +``--fetch`` Allow downloading sources ignoring OS and modules tool dependencies, implies --stop=fetch, --ignore-osdeps and ignore modules tool (default: False) +``--filter-deps=FILTER-DEPS`` List of dependencies that you do *not* want to install with EasyBuild, because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses) (type comma-separated list) +``--filter-env-vars=FILTER-ENV-VARS`` List of names of environment variables that should *not* be defined/updated by module files generated by EasyBuild (type comma-separated list) +``--fixed-installdir-naming-scheme`` Use fixed naming scheme for installation directories (default: True; disable with --disable-fixed-installdir-naming-scheme) +``--force-download=FORCE-DOWNLOAD`` Force re-downloading of sources and/or patches, even if they are available already in source path (type choice; default: sources) (choices: all, patches, sources) +``--group=GROUP`` Group to be used for software installations (only verified, not set) +``--group-writable-installdir`` Enable group write permissions on installation directory after installation (default: False) +``--hidden`` Install 'hidden' module file(s) by prefixing their version with '.' (default: False) +``--hide-deps=HIDE-DEPS`` Comma separated list of dependencies that you want automatically hidden, (e.g. --hide-deps=zlib,ncurses) (type comma-separated list) +``--hide-toolchains=HIDE-TOOLCHAINS`` Comma separated list of toolchains that you want automatically hidden, (e.g. --hide-toolchains=GCCcore) (type comma-separated list) +``--ignore-checksums`` Ignore failing checksum verification (default: False) +``--ignore-osdeps`` Ignore any listed OS dependencies (default: False) +``--install-latest-eb-release`` Install latest known version of easybuild (default: False) +``--lib64-fallback-sanity-check`` Fallback in sanity check to lib64/ equivalent for missing libraries (default: True; disable with --disable-lib64-fallback-sanity-check) +``--max-fail-ratio-adjust-permissions=MAX-FAIL-RATIO-ADJUST-PERMISSIONS`` Maximum ratio for failures to allow when adjusting permissions (type float; default: 0.5) +``--minimal-toolchains`` Use minimal toolchain when resolving dependencies (default: False) +``--module-only`` Only generate module file(s); skip all steps except for module, prepare, ready, postiter, sanitycheck (default: False) +``--modules-tool-version-check`` Check version of modules tool being used (default: True; disable with --disable-modules-tool-version-check) +``--mpi-cmd-template=MPI-CMD-TEMPLATE`` Template for MPI commands (template keys: %(nr_ranks)s, %(cmd)s) +``--mpi-tests`` Run MPI tests (when relevant) (default: True; disable with --disable-mpi-tests) +``--optarch=OPTARCH`` Set architecture optimization, overriding native architecture optimizations +``--output-format=OUTPUT-FORMAT`` Set output format (type choice; default: txt) (choices: txt, rst) +``--parallel=PARALLEL`` Specify (maximum) level of parallellism used during build procedure (type int) +``--pre-create-installdir`` Create installation directory before submitting build jobs (default: True; disable with --disable-pre-create-installdir) +``-p, --pretend`` Does the build/installation in a test directory located in $HOME/easybuildinstall (default: False) +``--read-only-installdir`` Set read-only permissions on installation directory after installation (default: False) +``--remove-ghost-install-dirs`` Remove ghost installation directories when --force or --rebuild is used, rather than just warning about them (default: False) +``--rpath`` Enable use of RPATH for linking with libraries (default: False) +``--rpath-filter=RPATH-FILTER`` List of regex patterns to use for filtering out RPATH paths (type comma-separated list) +``--set-default-module`` Set the generated module as default (default: False) +``--set-gid-bit`` Set group ID bit on newly created directories (default: False) +``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` Silence specified deprecation warnings (type comma-separated list) +``-t, --skip-test-cases`` Skip running test cases (default: False) +``--sticky-bit`` Set sticky bit on newly created directories (default: False) +``-T, --trace`` Provide more information in output to stdout on progress (default: False) +``--umask=UMASK`` umask to use (e.g. '022'); non-user write permissions on install directories are removed +``--update-modules-tool-cache`` Update modules tool cache file(s) after generating module file (default: False) +``--use-ccache=PATH`` Enable use of ccache to speed up compilation, with specified cache dir (type ; default: False) +``--use-existing-modules`` Use existing modules when resolving dependencies with minimal toolchains (default: False) +``--use-f90cache=PATH`` Enable use of f90cache to speed up compilation, with specified cache dir (type ; default: False) +``--verify-easyconfig-filenames`` Verify whether filename of specified easyconfigs matches with contents (default: False) +``--wait-on-lock=WAIT-ON-LOCK`` Wait for lock to be released; 0 implies no waiting (exit with an error if the lock already exists), non-zero value specified waiting interval [DEPRECATED: use --wait-on-lock-interval and --wait-on-lock-limit instead] (type ) +``--wait-on-lock-interval=WAIT-ON-LOCK-INTERVAL`` Wait interval (in seconds) to use when waiting for existing lock to be removed (type ; default: 60) +``--wait-on-lock-limit=WAIT-ON-LOCK-LIMIT`` Maximum amount of time (in seconds) to wait until lock is released (0 means no waiting at all, exit with error; -1 means no waiting limit, keep waiting) (type ; default: 0) +``--zip-logs=ZIP-LOGS`` Zip logs that are copied to install directory, using specified command (default: gzip) +========================================================================= ============================================================================================================================================================================================================================================ Package options From 6ad67d7e27ec50e6ef30d9343e4e068693b59991 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 May 2020 21:02:23 +0800 Subject: [PATCH 055/286] release EasyBuild v4.2.1 --- setup.py | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/setup.py b/setup.py index cb2ece20..6336760d 100644 --- a/setup.py +++ b/setup.py @@ -36,13 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware - -# note: using '4.2.0.post0' as version for EasyBuild v4.2.0 because of -# mistake in easybuild-4.2.0 package that was pushed to PyPI; -# the version of easyblocks/easyconfigs was accidentally still locked to '==4.1.1', -# see https://github.com/easybuilders/easybuild/pull/615/commits/3a8c81b1baaff93d3dc94b9b0cadc9bdf43d8fae -PYPI_VERSION = '4.2.0.post0' -VERSION = '4.2.0' +VERSION = '4.2.1' # Utility function to read README file @@ -57,7 +51,7 @@ def read(fname): setup( name="easybuild", - version=PYPI_VERSION, + version=str(VERSION), author="EasyBuild community", author_email="easybuild@lists.ugent.be", description="""EasyBuild is a software build \ From 24565487db284be07985908d5091991de91b491c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 May 2020 16:34:41 +0200 Subject: [PATCH 056/286] add definitions for foss/2020a + intel/2020a common toolchains to docs --- docs/Common-toolchains.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/Common-toolchains.rst b/docs/Common-toolchains.rst index 0b1f2ef2..f95ea1cf 100644 --- a/docs/Common-toolchains.rst +++ b/docs/Common-toolchains.rst @@ -174,6 +174,8 @@ Component versions in ``foss`` toolchain +----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ | ``2019b`` | Sept '19 | 2.32 | 8.3.0 | 3.1.4 | 0.3.7 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | +----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ +| ``2020a`` | May '20 | 2.34 | 9.3.0 | 4.0.3 | 0.3.9 | (incl. with OpenBLAS) | 2.1.0 | 3.3.8 | ++----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ *(components marked with* * *were patched)* @@ -208,6 +210,8 @@ Component versions in ``intel`` toolchain +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ | ``2019b`` | Sept '19 | 2.32 | 8.3.0 | 2019.5.281 | 2018.5.288 | 2019.5.281 | +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ +| ``2020a`` | May'20 | 2.34 | 9.3.0 | 2020.1.217 | 2019.7.217 | 2020.1.217 | ++----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ ``(*)``: This toolchain is deprecated, see :ref:`deprecated_easyconfigs_toolchains` for more information. From 6cfd6f8dded04e00fba9ab21ae4d666445774c42 Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Tue, 9 Jun 2020 10:27:36 -0700 Subject: [PATCH 057/286] Updated extensions section to reflect PR #3294 using 'sources', not 'git_config' directly. --- docs/Writing_easyconfig_files.rst | 33 ++++++++++++++++--------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index d0fa83e1..e5f1064a 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -525,7 +525,7 @@ Besides dependencies, which are found outside the module being built but are par it is also possible to incorporate extensions to the module within the build. This is done via the ``exts_list`` array. Each entry in ``exts_list`` is a three-component tuple, with the name and -version number, and a dictionary of source options: +version number, and a dictionary of configuration options for the entry: .. code:: python @@ -533,16 +533,16 @@ version number, and a dictionary of source options: ('name', 'version', { 'option':'value', 'option':'value' }) ] -The latter consist of most of the allowed keys as in the dictionary structure of ``sources`` (see -:ref:`_common_easyconfig_param_sources_alt`). Among those options, the following exceptions and -special cases should be noted: +The latter may contain essentially any of the full EasyConfig parameters, including ``buildopts``, ``installopts``, etc. +Among those options, the following exceptions and special cases should be noted: * **nosource**: If set ``True``, no download will be done -* **filename** and **download_filename** are ignored; use ``'source_tmpl'`` * **source_tmpl**: Template string for the file to be downloaded * default is ``'%(name)s-%(version)s.tar.gz'`` * ``%(name)s`` and ``%(version)s`` come from the ``exts_list`` entry (above) -* **git_config**: Dictionary specifying download from a Git repository +* **sources**: Dictionary specifying details of where to download the extension + * equivalent to a single entry from the EasyConfig ``sources`` list + * preffered to use of ``source_tmpl`` * **start_dir**: If not set, will be derived; the EasyConfigs value will not be used .. code:: python @@ -566,22 +566,23 @@ special cases should be noted: }), ] -That third instance uses the ``name`` and ``version`` variables defined in the EasyConfigs file. - -Since EasyBuild v4.2.1, the ``git_config`` dictionary (see :ref:`downloading-from-a-git-repository`) -may be included in the ``exts_list`` source definition. For example, to download Git sources from a -private repository and convert them to a tar-ball for installation: +That third instance uses the ``name`` and ``version`` variables defined in the EasyConfigs file. Since EasyBuild +v4.2.2, a single-entry ``sources`` dictionary (see :ref:`_common_easyconfig_param_sources_alt`) may be included in an +``exts_list`` entry. For example, to download Git sources from a private repository and convert them to a tar-ball for +installation: .. code:: python exts_defaultclass = 'PythonPackage' exts_list = [ ('pyCAP', '0.1', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'ssh://nero.stanford.edu/data/git/Analysis', - 'repo_name': 'pyCAP', - 'tag': '%(version)s', + 'sources': { + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'ssh://nero.stanford.edu/data/git/Analysis', + 'repo_name': 'pyCAP', + 'tag': '%(version)s', + } } }), ] From 03b3ee9b239cd15637d5c2428c3f250852facf02 Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Tue, 9 Jun 2020 13:00:36 -0700 Subject: [PATCH 058/286] Fix misspelling of 'preferred'. --- docs/Writing_easyconfig_files.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index e5f1064a..ce9ba488 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -542,7 +542,7 @@ Among those options, the following exceptions and special cases should be noted: * ``%(name)s`` and ``%(version)s`` come from the ``exts_list`` entry (above) * **sources**: Dictionary specifying details of where to download the extension * equivalent to a single entry from the EasyConfig ``sources`` list - * preffered to use of ``source_tmpl`` + * preferred to use of ``source_tmpl`` * **start_dir**: If not set, will be derived; the EasyConfigs value will not be used .. code:: python From 25ff2e29239b00276addb24406d20ba249a6b09d Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Tue, 9 Jun 2020 13:12:41 -0700 Subject: [PATCH 059/286] Per @ocaisa, add 'namd' to Codespell 'ignore-words-list'. --- .github/workflows/check_with_codespell.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check_with_codespell.sh b/.github/workflows/check_with_codespell.sh index 4d8ed081..c1fa4b05 100644 --- a/.github/workflows/check_with_codespell.sh +++ b/.github/workflows/check_with_codespell.sh @@ -1 +1 @@ -codespell --skip='.git,version-specific,scripts' --ignore-words-list=atleast,ninjs,simpy,proovread --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!'; else $(exit $retVal); fi; +codespell --skip='.git,version-specific,scripts' --ignore-words-list=atleast,ninjs,simpy,proovread,namd --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!'; else $(exit $retVal); fi; From ba320e2b9298a0c06fcdea87e80c3eb5184e0608 Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Tue, 9 Jun 2020 14:46:04 -0700 Subject: [PATCH 060/286] Add 'namd' to igore-words-list for Travis CI as well, per @ocaisa. --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index a330ae7b..eac21d13 100644 --- a/.travis.yml +++ b/.travis.yml @@ -13,7 +13,7 @@ script: # still added to the exit code (which is a just a count of spelling # suggestions). Since we know we have one of these, we allow for that. # see https://github.com/easybuilders/easybuild/pull/485 for details - - codespell --skip=".git,version-specific,scripts" --ignore-words-list=atleast,ninjs,simpy,proovread --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo "Got one expected warning, so success!"; else $(exit $retVal); fi; + - codespell --skip=".git,version-specific,scripts" --ignore-words-list=atleast,ninjs,simpy,proovread,namd --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo "Got one expected warning, so success!"; else $(exit $retVal); fi; - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - READTHEDOCS=1 sphinx-build docs build # test installation too (using options that don't require to have a modules tool installed) From fb06f793e90bcf81ae369e7ddab9a1288fb4e060 Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Mon, 22 Jun 2020 10:45:26 -0700 Subject: [PATCH 061/286] Improve explanation of using self.cfg['key'] vs. self.key; replace EasyConfig with easyconfig in new documentation sections. --- docs/Implementing-easyblocks.rst | 23 ++++++++++++++--------- docs/Writing_easyconfig_files.rst | 12 ++++++------ 2 files changed, 20 insertions(+), 15 deletions(-) diff --git a/docs/Implementing-easyblocks.rst b/docs/Implementing-easyblocks.rst index 37f30ee4..692a2496 100644 --- a/docs/Implementing-easyblocks.rst +++ b/docs/Implementing-easyblocks.rst @@ -260,8 +260,7 @@ Default easyconfig parameters ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ All of the parameters which are "set" in an easyconfig file (see :ref:`vsd_avail_easyconfig_params`) -become key-value pairs in the ``self.cfg`` dictionary. For instance, where the easyconfig file might -specify +become key-value pairs in the ``self.cfg`` dictionary. For instance, if the easyconfig file specifies .. code:: python @@ -269,23 +268,29 @@ specify version = '2.5.3' versionsuffix = '-Python-3.7.4' -these are accessible within an easyblock via +then these three parameters are accessible within an easyblock via .. code:: python longform = ''.join(self.cfg['name'],'/',self.cfg['version'],self.cfg['versionsuffix']) -For these "universal" arguments, this mapping is done for you in the ``EasyBlock`` base class, so -they are also available as local Python variables (``self.name``, ``self.version``, etc.): +You can use this notation successfully in your easyblock. For all of the variables listed +:ref:`vsd_avail_easyconfig_params`, the ``EasyBlock`` base class copies those dictionary entries into local Python +variables: + +* ``self.name = self.cfg['name']`` +* ``self.version = self.cfg['version']`` +* ``self.versionsuffix = self.cfg['versionsuffix']`` + +and so on. So in your easyblock code, you may replace the above expression +with .. code:: python longform = ''.join(self.name,'/',self.version,self.versionsuffix) -This is true for the variables listed in :ref:`vsd_avail_easyconfig_params`. Any additional -:ref:`custom parameters ` which you define for your own -easyblock, will not be automatically mapped. You will need to use ``self.cfg`` to access them in -your code. +Any additional :ref:`custom parameters ` which you define for your own +easyblock, will not be automatically mapped. You will need to use ``self.cfg`` to access them in your code. .. _implementing_easyblocks_custom_parameters: diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index ce9ba488..c7f85f9b 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -326,7 +326,7 @@ For example, to inject checksums in *every* easyconfig file required to build HP ... .. note:: We are clearing ``$MODULEPATH`` and specifying a custom (empty) location to ``--installpath`` to - avoid that EasyBuild skips any easyconfigs because a corresponding module is already available. + avoid that EasyBuild skips any easyconfig because a corresponding module is already available. .. _inject_checksums_type: @@ -533,7 +533,7 @@ version number, and a dictionary of configuration options for the entry: ('name', 'version', { 'option':'value', 'option':'value' }) ] -The latter may contain essentially any of the full EasyConfig parameters, including ``buildopts``, ``installopts``, etc. +The latter may contain essentially any of the full easyconfig parameters, including ``buildopts``, ``installopts``, etc. Among those options, the following exceptions and special cases should be noted: * **nosource**: If set ``True``, no download will be done @@ -541,9 +541,9 @@ Among those options, the following exceptions and special cases should be noted: * default is ``'%(name)s-%(version)s.tar.gz'`` * ``%(name)s`` and ``%(version)s`` come from the ``exts_list`` entry (above) * **sources**: Dictionary specifying details of where to download the extension - * equivalent to a single entry from the EasyConfig ``sources`` list + * equivalent to a single entry from the easyconfig ``sources`` list * preferred to use of ``source_tmpl`` -* **start_dir**: If not set, will be derived; the EasyConfigs value will not be used +* **start_dir**: If not set, will be derived; the easyconfig value will not be used .. code:: python @@ -566,7 +566,7 @@ Among those options, the following exceptions and special cases should be noted: }), ] -That third instance uses the ``name`` and ``version`` variables defined in the EasyConfigs file. Since EasyBuild +That third instance uses the ``name`` and ``version`` variables defined in the easyconfig file. Since EasyBuild v4.2.2, a single-entry ``sources`` dictionary (see :ref:`_common_easyconfig_param_sources_alt`) may be included in an ``exts_list`` entry. For example, to download Git sources from a private repository and convert them to a tar-ball for installation: @@ -588,7 +588,7 @@ installation: ] Here, the template strings ``%(name)s`` and ``%(version)s`` will be substituted from the -``exts_list`` entry elements ("pyCAP" and "0.1", respectively), not from the EasyConfigs values. +``exts_list`` entry elements ("pyCAP" and "0.1", respectively), not from the easyconfig values. .. _configure_build_install_command_options: From cbeee49b9dda2dfddc2235f07acaea4e23756ef7 Mon Sep 17 00:00:00 2001 From: Michael Kelsey Date: Fri, 3 Jul 2020 13:42:01 -0700 Subject: [PATCH 062/286] Clarify use of easyblock 'properties' (look like data member names) which reference self.cfg dictionary entries. Don't use 'module' qualifier for extensions. --- docs/Implementing-easyblocks.rst | 22 +++++++++++----------- docs/Writing_easyconfig_files.rst | 8 ++++---- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/docs/Implementing-easyblocks.rst b/docs/Implementing-easyblocks.rst index 692a2496..f131bd8b 100644 --- a/docs/Implementing-easyblocks.rst +++ b/docs/Implementing-easyblocks.rst @@ -274,23 +274,23 @@ then these three parameters are accessible within an easyblock via longform = ''.join(self.cfg['name'],'/',self.cfg['version'],self.cfg['versionsuffix']) -You can use this notation successfully in your easyblock. For all of the variables listed -:ref:`vsd_avail_easyconfig_params`, the ``EasyBlock`` base class copies those dictionary entries into local Python -variables: +You can use this notation successfully in your easyblock. A few of the most commonly used parameters can be referenced +directly, -* ``self.name = self.cfg['name']`` -* ``self.version = self.cfg['version']`` -* ``self.versionsuffix = self.cfg['versionsuffix']`` +* **self.name** = ``self.cfg['name']`` +* **self.version** = ``self.cfg['version']`` +* **self.toolchain** = ``self.cfg['toolchain']`` +* **self.all_dependencies**: combines ``builddependencies``, ``dependencies``, and ``toolchain``, in one dictionary -and so on. So in your easyblock code, you may replace the above expression -with +So in your easyblock code, you may replace the above expression with .. code:: python - longform = ''.join(self.name,'/',self.version,self.versionsuffix) + longform = ''.join(self.name,'/',self.version,self.cfg['versionsuffix']) -Any additional :ref:`custom parameters ` which you define for your own -easyblock, will not be automatically mapped. You will need to use ``self.cfg`` to access them in your code. +The other easyconfig parameters, and any additional :ref:`custom parameters +` which you define for your own easyblock, will not be automatically mapped. +You will need to use ``self.cfg`` to access them in your code. .. _implementing_easyblocks_custom_parameters: diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index c7f85f9b..81b623d6 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -518,11 +518,11 @@ Since EasyBuild v2.1, specifying modules that are not provided via EasyBuild as See :ref:`using_external_modules` for more information. -Module Extensions -~~~~~~~~~~~~~~~~~ +Extensions +~~~~~~~~~~ -Besides dependencies, which are found outside the module being built but are part of the site's EasyBuild installation, -it is also possible to incorporate extensions to the module within the build. This is done via the ``exts_list`` array. +Besides dependencies, which are found outside the software being built but are part of the site's EasyBuild installation, +it is also possible to incorporate extensions to the software within the build. This is done via the ``exts_list`` array. Each entry in ``exts_list`` is a three-component tuple, with the name and version number, and a dictionary of configuration options for the entry: From 1889b6c6d8d85309f132205c27210fd2236a7ec3 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Tue, 7 Jul 2020 15:48:57 -0500 Subject: [PATCH 063/286] Updated Davide Vanzo affiliation and email --- docs/Maintainers.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Maintainers.rst b/docs/Maintainers.rst index d63bd1a0..f593fd55 100644 --- a/docs/Maintainers.rst +++ b/docs/Maintainers.rst @@ -123,9 +123,9 @@ The EasyBuild maintainers all have admin access to the different EasyBuild GitHu * GitHub: `@casparvl `_ - e-mail: ``caspar.vanleeuwen (at) surfsara.nl`` - IRC/Slack: ``Caspar Van Leeuwen`` -* **Davide Vanzo** (`Vanderbilt University `_) +* **Davide Vanzo** (`Microsoft `_) - * GitHub: `@vanzod `_ - e-mail: ``davide.vanzo (at) vanderbilt.edu`` - IRC/Slack: ``vanzod`` + * GitHub: `@vanzod `_ - e-mail: ``davide.vanzo (at) microsoft.com`` - IRC/Slack: ``vanzod`` * **Lars Viklund** (`Umeå University, Sweden `_) From c75d13191818655c11684007001ef101e75a0734 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Jul 2020 16:41:51 +0800 Subject: [PATCH 064/286] update release notes for EasyBuild v4.2.2 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 135 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 135 insertions(+), 5 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index bcfbcd39..08990181 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20200708.01** (`July 8th 2020`): update release notes for EasyBuild v4.2.2 (see :ref:`release_notes_eb422`) * **release 20200520.01** (`May 20th 2020`): update release notes for EasyBuild v4.2.1 (see :ref:`release_notes_eb421`) * **release 20200414.01** (`Apr 14th 2020`): diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index f97b2234..e46a9626 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,141 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **1,978** different software packages, -including 31 different (compiler) toolchains. It contains 219 software-specific easyblocks and 37 generic easyblocks, -alongside 9,894 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,013** different software packages, +including 31 different (compiler) toolchains. It contains 222 software-specific easyblocks and 37 generic easyblocks, +alongside 10,147 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb422: + +EasyBuild v4.2.2 (July 8th 2020) +-------------------------------- + +bugfix/update release + +**framework** + +* various enhancements, including: + + * add support for using ``sources`` and ``git_config`` for extensions in ``exts_list`` (`#3294 `_) + * add support for software minver template (like ``%(pyminver)s``, etc.) (`#3344 `_, `#3345 `_) + * add support for updating dictionary or tuple easyconfig parameters with ``self.cfg.update`` (`#3356 `_) + +* various bug fixes, including: + + * fix crash in ``--avail-easyconfig-constants`` when using ``--output-format=rst`` + ensure sorted output (`#3341 `_) + * always take into account ``builddependencies`` when generating template values, also when we're not iterating over ``builddependencies`` (`#3346 `_) + * fix running command as ``easybuild`` user in generated Singularity definition file (`#3347 `_) + * allow ignoring ``versionsuffix`` in ``--try-update-deps`` (`#3350 `_, `#3353 `_) + * retain order of paths when generating ``prepend_path`` statements for module file (don't sort them alphabetically) (`#3367 `_) + * also put easyblocks used by extensions in ``reprod`` directory (`#3375 `_) + * also copy template values in ``EasyConfig.copy`` method to ensure they are defined when installing extensions (`#3377 `_) + * skip lines that start with ``module-version`` when determining whether a module exists in ``ModulesTool.exist`` (`#3379 `_) + +**easyblocks** + +* 3 new software-specific easyblocks: + + * LLVM (`#2065 `_), Scipion (`#1847 `_), XALT (`#1942 `_) + +* minor enhancements, including: + + * use ``wclean -platform`` instead of ``wcleanPlatform`` for OpenFOAM v2006 & newer (`#2088 `_) + +* various bug fixes, including: + + * only build OpenCV with IPP support on x86_64 systems (`#2056 `_) + * make sure ``CFLAGS`` and ``MYCFLAGS`` are used in Lua easyblock (`#2062 `_) + * also accept ``exist_lic`` as valid value for ``license_file`` in IntelBase easyblock (`#2067 `_) + * fix minor bug in shared libs handling and correctly setup SuiteSparse variables in Trilinos easyblock (`#2071 `_) + * make sure ``PythonBundle`` uses correct ``python`` command in extensions filter + also add ``lib64/python*/site-packages`` to ``$PYTHONPATH`` (if it exists) (`#2075 `_, `#2081 `_) + * fix build environment for WRF by patching shebang in compile script (`#2079 `_) + * fix order of ``intel64/lib`` paths in generated module for impi (and drop ``intel64/lib/release_mt``) (`#2080 `_) + * set ``$XDG_CACHE_HOME`` to avoid abuse of ``$HOME/.cache/pip`` when installing DOLFIN (`#2082 `_) + * make VMD easyblock Python 3 compatible (`#2083 `_) + * rename include-fixed subdirectory in GCC installation to avoid problems after OS upgrade (`#2087 `_, `#2093 `_, `#2094 `_) + * use glob pattern to determine name of Mathematica installation script (`#2089 `_) + * use ``mpirun`` for sanity check commands in LAMMPS easyblock (`#2096 `_) + +**easyconfigs** + +* added easyconfigs for 2 new toolchains: + + * golf/2020a (`#10672 `_) + + * intel/2020.06, based on intel/2020a but with impi 2018 update 5 (`#10864 `_) + +* added example easyconfig files for 36 new software packages: + + * AmrPlusPlus (`#9919 `_), arrow (`#10882 `_), attrdict (`#10827 `_), Cartopy (`#10685 `_), dm-tree (`#10775 `_), dotNET-SDK (`#10661 `_), + FLAIR (`#10860 `_), fastqsplitter (`#10706 `_), GLFW (`#10709 `_), git-extras (`#10440 `_), hl7apy (`#10728 `_), hyperopt (`#10735 `_), + IgBLAST (`#10889 `_), IntelDAAL (`#9848 `_), ichorCNA (`#10595 `_), MARS (`#10691 `_), MITObim (`#10897 `_), MUST (`#10849 `_), + mhcnuggets (`#9743 `_), PAUP (`#10830 `_), Percolator (`#10665 `_), PyBerny (`#10885 `_), poetry (`#10884 `_), pycocotools (`#10806 `_), + python-hl7 (`#10673 `_), SHAPEIT4 (`#10814 `_), SYMPHONY (`#10058 `_), SunPy (`#10676 `_), sdsl-lite (`#10691 `_), + TEtranscripts (`#10909 `_, `#10921 `_), Tombo (`#10646 `_), tensorboardX (`#10774 `_), Unidecode (`#10828 `_), WHAM (`#10736 `_), XALT (`#9792 `_), + Xvfb (`#10512 `_) + +* added additional easyconfigs for various supported software packages, including: + + * Armadillo 9.900.1, astropy 4.0.1, BLAST+ 2.10.1, BioPerl 1.7.7, Blitz++ 1.0.2, + Bonito 0.2.0, bokeh 2.0.2, CFITSIO 3.48, CGAL 4.14.3, CLHEP 2.4.1.3, cutadapt 2.10, + dask 2.18.1, Elk 6.3.2, GATE 9.0, GLM 0.9.9.8, GRASS 7.8.3, Geant4 10.6, + geopandas 0.8.0, giflib 5.2.1, HDF5 1.12.0, HISAT2 2.2.0, Hadoop 2.10.0, + IPython 7.15.0, inferCNV 1.2.1, Julia 1.4.2, LibSoup 2.70.0, MATIO 1.5.17, + MRtrix 3.0.0, Mathematica 12.1.1 MultiQC 1.9, NGS 2.10.5, NiBabel 3.1.0, + Nipype 1.4.2, ncbi-vdb 20.10.7, numba 0.50.0, OpenBabel 3.1.1, OpenFOAM v2006, + PDT 3.25.1, PRSice 2.3.1, ParaView 5.8.0, ParmEd 3.2.0, PyQt5 5.13.2, + Pysam 0.16.0.1, parallel 20200522, plotly.py 4.8.1, pybedtools 0.8.1, + ROOT 6.20.04, ReFrame 3.0, Roary 3.13.0, rjags 4-10, rstudio 1.3.959, + SPAdes 3.14.1, SRA-Toolkit 2.10.8, Saxon-HE 9.9.1.7, Seaborn 0.10.1, + Seurat 3.1.5, SimPEG 0.14.1, Spark 2.4.5, StringTie 2.1.3, scikit-allel 1.2.1, + scikit-learn 0.23.1, snpEff 4.3t, Valgrind 3.16.1, VarScan 2.4.4, + vsc-mympirun 5.1.0, WebKitGTK+ 2.27.4, wxPython 4.0.7.post2, zarr 2.4.0 + +* minor enhancements, including: + + * add extensions to R 4.0.0 easyconfig: drgee + stdReg (`#10833 `_), copCAR (`#10911 `_), ngspatial (`#10913 `_), drugCombo (`#10914 `_) + * add extensions to R-bundle-Bioconductor 3.11 easyconfig: BSgenome.Cfamiliaris.UCSC.canFam3 (`#10840 `_), SingleR (`#10904 `_) + * include extra extension and support for MPI in MAFFT v7.453 and v7.470 (`#10853 `_) + * add Array::Transpose to Perl (`#10878 `_) + +* various bug fixes, including: + + * fix dependencies and configuration of CoinUtils ecosystem (`#10450 `_) + * fix Togl configure patch so that it completely ignores ``TCL_SRC_DIR`` and ``TK_SRC_DIR`` (`#10662 `_) + * change Xerces-C++ to official CMakeMake build (fixes missing links to curl) (`#10664 `_) + * add ``-fPIC`` to ``toolchainopts`` in easyconfig for Lua 5.3.5 with system toolchain (`#10671 `_) + * remove hardcoded X86 target in LLVM easyconfigs (`#10677 `_) + * switch to https ``homepage`` and ``source_urls`` in libGLU easyconfigs (`#10686 `_) + * add patch for h5py 2.10.0 to avoid triggering ``MPI_Init`` at import (`#10687 `_) + * add alternative checksum for pkgmaker, doRNG, cobs extension in R 3.6.0 easyconfigs (`#10692 `_) + * update UDUNITS ``source_urls`` to https sources (`#10693 `_) + * add missing M4 to netCDF-Fortran easyconfigs using 2020a toolchain (#10695, `#10697 `_) + * add Rgraphviz patch to R-bundle-Bioconductor easyconfigs (`#10710 `_) + * add M4 builddependency to SuiteSparse 2019b easyconfigs (`#10720 `_) + * make sure WHAM is built with correct compiler (`#10736 `_) + * define ``MAX_JOBS`` in easyconfigs of PyTorch from v1.1.0 to v1.4.0 (`#10772 `_) + * add dm-tree and lz4 as dependencies to Ray v0.8.4 (`#10775 `_) + * fix source URL in recent ant easyconfigs (`#10790 `_) + * bump versions of GO.gb/org.Hs.eg.db/PFAM.db extensions in Bioconductor 3.11 bundle, since sources for old versions have disappeared (`#10791 `_) + * add patch to Armadillo easyconfigs using the foss toolchain to prevent it from picking up MKL if installed system-wide (`#10812 `_) + * add missing kerneltree extension in FLAIR easyconfig (`#10860 `_) + * fix source URLs in Eigen 3.2.* (`#10872 `_) and 3.3.* (`#10869 `_) easyconfigs + * refer to issue in GitHub repo in configparser patch, since Bitbucket repo is disappearing (`#10873 `_) + * switch to github.com source URL for MetaPhlAn (`#10874 `_) + * switch to GitHub sources for ScientificPython 2.9.4 (`#10875 `_) + * switch to GitHub source URL for HPDBSCAN (`#10876 `_) + * download x265 3.2/3.3 sources from ``bitbucket.org/multicoreware/x265_git`` (`#10905 `_) + * fix download URL for libatomic in gc 7.6.12 easyconfigs (`#10915 `_) + * fix ``sanity_check_paths`` in CFITSIO-3.48-GCCcore-9.3.0.eb easyconfig (`#10917 `_) + * add missing dependencies for geopandas 0.7.0 (`#10923 `_) + +* other changes: + + * rename OpenPyXL 2.6.4 easyconfig to openpyxl (`#10916 `_) + + .. _release_notes_eb421: EasyBuild v4.2.1 (May 20th 2020) diff --git a/docs/conf.py b/docs/conf.py index 6de1da7d..b5a15be8 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.2.1' # this is meant to reference the version of EasyBuild +version = '4.2.2' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20200520.0' # this is meant to reference the version of the documentation itself +release = '20200708.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 1023f01a2513c0877d87d377a20d897ed00a29c1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jul 2020 12:14:22 +0200 Subject: [PATCH 065/286] auto-update docs for EasyBuild v4.2.2 --- docs/version-specific/Supported_software.rst | 1897 ++++++++++++------ docs/version-specific/easyblocks.rst | 4 + docs/version-specific/help.rst | 1 + 3 files changed, 1295 insertions(+), 607 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 46a21ceb..15242bac 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 1978 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2013 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -723,6 +723,22 @@ version toolchain ========= ================= +.. _list_software_AmrPlusPlus_1128: + +*AmrPlusPlus* ++++++++++++++ + +AmrPlusPlus v2.0 can process the raw data from the sequencer, identify the fragments of DNA, and count them. It also provides a count of the polymorphisms that occur in each DNA fragment with respect to the reference database. + +*homepage*: https://megares.meglab.org/amrplusplus/latest/html/v2 + +================ ============= +version toolchain +================ ============= +``2.0-20200114`` ``GCC/8.3.0`` +================ ============= + + .. _list_software_Anaconda2_839: *Anaconda2* @@ -908,6 +924,7 @@ version versionsuffix toolchain ``1.10.5`` ``-Java-1.8`` ``system`` ``1.10.6`` ``-Java-1.8`` ``system`` ``1.10.7`` ``-Java-11`` ``system`` +``1.10.8`` ``-Java-11`` ``system`` ========== =================== ========== @@ -1194,7 +1211,10 @@ version versionsuffix toolchain ``7.950.1`` ``-Python-2.7.12`` ``intel/2016b`` ``8.300.1`` ``foss/2017b``, ``intel/2017b`` ``8.400.0`` ``foss/2018a`` +``9.600.5`` ``foss/2018b`` ``9.700.2`` ``foss/2019a`` +``9.880.1`` ``foss/2020a`` +``9.900.1`` ``foss/2019b``, ``foss/2020a`` =========== ================== =============================== @@ -1230,7 +1250,7 @@ version toolchain ``3.4.0`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b``, ``intel/2017a`` ``3.5.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b`` ``3.6.2`` ``intel/2018a`` -``3.7.0`` ``foss/2019a``, ``foss/2019b``, ``intel/2019b`` +``3.7.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019b`` ========= ================================================================================ @@ -1283,9 +1303,26 @@ version versionsuffix toolchain ``0.12.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.12.0`` ``-Python-3.6.6`` ``intel/2018b`` ``0.16.0`` ``-Python-3.7.4`` ``intel/2019b`` +``0.17.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ================== =============================== +.. _list_software_arrow_555: + +*arrow* ++++++++ + +R interface to the Apache Arrow C++ library + +*homepage*: https://cran.r-project.org/web/packages/arrow + +========== ============= ============== +version versionsuffix toolchain +========== ============= ============== +``0.17.1`` ``-R-4.0.0`` ``foss/2020a`` +========== ============= ============== + + .. _list_software_ART_231: *ART* @@ -1492,15 +1529,16 @@ version toolchain *astropy* +++++++++ -The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages. +The Astropy Project is a community effort to develop a core package for astronomy using the Python programming language and improve usability, interoperability, and collaboration between astronomy Python packages. The core astropy package contains functionality aimed at professional astronomers and astrophysicists, but may be useful to anyone developing astronomy software. The Astropy Project also includes "affiliated packages," Python packages that are not necessarily developed by the core development team, but share the goals of Astropy, and often build from the core package's code and infrastructure. -*homepage*: http://www.astropy.org/ +*homepage*: https://www.astropy.org/ ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``2.0.12`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.0.14`` ``foss/2019a`` +``4.0.1`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================== =============================== @@ -1668,6 +1706,22 @@ version toolchain ========== ================= +.. _list_software_attrdict_863: + +*attrdict* +++++++++++ + +AttrDict is a Python library that provides mapping objects that allow their elements to be accessed both as keys and as attributes. + +*homepage*: https://github.com/bcj/AttrDict + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``2.0.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= + + .. _list_software_augur_548: *augur* @@ -1875,6 +1929,7 @@ version versionsuffix toolchain ``1.11.56`` ``-Python-2.7.12`` ``foss/2016b`` ``1.16.290`` ``-Python-3.6.6`` ``foss/2018b`` ``1.17.7`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``1.18.89`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ============ ================== ================= @@ -1994,14 +2049,14 @@ BamTools provides both a programmer's API and an end-user's toolkit for handling *homepage*: https://github.com/pezmaster31/bamtools -========= ======================================================================================================================================================================================== -version toolchain -========= ======================================================================================================================================================================================== -``2.4.0`` ``foss/2016b`` -``2.4.1`` ``intel/2017a`` -``2.5.0`` ``foss/2016b``, ``intel/2017b`` -``2.5.1`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017b``, ``intel/2018b`` -========= ======================================================================================================================================================================================== +========= ======================================================================================================================================================================================================= +version toolchain +========= ======================================================================================================================================================================================================= +``2.4.0`` ``foss/2016b`` +``2.4.1`` ``intel/2017a`` +``2.5.0`` ``foss/2016b``, ``intel/2017b`` +``2.5.1`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017b``, ``intel/2018b`` +========= ======================================================================================================================================================================================================= .. _list_software_BamUtil_686: @@ -2331,7 +2386,7 @@ version toolchain ``1.3`` ``foss/2016a``, ``intel/2016a`` ``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` ``1.9`` ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``1.10.2`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ========== ========================================================================================= @@ -2377,12 +2432,13 @@ version versionsuffix toolchain bcolz provides columnar, chunked data containers that can be compressed either in-memory and on-disk. Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, but it also comes with support for import/export facilities to/from HDF5/PyTables tables and pandas dataframes. -*homepage*: http://bcolz.blosc.org/en/latest/ +*homepage*: https://bcolz.blosc.org/en/latest/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.1.1`` ``-Python-2.7.13`` ``foss/2017a`` +``1.2.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ============== @@ -2411,15 +2467,15 @@ beagle-lib is a high-performance library that can perform the core calculations *homepage*: https://github.com/beagle-dev/beagle-lib -========= ================ =============================== -version versionsuffix toolchain -========= ================ =============================== -``2.1.2`` ``foss/2016a``, ``foss/2017a`` -``3.0.1`` ``foss/2018a``, ``intel/2018a`` -``3.0.2`` ``foss/2018b`` -``3.0.2`` ``-CUDA-9.2.88`` ``foss/2018b`` -``3.1.2`` ``GCC/8.2.0-2.31.1`` -========= ================ =============================== +========= ================ =================================== +version versionsuffix toolchain +========= ================ =================================== +``2.1.2`` ``foss/2016a``, ``foss/2017a`` +``3.0.1`` ``foss/2018a``, ``intel/2018a`` +``3.0.2`` ``foss/2018b`` +``3.0.2`` ``-CUDA-9.2.88`` ``foss/2018b`` +``3.1.2`` ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0`` +========= ================ =================================== .. _list_software_Beast_495: @@ -2461,6 +2517,7 @@ version versionsuffix toolchain ``4.6.3`` ``-Python-3.6.4`` ``intel/2018a`` ``4.7.1`` ``-Python-3.6.6`` ``intel/2018b`` ``4.8.0`` ``GCCcore/8.2.0`` +``4.9.1`` ``GCCcore/8.3.0`` ========= ================= ================= @@ -2501,8 +2558,8 @@ version toolchain ``2.25.0`` ``foss/2016a`` ``2.26.0`` ``GCCcore/6.4.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``2.27.1`` ``GCCcore/6.4.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` -``2.28.0`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2.29.2`` ``GCC/8.3.0`` +``2.28.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.29.2`` ``GCC/8.3.0``, ``GCC/9.3.0`` ========== ==================================================================================== @@ -2754,7 +2811,7 @@ version versionsuffix toolchain Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. -*homepage*: http://www.bioperl.org/ +*homepage*: https://bioperl.org/ =========== ================ =============================== version versionsuffix toolchain @@ -2769,6 +2826,7 @@ version versionsuffix toolchain ``1.7.2`` ``-Perl-5.26.1`` ``intel/2018a`` ``1.7.2`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` ``1.7.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``1.7.7`` ``GCCcore/9.3.0`` =========== ================ =============================== @@ -2967,6 +3025,7 @@ version versionsuffix toolchain ``2.7.1`` ``-Python-2.7.14`` ``intel/2017b`` ``2.8.1`` ``foss/2018b`` ``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a``, ``iimpi/2019b`` +``2.10.1`` ``gompi/2020a`` ========== ================== ================================================================== @@ -3029,15 +3088,16 @@ version versionsuffix toolchain *Blitz++* +++++++++ -Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface +Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface -*homepage*: http://blitz.sourceforge.net/ +*homepage*: https://github.com/blitzpp/blitz -======== ================================= -version toolchain -======== ================================= -``0.10`` ``GCCcore/6.4.0``, ``foss/2016a`` -======== ================================= +========= ================================= +version toolchain +========= ================================= +``0.10`` ``GCCcore/6.4.0``, ``foss/2016a`` +``1.0.2`` ``GCCcore/9.3.0`` +========= ================================= .. _list_software_BlobTools_912: @@ -3143,6 +3203,7 @@ version versionsuffix toolchain ``1.0.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.3.4`` ``-Python-3.7.2`` ``foss/2019a`` ``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.0.2`` ``-Python-3.8.2`` ``foss/2020a`` =========== ================== ================================== @@ -3176,6 +3237,7 @@ version versionsuffix toolchain ========= ================= ================================== ``0.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``0.1.4`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``0.2.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ================= ================================== @@ -3264,6 +3326,7 @@ version versionsuffix toolchain ``1.70.0`` ``gompi/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` ``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b`` ``1.72.0`` ``gompi/2020a``, ``iimpi/2020a`` +``1.72.0`` ``-no_mpi`` ``GCCcore/9.3.0`` ========== ================== ==================================================================== @@ -3742,7 +3805,7 @@ version toolchain --- -:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_charmm_632` - :ref:`list_software_CHARMM_440` - :ref:`list_software_CHASE_356` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_charmm_632` - :ref:`list_software_CHARMM_440` - :ref:`list_software_CHASE_356` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_C3D_186: @@ -3959,6 +4022,22 @@ version toolchain ========== ============== +.. _list_software_Cartopy_738: + +*Cartopy* ++++++++++ + +Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy. + +*homepage*: https://scitools.org.uk/cartopy/docs/latest/ + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.18.0`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_CaSpER_510: *CaSpER* @@ -4062,7 +4141,7 @@ version toolchain *Cbc* +++++ -Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable. +Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable. *homepage*: https://github.com/coin-or/Cbc @@ -4129,15 +4208,16 @@ version toolchain *cclib* +++++++ -cclib is a Python library that provides parsers for computational chemistry log files. It alsoprovides a platform to implement algorithms in a package-independent manner. +cclib is a Python library that provides parsers for computational chemistry log files. It also provides a platform to implement algorithms in a package-independent manner. -*homepage*: http://cclib.github.io/ +*homepage*: https://cclib.github.io/ -======= ================= ============== -version versionsuffix toolchain -======= ================= ============== -``1.5`` ``-Python-3.5.2`` ``foss/2016b`` -======= ================= ============== +========= ================= =============================== +version versionsuffix toolchain +========= ================= =============================== +``1.5`` ``-Python-3.5.2`` ``foss/2016b`` +``1.6.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +========= ================= =============================== .. _list_software_CD-HIT_409: @@ -4155,7 +4235,7 @@ version versionsuffix toolchain ``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` ``4.6.6`` ``foss/2016b`` ``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` -``4.8.1`` ``foss/2018b`` +``4.8.1`` ``GCC/9.3.0``, ``foss/2018b`` ========= ============== ================================================ @@ -4286,14 +4366,14 @@ version toolchain Classifier for metagenomic sequences -*homepage*: https://ccb.jhu.edu/software/centrifuge/ +*homepage*: https://ccb.jhu.edu/software/centrifuge -============== ============== -version toolchain -============== ============== -``1.0.3`` ``foss/2018b`` -``1.0.4-beta`` ``foss/2018b`` -============== ============== +============== =============================== +version toolchain +============== =============================== +``1.0.3`` ``foss/2018b`` +``1.0.4-beta`` ``foss/2018b``, ``gompi/2020a`` +============== =============================== .. _list_software_CESM-deps_769: @@ -4328,7 +4408,8 @@ version toolchain ``3.41`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``intel/2016b`` ``3.42`` ``GCCcore/6.4.0``, ``intel/2017b`` ``3.45`` ``GCCcore/7.3.0``, ``intel/2018b`` -``3.47`` ``GCCcore/8.2.0`` +``3.47`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.48`` ``GCCcore/9.3.0`` ======== ===================================================== @@ -4377,6 +4458,7 @@ version versionsuffix toolchain ``4.11.1`` ``-Python-3.6.6`` ``foss/2018b`` ``4.14`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``4.14.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``4.14.3`` ``-Python-3.8.2`` ``gompi/2020a`` ========== ================== =============================== @@ -4401,7 +4483,7 @@ version versionsuffix toolchain *Cgl* +++++ -The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver. +The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver. *homepage*: https://github.com/coin-or/Cgl @@ -4790,7 +4872,7 @@ version toolchain The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package. -*homepage*: http://proj-clhep.web.cern.ch/proj-clhep/ +*homepage*: https://proj-clhep.web.cern.ch/proj-clhep/ =========== ================================================================ version toolchain @@ -4802,6 +4884,7 @@ version toolchain ``2.3.4.3`` ``foss/2017b``, ``intel/2017b`` ``2.4.0.0`` ``intel/2017b`` ``2.4.1.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018b`` +``2.4.1.3`` ``foss/2019b`` =========== ================================================================ @@ -4858,7 +4941,7 @@ version toolchain *Clp* +++++ -Clp (Coin-or linear programming) is an open-source linear programming solver. It is primarily meant to be used as a callable library, but a basic, stand-alone executable version is also available. +Clp (Coin-or linear programming) is an open-source linear programming solver. It is primarily meant to be used as a callable library, but a basic, stand-alone executable version is also available. *homepage*: https://github.com/coin-or/Clp @@ -5068,15 +5151,15 @@ version versionsuffix toolchain *CoinUtils* +++++++++++ -CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project. +CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project. *homepage*: https://github.com/coin-or/CoinUtils -========== ================= -version toolchain -========== ================= -``2.11.3`` ``GCCcore/7.3.0`` -========== ================= +========== ================================= +version toolchain +========== ================================= +``2.11.3`` ``GCCcore/7.3.0``, ``foss/2018b`` +========== ================================= .. _list_software_Commet_613: @@ -5137,7 +5220,7 @@ version versionsuffix toolchain configparser is a Python library that brings the updated configparser from Python 3.5 to Python 2.6-3.5 -*homepage*: http://docs.python.org/3/library/configparser.html +*homepage*: https://docs.python.org/3/library/configparser.html ========= ================== =============================== version versionsuffix toolchain @@ -5192,11 +5275,11 @@ Copy number and genotype annotation from whole genome and whole exome sequencin *homepage*: https://github.com/BoevaLab/FREEC -======== ==================== -version toolchain -======== ==================== -``11.5`` ``GCC/8.2.0-2.31.1`` -======== ==================== +======== ======================================== +version toolchain +======== ======================================== +``11.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1`` +======== ======================================== .. _list_software_CoordgenLibs_1211: @@ -5382,7 +5465,7 @@ CppUnit is the C++ port of the famous JUnit framework for unit testing. version toolchain ========== ==================================================== ``1.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a`` -``1.15.1`` ``GCCcore/8.3.0`` +``1.15.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ==================================================== @@ -5686,11 +5769,11 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is *homepage*: https://www.scalasca.org/software/cube-4.x/download.html -========= ================= -version toolchain -========= ================= -``4.4.4`` ``GCCcore/8.2.0`` -========= ================= +========= ==================================== +version toolchain +========= ==================================== +``4.4.4`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +========= ==================================== .. _list_software_CubeLib_662: @@ -5702,11 +5785,11 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is *homepage*: https://www.scalasca.org/software/cube-4.x/download.html -========= ==================================== -version toolchain -========= ==================================== -``4.4.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= ==================================== +========= ======================================================= +version toolchain +========= ======================================================= +``4.4.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================= .. _list_software_CubeWriter_1020: @@ -5718,11 +5801,11 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is *homepage*: https://www.scalasca.org/software/cube-4.x/download.html -========= ==================================== -version toolchain -========= ==================================== -``4.4.3`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= ==================================== +========= ======================================================= +version toolchain +========= ======================================================= +``4.4.3`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================= .. _list_software_CUDA_285: @@ -5893,6 +5976,8 @@ version versionsuffix toolchain ``2.1`` ``-Python-3.6.6`` ``foss/2018b`` ``2.7`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``2.8`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.10`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.10`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ================== ================================================ @@ -6042,7 +6127,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` .. _list_software_dadi_402: @@ -6170,6 +6255,7 @@ version versionsuffix toolchain ``1.1.4`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``2.3.0`` ``-Python-3.7.2`` ``foss/2019a`` ``2.8.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.18.1`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================== =================================================== @@ -6235,12 +6321,13 @@ Perl5 access to Berkeley DB version 1.x. *homepage*: http://perldoc.perl.org/DB_File.html -========= ================ =============== -version versionsuffix toolchain -========= ================ =============== -``1.835`` ``-Perl-5.20.3`` ``intel/2016a`` -``1.835`` ``-Perl-5.22.1`` ``foss/2016a`` -========= ================ =============== +========= ================ ================= +version versionsuffix toolchain +========= ================ ================= +``1.835`` ``GCCcore/9.3.0`` +``1.835`` ``-Perl-5.20.3`` ``intel/2016a`` +``1.835`` ``-Perl-5.22.1`` ``foss/2016a`` +========= ================ ================= .. _list_software_DBD-mysql_813: @@ -6314,13 +6401,13 @@ D-Bus is a message bus system, a simple way for applications to talk to one anot *homepage*: http://dbus.freedesktop.org/doc/dbus-glib -========= ===================================================== -version toolchain -========= ===================================================== -``0.106`` ``foss/2016a``, ``intel/2016a`` -``0.108`` ``intel/2016b``, ``intel/2017a`` -``0.110`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``intel/2017b`` -========= ===================================================== +========= ======================================================================== +version toolchain +========= ======================================================================== +``0.106`` ``foss/2016a``, ``intel/2016a`` +``0.108`` ``intel/2016b``, ``intel/2017a`` +``0.110`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b`` +========= ======================================================================== .. _list_software_dcm2niix_798: @@ -6470,6 +6557,7 @@ version versionsuffix toolchain ``2.5.4`` ``-Python-3.6.3`` ``intel/2017b`` ``3.3.1`` ``-Python-3.6.6`` ``foss/2018b`` ``3.3.1`` ``-Python-3.7.4`` ``intel/2019b`` +``3.3.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= =============== @@ -6723,6 +6811,22 @@ version versionsuffix toolchain ======== ================= =============================== +.. _list_software_dm-tree_686: + +*dm-tree* ++++++++++ + +dm-tree provides tree, a library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows to apply a function to each "leaf" preserving the overall structure. + +*homepage*: https://github.com/deepmind/tree + +========= ================= +version toolchain +========= ================= +``0.1.1`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_DMTCP_376: *DMTCP* @@ -6732,14 +6836,14 @@ DMTCP is a tool to transparently checkpoint the state of multiple simultaneous a *homepage*: https://github.com/dmtcp/dmtcp -========= ============================== -version toolchain -========= ============================== -``2.4.5`` ``system`` -``2.5.0`` ``foss/2016a`` -``2.5.1`` ``system`` -``2.5.2`` ``foss/2016b``, ``foss/2018b`` -========= ============================== +========= ================================================= +version toolchain +========= ================================================= +``2.4.5`` ``system`` +``2.5.0`` ``foss/2016a`` +``2.5.1`` ``system`` +``2.5.2`` ``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2018b`` +========= ================================================= .. _list_software_DOLFIN_444: @@ -6792,6 +6896,22 @@ version toolchain ========= ================= +.. _list_software_dotNET-SDK_829: + +*dotNET-SDK* +++++++++++++ + +.NET is a free, cross-platform, open source developer platform for building many different types of applications. + +*homepage*: https://www.microsoft.com/net/ + +=========== ============== ========== +version versionsuffix toolchain +=========== ============== ========== +``3.1.300`` ``-linux-x64`` ``system`` +=========== ============== ========== + + .. _list_software_double-conversion_1774: *double-conversion* @@ -6934,15 +7054,15 @@ version toolchain *dtcmp* +++++++ -Datatype Compare (DTCMP) Library for sorting and ranking distributed data using MPI +Datatype Compare (DTCMP) Library for sorting and ranking distributed data using MPI. *homepage*: https://github.com/llnl/dtcmp -========= ================================ -version toolchain -========= ================================ -``1.1.0`` ``gompi/2019a``, ``iimpi/2019a`` -========= ================================ +========= ================================================================== +version toolchain +========= ================================================================== +``1.1.0`` ``gompi/2019a``, ``gompi/2020a``, ``iimpi/2019a``, ``iimpi/2020a`` +========= ================================================================== .. _list_software_dtcwt_550: @@ -7121,6 +7241,7 @@ version toolchain ``4.1.1`` ``system`` ``4.1.2`` ``system`` ``4.2.0`` ``system`` +``4.2.1`` ``system`` ========== ========== @@ -7218,7 +7339,7 @@ version versionsuffix toolchain Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. -*homepage*: http://eigen.tuxfamily.org/index.php?title=Main_Page +*homepage*: https://eigen.tuxfamily.org ========== =========================================== version toolchain @@ -7287,6 +7408,7 @@ version toolchain ========== =============== ``4.0.15`` ``intel/2016b`` ``4.3.6`` ``intel/2017a`` +``6.3.2`` ``intel/2019b`` ========== =============== @@ -7540,9 +7662,9 @@ version versionsuffix toolchain *ESMF* ++++++ -The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models. +The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. -*homepage*: https://sourceforge.net/projects/esmf +*homepage*: https://www.earthsystemcog.org/projects/esmf/ ============ ================ ================================================================= version versionsuffix toolchain @@ -7553,6 +7675,7 @@ version versionsuffix toolchain ``7.0.2`` ``intel/2017b`` ``7.1.0r`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``8.0.0`` ``intel/2019b`` +``8.0.1`` ``foss/2020a`` ============ ================ ================================================================= @@ -7765,7 +7888,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FIAT_292` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FIAT_292` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -8039,10 +8162,27 @@ version versionsuffix toolchain ``0.11.7`` ``-Java-1.8.0_162`` ``system`` ``0.11.8`` ``-Java-1.8`` ``system`` ``0.11.8`` ``-Java-11`` ``system`` +``0.11.9`` ``-Java-1.8`` ``system`` ``0.11.9`` ``-Java-11`` ``system`` ========== =================== ========== +.. _list_software_fastqsplitter_1430: + +*fastqsplitter* ++++++++++++++++ + +Splits fastq files evenly. + +*homepage*: https://github.com/LUMC/fastqsplitter + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``1.2.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +========= ================= ================= + + .. _list_software_FastQTL_639: *FastQTL* @@ -8123,7 +8263,7 @@ FastTree infers approximately-maximum-likelihood phylogenetic trees from alignme version toolchain ========== ================================================================= ``2.1.10`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``2.1.11`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.1.11`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ================================================================= @@ -8395,6 +8535,7 @@ version versionsuffix toolchain ``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` ``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` ``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``iomkl/2018b`` +``3.3.8`` ``-serial`` ``GCC/9.3.0`` ========= ============= ================================================================================================================================================================================================================================ @@ -8473,17 +8614,17 @@ The file command is 'a file type guesser', that is, a command-line tool that te *homepage*: https://www.darwinsys.com/file/ -======== ================= -version toolchain -======== ================= -``5.17`` ``GCC/4.8.2`` -``5.25`` ``intel/2016a`` -``5.28`` ``foss/2016b`` -``5.30`` ``intel/2017a`` -``5.33`` ``GCCcore/6.4.0`` -``5.35`` ``GCCcore/7.3.0`` -``5.38`` ``GCCcore/8.3.0`` -======== ================= +======== ==================================== +version toolchain +======== ==================================== +``5.17`` ``GCC/4.8.2`` +``5.25`` ``intel/2016a`` +``5.28`` ``foss/2016b`` +``5.30`` ``intel/2017a`` +``5.33`` ``GCCcore/6.4.0`` +``5.35`` ``GCCcore/7.3.0`` +``5.38`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======== ==================================== .. _list_software_Filtlong_831: @@ -8591,11 +8732,12 @@ Fiona is designed to be simple and dependable. It focuses on reading and writing *homepage*: https://github.com/Toblerity/Fiona -========== ================= ============== -version versionsuffix toolchain -========== ================= ============== -``1.8.13`` ``-Python-3.7.4`` ``foss/2019b`` -========== ================= ============== +================ ================= ============== +version versionsuffix toolchain +================ ================= ============== +``1.8.13`` ``-Python-3.7.4`` ``foss/2019b`` +``1.8.13.post1`` ``-Python-3.7.2`` ``foss/2019a`` +================ ================= ============== .. _list_software_Firefox_723: @@ -8662,6 +8804,22 @@ version toolchain ======= ================================================= +.. _list_software_FLAIR_366: + +*FLAIR* ++++++++ + +FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads. + +*homepage*: https://github.com/BrooksLabUCSC/flair + +======= ================= ============== +version versionsuffix toolchain +======= ================= ============== +``1.5`` ``-Python-3.7.4`` ``foss/2019b`` +======= ================= ============== + + .. _list_software_FLANN_367: *FLANN* @@ -8705,11 +8863,12 @@ version toolchain *homepage*: https://www.palletsprojects.com/p/flask/ -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``1.0.2`` ``-Python-3.6.6`` ``foss/2018b`` -========= ================= ============== +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``1.0.2`` ``-Python-3.6.6`` ``foss/2018b`` +``1.1.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= .. _list_software_FLEUR_382: @@ -8737,17 +8896,17 @@ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, some *homepage*: http://flex.sourceforge.net/ -========== ==================================================================================================================================================================================================================================================================================================================================================================== -version toolchain -========== ==================================================================================================================================================================================================================================================================================================================================================================== -``2.5.35`` ``system`` -``2.5.38`` ``GCC/4.8.2`` -``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` -``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.6.2`` ``intel/2016b`` -``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` -``2.6.4`` ``GCCcore/10.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` -========== ==================================================================================================================================================================================================================================================================================================================================================================== +========== ======================================================================================================================================================================================================================================================================================================================================================================================= +version toolchain +========== ======================================================================================================================================================================================================================================================================================================================================================================================= +``2.5.35`` ``system`` +``2.5.38`` ``GCC/4.8.2`` +``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` +``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +``2.6.2`` ``intel/2016b`` +``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` +``2.6.4`` ``GCCcore/10.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` +========== ======================================================================================================================================================================================================================================================================================================================================================================================= .. _list_software_FlexiDot_799: @@ -9126,7 +9285,7 @@ version versionsuffix toolchain ========= ================ ====================================================================================================================================================================================== ``3.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` -``3.2.1`` ``GCCcore/8.3.0`` +``3.2.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ================ ====================================================================================================================================================================================== @@ -9139,11 +9298,11 @@ FreeImage is an Open Source library project for developers who would like to sup *homepage*: http://freeimage.sourceforge.net -========== ==================================== -version toolchain -========== ==================================== -``3.18.0`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` -========== ==================================== +========== ======================================================= +version toolchain +========== ======================================================= +``3.18.0`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ======================================================= .. _list_software_FreeSurfer_1017: @@ -9200,13 +9359,13 @@ FreeXL is an open source library to extract valid data from within an Excel (.x *homepage*: https://www.gaia-gis.it/fossil/freexl/index -========= ==================================== -version toolchain -========= ==================================== -``1.0.2`` ``foss/2016b``, ``intel/2016b`` -``1.0.3`` ``GCCcore/6.4.0`` -``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -========= ==================================== +========= ======================================================= +version toolchain +========= ======================================================= +``1.0.2`` ``foss/2016b``, ``intel/2016b`` +``1.0.3`` ``GCCcore/6.4.0`` +``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ======================================================= .. _list_software_FriBidi_665: @@ -9410,7 +9569,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gblocks_709` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_gtest_551` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gblocks_709` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_gtest_551` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -9599,6 +9758,7 @@ version versionsuffix toolchain ``8.1.p01`` ``-Python-2.7.15`` ``foss/2018b`` ``8.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``8.2`` ``-Python-2.7.15`` ``foss/2018b`` +``9.0`` ``-Python-3.7.4`` ``foss/2019b`` =========== =============================== =============================== @@ -9853,11 +10013,11 @@ GConf is a system for storing application preferences. It is intended for user *homepage*: https://projects.gnome.org/gconf/ -========= ===================================================================================================================== -version toolchain -========= ===================================================================================================================== -``3.2.6`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -========= ===================================================================================================================== +========= ======================================================================================================================================== +version toolchain +========= ======================================================================================================================================== +``3.2.6`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +========= ======================================================================================================================================== .. _list_software_Gctf_388: @@ -9926,7 +10086,7 @@ version versionsuffix toolchain ``2.2.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.0.0`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ``3.0.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.0.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.0.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``3.0.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========= ============================== ================================================================ @@ -10103,6 +10263,7 @@ version toolchain ``10.03.p03`` ``foss/2017b``, ``intel/2017b`` ``10.04`` ``intel/2017b`` ``10.5`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018b`` +``10.6`` ``foss/2019b`` ============= ================================================================ @@ -10301,6 +10462,7 @@ GeoPandas is a project to add support for geographic data to pandas objects. It version versionsuffix toolchain ========= ================= ============== ``0.7.0`` ``-Python-3.7.4`` ``foss/2019b`` +``0.8.0`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= ============== @@ -10523,12 +10685,13 @@ version versionsuffix toolchain giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented. -*homepage*: http://libungif.sourceforge.net/ +*homepage*: http://giflib.sourceforge.net/ ========= ==================================== version toolchain ========= ==================================== ``5.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``5.2.1`` ``GCCcore/8.3.0`` ========= ==================================== @@ -10697,6 +10860,22 @@ version versionsuffix toolchain =========== ============= ================= +.. _list_software_git-extras_1032: + +*git-extras* +++++++++++++ + +Extra useful scripts for git + +*homepage*: https://github.com/tj/git-extras + +========= ============== +version toolchain +========= ============== +``5.1.0`` ``foss/2016a`` +========= ============== + + .. _list_software_git-lfs_694: *git-lfs* @@ -10706,12 +10885,13 @@ Git Large File Storage (LFS) replaces large files such as audio samples, videos *homepage*: https://git-lfs.github.com -========= ========== -version toolchain -========= ========== -``1.1.1`` ``system`` -``2.7.1`` ``system`` -========= ========== +========== ========== +version toolchain +========== ========== +``1.1.1`` ``system`` +``2.7.1`` ``system`` +``2.11.0`` ``system`` +========== ========== .. _list_software_GitPython_934: @@ -10817,6 +10997,23 @@ version toolchain ========= ======================================================================= +.. _list_software_GLFW_304: + +*GLFW* +++++++ + +GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop + +*homepage*: https://www.glfw.org + +========= ================= +version toolchain +========= ================= +``3.2.1`` ``intel/2018a`` +``3.3.2`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_GLib_350: *GLib* @@ -10926,6 +11123,7 @@ version toolchain ``0.9.7.6`` ``intel/2016a`` ``0.9.8.3`` ``GCCcore/5.4.0`` ``0.9.9.0`` ``GCCcore/6.4.0`` +``0.9.9.8`` ``GCCcore/8.3.0`` =========== ================= @@ -11139,16 +11337,17 @@ version versionsuffix toolchain Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. -*homepage*: https://gmsh.info/ +*homepage*: https://gmsh.info -========= ================== ============== -version versionsuffix toolchain -========= ================== ============== -``3.0.6`` ``-Python-2.7.14`` ``foss/2017b`` -``3.0.6`` ``-Python-3.6.6`` ``foss/2018b`` -``4.2.2`` ``-Python-3.6.6`` ``foss/2018b`` -``4.5.6`` ``-Python-3.7.4`` ``foss/2019b`` -========= ================== ============== +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``3.0.6`` ``-Python-2.7.14`` ``foss/2017b`` +``3.0.6`` ``-Python-3.6.6`` ``foss/2018b`` +``4.2.2`` ``-Python-3.6.6`` ``foss/2018b`` +``4.5.6`` ``-Python-2.7.16`` ``intel/2019b`` +``4.5.6`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================== =============== .. _list_software_GMT_232: @@ -11345,6 +11544,7 @@ GNU Compiler Collection (GCC) based compiler toolchain, including OpenBLAS (BLA version toolchain ========= ========== ``2018a`` ``system`` +``2020a`` ``system`` ========= ========== @@ -11543,13 +11743,13 @@ gperftools are for use by developers so that they can create more robust applica *homepage*: https://github.com/gperftools/gperftools -========== =============================== -version toolchain -========== =============================== -``2.5`` ``foss/2016a``, ``intel/2016b`` -``2.6.3`` ``GCCcore/6.4.0`` -``2.7.90`` ``GCCcore/8.3.0`` -========== =============================== +========== ==================================== +version toolchain +========== ==================================== +``2.5`` ``foss/2016a``, ``intel/2016b`` +``2.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.7.90`` ``GCCcore/8.3.0`` +========== ==================================== .. _list_software_gpustat_776: @@ -11766,13 +11966,14 @@ version toolchain The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization -*homepage*: http://grass.osgeo.org +*homepage*: https://grass.osgeo.org -========= ================== ============== -version versionsuffix toolchain -========= ================== ============== -``7.6.0`` ``-Python-2.7.15`` ``foss/2018b`` -========= ================== ============== +========= ================== ================== +version versionsuffix toolchain +========= ================== ================== +``7.6.0`` ``-Python-2.7.15`` ``foss/2018b`` +``7.8.3`` ``-Python-3.7.4`` ``fosscuda/2019b`` +========= ================== ================== .. _list_software_Greenlet_822: @@ -12192,12 +12393,12 @@ GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free *homepage*: http://gts.sourceforge.net/ -============ ================================================================================================================= -version toolchain -============ ================================================================================================================= -``0.7.6`` ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` -``20121130`` ``foss/2017b`` -============ ================================================================================================================= +============ ================================================================================================================================= +version toolchain +============ ================================================================================================================================= +``0.7.6`` ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` +``20121130`` ``foss/2017b`` +============ ================================================================================================================================= .. _list_software_gubbins_746: @@ -12316,7 +12517,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_hyperopt_891` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -12328,11 +12529,12 @@ The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, a *homepage*: http://www.hdfgroup.org/h4toh5/ -========= ======================== ========== -version versionsuffix toolchain -========= ======================== ========== -``2.2.2`` ``-linux-x86_64-static`` ``system`` -========= ======================== ========== +========= ======================== =============================== +version versionsuffix toolchain +========= ======================== =============================== +``2.2.2`` ``-linux-x86_64-static`` ``system`` +``2.2.3`` ``foss/2018b``, ``gompi/2019b`` +========= ======================== =============================== .. _list_software_H5hut_462: @@ -12392,7 +12594,7 @@ version versionsuffix toolchain ``2.8.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.9.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` ``2.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``2.10.0`` ``-Python-3.8.2`` ``foss/2020a`` +``2.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ===================================== ==================================================================================== @@ -12415,6 +12617,7 @@ version versionsuffix toolchain ``2.6.0-cdh5.8.0`` ``-native`` ``system`` ``2.6.0-cdh5.12.0`` ``-native`` ``system`` ``2.9.2`` ``-native`` ``GCCcore/7.3.0`` +``2.10.0`` ``-native`` ``GCCcore/8.3.0`` =================== ========================== ================= @@ -12588,11 +12791,11 @@ HDF-EOS libraries are software libraries built on HDF libraries. It supports th *homepage*: https://hdfeos.org/ -======== ================= -version toolchain -======== ================= -``2.20`` ``GCCcore/7.3.0`` -======== ================= +======== ==================================== +version toolchain +======== ==================================== +``2.20`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +======== ==================================== .. _list_software_HDF-EOS5_539: @@ -12604,11 +12807,11 @@ HDF-EOS libraries are software libraries built on HDF libraries. It supports th *homepage*: https://hdfeos.org/ -======== ============== -version toolchain -======== ============== -``1.16`` ``foss/2018b`` -======== ============== +======== =============================== +version toolchain +======== =============================== +``1.16`` ``foss/2018b``, ``gompi/2019b`` +======== =============================== .. _list_software_HDF5_263: @@ -12640,6 +12843,7 @@ version versionsuffix toolchain ``1.10.2`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``1.10.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompic/2019a``, ``gompic/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpic/2019a``, ``iimpic/2019b`` ``1.10.6`` ``gompi/2020a``, ``iimpi/2020a`` +``1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` ================= ============= ================================================================================================================================================================================================================== @@ -12828,9 +13032,26 @@ version toolchain ``2.0.4`` ``foss/2016b`` ``2.0.5`` ``intel/2017a`` ``2.1.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +``2.2.0`` ``foss/2018b`` ============== ================================================================================= +.. _list_software_hl7apy_597: + +*hl7apy* +++++++++ + +Python library to parse, create and handle HL7 v2 messages. + +*homepage*: https://github.com/crs4/hl7apy + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``1.3.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= + + .. _list_software_HLAminer_752: *HLAminer* @@ -12989,7 +13210,7 @@ version toolchain Highly parallel density based spatial clustering for application with noise -*homepage*: https://bitbucket.org/markus.goetz/hpdbscan +*homepage*: https://github.com/Markus-Goetz/hpdbscan ============ ============== version toolchain @@ -13012,7 +13233,7 @@ version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``fosscuda/2019b``, ``gomkl/2019a``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020a``, ``intelcuda/2019b``, ``iomkl/2019.01`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``fosscuda/2019b``, ``gomkl/2019a``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020a``, ``intelcuda/2019b``, ``iomkl/2019.01`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= @@ -13154,6 +13375,22 @@ version toolchain =========== ===================================================================================================================================================================================================================================================== +.. _list_software_hyperopt_891: + +*hyperopt* +++++++++++ + +Distributed Asynchronous Hyperparameter Optimization in Python + +*homepage*: https://github.com/hyperopt/hyperopt + +========= ========================== =============== +version versionsuffix toolchain +========= ========================== =============== +``0.2.4`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` +========= ========================== =============== + + .. _list_software_Hyperopt_859: *Hyperopt* @@ -13263,7 +13500,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_ITSTool_654` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_ITSTool_654` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -13436,6 +13673,22 @@ version versionsuffix toolchain ============== =================== ========== +.. _list_software_ichorCNA_743: + +*ichorCNA* +++++++++++ + +ichorCNA is a tool for estimating the fraction of tumor in cell-free DNA from ultra-low-pass whole genome sequencing + +*homepage*: https://github.com/broadinstitute/ichorCNA/wiki + +========= ============== +version toolchain +========= ============== +``0.2.0`` ``foss/2019b`` +========= ============== + + .. _list_software_icmake_618: *icmake* @@ -13560,6 +13813,22 @@ version versionsuffix toolchain ============== ===================== ========== +.. _list_software_IgBLAST_550: + +*IgBLAST* ++++++++++ + +IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences. + +*homepage*: https://ncbi.github.io/igblast + +========== ============== ========== +version versionsuffix toolchain +========== ============== ========== +``1.15.0`` ``-x64-linux`` ``system`` +========== ============== ========== + + .. _list_software_IGMPlot_636: *IGMPlot* @@ -13656,40 +13925,41 @@ Intel C/C++ and Fortran compilers, alongside Intel MPI. *homepage*: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ -=========== ==================== ========== -version versionsuffix toolchain -=========== ==================== ========== -``8.1.5`` ``-GCC-4.9.3-2.25`` ``system`` -``2016.00`` ``-GCC-4.9.3-2.25`` ``system`` -``2016.01`` ``-GCC-4.9.3-2.25`` ``system`` -``2016.02`` ``-GCC-4.9.3-2.25`` ``system`` -``2016.02`` ``-GCC-5.3.0-2.26`` ``system`` -``2016.03`` ``-GCC-4.9.3-2.25`` ``system`` -``2016.03`` ``-GCC-5.3.0-2.26`` ``system`` -``2016.03`` ``-GCC-5.4.0-2.26`` ``system`` -``2016b`` ``system`` -``2017.00`` ``-GCC-5.4.0-2.26`` ``system`` -``2017.01`` ``-GCC-5.4.0-2.26`` ``system`` -``2017.02`` ``-GCC-6.3.0-2.27`` ``system`` -``2017.09`` ``system`` -``2017a`` ``system`` -``2017b`` ``system`` -``2018.00`` ``system`` -``2018.01`` ``system`` -``2018.02`` ``system`` -``2018.04`` ``system`` -``2018a`` ``system`` -``2018b`` ``system`` -``2019.00`` ``system`` -``2019.01`` ``system`` -``2019.02`` ``system`` -``2019.03`` ``system`` -``2019a`` ``system`` -``2019b`` ``system`` -``2020.00`` ``system`` -``2020a`` ``system`` -``system`` ``-GCC-system-2.29`` ``system`` -=========== ==================== ========== +===================== ==================== ========== +version versionsuffix toolchain +===================== ==================== ========== +``8.1.5`` ``-GCC-4.9.3-2.25`` ``system`` +``2016.00`` ``-GCC-4.9.3-2.25`` ``system`` +``2016.01`` ``-GCC-4.9.3-2.25`` ``system`` +``2016.02`` ``-GCC-4.9.3-2.25`` ``system`` +``2016.02`` ``-GCC-5.3.0-2.26`` ``system`` +``2016.03`` ``-GCC-4.9.3-2.25`` ``system`` +``2016.03`` ``-GCC-5.3.0-2.26`` ``system`` +``2016.03`` ``-GCC-5.4.0-2.26`` ``system`` +``2016b`` ``system`` +``2017.00`` ``-GCC-5.4.0-2.26`` ``system`` +``2017.01`` ``-GCC-5.4.0-2.26`` ``system`` +``2017.02`` ``-GCC-6.3.0-2.27`` ``system`` +``2017.09`` ``system`` +``2017a`` ``system`` +``2017b`` ``system`` +``2018.00`` ``system`` +``2018.01`` ``system`` +``2018.02`` ``system`` +``2018.04`` ``system`` +``2018a`` ``system`` +``2018b`` ``system`` +``2019.00`` ``system`` +``2019.01`` ``system`` +``2019.02`` ``system`` +``2019.03`` ``system`` +``2019a`` ``system`` +``2019b`` ``system`` +``2020.00`` ``system`` +``2020.06-impi-18.5`` ``system`` +``2020a`` ``system`` +``system`` ``-GCC-system-2.29`` ``system`` +===================== ==================== ========== .. _list_software_iimpic_635: @@ -13914,7 +14184,7 @@ version toolchain ``2019.3.199`` ``iimpi/2019.03`` ``2019.5.281`` ``iimpi/2019b``, ``iimpic/2019b`` ``2020.0.166`` ``iimpi/2020.00`` -``2020.1.217`` ``iimpi/2020a`` +``2020.1.217`` ``iimpi/2020.06-impi-18.5``, ``iimpi/2020a`` ============== ====================================================================================================================================================================================================================================================================== @@ -13986,7 +14256,7 @@ version versionsuffix toolchain ``2018.2.199`` ``iccifort/2018.2.199-GCC-6.4.0-2.28`` ``2018.3.222`` ``GCC/7.3.0-2.30``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` ``2018.4.274`` ``iccifort/2018.5.274-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifortcuda/2019a`` -``2018.5.288`` ``iccifort/2019.5.281``, ``iccifortcuda/2019b`` +``2018.5.288`` ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifortcuda/2019b`` ``2019.0.117`` ``iccifort/2019.0.117-GCC-8.2.0-2.31.1`` ``2019.1.144`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2019.2.187`` ``iccifort/2019.2.187-GCC-8.2.0-2.31.1`` @@ -14045,6 +14315,7 @@ InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence version versionsuffix toolchain ========= ========================= ============== ``1.0.4`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` +``1.2.1`` ``-Python-3.7.4`` ``foss/2019b`` ========= ========================= ============== @@ -14179,39 +14450,40 @@ Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Li *homepage*: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain -=========== ============= ========== -version versionsuffix toolchain -=========== ============= ========== -``2016.00`` ``system`` -``2016.01`` ``system`` -``2016.02`` ``-GCC-4.9`` ``system`` -``2016.02`` ``-GCC-5.3`` ``system`` -``2016.03`` ``-GCC-4.9`` ``system`` -``2016.03`` ``-GCC-5.3`` ``system`` -``2016.03`` ``-GCC-5.4`` ``system`` -``2016a`` ``system`` -``2016b`` ``system`` -``2017.00`` ``system`` -``2017.01`` ``system`` -``2017.02`` ``system`` -``2017.09`` ``system`` -``2017a`` ``system`` -``2017b`` ``system`` -``2018.00`` ``system`` -``2018.01`` ``system`` -``2018.02`` ``system`` -``2018.04`` ``system`` -``2018a`` ``system`` -``2018b`` ``system`` -``2019.00`` ``system`` -``2019.01`` ``system`` -``2019.02`` ``system`` -``2019.03`` ``system`` -``2019a`` ``system`` -``2019b`` ``system`` -``2020.00`` ``system`` -``2020a`` ``system`` -=========== ============= ========== +===================== ============= ========== +version versionsuffix toolchain +===================== ============= ========== +``2016.00`` ``system`` +``2016.01`` ``system`` +``2016.02`` ``-GCC-4.9`` ``system`` +``2016.02`` ``-GCC-5.3`` ``system`` +``2016.03`` ``-GCC-4.9`` ``system`` +``2016.03`` ``-GCC-5.3`` ``system`` +``2016.03`` ``-GCC-5.4`` ``system`` +``2016a`` ``system`` +``2016b`` ``system`` +``2017.00`` ``system`` +``2017.01`` ``system`` +``2017.02`` ``system`` +``2017.09`` ``system`` +``2017a`` ``system`` +``2017b`` ``system`` +``2018.00`` ``system`` +``2018.01`` ``system`` +``2018.02`` ``system`` +``2018.04`` ``system`` +``2018a`` ``system`` +``2018b`` ``system`` +``2019.00`` ``system`` +``2019.01`` ``system`` +``2019.02`` ``system`` +``2019.03`` ``system`` +``2019a`` ``system`` +``2019b`` ``system`` +``2020.00`` ``system`` +``2020.06-impi-18.5`` ``system`` +``2020a`` ``system`` +===================== ============= ========== .. _list_software_IntelClusterChecker_1939: @@ -14249,6 +14521,22 @@ version toolchain =========== ========== +.. _list_software_IntelDAAL_782: + +*IntelDAAL* ++++++++++++ + +Intel® Data Analytics Acceleration Library (Intel® DAAL) is the library of Intel® architecture optimized building blocks covering all stages of data analytics: data acquisition from a data source, preprocessing, transformation, data mining, modeling, validation, and decision making. + +*homepage*: https://software.intel.com/en-us/daal + +============== ========== +version toolchain +============== ========== +``2019.4.007`` ``system`` +============== ========== + + .. _list_software_IntelPython_1150: *IntelPython* @@ -14521,6 +14809,7 @@ version versionsuffix toolchain ``7.7.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``7.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``7.13.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``7.15.0`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================== ======================================================================================= @@ -14631,6 +14920,7 @@ version toolchain ``2018.1.017`` ``system`` ``2018.3.022`` ``system`` ``2019.2.026`` ``system`` +``2019.4.036`` ``system`` ============== ========== @@ -14711,12 +15001,12 @@ JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian *homepage*: http://mcmc-jags.sourceforge.net/ -========= =============================================================== -version toolchain -========= =============================================================== -``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` -``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b`` -========= =============================================================== +========= =============================================================================== +version toolchain +========= =============================================================================== +``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` +``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``intel/2017b`` +========= =============================================================================== .. _list_software_Jansson_732: @@ -15038,6 +15328,7 @@ version versionsuffix toolchain ``1.3.1`` ``-linux-x86_64`` ``system`` ``1.4.0`` ``-linux-x86_64`` ``system`` ``1.4.1`` ``-linux-x86_64`` ``system`` +``1.4.2`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -15408,6 +15699,7 @@ version versionsuffix toolchain ``0.10.5-beta`` ``-Perl-5.24.0`` ``foss/2016b`` ``1.0`` ``-Perl-5.26.1`` ``intel/2018a`` ``1.1`` ``-Perl-5.28.0`` ``foss/2018b`` +``1.1.1`` ``GCCcore/9.3.0`` ``1.1.1`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` =============== ================ ================= @@ -15428,6 +15720,7 @@ version versionsuffix toolchain ``2.0.7-beta`` ``-Perl-5.28.0`` ``foss/2018b`` ``2.0.8-beta`` ``-Perl-5.30.0`` ``gompi/2019b`` ``2.0.9-beta`` ``-Perl-5.28.0`` ``foss/2018b`` +``2.0.9-beta`` ``-Perl-5.30.2`` ``gompi/2020a`` ============== ================ =============== @@ -15521,11 +15814,11 @@ Kyoto Cabinet is a library of routines for managing a database. *homepage*: https://fallabs.com/kyotocabinet -========== ================= -version toolchain -========== ================= -``1.2.77`` ``GCCcore/7.3.0`` -========== ================= +========== ==================================== +version toolchain +========== ==================================== +``1.2.77`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +========== ==================================== .. _list_software_letter_l: @@ -15583,7 +15876,7 @@ LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale At version versionsuffix toolchain ============ ======================== =============================== ``3Mar2020`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` -``3Mar2020`` ``-Python-3.8.2-kokkos`` ``foss/2020a`` +``3Mar2020`` ``-Python-3.8.2-kokkos`` ``foss/2020a``, ``intel/2020a`` ``7Aug2019`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` ============ ======================== =============================== @@ -16199,6 +16492,7 @@ version toolchain ========= ==================================== ``1.6.5`` ``intel/2016a`` ``1.8.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.8.5`` ``GCCcore/8.3.0`` ========= ==================================== @@ -16278,7 +16572,7 @@ version toolchain The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. -*homepage*: ftp://ftp.freedesktop.org/pub/mesa/glu/ +*homepage*: https://mesa.freedesktop.org/archive/glu/ ========= ================ =========================================================================================================================================================================================================================================================================================================================================== version versionsuffix toolchain @@ -16320,6 +16614,7 @@ version toolchain ``1.21`` ``intel/2016a`` ``1.35`` ``GCCcore/7.3.0`` ``1.36`` ``GCCcore/8.2.0`` +``1.38`` ``GCCcore/8.3.0`` ======== ================= @@ -16471,7 +16766,7 @@ version toolchain ======== ====================================================================================== ``1.32`` ``GCCcore/5.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` ``1.34`` ``GCCcore/6.4.0`` -``1.35`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +``1.35`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ======== ====================================================================================== @@ -16562,11 +16857,11 @@ libMemcached is an open source C/C++ client library and tools for the memcached *homepage*: https://memcached.org -========== ================= -version toolchain -========== ================= -``1.0.18`` ``GCCcore/6.4.0`` -========== ================= +========== ==================================== +version toolchain +========== ==================================== +``1.0.18`` ``GCCcore/6.4.0``, ``GCCcore/9.3.0`` +========== ==================================== .. _list_software_libpciaccess_1253: @@ -16624,12 +16919,12 @@ C library for the Public Suffix List *homepage*: https://rockdaboot.github.io/libpsl -========== ================= -version toolchain -========== ================= -``0.20.2`` ``GCCcore/7.3.0`` -``0.21.0`` ``GCCcore/8.2.0`` -========== ================= +========== ==================================== +version toolchain +========== ==================================== +``0.20.2`` ``GCCcore/7.3.0`` +``0.21.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========== ==================================== .. _list_software_libpsml_755: @@ -16886,6 +17181,7 @@ libsoup is an HTTP client/server library for GNOME. It uses GObjects and the gli version toolchain ========== ================= ``2.66.1`` ``GCCcore/8.2.0`` +``2.70.0`` ``GCCcore/8.3.0`` ========== ================= @@ -16919,6 +17215,7 @@ version versionsuffix toolchain ========== ================= =============================================== ``4.3.0a`` ``foss/2016b``, ``foss/2018b``, ``intel/2016b`` ``4.3.0a`` ``-Python-3.7.2`` ``foss/2019a`` +``4.3.0a`` ``-Python-3.7.4`` ``GCC/8.3.0`` ========== ================= =============================================== @@ -16980,13 +17277,14 @@ Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages *homepage*: https://www.gnu.org/software/libtasn1/ -======== =================================================== -version toolchain -======== =================================================== -``4.7`` ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` -``4.12`` ``GCCcore/5.4.0`` -``4.13`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -======== =================================================== +========== =================================================== +version toolchain +========== =================================================== +``4.7`` ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` +``4.12`` ``GCCcore/5.4.0`` +``4.13`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``4.16.0`` ``GCCcore/8.3.0`` +========== =================================================== .. _list_software_LibTIFF_576: @@ -17160,6 +17458,7 @@ version toolchain ========= ==================================== ``1.0.0`` ``foss/2018b`` ``1.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.1.0`` ``GCCcore/8.3.0`` ========= ==================================== @@ -18110,11 +18409,11 @@ The Light-weight Group Library provides methods for MPI codes to quickly create *homepage*: https://github.com/llnl/lwgrp -========= ================================ -version toolchain -========= ================================ -``1.0.2`` ``gompi/2019a``, ``iimpi/2019a`` -========= ================================ +========= ================================================================== +version toolchain +========= ================================================================== +``1.0.2`` ``gompi/2019a``, ``gompi/2020a``, ``iimpi/2019a``, ``iimpi/2020a`` +========= ================================================================== .. _list_software_lxml_445: @@ -18201,7 +18500,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_magma_515` - :ref:`list_software_MAGMA_355` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_magma_515` - :ref:`list_software_MAGMA_355` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -18278,19 +18577,20 @@ version toolchain *MAFFT* +++++++ -MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc. +MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. *homepage*: https://mafft.cbrc.jp/alignment/software/source.html -========= ==================== ====================================== -version versionsuffix toolchain -========= ==================== ====================================== -``7.305`` ``-with-extensions`` ``foss/2016b`` -``7.397`` ``-with-extensions`` ``intel/2018a`` -``7.427`` ``-with-extensions`` ``foss/2018b``, ``intel/2018b`` -``7.429`` ``-with-extensions`` ``GCC/8.2.0-2.31.1`` -``7.453`` ``-with-extensions`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -========= ==================== ====================================== +========= ==================== ====================================================================== +version versionsuffix toolchain +========= ==================== ====================================================================== +``7.305`` ``-with-extensions`` ``foss/2016b`` +``7.397`` ``-with-extensions`` ``intel/2018a`` +``7.427`` ``-with-extensions`` ``foss/2018b``, ``intel/2018b`` +``7.429`` ``-with-extensions`` ``GCC/8.2.0-2.31.1`` +``7.453`` ``-with-extensions`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``gompi/2020a``, ``iccifort/2019.5.281`` +``7.470`` ``-with-extensions`` ``GCC/9.3.0``, ``gompi/2020a`` +========= ==================== ====================================================================== .. _list_software_magick_620: @@ -18338,11 +18638,12 @@ MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data *homepage*: https://ctg.cncr.nl/software/magma -========= ============== -version toolchain -========= ============== -``1.07b`` ``foss/2018b`` -========= ============== +========== ============== +version toolchain +========== ============== +``1.07b`` ``foss/2018b`` +``1.07bb`` ``GCC/8.3.0`` +========== ============== .. _list_software_MagresPython_1249: @@ -18477,12 +18778,13 @@ Manta calls structural variants (SVs) and indels from mapped paired-end sequenci *homepage*: https://github.com/Illumina/manta -========= ========== -version toolchain -========= ========== -``1.1.1`` ``system`` -``1.6.0`` ``system`` -========= ========== +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``1.1.1`` ``system`` +``1.6.0`` ``system`` +``1.6.0`` ``-Python-2.7.16`` ``gompi/2019b`` +========= ================== =============== .. _list_software_Maple_495: @@ -18578,6 +18880,22 @@ version toolchain ========= ==================================================== +.. _list_software_MARS_307: + +*MARS* +++++++ + +improving Multiple circular sequence Alignment using Refined Sequences + +*homepage*: https://github.com/lorrainea/MARS + +============ ================= +version toolchain +============ ================= +``20191101`` ``GCCcore/8.3.0`` +============ ================= + + .. _list_software_Mash_393: *Mash* @@ -18635,6 +18953,7 @@ version toolchain ``11.1.1`` ``system`` ``11.3.0`` ``system`` ``12.0.0`` ``system`` +``12.1.1`` ``system`` ========== ========== @@ -18669,6 +18988,7 @@ version toolchain ``1.5.9`` ``GCCcore/5.4.0`` ``1.5.11`` ``foss/2017b`` ``1.5.12`` ``GCCcore/6.4.0`` +``1.5.17`` ``GCCcore/8.3.0`` ========== ================= @@ -18908,14 +19228,14 @@ The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable *homepage*: http://micans.org/mcl/ -========== ================ ================================================== -version versionsuffix toolchain -========== ================ ================================================== -``02.063`` ``intel/2016b`` -``14.137`` ``GCCcore/8.3.0``, ``foss/2016a``, ``intel/2016b`` -``14.137`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``14.137`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -========== ================ ================================================== +========== ================ ===================================================================== +version versionsuffix toolchain +========== ================ ===================================================================== +``02.063`` ``intel/2016b`` +``14.137`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``intel/2016b`` +``14.137`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``14.137`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +========== ================ ===================================================================== .. _list_software_MCR_226: @@ -18969,11 +19289,11 @@ MDBM is a super-fast memory-mapped key/value store *homepage*: https://github.com/yahoo/mdbm -========== ================= -version toolchain -========== ================= -``4.13.0`` ``GCCcore/6.4.0`` -========== ================= +========== ==================================== +version toolchain +========== ==================================== +``4.13.0`` ``GCCcore/6.4.0``, ``GCCcore/9.3.0`` +========== ==================================== .. _list_software_MDSplus_680: @@ -19193,6 +19513,7 @@ version versionsuffix toolchain ========= ============================== =============================== ``5.0.4`` ``-Perl-5.26.0-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``5.0.4`` ``-Perl-5.26.0-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``5.1.1`` ``-Python-3.6.6`` ``foss/2018b`` ``5.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========= ============================== =============================== @@ -19575,6 +19896,22 @@ version versionsuffix toolchain ========= ================= ================================== +.. _list_software_mhcnuggets_1077: + +*mhcnuggets* +++++++++++++ + +MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II. + +*homepage*: https://github.com/KarchinLab/mhcnuggets + +======= ================= ================================== +version versionsuffix toolchain +======= ================= ================================== +``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` +======= ================= ================================== + + .. _list_software_MiGEC_389: *MiGEC* @@ -19775,13 +20112,13 @@ MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solex *homepage*: https://sourceforge.net/projects/mira-assembler/ -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``4.0.2`` ``intel/2017b`` -``4.0.2`` ``-Python-2.7.11`` ``foss/2016a`` -``4.9.6`` ``intel/2017b`` -========= ================== =============== +========= ================== ================================================ +version versionsuffix toolchain +========= ================== ================================================ +``4.0.2`` ``foss/2018b``, ``gompi/2019b``, ``intel/2017b`` +``4.0.2`` ``-Python-2.7.11`` ``foss/2016a`` +``4.9.6`` ``intel/2017b`` +========= ================== ================================================ .. _list_software_miRDeep2_728: @@ -19801,6 +20138,22 @@ version versionsuffix toolchain =========== ================= =============== +.. _list_software_MITObim_625: + +*MITObim* ++++++++++ + +The MITObim procedure (mitochondrial baiting and iterative mapping) represents a highly efficient approach to assembling novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads. + +*homepage*: https://github.com/chrishah/MITObim + +========= =============================== +version toolchain +========= =============================== +``1.9.1`` ``foss/2018b``, ``gompi/2019b`` +========= =============================== + + .. _list_software_MitoZ_499: *MitoZ* @@ -20181,13 +20534,13 @@ Motif refers to both a graphical user interface (GUI) specification and the widg *homepage*: https://motif.ics.com/ -========= ==================================================================================================================================== -version toolchain -========= ==================================================================================================================================== -``2.3.5`` ``foss/2016a``, ``intel/2016a`` -``2.3.7`` ``intel/2017a`` -``2.3.8`` ``GCCcore/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` -========= ==================================================================================================================================== +========= ======================================================================================================================================================= +version toolchain +========= ======================================================================================================================================================= +``2.3.5`` ``foss/2016a``, ``intel/2016a`` +``2.3.7`` ``intel/2017a`` +``2.3.8`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` +========= ======================================================================================================================================================= .. _list_software_MotionCor2_972: @@ -20448,6 +20801,7 @@ version versionsuffix toolchain =================== ================== =============== ``0.3.14`` ``-Python-2.7.11`` ``intel/2016a`` ``0.3.15`` ``-Python-2.7.12`` ``intel/2016b`` +``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` ``3.0-rc-20191217`` ``-Python-2.7.16`` ``foss/2019b`` ``3.0-rc-20191217`` ``-Python-3.7.4`` ``foss/2019b`` ``3.0_RC2`` ``-Python-2.7.13`` ``foss/2017a`` @@ -20556,7 +20910,9 @@ version versionsuffix toolchain ``1.7`` ``-Python-2.7.15`` ``intel/2018b`` ``1.7`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.8`` ``-Python-2.7.16`` ``intel/2019b`` -``1.8`` ``-Python-3.7.4`` ``intel/2019b`` +``1.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.9`` ``-Python-3.7.4`` ``foss/2019b`` +``1.9`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ======= ================== =============================== @@ -20678,6 +21034,23 @@ version versionsuffix toolchain ========= ============= ============== +.. _list_software_MUST_329: + +*MUST* +++++++ + +MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user. As MPI calls are complex and usage errors common, this functionality is extremely helpful for application developers that want to develop correct MPI applications. This includes errors that already manifest – segmentation faults or incorrect results – as well as many errors that are not visible to the application developer or do not manifest on a certain system or MPI implementation. + +*homepage*: https://hpc.rwth-aachen.de/must/ + +======= ================= ============== +version versionsuffix toolchain +======= ================= ============== +``1.6`` ``-Python-3.6.6`` ``foss/2018b`` +``1.6`` ``-Python-3.7.4`` ``foss/2019b`` +======= ================= ============== + + .. _list_software_MuTect_594: *MuTect* @@ -21146,6 +21519,7 @@ version toolchain ``2.9.1-1`` ``foss/2018a``, ``intel/2018a`` ``2.9.3`` ``foss/2018b`` ``2.10.4`` ``gompi/2019b`` +``2.10.7`` ``gompi/2020a`` =========== ================================================ @@ -21634,7 +22008,7 @@ version toolchain *networkx* ++++++++++ -NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. +NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. *homepage*: https://pypi.python.org/pypi/networkx @@ -21653,7 +22027,7 @@ version versionsuffix toolchain ``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``2.4`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``2.4`` ``-Python-3.8.2`` ``foss/2020a`` +``2.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ======== ================== =============================================== @@ -21778,6 +22152,7 @@ version versionsuffix toolchain ``2.10.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` ``2.10.0`` ``-Java-11`` ``GCCcore/8.2.0`` ``2.10.4`` ``-Java-11`` ``GCCcore/8.3.0`` +``2.10.5`` ``GCCcore/9.3.0`` ========== =================== ================================== @@ -21851,6 +22226,7 @@ version versionsuffix toolchain ``2.3.0`` ``-Python-3.6.6`` ``foss/2018b`` ``2.4.0`` ``foss/2019a``, ``intel/2019a`` ``2.5.1`` ``-Python-3.6.6`` ``foss/2018b`` +``3.1.0`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================================= =============================== @@ -21963,13 +22339,14 @@ version toolchain Nipype is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. -*homepage*: http://nipy.org/nipype +*homepage*: https://nipype.readthedocs.io ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``1.0.2`` ``-Python-3.6.4`` ``intel/2018a`` ``1.1.3`` ``-Python-3.6.6`` ``foss/2018b`` +``1.4.2`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================= =============== @@ -22048,16 +22425,16 @@ Node.js is a platform built on Chrome's JavaScript runtime for easily building *homepage*: http://nodejs.org -=========== ==================================== -version toolchain -=========== ==================================== -``4.4.7`` ``foss/2016a`` -``6.10.3`` ``foss/2017a`` -``8.9.4`` ``foss/2017a`` -``10.15.1`` ``foss/2018b`` -``10.15.3`` ``GCCcore/8.2.0`` -``12.16.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` -=========== ==================================== +=========== ======================================================= +version toolchain +=========== ======================================================= +``4.4.7`` ``foss/2016a`` +``6.10.3`` ``foss/2017a`` +``8.9.4`` ``foss/2017a`` +``10.15.1`` ``foss/2018b`` +``10.15.3`` ``GCCcore/8.2.0`` +``12.16.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +=========== ======================================================= .. _list_software_Normaliz_844: @@ -22303,6 +22680,7 @@ version versionsuffix toolchain ``0.43.1`` ``intel/2019a`` ``0.46.0`` ``foss/2019a`` ``0.47.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``0.50.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ================== ================================== @@ -22332,7 +22710,7 @@ version versionsuffix toolchain ``2.7.0`` ``intel/2019a`` ``2.7.1`` ``-Python-2.7.16`` ``intel/2019b`` ``2.7.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``2.7.1`` ``-Python-3.8.2`` ``intel/2020a`` +``2.7.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========= ================== =================================================== @@ -22415,7 +22793,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenPyXL_767` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_orca_421` - :ref:`list_software_ORCA_293` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_orca_421` - :ref:`list_software_ORCA_293` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -22563,12 +22941,12 @@ OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-sour *homepage*: https://www.score-p.org -========= ==================================== -version toolchain -========= ==================================== -``2.0`` ``foss/2016a`` -``2.0.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= ==================================== +========= ======================================================= +version toolchain +========= ======================================================= +``2.0`` ``foss/2016a`` +``2.0.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================= .. _list_software_OpenAI-Gym_886: @@ -22605,6 +22983,7 @@ version versionsuffix toolchain ``2.4.1`` ``-Python-3.6.6`` ``intel/2018b`` ``2.4.1`` ``-Python-3.7.2`` ``intel/2019a`` ``3.0.0`` ``-Python-3.7.4`` ``gompi/2019b`` +``3.1.1`` ``-Python-3.7.4`` ``gompi/2019b`` ========= ================== =============== @@ -22749,29 +23128,31 @@ OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive *homepage*: https://www.openfoam.com/ -================ ================================================ -version toolchain -================ ================================================ -``2.2.2`` ``intel/2016a``, ``intel/2017a`` -``2.2.x`` ``intel/2019a`` -``2.3.1`` ``intel/2017a``, ``intel/2019b`` -``2.4.0`` ``intel/2017a``, ``intel/2019a`` -``3.0.0`` ``foss/2016a`` -``3.0.1`` ``intel/2016b``, ``intel/2018a`` -``4.0`` ``foss/2016b``, ``intel/2016b`` -``4.1`` ``foss/2016b``, ``intel/2017a`` -``5.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``5.0-20180108`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``6`` ``foss/2018b``, ``foss/2019b``, ``intel/2018a`` -``7`` ``foss/2019b`` -``v1606+`` ``foss/2018b`` -``v1612+`` ``foss/2018b`` -``v1712`` ``foss/2017b``, ``intel/2017b`` -``v1806`` ``foss/2018b`` -``v1812`` ``foss/2018b`` -``v1906`` ``foss/2019b`` -``v1912`` ``foss/2019b``, ``intel/2019b`` -================ ================================================ +================ ============= ================================================ +version versionsuffix toolchain +================ ============= ================================================ +``2.2.2`` ``intel/2016a``, ``intel/2017a`` +``2.2.x`` ``intel/2019a`` +``2.3.1`` ``intel/2017a``, ``intel/2019b`` +``2.4.0`` ``intel/2017a``, ``intel/2019a`` +``3.0.0`` ``foss/2016a`` +``3.0.1`` ``intel/2016b``, ``intel/2018a`` +``4.0`` ``foss/2016b``, ``intel/2016b`` +``4.1`` ``foss/2016b``, ``intel/2017a`` +``5.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``5.0-20180108`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``6`` ``foss/2018b``, ``foss/2019b``, ``intel/2018a`` +``7`` ``foss/2019b`` +``7`` ``-20200508`` ``foss/2019b`` +``v1606+`` ``foss/2018b`` +``v1612+`` ``foss/2018b`` +``v1712`` ``foss/2017b``, ``intel/2017b`` +``v1806`` ``foss/2018b`` +``v1812`` ``foss/2018b`` +``v1906`` ``foss/2019b`` +``v1912`` ``foss/2019b``, ``intel/2019b`` +``v2006`` ``foss/2020a`` +================ ============= ================================================ .. _list_software_OpenFOAM-Extend_1354: @@ -22791,6 +23172,7 @@ version versionsuffix toolchain ``4.0`` ``intel/2017a`` ``4.0`` ``-Python-2.7.16`` ``intel/2019b`` ``4.1-20191120`` ``-Python-2.7.16`` ``intel/2019b`` +``4.1-20200408`` ``-Python-2.7.16`` ``foss/2019b`` ================ ================== ================================= @@ -22820,14 +23202,14 @@ version toolchain OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software. -*homepage*: http://www.openjpeg.org/ +*homepage*: https://www.openjpeg.org/ ========= ==================================== version toolchain ========= ==================================== ``2.1`` ``GCCcore/6.4.0`` ``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.3.1`` ``GCCcore/8.2.0`` +``2.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ==================================== @@ -23002,28 +23384,13 @@ A Python library to read/write Excel 2010 xlsx/xlsm files *homepage*: https://openpyxl.readthedocs.io -========= ================= ================= -version versionsuffix toolchain -========= ================= ================= -``2.6.2`` ``GCCcore/8.2.0`` -``3.0.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -========= ================= ================= - - -.. _list_software_OpenPyXL_767: - -*OpenPyXL* -++++++++++ - -A Python library to read/write Excel 2010 xlsx/xlsm files - -*homepage*: https://openpyxl.readthedocs.io - -========= ================= -version toolchain -========= ================= -``2.6.4`` ``GCCcore/8.3.0`` -========= ================= +========= ================== ================= +version versionsuffix toolchain +========= ================== ================= +``2.6.2`` ``GCCcore/8.2.0`` +``2.6.4`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +``3.0.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================== ================= .. _list_software_OpenRefine_1003: @@ -23051,11 +23418,12 @@ OpenSlide is a C library that provides a simple interface to read whole-slide im *homepage*: https://openslide.org/ -========= ================= -version toolchain -========= ================= -``3.4.1`` ``GCCcore/8.2.0`` -========= ================= +========= =============== ================= +version versionsuffix toolchain +========= =============== ================= +``3.4.1`` ``GCCcore/8.2.0`` +``3.4.1`` ``-largefiles`` ``GCCcore/8.2.0`` +========= =============== ================= .. _list_software_openslide-python_1682: @@ -23261,15 +23629,15 @@ version versionsuffix toolchain *Osi* +++++ -Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver. That is, programs written to the OSI standard may be linked to any solver with an OSI interface and should produce correct results. The OSI has been significantly extended compared to its first incarnation. Currently, the OSI supports linear programming solvers and has rudimentary support for integer programming. +Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver. That is, programs written to the OSI standard may be linked to any solver with an OSI interface and should produce correct results. The OSI has been significantly extended compared to its first incarnation. Currently, the OSI supports linear programming solvers and has rudimentary support for integer programming. *homepage*: https://github.com/coin-or/Osi -=========== ================= -version toolchain -=========== ================= -``0.108.5`` ``GCCcore/7.3.0`` -=========== ================= +=========== ================================= +version toolchain +=========== ================================= +``0.108.5`` ``GCCcore/7.3.0``, ``foss/2018b`` +=========== ================================= .. _list_software_OSU-Micro-Benchmarks_1865: @@ -23298,12 +23666,12 @@ The Open Trace Format 2 is a highly scalable, memory efficient event trace data *homepage*: https://www.score-p.org -======= ==================================== -version toolchain -======= ==================================== -``2.0`` ``foss/2016a``, ``foss/2017a`` -``2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -======= ==================================== +======= ======================================================= +version toolchain +======= ======================================================= +``2.0`` ``foss/2016a``, ``foss/2017a`` +``2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ======================================================= .. _list_software_ownCloud_843: @@ -23345,7 +23713,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_pip_329` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-mpi_1052` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_pip_329` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-mpi_1052` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -23566,7 +23934,7 @@ version toolchain ``5.5.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``5.6.0`` ``GCCcore/6.4.0`` ``5.7.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``6.0.0`` ``GCCcore/8.3.0`` +``6.0.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ==================================== @@ -23596,6 +23964,7 @@ version toolchain ``20190622`` ``GCCcore/8.2.0`` ``20190922`` ``GCCcore/8.3.0`` ``20200422`` ``GCCcore/9.3.0`` +``20200522`` ``GCCcore/9.3.0`` ============ =============================== @@ -23685,6 +24054,7 @@ version versionsuffix toolchain ``5.4.1`` ``-mpi`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``5.5.2`` ``-Python-2.7.15-mpi`` ``foss/2018b`` ``5.6.2`` ``-Python-3.7.4-mpi`` ``foss/2019b``, ``intel/2019b`` +``5.8.0`` ``-Python-3.8.2-mpi`` ``foss/2020a``, ``intel/2020a`` ========= ====================== ================================================================================================= @@ -23709,14 +24079,15 @@ version toolchain *ParmEd* ++++++++ -ParmEd is a general tool for aiding in investigations of biomolecular systems using popular molecular simulation packages, like Amber, CHARMM, and OpenMM written in Python. +ParmEd is a general tool for aiding in investigations of biomolecular systems using popular molecular simulation packages, like Amber, CHARMM, and OpenMM written in Python. -*homepage*: http://parmed.github.io/ParmEd/html/index.html +*homepage*: https://parmed.github.io/ParmEd ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``2.7.3`` ``-Python-3.6.3`` ``intel/2017b`` +``3.2.0`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================= =============== @@ -23745,11 +24116,11 @@ ParMGridGen is an MPI-based parallel library that is based on the serial package *homepage*: http://www-users.cs.umn.edu/~moulitsa/software.html -======= =================================================================== -version toolchain -======= =================================================================== -``1.0`` ``gimkl/2.11.5``, ``iimpi/2019b``, ``intel/2016a``, ``intel/2017a`` -======= =================================================================== +======= ==================================================================================== +version toolchain +======= ==================================================================================== +``1.0`` ``gimkl/2.11.5``, ``gompi/2019b``, ``iimpi/2019b``, ``intel/2016a``, ``intel/2017a`` +======= ==================================================================================== .. _list_software_PartitionFinder_1554: @@ -23838,6 +24209,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_PAUP_310: + +*PAUP* +++++++ + +PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computational phylogenetics program for inferring evolutionary trees. + +*homepage*: https://paup.phylosolutions.com/ + +=========== ============= ========== +version versionsuffix toolchain +=========== ============= ========== +``4.0a166`` ``-centos64`` ``system`` +=========== ============= ========== + + .. _list_software_pauvre_659: *pauvre* @@ -24086,12 +24473,13 @@ Program Database Toolkit (PDT) is a framework for analyzing source code written *homepage*: https://www.cs.uoregon.edu/research/pdt/ -======== ==================================== -version toolchain -======== ==================================== -``3.22`` ``foss/2016a`` -``3.25`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -======== ==================================== +========== ==================================== +version toolchain +========== ==================================== +``3.22`` ``foss/2016a`` +``3.25`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.25.1`` ``GCCcore/9.3.0`` +========== ==================================== .. _list_software_PEAR_296: @@ -24112,6 +24500,22 @@ version toolchain ========== ========================================================== +.. _list_software_Percolator_1051: + +*Percolator* +++++++++++++ + +Semi-supervised learning for peptide identification from shotgun proteomics datasets + +*homepage*: https://github.com/percolator/percolator + +======= =============== +version toolchain +======= =============== +``3.4`` ``gompi/2019a`` +======= =============== + + .. _list_software_Perl_403: *Perl* @@ -24551,6 +24955,7 @@ version versionsuffix toolchain ``2.18.14`` ``-Java-1.8`` ``system`` ``2.18.17`` ``-Java-1.8`` ``system`` ``2.18.27`` ``-Java-1.8`` ``system`` +``2.20.6`` ``-Java-1.8`` ``system`` ``2.21.1`` ``-Java-11`` ``system`` ``2.21.6`` ``-Java-11`` ``system`` =========== =================== ========== @@ -24975,6 +25380,7 @@ version toolchain ``1.07`` ``foss/2016a``, ``foss/2016b`` ``1.07-x86_64`` ``system`` ``1.9b_4.1-x86_64`` ``system`` +``1.9b_6.17-x86_64`` ``system`` ``2.00-alpha1-x86_64`` ``system`` ``2.00-alpha2-x86_64`` ``system`` ``2.00-alpha2-x86_64_avx2`` ``system`` @@ -25040,12 +25446,13 @@ An open-source, interactive graphing library for Python *homepage*: https://plot.ly/python -========= =============== -version toolchain -========= =============== -``4.1.0`` ``intel/2019a`` -``4.4.1`` ``intel/2019b`` -========= =============== +========= ================= +version toolchain +========= ================= +``4.1.0`` ``intel/2019a`` +``4.4.1`` ``intel/2019b`` +``4.8.1`` ``GCCcore/9.3.0`` +========= ================= .. _list_software_PLplot_603: @@ -25172,6 +25579,22 @@ version toolchain ======= ================================ +.. _list_software_poetry_675: + +*poetry* +++++++++ + +Python packaging and dependency management made easy + +*homepage*: https://python-poetry.org/ + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``1.0.9`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +========= ================= ================= + + .. _list_software_polymake_866: *polymake* @@ -25454,11 +25877,11 @@ PRANK is a probabilistic multiple alignment program for DNA, codon and amino-a *homepage*: http://wasabiapp.org/software/prank/ -========== =============== -version toolchain -========== =============== -``170427`` ``intel/2018a`` -========== =============== +========== ============================== +version toolchain +========== ============================== +``170427`` ``GCC/9.3.0``, ``intel/2018a`` +========== ============================== .. _list_software_PRC_229: @@ -25762,7 +26185,7 @@ Google Protocol Buffers =========== =================================================== version toolchain =========== =================================================== -``2.5.0`` ``GCCcore/7.3.0``, ``system`` +``2.5.0`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``system`` ``2.6.1`` ``system`` ``3.0.2`` ``foss/2016a`` ``3.2.0`` ``foss/2016b``, ``intel/2016b`` @@ -25835,6 +26258,7 @@ PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculatin version toolchain ========== ================= ``2.2.12`` ``GCCcore/8.3.0`` +``2.3.1`` ``GCCcore/9.3.0`` ========== ================= @@ -26192,9 +26616,26 @@ version versionsuffix toolchain ``0.7.10`` ``-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` ``0.7.10`` ``-Python-3.6.6`` ``foss/2018b`` ``0.8.0`` ``foss/2019a``, ``intel/2019a`` +``0.8.1`` ``foss/2019b`` ========== ================== ================================ +.. _list_software_PyBerny_713: + +*PyBerny* ++++++++++ + +PyBerny is an optimizer of molecular geometries with respect to the total energy, using nuclear gradient information. + +*homepage*: https://github.com/jhrmnn/pyberny + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.6.2`` ``-Python-3.8.2`` ``intel/2020a`` +========= ================= =============== + + .. _list_software_pyBigWig_802: *pyBigWig* @@ -26287,6 +26728,22 @@ version toolchain ========= =============== +.. _list_software_pycocotools_1214: + +*pycocotools* ++++++++++++++ + +Tools for working with the MSCOCO dataset + +*homepage*: https://github.com/cocodataset/cocoapi + +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``2.0.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +========= ================= ================== + + .. _list_software_pycodestyle_1205: *pycodestyle* @@ -27009,6 +27466,7 @@ version versionsuffix toolchain ``5.11.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``5.13.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========== ================== =============================== @@ -27123,6 +27581,7 @@ version versionsuffix toolchain ``0.15.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``0.15.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``0.15.3`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``0.16.0.1`` ``GCC/9.3.0`` ============ ================== ============================================================== @@ -27284,7 +27743,7 @@ version versionsuffix toolchain ``3.5.2`` ``-Python-2.7.14`` ``intel/2018a`` ``3.5.2`` ``-Python-2.7.16`` ``intel/2019b`` ``3.6.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``3.6.1`` ``-Python-3.8.2`` ``intel/2020a`` +``3.6.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` =========== ================== =================================================== @@ -27388,6 +27847,22 @@ version versionsuffix toolchain ========== ================= ================================================================================================================================================================= +.. _list_software_python-hl7_986: + +*python-hl7* +++++++++++++ + +A simple library for parsing messages of Health Level 7 (HL7) version 2.x into Python objects. + +*homepage*: https://github.com/johnpaulett/python-hl7 + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``0.3.4`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= + + .. _list_software_python-igraph_1354: *python-igraph* @@ -28062,6 +28537,7 @@ version versionsuffix toolchain ``4.6.3`` ``-Python-3.6.4`` ``foss/2018a`` ``5.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` ``5.0.2`` ``-Python-3.7.2`` ``foss/2019a`` +``5.0.2`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ============================== @@ -28683,6 +29159,7 @@ version toolchain ``2.19`` ``system`` ``2.20`` ``system`` ``2.21`` ``system`` +``3.0`` ``system`` ======== ========== @@ -28825,6 +29302,7 @@ version versionsuffix toolchain ========= ============= ============== ``1.4-4`` ``-R-3.6.0`` ``foss/2019a`` ``1.4-8`` ``-R-3.6.2`` ``foss/2019b`` +``1.4-8`` ``-R-4.0.0`` ``foss/2020a`` ========= ============= ============== @@ -28905,14 +29383,15 @@ The rjags package is an interface to the JAGS library. *homepage*: https://cran.r-project.org/web/packages/rjags -======= ============= =============== -version versionsuffix toolchain -======= ============= =============== -``4-6`` ``-R-3.4.0`` ``intel/2017a`` -``4-6`` ``-R-3.4.3`` ``intel/2017b`` -``4-8`` ``-R-3.5.1`` ``foss/2018b`` -``4-9`` ``-R-3.6.0`` ``foss/2019a`` -======= ============= =============== +======== ============= =============== +version versionsuffix toolchain +======== ============= =============== +``4-6`` ``-R-3.4.0`` ``intel/2017a`` +``4-6`` ``-R-3.4.3`` ``intel/2017b`` +``4-8`` ``-R-3.5.1`` ``foss/2018b`` +``4-9`` ``-R-3.6.0`` ``foss/2019a`` +``4-10`` ``foss/2019b`` +======== ============= =============== .. _list_software_Rmath_508: @@ -29077,6 +29556,7 @@ version versionsuffix toolchain ========== ================ =============== ``3.12.0`` ``system`` ``3.12.0`` ``-Perl-5.26.1`` ``intel/2018a`` +``3.13.0`` ``foss/2020a`` ========== ================ =============== @@ -29129,6 +29609,7 @@ version versionsuffix toolchain ``6.10.08`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``6.14.06`` ``-Python-2.7.15`` ``foss/2018b`` ``6.14.06`` ``-Python-3.6.6`` ``foss/2018b`` +``6.20.04`` ``-Python-3.7.4`` ``foss/2019b`` ``v5.34.34`` ``-Python-2.7.11`` ``intel/2016a`` ``v5.34.36`` ``-Python-2.7.11`` ``intel/2016a`` ``v6.06.02`` ``-Python-2.7.12`` ``intel/2016b`` @@ -29317,12 +29798,13 @@ This RStudio Server version. RStudio is a set of integrated tools designed to he *homepage*: https://www.rstudio.com/ -============ ============= ================== -version versionsuffix toolchain -============ ============= ================== -``1.2.5033`` ``-Java-11`` ``fosscuda/2019b`` -``1.2.5042`` ``-Java-11`` ``foss/2019b`` -============ ============= ================== +============ ==================== ================== +version versionsuffix toolchain +============ ==================== ================== +``1.2.5033`` ``-Java-11`` ``fosscuda/2019b`` +``1.2.5042`` ``-Java-11`` ``foss/2019b`` +``1.3.959`` ``-Java-11-R-4.0.0`` ``foss/2020a`` +============ ==================== ================== .. _list_software_RTG-Tools_811: @@ -29414,7 +29896,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_Stata_509` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDSL_310` - :ref:`list_software_sdsl-lite_913` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_Stata_509` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -29664,6 +30146,7 @@ version versionsuffix toolchain ============ =================== ========== ``9.7.0.4`` ``-Java-1.7.0_79`` ``system`` ``9.7.0.21`` ``-Java-1.8.0_162`` ``system`` +``9.9.1.7`` ``-Java-13`` ``system`` ============ =================== ========== @@ -29735,12 +30218,12 @@ Scalasca is a software tool that supports the performance optimization of paral *homepage*: https://www.scalasca.org/ -======= =============== -version toolchain -======= =============== -``2.3`` ``foss/2016a`` -``2.5`` ``gompi/2019a`` -======= =============== +======= ================================ +version toolchain +======= ================================ +``2.3`` ``foss/2016a`` +``2.5`` ``gompi/2019a``, ``gompi/2020a`` +======= ================================ .. _list_software_SCALCE_427: @@ -29782,7 +30265,7 @@ version versionsuffix toolchain ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization. -*homepage*: https://sourcesup.cru.fr/projects/scientific-py/ +*homepage*: http://dirac.cnrs-orleans.fr/ScientificPython ========= ================== =============================== version versionsuffix toolchain @@ -29798,12 +30281,13 @@ version versionsuffix toolchain This package provides utilities for exploratory analysis of large scale genetic variation data. It is based on numpy, scipy and other general-purpose Python scientific libraries. -*homepage*: http://scikit-allel.readthedocs.io/en/latest/ +*homepage*: https://scikit-allel.readthedocs.io/en/latest/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.1.8`` ``-Python-2.7.13`` ``foss/2017a`` +``1.2.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ============== @@ -29888,6 +30372,7 @@ version versionsuffix toolchain ``0.20.3`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``0.20.4`` ``-Python-2.7.16`` ``intel/2019b`` ``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``0.23.1`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================================= ======================================================================== @@ -30069,12 +30554,12 @@ The Score-P measurement infrastructure is a highly scalable and easy-to-use too *homepage*: https://www.score-p.org -========= ================================= -version toolchain -========= ================================= -``2.0.1`` ``foss/2016a`` -``6.0`` ``gompi/2019a``, ``gompic/2019b`` -========= ================================= +========= ================================================== +version toolchain +========= ================================================== +``2.0.1`` ``foss/2016a`` +``6.0`` ``gompi/2019a``, ``gompi/2020a``, ``gompic/2019b`` +========= ================================================== .. _list_software_SCOTCH_452: @@ -30214,6 +30699,22 @@ version toolchain ================== ============= +.. _list_software_sdsl-lite_913: + +*sdsl-lite* ++++++++++++ + +Succinct Data Structure Library 2.0 + +*homepage*: https://github.com/simongog/sdsl-lite + +========= ================= +version toolchain +========= ================= +``2.1.1`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_Seaborn_714: *Seaborn* @@ -30236,6 +30737,7 @@ version versionsuffix toolchain ``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``0.9.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``0.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.10.1`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================== ========================================================================================= @@ -30410,13 +30912,13 @@ SeqAn is an open source C++ library of efficient algorithms and data structures *homepage*: https://www.seqan.de/ -========= ============= ======================================================================== -version versionsuffix toolchain -========= ============= ======================================================================== -``1.4.2`` ``-library`` ``system`` -``2.3.2`` ``foss/2016b`` -``2.4.0`` ``GCC/8.2.0-2.31.1``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2018b`` -========= ============= ======================================================================== +========= ============= =========================================================================================== +version versionsuffix toolchain +========= ============= =========================================================================================== +``1.4.2`` ``-library`` ``system`` +``2.3.2`` ``foss/2016b`` +``2.4.0`` ``GCC/8.2.0-2.31.1``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2018b`` +========= ============= =========================================================================================== .. _list_software_SeqAn3_523: @@ -30477,12 +30979,12 @@ Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FA *homepage*: https://github.com/lh3/seqtk/ -======= =================================================================== -version toolchain -======= =================================================================== -``1.2`` ``foss/2016b``, ``intel/2017a`` -``1.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2018a``, ``foss/2018b`` -======= =================================================================== +======= ================================================================================== +version toolchain +======= ================================================================================== +``1.2`` ``foss/2016b``, ``intel/2017a`` +``1.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` +======= ================================================================================== .. _list_software_Serf_400: @@ -30534,6 +31036,7 @@ version versionsuffix toolchain ``2.3.4`` ``-R-3.4.4`` ``intel/2018a`` ``2.3.4`` ``-R-3.5.1`` ``foss/2018b`` ``3.1.2`` ``-R-3.6.0`` ``foss/2019a`` +``3.1.5`` ``-R-4.0.0`` ``foss/2020a`` ============ ============= =============== @@ -30602,6 +31105,22 @@ version versionsuffix toolchain ========== =============== ========== +.. _list_software_SHAPEIT4_578: + +*SHAPEIT4* +++++++++++ + +SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data. + +*homepage*: https://odelaneau.github.io/shapeit4/ + +========= ============== +version toolchain +========= ============== +``4.1.3`` ``foss/2019b`` +========= ============== + + .. _list_software_Shapely_726: *Shapely* @@ -30614,6 +31133,7 @@ Shapely is a BSD-licensed Python package for manipulation and analysis of planar ========= ================= ====================================== version versionsuffix toolchain ========= ================= ====================================== +``1.7.0`` ``-Python-3.7.2`` ``foss/2019a`` ``1.7.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ========= ================= ====================================== @@ -30779,11 +31299,12 @@ Simulation and Parameter Estimation in Geophysics: a python package for simulati *homepage*: http://simpeg.xyz -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``0.3.1`` ``-Python-2.7.12`` ``intel/2016b`` -========= ================== =============== +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``0.3.1`` ``-Python-2.7.12`` ``intel/2016b`` +``0.14.1`` ``-Python-3.8.2`` ``intel/2020a`` +========== ================== =============== .. _list_software_SIMPLE_458: @@ -30913,16 +31434,16 @@ SIONlib is a scalable I/O library for parallel access to task-local files. The *homepage*: https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html -========= ============= ================= -version versionsuffix toolchain -========= ============= ================= -``1.6.1`` ``foss/2016a`` -``1.6.1`` ``-tools`` ``foss/2016a`` -``1.7.1`` ``foss/2017a`` -``1.7.1`` ``-tools`` ``foss/2017a`` -``1.7.4`` ``-tools`` ``GCCcore/8.2.0`` -``1.7.6`` ``-tools`` ``GCCcore/8.3.0`` -========= ============= ================= +========= ============= ==================================== +version versionsuffix toolchain +========= ============= ==================================== +``1.6.1`` ``foss/2016a`` +``1.6.1`` ``-tools`` ``foss/2016a`` +``1.7.1`` ``foss/2017a`` +``1.7.1`` ``-tools`` ``foss/2017a`` +``1.7.4`` ``-tools`` ``GCCcore/8.2.0`` +``1.7.6`` ``-tools`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ============= ==================================== .. _list_software_SIP_236: @@ -31280,6 +31801,7 @@ version versionsuffix toolchain ======== ================== ========== ``3.6`` ``-Java-1.7.0_80`` ``system`` ``4.1d`` ``-Java-1.7.0_80`` ``system`` +``4.3t`` ``-Java-1.8`` ``system`` ======== ================== ========== @@ -31484,6 +32006,7 @@ version versionsuffix toolchain ``3.13.1`` ``GCC/8.2.0-2.31.1`` ``3.14.0`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` ``3.14.0`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``3.14.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` ========== ================= ============================================== @@ -31531,6 +32054,7 @@ version versionsuffix toolchain ``2.4.0`` ``-Hadoop-2.7-Java-1.8-Python-3.6.6`` ``intel/2018b`` ``2.4.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.4.0`` ``-Python-3.6.6`` ``intel/2018b`` +``2.4.5`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` ========= =========================================== =============================== @@ -31862,6 +32386,7 @@ version versionsuffix toolchain ``2.9.6-1`` ``-centos_linux64`` ``system`` ``2.10.4`` ``gompi/2019b`` ``2.10.5`` ``-centos_linux64`` ``system`` +``2.10.8`` ``gompi/2020a`` =========== =================== =============== @@ -32024,23 +32549,23 @@ STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays *homepage*: https://github.com/alexdobin/STAR -========== =============================================== -version toolchain -========== =============================================== -``2.4.2a`` ``foss/2018b`` -``2.5.0a`` ``GNU/4.9.3-2.25`` -``2.5.2a`` ``foss/2016a`` -``2.5.2b`` ``intel/2016b`` -``2.5.3a`` ``intel/2017a``, ``intel/2017b`` -``2.5.4b`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` -``2.6.0c`` ``foss/2018a``, ``intel/2018a`` -``2.6.1c`` ``foss/2018b`` -``2.7.0d`` ``foss/2018b`` -``2.7.0f`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` -``2.7.1a`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` -``2.7.2b`` ``GCC/8.3.0`` -``2.7.3a`` ``GCC/8.3.0`` -========== =============================================== +========== ============================================================== +version toolchain +========== ============================================================== +``2.4.2a`` ``foss/2018b`` +``2.5.0a`` ``GNU/4.9.3-2.25`` +``2.5.2a`` ``foss/2016a`` +``2.5.2b`` ``intel/2016b`` +``2.5.3a`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``intel/2017a``, ``intel/2017b`` +``2.5.4b`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` +``2.6.0c`` ``foss/2018a``, ``intel/2018a`` +``2.6.1c`` ``foss/2018b`` +``2.7.0d`` ``foss/2018b`` +``2.7.0f`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` +``2.7.1a`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` +``2.7.2b`` ``GCC/8.3.0`` +``2.7.3a`` ``GCC/8.3.0``, ``GCC/9.3.0`` +========== ============================================================== .. _list_software_STAR-Fusion_987: @@ -32095,6 +32620,7 @@ version versionsuffix toolchain ``0.6.1`` ``-Python-3.5.2`` ``intel/2016b`` ``0.8.0`` ``-Python-2.7.13`` ``intel/2017a`` ``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.9.0`` ``-Python-2.7.16`` ``intel/2019b`` ``0.9.0`` ``-Python-3.6.6`` ``intel/2018b`` ``0.10.1`` ``foss/2019a`` ``0.11.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` @@ -32203,6 +32729,7 @@ version toolchain ``2.0.3`` ``GCCcore/7.3.0`` ``2.1.0`` ``foss/2018b`` ``2.1.1`` ``GCC/8.3.0`` +``2.1.3`` ``GCC/8.3.0``, ``GCC/9.3.0`` ========== ================================== @@ -32344,13 +32871,29 @@ SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers *homepage*: https://computation.llnl.gov/projects/sundials -========= ================================================================================================================== -version toolchain -========= ================================================================================================================== -``2.6.2`` ``intel/2016b``, ``intel/2018b`` -``2.7.0`` ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``5.1.0`` ``intel/2019b`` -========= ================================================================================================================== +========= ================================================================================================================================== +version toolchain +========= ================================================================================================================================== +``2.6.2`` ``intel/2016b``, ``intel/2018b`` +``2.7.0`` ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +``5.1.0`` ``foss/2019b``, ``intel/2019b`` +========= ================================================================================================================================== + + +.. _list_software_SunPy_511: + +*SunPy* ++++++++ + +The community-developed, free and open-source solar data analysis environment for Python. + +*homepage*: https://sunpy.org/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.1.3`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== .. _list_software_SuperLU_688: @@ -32501,7 +33044,7 @@ version versionsuffix toolchain ``3.0.10`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``3.0.10`` ``-Python-2.7.12-PCRE-8.39`` ``intel/2016b`` ``3.0.11`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.0.12`` ``GCCcore/8.2.0`` +``3.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.0.12`` ``-Python-2.7.13`` ``intel/2017a`` ``3.0.12`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``3.0.12`` ``-Python-2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``intel/2018b`` @@ -32548,6 +33091,22 @@ version versionsuffix toolchain ========= ============= ==================== +.. _list_software_SYMPHONY_647: + +*SYMPHONY* +++++++++++ + +SYMPHONY is an open-source solver for mixed-integer linear programs (MILPs) written in C. + +*homepage*: https://projects.coin-or.org/SYMPHONY + +========== ============== +version toolchain +========== ============== +``5.6.16`` ``foss/2018b`` +========== ============== + + .. _list_software_sympy_578: *sympy* @@ -32593,7 +33152,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_texinfo_765` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` +:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` .. _list_software_tabix_536: @@ -32814,7 +33373,7 @@ version toolchain =========== ======================================================= ``6.19.00`` ``intel/2016a`` ``6.20.00`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``6.22.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``6.22.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` =========== ======================================================= @@ -32834,6 +33393,22 @@ version toolchain =========== ========== +.. _list_software_tensorboardX_1275: + +*tensorboardX* +++++++++++++++ + +Tensorboard for PyTorch. + +*homepage*: https://github.com/lanpa/tensorboardX + +======= ================= ============== +version versionsuffix toolchain +======= ================= ============== +``2.0`` ``-Python-3.7.4`` ``foss/2019b`` +======= ================= ============== + + .. _list_software_TensorFlow_1043: *TensorFlow* @@ -32884,7 +33459,7 @@ version versionsuffix toolchain ``2.0.1`` ``-Python-3.7.2`` ``foss/2019a`` ``2.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``2.2.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========== ============================= =================================================== @@ -32988,6 +33563,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_TEtranscripts_1366: + +*TEtranscripts* ++++++++++++++++ + +TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements. TEtranscripts then performs differential analysis using DESeq2. + +*homepage*: https://github.com/mhammell-laboratory/TEtranscripts + +========= ============== +version toolchain +========= ============== +``2.2.0`` ``foss/2020a`` +========= ============== + + .. _list_software_texinfo_765: *texinfo* @@ -33311,6 +33902,22 @@ version toolchain ======= ================= +.. _list_software_Tombo_513: + +*Tombo* ++++++++ + +Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data. + +*homepage*: https://github.com/nanoporetech/tombo + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.5.1`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_TopHat_592: *TopHat* @@ -33325,7 +33932,7 @@ version versionsuffix toolchain ========= ================== ================================================================================ ``2.1.0`` ``-Python-2.7.14`` ``intel/2018a`` ``2.1.1`` ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``2.1.2`` ``foss/2018b`` +``2.1.2`` ``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` ========= ================== ================================================================================ @@ -33377,7 +33984,7 @@ version versionsuffix toolchain ``0.2.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` ``0.2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` -``0.4.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``0.4.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``0.5.0`` ``-Python-3.7.4-PyTorch-1.4.0`` ``fosscuda/2019b`` ========= =============================== ================================== @@ -33564,6 +34171,7 @@ version versionsuffix toolchain =========== ================== =============================== ``12.12.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``12.12.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``12.12.1`` ``-Python-3.7.4`` ``foss/2019b`` =========== ================== =============================== @@ -33626,6 +34234,7 @@ version versionsuffix toolchain ``0.36`` ``-Java-1.8.0_92`` ``system`` ``0.38`` ``-Java-1.8`` ``system`` ``0.38`` ``-Java-1.8.0_162`` ``system`` +``0.39`` ``-Java-1.8`` ``system`` ``0.39`` ``-Java-11`` ``system`` ======== =================== ========== @@ -33842,7 +34451,7 @@ version versionsuffix toolchain --- -:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` +:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` .. _list_software_UCLUST_480: @@ -33906,7 +34515,7 @@ version versionsuffix toolchain UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. -*homepage*: http://www.unidata.ucar.edu/software/udunits/ +*homepage*: https://www.unidata.ucar.edu/software/udunits/ ========== =========================================================================================================================================================== version toolchain @@ -33948,6 +34557,7 @@ version versionsuffix toolchain ========= ================= ============== ``1.0.0`` ``-Python-3.6.6`` ``foss/2018b`` ``1.0.1`` ``-Python-3.7.4`` ``foss/2019b`` +``1.0.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -33999,6 +34609,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_Unidecode_912: + +*Unidecode* ++++++++++++ + +Python library for lossy ASCII transliterations of Unicode text (port of Text::Unidecode Perl module) + +*homepage*: https://github.com/avian2/unidecode + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``1.1.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= + + .. _list_software_units_563: *units* @@ -34193,7 +34819,7 @@ version versionsuffix toolchain Valgrind: Debugging and profiling tools -*homepage*: http://valgrind.org +*homepage*: https://valgrind.org ========== ================================================================================= version toolchain @@ -34201,6 +34827,7 @@ version toolchain ``3.11.0`` ``foss/2016a``, ``intel/2016a`` ``3.13.0`` ``foss/2017b``, ``foss/2018a``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.14.0`` ``foss/2018b`` +``3.16.1`` ``gompi/2019b`` ========== ================================================================================= @@ -34267,6 +34894,7 @@ version versionsuffix toolchain ========= ================== ========== ``2.3.6`` ``-Java-1.7.0_80`` ``system`` ``2.4.1`` ``-Java-1.7.0_80`` ``system`` +``2.4.4`` ``-Java-1.8`` ``system`` ========= ================== ========== @@ -34641,6 +35269,7 @@ version versionsuffix toolchain ``4.1.6`` ``system`` ``4.1.8`` ``system`` ``4.1.9`` ``system`` +``5.1.0`` ``system`` =========== ================================== =============== @@ -34810,7 +35439,7 @@ version toolchain --- -:ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` +:ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_WHAM_301` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` .. _list_software_Wannier90_829: @@ -34881,6 +35510,7 @@ WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for version toolchain ========== ==================== ``2.24.1`` ``GCC/8.2.0-2.31.1`` +``2.27.4`` ``GCC/8.3.0`` ========== ==================== @@ -34924,7 +35554,7 @@ version versionsuffix toolchain GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. -*homepage*: https://www.gnu.org/software/wget/ +*homepage*: https://www.gnu.org/software/wget ========== ==================================== version toolchain @@ -34932,9 +35562,27 @@ version toolchain ``1.17.1`` ``foss/2016a``, ``foss/2016b`` ``1.19.4`` ``GCCcore/6.4.0`` ``1.20.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +``1.20.3`` ``GCCcore/9.3.0`` ========== ==================================== +.. _list_software_WHAM_301: + +*WHAM* +++++++ + +An implementation of WHAM: the Weighted Histogram Analysis Method + +*homepage*: http://membrane.urmc.rochester.edu/?page_id=126 + +=========== ============= =============== +version versionsuffix toolchain +=========== ============= =============== +``2.0.9.1`` ``intel/2019a`` +``2.0.9.1`` ``-kj_mol`` ``intel/2019a`` +=========== ============= =============== + + .. _list_software_wheel_533: *wheel* @@ -35176,19 +35824,20 @@ version toolchain wxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. It is implemented as a Python extension module (native code) that wraps the popular wxWidgets cross platform GUI library, which is written in C++. -*homepage*: http://www.wxpython.org +*homepage*: https://www.wxpython.org -=========== ================== =============================== -version versionsuffix toolchain -=========== ================== =============================== -``3.0.2.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``3.0.2.0`` ``-Python-2.7.12`` ``intel/2016b`` -``3.0.2.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.0.2.0`` ``-Python-2.7.14`` ``intel/2017b`` -``3.0.2.0`` ``-Python-2.7.15`` ``foss/2018b`` -``4.0.4`` ``-Python-2.7.15`` ``GCC/8.2.0-2.31.1`` -``4.0.4`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` -=========== ================== =============================== +=============== ================== =============================== +version versionsuffix toolchain +=============== ================== =============================== +``3.0.2.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``3.0.2.0`` ``-Python-2.7.12`` ``intel/2016b`` +``3.0.2.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.0.2.0`` ``-Python-2.7.14`` ``intel/2017b`` +``3.0.2.0`` ``-Python-2.7.15`` ``foss/2018b`` +``4.0.4`` ``-Python-2.7.15`` ``GCC/8.2.0-2.31.1`` +``4.0.4`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` +``4.0.7.post2`` ``-Python-3.7.4`` ``GCC/8.3.0`` +=============== ================== =============================== .. _list_software_wxWidgets_966: @@ -35215,7 +35864,7 @@ version toolchain --- -:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCfun_484` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_XZ_178` +:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCfun_484` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_XZ_178` .. _list_software_X11_186: @@ -35293,6 +35942,22 @@ version toolchain ======= ================================== +.. _list_software_XALT_313: + +*XALT* +++++++ + +XALT 2 is a tool to allow a site to track user executables and library usage on a cluster. When installed it can tell a site what are the top executables by Node-Hours or by the number of users or the number of times it is run. XALT 2 also tracks library usage as well. XALT 2 can also track package use by R, MATLAB or Python. It tracks both MPI and non-MPI programs. + +*homepage*: https://github.com/xalt/xalt + +========= ========== +version toolchain +========= ========== +``2.8.4`` ``system`` +========= ========== + + .. _list_software_xarray_663: *xarray* @@ -35636,6 +36301,7 @@ version versionsuffix toolchain ``2.0132`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` ``2.0200`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` ``2.0201`` ``GCCcore/8.3.0`` +``2.0205`` ``GCCcore/9.3.0`` ========== ================ =============================== @@ -35846,6 +36512,22 @@ version toolchain ========= ================================================= +.. _list_software_Xvfb_406: + +*Xvfb* +++++++ + +Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory. + +*homepage*: https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml + +========== ==================================== +version toolchain +========== ==================================== +``1.20.8`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========== ==================================== + + .. _list_software_XZ_178: *XZ* @@ -35864,7 +36546,7 @@ version versionsuffix toolchain ``5.2.2`` ``-gettext-0.19.7`` ``foss/2016a``, ``intel/2016a`` ``5.2.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``gimkl/2017a`` ``5.2.4`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` -``5.2.5`` ``GCCcore/9.3.0`` +``5.2.5`` ``GCCcore/10.1.0``, ``GCCcore/9.3.0`` ========= =================== =========================================================================================================================================================== @@ -35918,7 +36600,7 @@ version versionsuffix toolchain ``1.5.0`` ``-Python-3.7.2`` ``intel/2019a`` ``1.6.0`` ``-Python-3.7.2`` ``intel/2019a`` ``1.6.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.6.0`` ``-Python-3.8.2`` ``foss/2020a`` +``1.6.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ==================== ============================== ================================================ @@ -36005,12 +36687,13 @@ version toolchain Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing. -*homepage*: http://zarr.readthedocs.io/en/stable/ +*homepage*: https://zarr.readthedocs.io/en/stable/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.1.4`` ``-Python-2.7.13`` ``foss/2017a`` +``2.4.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ============== @@ -36146,11 +36829,11 @@ Zstandard is a real-time compression algorithm, providing high compression ratio *homepage*: https://facebook.github.io/zstd -========= ================================= -version toolchain -========= ================================= -``1.3.4`` ``foss/2016b`` -``1.4.0`` ``GCCcore/8.2.0``, ``foss/2018b`` -``1.4.4`` ``GCCcore/9.3.0`` -========= ================================= +========= ==================================== +version toolchain +========= ==================================== +``1.3.4`` ``foss/2016b`` +``1.4.0`` ``GCCcore/8.2.0``, ``foss/2018b`` +``1.4.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ==================================== diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index d6a01d22..9566efcf 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -74,6 +74,7 @@ * EB_Geant4 * EB_GROMACS * EB_LAMMPS + * EB_LLVM * EB_netCDF * EB_OpenBabel * EB_OpenCV @@ -182,6 +183,7 @@ * EB_tbb * EB_Velvet * EB_VMD + * EB_XALT * EB_XCrySDen * MakeCp @@ -235,6 +237,7 @@ * EB_WRF_minus_Fire * ExtensionEasyBlock + * EB_Scipion * OCamlPackage * OctavePackage * PerlModule @@ -359,6 +362,7 @@ * ExtensionEasyBlock + * EB_Scipion * OCamlPackage * OctavePackage * PerlModule diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index f4a51094..40e86b30 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -357,6 +357,7 @@ Option flag Option description ``--toolchain-name=NAME`` Search and build with given toolchain name ``--toolchain-version=VERSION`` Search and build with given toolchain version ``--try-amend=VAR=VALUE[,VALUE]`` Try to specify additional search and build parameters (can be used multiple times); for example: versionprefix=foo or patches=one.patch,two.patch) (USE WITH CARE!) +``--try-ignore-versionsuffixes`` Ignore versionsuffix differences when --try-update-deps is used (default: False) ``--try-software=NAME,VERSION`` Try to search and build software with given name and version (USE WITH CARE!) (type comma-separated list) ``--try-software-name=NAME`` Try to search and build software with given name (USE WITH CARE!) ``--try-software-version=VERSION`` Try to search and build software with given version (USE WITH CARE!) From 928282fa9d7f76fab2da8b604896577b8a5cae2d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 8 Jul 2020 20:46:59 +0800 Subject: [PATCH 066/286] bump version to 4.2.2 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 6336760d..8218c5c2 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.2.1' +VERSION = '4.2.2' # Utility function to read README file From 35001ecbfa40288dabdf2a813a697b95016c69d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Aug 2020 10:33:33 +0200 Subject: [PATCH 067/286] refer to GitHub Actions rather than Travis w.r.t. CI tests --- docs/Contributing.rst | 23 ++++++++++++----------- docs/Integration_with_GitHub.rst | 4 ++-- 2 files changed, 14 insertions(+), 13 deletions(-) diff --git a/docs/Contributing.rst b/docs/Contributing.rst index 786c6f01..ff1469b6 100644 --- a/docs/Contributing.rst +++ b/docs/Contributing.rst @@ -448,7 +448,7 @@ Updating existing pull requests Please consider using ``eb --update-pr`` instead, see :ref:`github_update_pr`. It is quite common to update a pull request after creating it, -for example if Travis reports problems with the changes being made, or as a response +for example if the test suite run in GitHub Actions reports problems with the changes being made, or as a response to someone reviewing your contribution. To update an existing pull request, it suffices to add commits to the branch @@ -464,7 +464,7 @@ For example, to update the pull request that was created using the ``mybranch`` git commit -m "example commit message for additional changes" git push origin mybranch -Updating a pull request will trigger Travis to re-test your contribution, +Updating a pull request will trigger GitHub Actions to re-test your contribution, and a notification will be sent out to whoever is 'watching' your pull request. @@ -473,7 +473,7 @@ and a notification will be sent out to whoever is 'watching' your pull request. Merging of pull requests ~~~~~~~~~~~~~~~~~~~~~~~~ -Once your pull request has been given the green light by Travis and one or more +Once your pull request has been given the green light by GitHub Actions and one or more people reviewing have approved the changes, it can be merged into the ``develop`` branch. @@ -501,7 +501,7 @@ Requirements for pull requests (i) *the PR must target the* ``develop`` *branch of the repository*; see :ref:`contributing_review_process_develop_branch` -(ii) *the test suite must (still) pass*, i.e. Travis *must* give a green light; see :ref:`contributing_review_process_travis` +(ii) *the test suite must (still) pass*, i.e. GitHub Actions *must* give a green light; see :ref:`contributing_review_process_travis` * *tests should be added or enhanced when appropriate*; see :ref:`contributing_review_process_adding_tests`, especially for PRs to the ``easybuild-framework`` repository @@ -532,17 +532,18 @@ when preparing a new EasyBuild release. Occasionally, an additional version branch (e.g. '``3.3.x``') may be introduced temporarily, in case an intermittent bugfix release is being worked on. -.. _contributing_review_process_travis: +.. _contributing_review_process_github_actions: -Test suite (Travis) -~~~~~~~~~~~~~~~~~~~ +Test suite (GitHub Actions) +~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Each pull request is tested automatically by Travis and the test result is reported in the pull request. +Each pull request is tested automatically by `GitHub Actions `_ +and the test result is reported in the pull request. -**Only pull requests that have been tested and approved by Travis are +**Only pull requests that have been tested and approved by GitHub Actions are eligible for being merged!** -Note that Travis will only run the *test suite* for that particular repository. +Note that GitHub Actions will only run the *test suite* for that particular repository. That is, for easyconfig contributions it does *not* include actually building and installing software. @@ -612,7 +613,7 @@ be contributed can be performed via ``eb --check-contrib``. This will check: * style aspects for the specified easyconfig files * whether SHA256 checksums are included for all source files & patches -This check is also a part of the test suite run by Travis for easyconfig PRs. +This check is also a part of the test suite run by GitHub Actions for easyconfig PRs. .. _contributing_review_process_review_pr: diff --git a/docs/Integration_with_GitHub.rst b/docs/Integration_with_GitHub.rst index d9c7770c..2eb48350 100644 --- a/docs/Integration_with_GitHub.rst +++ b/docs/Integration_with_GitHub.rst @@ -238,7 +238,7 @@ for pull requests based on an outdated branch in which easyconfigs are changed t as well. As such, the exact semantics of ``--from-pr`` depends on the state of the specified pull request, i.e. whether or not -the pull request was merged already, whether the pull request is mergeable and stable (as indicated by Travis), etc. +the pull request was merged already, whether the pull request is mergeable and stable (as indicated by GitHub Actions), etc. .. _github_from_pr_vs_develop_open_stable_prs: @@ -279,7 +279,7 @@ For closed and unstable pull requests, only the branch corresponding to the pull which aligns with the semantics of ``--from-pr`` as it was before EasyBuild v2.9.0. In this case, the current ``develop`` branch is *not* taken into account. -.. note:: A pull request is considered unstable when GitHub reports merge conflicts or when Travis reports +.. note:: A pull request is considered unstable when GitHub reports merge conflicts or when GitHub Actions reports one or more failing tests. From 2f542b52ceabc016a61c8e0d37a7837ea621a065 Mon Sep 17 00:00:00 2001 From: darkless Date: Tue, 18 Aug 2020 16:54:57 +0200 Subject: [PATCH 068/286] Add documentation for patches --- docs/Writing_easyconfig_files.rst | 46 +++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index 81b623d6..d9f000cf 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -128,6 +128,7 @@ Remarks: * unified diff format (``diff -ru``) * patched locations relative to unpacked sources +* see :ref:`common_easyconfig_param_sources_patches` for more information on ``patches`` * see :ref:`common_easyconfig_param_sources_checksums` for more information on ``checksums`` * ``sources`` is usually specified as a list of strings representing filenames for source files, but other formats are supported too, see :ref:`common_easyconfig_param_sources_alt` @@ -154,6 +155,51 @@ Example: .. note:: Rather than hardcoding the version (and name) in the list of sources, a string template `%(version)s` can be used, see also :ref:`easyconfig_param_templates`. +.. _common_easyconfig_param_sources_patches: + +Patches +^^^^^^^ + +Patches can be provided via the ``patches`` easyconfig parameter (list). And patch could be defined as: + +* string +* tuple +* dict + +The most straight-forward use-case is ``string``, which contains the name of the patch file +and has to have ``.patch`` extension. + +``Tuple`` adds possibility to specify patch level, which is used in patch command. +This is mostly needed, if patch file just adds new files and generally is not possible to determine starting directory. + +.. note:: ``Tuple`` also have special usage, if the patch file have any other extension than ``.patch`` + In this case, first tuple argument is file which should be coppied to unpacked source dir and second tuple argument + is target path, where the files should be coppied relative to unpacked source dir. See more in example below. + +``Dict`` adds ability to pass ``patch`` command additional arguments. For example ``--binary`` flag is needed to patch +files with CRLF endings. +The ``dict`` has required ``filename`` key, and ``level`` and ``opts`` optional ones. + +.. note:: Filling just ``filename`` in ``dict`` is same as using plain ``string`` definition. + Filling ``filename`` and ``level`` is same as using ``tuple`` definition. + +Example: +``` +patches = [ + # a simple patch file + 'name-versions-fix.patch', + + # when creating only new files by patch file, you need to specify level: + ('name-versions-fix.patch', 1), + + # copy file to target_path folder + ('Makefile', 'target_path'), + + # specify patch file and optionally level and opts for patch command + {'filename': 'name-versions-fix.patch', 'level': 1, 'opts': '-l'} +] +``` + .. _common_easyconfig_param_sources_checksums: Checksums From 00bcbb185d4edec94fee01466a2100b2a5b533d3 Mon Sep 17 00:00:00 2001 From: darkless Date: Tue, 18 Aug 2020 17:03:42 +0200 Subject: [PATCH 069/286] Fix typos --- docs/Writing_easyconfig_files.rst | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index d9f000cf..93d54544 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -166,15 +166,15 @@ Patches can be provided via the ``patches`` easyconfig parameter (list). And pat * tuple * dict -The most straight-forward use-case is ``string``, which contains the name of the patch file +The most straight-forward use-case is ``string``, which contains the name of the patch file and has to have ``.patch`` extension. -``Tuple`` adds possibility to specify patch level, which is used in patch command. +``Tuple`` adds possibility to specify patch level, which is used in patch command. This is mostly needed, if patch file just adds new files and generally is not possible to determine starting directory. .. note:: ``Tuple`` also have special usage, if the patch file have any other extension than ``.patch`` - In this case, first tuple argument is file which should be coppied to unpacked source dir and second tuple argument - is target path, where the files should be coppied relative to unpacked source dir. See more in example below. + In this case, first tuple argument is file which should be copied to unpacked source dir and second tuple argument + is target path, where the files should be copied relative to unpacked source dir. See more in example below. ``Dict`` adds ability to pass ``patch`` command additional arguments. For example ``--binary`` flag is needed to patch files with CRLF endings. @@ -188,13 +188,13 @@ Example: patches = [ # a simple patch file 'name-versions-fix.patch', - + # when creating only new files by patch file, you need to specify level: ('name-versions-fix.patch', 1), - + # copy file to target_path folder ('Makefile', 'target_path'), - + # specify patch file and optionally level and opts for patch command {'filename': 'name-versions-fix.patch', 'level': 1, 'opts': '-l'} ] @@ -491,7 +491,7 @@ Examples: the cloned repository), the (SHA256) checksum is not guaranteed to be the same across different systems. Whenever you have the option to download a source tarball (or equivalent) directly (for example from GitHub, - which also allows downloading a tarball of a specific commit), we strongly recommend you to do so, + which also allows downloading a tarball of a specific commit), we strongly recommend you to do so, ``git_config`` is intended for other Git repos. From 4d8947b98062da67b9eb11b0106aa901536ec642 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 20 Aug 2020 13:10:35 +0200 Subject: [PATCH 070/286] Add setup.cfg --- setup.cfg | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 setup.cfg diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 00000000..6deafc26 --- /dev/null +++ b/setup.cfg @@ -0,0 +1,2 @@ +[flake8] +max-line-length = 120 From 05d076f798a2397227d57335dd2bd11a3cead94b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 20 Aug 2020 13:13:29 +0200 Subject: [PATCH 071/286] Add docs/_build to gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 60627647..b5e22ad0 100644 --- a/.gitignore +++ b/.gitignore @@ -5,5 +5,6 @@ LICENSE_HEADER *.swp *.nja build/ +/docs/_build/ dist/ *egg-info/ From 9b28756fce6ae6f3d4dec63b884279a11da13907 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 20 Aug 2020 13:15:26 +0200 Subject: [PATCH 072/286] Fix flake8 issues --- docs/conf.py | 64 ++++++++++++++--------------- docs/scripts/gen_easyblocks_docs.py | 1 - 2 files changed, 32 insertions(+), 33 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index b5a15be8..3a9f859c 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -10,12 +10,12 @@ # All configuration values have a default value; values that are commented out # serve to show the default value. -import sys, os +import os # If your extensions are in another directory, add it here. If the directory # is relative to the documentation root, use os.path.abspath to make it # absolute, like shown here. -#sys.path.append(os.path.abspath('some/directory')) +# sys.path.append(os.path.abspath('some/directory')) # General configuration # --------------------- @@ -47,30 +47,30 @@ # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: -#today = '' +# today = '' # Else, today_fmt is used as the format for a strftime call. today_fmt = '%a, %d %b %Y %H:%M:%S' # e.g., Mon, 03 Nov 2014 22:14:42 # List of documents that shouldn't be included in the build. -#unused_docs = [] +# unused_docs = [] # List of directories, relative to source directories, that shouldn't be searched # for source files. -#exclude_dirs = [] +# exclude_dirs = [] # The reST default role (used for this markup: `text`) to use for all documents. -#default_role = None +# default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True +# add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). -#add_module_names = True +# add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. -#show_authors = False +# show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' @@ -96,18 +96,18 @@ html_title = project + " v" + version + " documentation (release " + release + ")" # A shorter title for the navigation bar. Default is the same as html_title. -#html_short_title = None +# html_short_title = None # The name of an image file (within the static path) to place at the top of # the sidebar. -#html_logo = None +# html_logo = None html_logo = 'easybuild_logo_alpha.png' # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. -#html_favicon = None +# html_favicon = None # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, @@ -120,41 +120,41 @@ # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. -#html_use_smartypants = True +# html_use_smartypants = True # Custom sidebar templates, maps document names to template names. -#html_sidebars = {} +# html_sidebars = {} html_sidebars = { - '**': ['searchbox.html', 'globaltoc.html', 'sourcelink.html'], - 'using/windows': ['searchbox.html', 'windowssidebar.html'], + '**': ['searchbox.html', 'globaltoc.html', 'sourcelink.html'], + 'using/windows': ['searchbox.html', 'windowssidebar.html'], } # Additional templates that should be rendered to pages, maps page names to # template names. -#html_additional_pages = {} +# html_additional_pages = {} # If false, no module index is generated. -#html_use_modindex = True +# html_use_modindex = True html_use_modindex = False # If false, no index is generated. -#html_use_index = True +# html_use_index = True html_use_index = False # If true, the index is split into individual pages for each letter. -#html_split_index = False +# html_split_index = False # If true, the reST sources are included in the HTML build as _sources/. -#html_copy_source = True +# html_copy_source = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. -#html_use_opensearch = '' +# html_use_opensearch = '' # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = '' +# html_file_suffix = '' # Output file base name for HTML help builder. htmlhelp_basename = 'easyBuild_docs' @@ -164,32 +164,32 @@ # ------------------------ # The paper size ('letter' or 'a4'). -#latex_paper_size = 'letter' +# latex_paper_size = 'letter' latex_paper_size = 'a4' # The font size ('10pt', '11pt' or '12pt'). -#latex_font_size = '10pt' +# latex_font_size = '10pt' # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, document class [howto/manual]). latex_documents = [ - ('index', 'easybuild.tex', 'EasyBuild Documentation', - 'Ghent University', 'manual'), + ('index', 'easybuild.tex', 'EasyBuild Documentation', + 'Ghent University', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. -#latex_logo = None +# latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. -#latex_use_parts = False +# latex_use_parts = False # Additional stuff for the LaTeX preamble. -#latex_preamble = '' +# latex_preamble = '' # Documents to append as an appendix to all manuals. -#latex_appendices = [] +# latex_appendices = [] # If false, no module index is generated. -#latex_use_modindex = True +# latex_use_modindex = True diff --git a/docs/scripts/gen_easyblocks_docs.py b/docs/scripts/gen_easyblocks_docs.py index 67df2ebc..e75f113c 100644 --- a/docs/scripts/gen_easyblocks_docs.py +++ b/docs/scripts/gen_easyblocks_docs.py @@ -71,4 +71,3 @@ print('%s updated' % so.options.out_file) else: print(txt) - From 8ec75c3108d42ba3913680e75427df51b2adc76b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 20 Aug 2020 13:17:11 +0200 Subject: [PATCH 073/286] Enable flake8 on CI --- .github/workflows/linting.yml | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 .github/workflows/linting.yml diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml new file mode 100644 index 00000000..5f76d7e5 --- /dev/null +++ b/.github/workflows/linting.yml @@ -0,0 +1,22 @@ +name: Static Analysis +on: [push, pull_request] +jobs: + python-linting: + runs-on: ubuntu-18.04 + steps: + - uses: actions/checkout@v2 + + - name: set up Python + uses: actions/setup-python@v1 + with: + python-version: 3.8 + + - name: install Python packages + run: | + pip install --upgrade pip + pip install --upgrade flake8 + + - name: Run flake8 + run: | + flake8 -j3 + \ No newline at end of file From 107f8e7161274d01efcb40282e85520d090e8358 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 20 Aug 2020 13:48:01 +0200 Subject: [PATCH 074/286] Make CI cfg consistent with EC repo --- .github/workflows/linting.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 5f76d7e5..09493c87 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -16,7 +16,5 @@ jobs: pip install --upgrade pip pip install --upgrade flake8 - - name: Run flake8 - run: | - flake8 -j3 - \ No newline at end of file + - name: Run flake8 to verify PEP8-compliance of Python code + run: flake8 -j3 From 600be4a538fdd951de033d71e04b81fda81ac462 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 12 Sep 2020 11:00:24 +0800 Subject: [PATCH 075/286] update release notes for EasyBuild v4.3.0 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 220 +++++++++++++++++++++++++++++++++++++++++ docs/conf.py | 4 +- 3 files changed, 223 insertions(+), 2 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 08990181..f2c22ea4 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20200913.01** (`Sep 13th 2020`): update release notes for EasyBuild v4.3.0 (see :ref:`release_notes_eb430`) * **release 20200708.01** (`July 8th 2020`): update release notes for EasyBuild v4.2.2 (see :ref:`release_notes_eb422`) * **release 20200520.01** (`May 20th 2020`): update release notes for EasyBuild v4.2.1 (see :ref:`release_notes_eb421`) * **release 20200414.01** (`Apr 14th 2020`): diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index e46a9626..12f439fe 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -9,6 +9,226 @@ alongside 10,147 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb430: + +EasyBuild v4.3.0 (September 13th 2020) +-------------------------------------- + +feature release + +**framework** + +* various enhancements, including: + + * add script to create ``sources`` entries for git submodules (`#3369 `_, `#3436 `_) + + * add templates for CUDA compute capabilities (`#3382 `_) + + * ``%(cuda_compute_capabilities)s``, ``%(cuda_sm_comma_sep)s``, ``%(cuda_sm_space_sep)s`` + + * add EasyBuild configuration option ``--generate-devel-module`` (`#3388 `_) + + * to allow disabling generating of "devel" modules via ``--disable-generate-devel-module`` + + * set up a minimal build environment when using system compiler (`#3399 `_) + + * by default, ``$CC`` is set to ``gcc`` and ``$CXX`` is set to ``g++`` when using ``system`` toolchain + * minimal build environment can be customized via ``--minimal-build-env`` configuration option + + * add ``--sysroot`` configuration option to specify alternative location of system root (`#3419 `_) + + * this is useful when installing software in a Gentoo Prefix environment (for example) + +* various bug fixes, including: + + * allow including easyblocks from multiple locations, by combining ``--include-easyblocks`` and ``--include-easyblocks-from-pr`` (`#3311 `_) + * also escape backslashes in ``quote_py_str()`` (`#3386 `_) + * use one argument ``module swap`` statements in Tcl modulefiles (required by Modules 4.2.3+) (`#3397 `_) + * fix copying of (non-existing) file with ``apply_patch`` (`#3400 `_) + * create symlink from ``lib64`` to ``lib`` subdir in installation directories to avoid that GCC prefers ``/lib64`` system directories (`#3401 `_) + * fix default value for ``lib64_fallback_sanity_check`` build option (`#3402 `_) + * correctly determine commit status in ``--merge-pr`` (`#3406 `_) + * stop installing ccache wrapper for Fortran compiler (`#3409 `_) + * fix issues with applying PR patch in ``--from-pr`` (`#3414 `_) + * make ``RPATH`` wrapper script more robust by using ``python -E -s -S`` to run ``rpath_args.py`` (`#3422 `_) + * don't inject ``-Wl,-rpath`` options when ``-x c++-header`` compiler option is used (`#3424 `_) + * fix lack of ``-mno-recip`` on aarch64 by tweaking GCC options used when ``precise`` toolchain option is enabled (`#3425 `_) + * make sure ``self.start_dir`` is set in ``ExtensionEasyBlock`` (#3426, `#3435 `_) + * exclude local variables from typo check in easyconfig files (`#3427 `_) + +* other changes: + + * stick to cryptography 2.9.2 when using Python 2.7 to avoid broken test suite in CI (`#3392 `_) + * automatically enable ``--ignore-locks`` with ``--fetch`` (`#3404 `_) + * switch to status badge based on tests run in GitHub Actions CI in README (`#3415 `_) + * make ``flake8`` code style checks pass (`#3416 `_, `#3417 `_) + * limit Travis to only test with Python 2.6 + Lmod 7 (`#3418 `_) + * ignore deprecation warning raised for cryptography when using Python 3.5 produced by output of test suite (`#3423 `_) + +**easyblocks** + +* 2 new software-specific easyblocks: + + * pybind11 (`#2115 `_), PyTorch (`#2104 `_) + +* minor enhancements, including: + + * update MATLAB easyblock to use new binary installer for versions >= 2020a (`#2058 `_) + * add ``use_pip_requirement`` custom easyconfig parameter to PythonPackage easyblock to allow providing a requirements file to the ``pip`` command, as a source (`#2064 `_) + * update CP2K easyblock for recent versions (>= 7.0) (`#2069 `_) + * add ``multi_deps`` support into custom easyblock for QScintilla (`#2077 `_) + * update Mothur easyblock for v1.44.0 and higher (`#2084 `_) + * update MotionCor2 easyblock to add support for v1.3.2 (`#2100 `_) + * update Tinker easyblock to handle skipping of tests depending on version and link with ``fftw_omp`` (`#2102 `_) + * launch test & sanity check commands through ``mpirun`` for netcdf4-python if MPI support is enabled (`#2106 `_) + * check for installation of pip & setuptools in Python 3.4+ (`#2108 `_) + * update QuantumESPRESSO easyblock to support version 6.6 (`#2112 `_) + * allow NAMD to be built on POWER, and also use the CUDA arch info (`#2113 `_, `#2123 `_) + * update Libint easyblock for versions >= 2.6.0 + add custom easyconfig parameter to enable Fortran support (`#2116 `_) + * update TensorFlow easyblock to use system/EasyBuild installed libraries (`#2117 `_, `#2165 `_, `#2163 `_, `#2172 `_) + * add support in NAMD easyblock to pass additional C++ compiler options for building Charm++ component with + wrap them in single quotes (`#2118 `_) + * automatically add required ``-G Ninja`` option when using CMakeNinja easyblock + add ``generator`` custom easyconfig parameter for CMakeMake (`#2120 `_) + * make several easyblocks aware of ``--sysroot`` EasyBuild configuration option: binutils (`#2147 `_, `#2159 `_), CMakeMake (`#2152 `_), GCC (`#2143 `_), Perl (`#2142 `_), Python (`#2148 `_, `#2149 `_) + * make Mesa easyblock aware of aarch64 (`#2153 `_) + * enhance sanity check in custom Doxygen easyblock to catch broken installation (`#2171 `_) + +* various bug fixes, including: + + * make TensorFlow easyblock ignore the ``PKG_REVISION`` identifier if NCCL version if it exists (`#2085 `_) + * remove version check against the ``version.txt`` file in CUDA easyblock (`#2097 `_) + * add ``lib`` symlink in tbb installation directory when building from source (`#2103 `_) + * handle GNUInstallDirs special cases in CMakeMake easyblock (`#2105 `_, `#2124 `_) + * patch ELPA's ``manual_cpp`` script to fix hardcoded ``/usr/bin/python`` (`#2107 `_) + * make TensorFlow easyblock also set ``$GCC_HOST_COMPILER_PREFIX`` to specify binutils location (`#2110 `_) + * ensure stand-alone Python package being installed is in view when running ``pip check`` by loading fake module first (`#2114 `_) + * be more patient when running interactive configure script for WRF (`#2119 `_) + * make sure ``self.start_dir`` is set to a full path before constructing installation command in RPackage easyblock (`#2125 `_) + * correctly check whether ``modinc`` easyconfig parameter is set to ``True`` in CP2K easyblock (`#2138 `_) + * update PSI easyblock to correctly find Python and enable PCMSolver/CheMPS2 (`#2141 `_) + * fix running GROMACS tests when using ``eb --rpath`` (`#2144 `_, `#2154 `_) + * remove existing Python installation directory if both ``eb --rpath`` and ``--enable-optimizations`` configuration option are used (`#2146 `_) + * ensure ``libQt5Core.so`` is compatible with older Linux kernels by disabling ``renameat2`` and ``getentropy`` features (`#2151 `_) + * solve issue where pybind11 picks up on the system Python instead of one provided by a module (`#2158 `_) + * fix Qt5 easyblock to support installation on Arm/aarch64 (requires platform to be ``linux-g++``) (`#2160 `_) + * fix OpenFOAM easyblock to support installation on Arm/aarch64 systems (`#2162 `_) + * explicitely enable/disable CUDA options in PyTorch easyblock + fix download check in sanity check + fix for disabling of *NNPACK on POWER systems (`#2164 `_) + * fix sanity check in Mathematica easyblock for 11.x versions older than 11.3 (`#2168 `_) + * unset ``$COLUMNS`` if it is set to ``0`` before running Perl's configure script (`#2169 `_) + +* other changes: + + * filter out Python in SLEPc configure (`#2101 `_) + * switch to status badge based on tests run in GitHub Actions CI in README (`#2126 `_) + * fix code style issues to make ``flake8`` checks pass (`#2128 `_ - `#2137 `_, `#2140 `_, `#2145 `_, `#2155 `_) + * limit test configurations in Travis CI to only Python 2.6 (`#2139 `_) + +**easyconfigs** + +* added easyconfigs for 2 new toolchains: + + * gomkl/2020a and iomkl/2020a (`#11036 `_) + +* added example easyconfig files for 49 new software packages: + + * almosthere (`#11152 `_), arcasHLA (`#10867 `_), BioPP (`#11113 `_), Bracken (`#10829 `_), BUFRLIB (`#11140 `_), Calib (`#11111 `_), + CellRanger-ATAC (`#11186 `_), edlib (#10470, `#11246 `_), flatbuffers (`#11109 `_), gengetopt (`#11117 `_), graphite2 (`#11168 `_), + HeFFTe (`#10990 `_), hierfstat (`#11249 `_), immunedeconv (`#11136 `_), ioapi (`#10959 `_), itpp (`#10958 `_), LiBis (`#11059 `_), + libosmium (`#11024 `_), limix-bgen (`#11152 `_), minibar (#10470, `#11246 `_), misha (`#11127 `_), MOABS (`#10747 `_), moonjit (`#11163 `_), + NGLess (`#11128 `_), nsync (`#11109 `_), openCARP (`#11117 `_), OpenForceField (`#11048 `_), OpenMMTools (`#11046 `_), OpenMS (`#10994 `_), + PennCNV (`#10986 `_), plantcv (`#10968 `_), PlasmaPy (`#10732 `_), Portcullis (`#11038 `_), PycURL (`#11169 `_), PyGEOS (`#11110 `_), + pySCENIC (`#11115 `_), Reapr (`#9296 `_), RnBeads (`#11142 `_), sf (`#11248 `_), SLiM (`#11172 `_), stars (#11215, `#11248 `_), Sumo (`#11071 `_), + Telescope (`#10943 `_), tensorflow-probability (`#10312 `_), texlive (`#11168 `_), tidymodels (`#11010 `_), Trycycler (`#11207 `_), + umi4cPackage (`#11127 `_), variant_tools (`#11169 `_) + +* added additional easyconfigs for various supported software packages, including: + + * Bazel 3.4.1, Bonito 0.2.2, binutils 2.35, CP2K 7.1, Clang 10.0.1, ccache 3.7.11, ctffind 4.1.14, datamash 1.5, + ELPA 2020.05.001, Emacs 26.3, Flye 2.8.1, GCC(core) 10.2.0, googletest 1.10.0, HDF 4.2.15, Horovod 0.19.5, + imageio 2.9.0, JUBE 2.4.0, Julia 1.5.1, Kent_tools 401, Libint 2.6.0, libxsmm 1.16.1, MDSplus 7.96.8, + MDTraj 1.9.4, MariaDB 10.4.13, Meson 0.55.1, MotionCor2 1.3.2, NAMD 2.14, NCO 4.9.3, OpenFOAM 8, OpenMPI 4.0.5, + OptiX 6.5.0, Pandoc 2.10, Perl 5.32.0, PostgreSQL 12.4, PyCUDA 2019.1.2, PyFR 1.9.0, PyTorch 1.6.0, + PyZMQ 18.1.1, patchelf 0.12, pocl 1.5, pycocotools 2.0.1, pyproj 2.6.1.post1, QuantumESPRESSO 6.6, + RDKit 2020.03.3, rgdal 1.5, Salmon 1.3.0, Spark 3.0.0, scikit-image 0.17.1, scipy 1.4.1, snpEff 5.0, + sympy 1.6.2, TINKER 8.7.2, tqdm 4.47.0, Unicycler 0.4.8, VMD 1.9.4a43 + +* minor enhancements, including: + + * also build Python libraries for ParaView 5.8.0 (`#10927 `_) + * add extensions to recent Bioconductor easyconfigs: FlowSorted.Blood.EPIC (`#11021 `_), DRIMSeq + stageR (`#11053 `_) + * add extensions to recent R easyconfigs: AICcmodavg + biomod2 (`#11030 `_), qqman (`#11052 `_), poLCA (`#11081 `_), coxed + (`#11094 `_), testit + data.tree (`#11135 `_), celestial + fasterize (`#11206 `_) + * add Config::Simple extension to Perl 5.30.x easyconfigs (`#11051 `_) + * update TensorFlow v2.1.0 (`#11109 `_) and v2.0.0 (`#11233 `_) easyconfigs to provide more dependencies via EasyBuild + * add CUDA compute capabilities to torchvision-0.5.0 (`#11241 `_) + +* various bug fixes, including: + + * patch to fix exporting images with PyQtGraph v0.10.0 (`#10848 `_) + * add missing Python dependency to PETSc 3.11.1 (`#10907 `_) and PETSc 3.12.x (`#10908 `_) easyconfigs + * use CMakeMake easyblock for installing magma to avoid C++11 related failures on POWER (`#10929 `_) + * fix source URL for Graphviz v2.40.1 (`#10944 `_) + * fix ``lapack.h`` for use with C++ in OpenBLAS 0.3.9 easyconfigs (`#10960 `_) + * add missing build dep on M4 for 2019b versions of netCDF-Fortran (`#10972 `_) + * update easyconfig for PyTorch 1.4 to use custom easyblock and run on POWER (`#11000 `_) + * create symlinks to incorrectly named directories in OpenBabel-3.1.1 so ``$BABEL_LIBDIR`` and ``$BABEL_DATADIR`` work properly (`#11004 `_) + * add missing Python build dep to recent ELPA easyconfigs (`#11011 `_) + * use ``is_generic_easyblock`` from filetools in easyconfigs test suite (`#11020 `_) + * fix sources in Portcullis v1.2.2 easyconfigs (`#11038 `_) + * add patch for FFTW 3.3.8 to avoid use of ``-no-gcc`` when building with Intel compilers, to fix installation on CentOS 8 (cfr. `#10932 `_) (`#11050 `_) + * add missing Python build dep for BEDTools 2.29.x (`#11054 `_) + * add missing SciPy-bundle and Kent_tools (for bedPartition command) dependencies to FLAIR (`#11057 `_) + * add patch to fix bug in LiBiS v20200428 easyconfig (`#11059 `_) + * use FFTW provided via EasyBuild for ScaFaCoS (`#11060 `_) + * fix undefined reference to ``qfloat16::mantissatable`` in Qt5.14.1 (`#11063 `_) + * add alternative checksum for rstantools 2.0.0 extension (`#11081 `_) + * update checksums for R 3.6.0 packages and add patch for ppc (`#11088 `_) + * install scikit-learn 0.23.1 as a bundle and include required threadpoolctl extension (`#11089 `_) + * update pybind11 easyconfigs to use custom easyblock to install with pip (`#11091 `_) + * add recent six as extension to archspec installed on top of Python 3.7.4 (`#11092 `_) + * add missing Seaborn dependency to LiBis easyconfig (`#11095 `_) + * add missing dependencies for OpenPIV + switch to PythonBundle easyblock and include progressbar2 as extension (`#11096 `_) + * add missing argparse dep to TEtranscripts easyconfig (`#11097 `_) + * add missing pkg-config build dep in Octave 5.1.0 easyconfigs (`#11100 `_) + * don't statically link MUSCLE, to avoid requiring that glibc-static is installed in OS (`#11102 `_) + * add missing pkg-config build dependency in recent R-bundle-Bioconductor easyconfigs (`#11104 `_) + * add patch to h5py 2.8.0 (`#11119 `_) and 2.9.0 (`#11118 `_) easyconfigs to avoid MPI_Init on ``import h5py`` + * add patch to support libbfd 2.34 API change in Score-P 6.0 (`#11123 `_) + * use pip to install protobuf-python in 2019b toolchain (requires re-downloading source tarball!) (#11143, `#11260 `_) + * add missing Keras-Applications extension to TensorFlow 2.2.0 easyconfigs with foss*/2019b toolchain (`#11156 `_) + * add missing pocl dependency in R 3.6.0 (`#11157 `_) + * update Meson build dep to 0.55.1 for GLib, X11, Mesa & co to fix aggressive RPATH stripping (`#11178 `_) + * disable generating of man pages in recent libdrm easyconfigs to avoid installation failure if docbook-xsl is not installed (`#11182 `_) + * add fontconfig and bzip2 as direct dependencies for Qt5 to fix installation with --rpath (`#11183 `_) + * fix failing ``make check`` for MPFR 4.x (`#11187 `_) and GMP (`#11188 `_) when installing with ``eb --rpath`` + * add pkg-config as a build dependency for libglvnd (`#11189 `_) + * add missing libiconv build dep in recent Doxygen easyconfigs (`#11191 `_, `#11257 `_) + * enhance Java/11 wrapper to also support for aarch64/Arm (`#11192 `_) + * add pkg-config as a build dependency to Ghostscript 9.52, needed on aarch64/arm (`#11194 `_) + * add patch for pycrypto extension in recent Python easyconfigs to remove hardcoded ``/usr/include`` which causes problems when ``eb --sysroot`` is used (`#11202 `_) + * fix installation of R v3.6.3 and v4.0.0 with foss/2020a on Arm (aarch64) (`#11213 `_) + * update PyTorch 1.4 easyconfigs to use custom easyblock (and do less downloading during installations) (`#11219 `_) + +* other changes: + + * don't require custom sanity_check_paths for CUDA bundle easyconfigs (`#10936 `_) + * move intervaltree and sortedcontainers to main Python easyconfigs (`#10969 `_, `#10970 `_) + * disable qtwayland in Qt5 v5.14.1 (`#11107 `_) + * remove mklml (small MKL) from PyTorch 1.3.1 and 1.4.0 easyconfigs (`#11019 `_) + * use pip to install h5py 2.10.0 (`#11044 `_) + * stop testing easyconfig PRs with Travis, only use GitHub Actions from now on (`#11008 `_, `#11055 `_) + * switch to Kent_tools built from source as dep for FusionCatcher (`#11057 `_) + * fall back to using PR target branch when determining "merge base" between PR branch & target branch fails in test suite (`#11069 `_) + * rename gtest to googletest (`#11082 `_) + * rename sdsl-lite to SDSL (to use one single name) (`#11084 `_) + * stop using ``remove_usr_bin`` patch in TensorFlow easyconfig, no longer required with updated TensorFlow easyblock (`#11087 `_) + * extend timeout for libxc-4.3.4 to avoid failing tests (`#11126 `_) + * move GitHub Actions status badge to top of README (`#11138 `_) + * fix code style issues in test (`#11146 `_) + * enable ``flake8`` on CI and fix issues (`#11147 `_) + * prefer gc GitHub site for source downloads (`#11208 `_) + * prefer ``https`` over ``ftp`` in ``source_urls`` of IgBLAST easyconfig (`#11244 `_) + + .. _release_notes_eb422: EasyBuild v4.2.2 (July 8th 2020) diff --git a/docs/conf.py b/docs/conf.py index 3a9f859c..b325ea80 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.2.2' # this is meant to reference the version of EasyBuild +version = '4.3.0' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20200708.0' # this is meant to reference the version of the documentation itself +release = '20200913.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 1c29d3724f85e2a892f5f552f719e292ee37c603 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Sep 2020 08:31:33 +0200 Subject: [PATCH 076/286] auto-update docs for EasyBuild v4.3.0 --- docs/version-specific/Supported_software.rst | 1871 ++++++++++++----- docs/version-specific/easyblocks.rst | 5 + .../easyconfig_parameters.rst | 77 +- docs/version-specific/generic_easyblocks.rst | 13 +- docs/version-specific/help.rst | 4 + 5 files changed, 1418 insertions(+), 552 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 15242bac..a5abf6b4 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2013 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2059 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -209,11 +209,11 @@ ACTC converts independent triangles into triangle strips or fans. *homepage*: https://sourceforge.net/projects/actc -======= ===================================================== -version toolchain -======= ===================================================== -``1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``intel/2016b`` -======= ===================================================== +======= ======================================================================== +version toolchain +======= ======================================================================== +``1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``intel/2016b`` +======= ======================================================================== .. _list_software_ada_294: @@ -347,6 +347,7 @@ The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitates version toolchain ========= =============== ``2.7.0`` ``gompi/2019a`` +``2.7.2`` ``gompi/2020a`` ========= =============== @@ -521,6 +522,22 @@ version toolchain ========= ============== +.. _list_software_almosthere_1076: + +*almosthere* +++++++++++++ + +Progress indicator C library. ATHR is a simple yet powerful progress indicator library that works on Windows, Linux, and macOS. It is non-blocking as the progress update is done via a dedicated, lightweight thread, as to not impair the performance of the calling program. + +*homepage*: https://github.com/horta/almosthere + +========== ================= +version toolchain +========== ================= +``1.0.10`` ``GCCcore/9.3.0`` +========== ================= + + .. _list_software_Alpha_486: *Alpha* @@ -608,6 +625,7 @@ version versionsuffix toolchain ``16`` ``-AmberTools-17-patchlevel-10-15-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``16`` ``-AmberTools-17-patchlevel-8-12`` ``intel/2017b`` ``18`` ``-AmberTools-18-patchlevel-10-8`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017b`` +``18`` ``-AmberTools-19-patchlevel-12-17-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b`` ======= ================================================= ======================================================================== @@ -620,11 +638,11 @@ A stripped-down set of just antechamber, sqm, and tleap. *homepage*: https://github.com/choderalab/ambermini -=========== =============== -version toolchain -=========== =============== -``16.16.0`` ``intel/2017b`` -=========== =============== +=========== ================================ +version toolchain +=========== ================================ +``16.16.0`` ``intel/2017b``, ``intel/2020a`` +=========== ================================ .. _list_software_AmberTools_1016: @@ -957,6 +975,7 @@ ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language to version versionsuffix toolchain ========= ================== ===================================================================================================== ``2.7.7`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b`` +``2.7.7`` ``-Java-11`` ``GCCcore/8.3.0`` ``2.7.7`` ``-Python-2.7.11`` ``foss/2016a`` ``2.7.7`` ``-Python-2.7.13`` ``intel/2017a`` ``2.7.7`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` @@ -1113,6 +1132,22 @@ version toolchain ========== ================================================================================ +.. _list_software_arcasHLA_735: + +*arcasHLA* +++++++++++ + +arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples. + +*homepage*: https://github.com/RabadanLab/arcasHLA + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.2.0`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_ARCH_286: *ARCH* @@ -1418,28 +1453,28 @@ ASE is a python package providing an open source Atomic Simulation Environment *homepage*: https://wiki.fysik.dtu.dk/ase/ -============== ================== ================================================ -version versionsuffix toolchain -============== ================== ================================================ -``3.9.1.4567`` ``-Python-2.7.11`` ``intel/2016a`` -``3.10.0`` ``-Python-2.7.11`` ``intel/2016.02-GCC-4.9`` -``3.11.0`` ``-Python-2.7.12`` ``intel/2016b`` -``3.13.0`` ``-Python-2.7.12`` ``foss/2016b`` -``3.13.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.15.0`` ``-Python-2.7.12`` ``foss/2016b`` -``3.15.0`` ``-Python-2.7.14`` ``intel/2017b`` -``3.15.0`` ``-Python-3.5.2`` ``foss/2016b`` -``3.15.0`` ``-Python-3.6.2`` ``foss/2017b`` -``3.15.0`` ``-Python-3.6.3`` ``foss/2017b`` -``3.16.2`` ``-Python-3.6.4`` ``iomkl/2018.02``, ``iomkl/2018a`` -``3.16.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.17.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.17.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.18.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.18.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -============== ================== ================================================ +============== ================== =================================================== +version versionsuffix toolchain +============== ================== =================================================== +``3.9.1.4567`` ``-Python-2.7.11`` ``intel/2016a`` +``3.10.0`` ``-Python-2.7.11`` ``intel/2016.02-GCC-4.9`` +``3.11.0`` ``-Python-2.7.12`` ``intel/2016b`` +``3.13.0`` ``-Python-2.7.12`` ``foss/2016b`` +``3.13.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.15.0`` ``-Python-2.7.12`` ``foss/2016b`` +``3.15.0`` ``-Python-2.7.14`` ``intel/2017b`` +``3.15.0`` ``-Python-3.5.2`` ``foss/2016b`` +``3.15.0`` ``-Python-3.6.2`` ``foss/2017b`` +``3.15.0`` ``-Python-3.6.3`` ``foss/2017b`` +``3.16.2`` ``-Python-3.6.4`` ``iomkl/2018.02``, ``iomkl/2018a`` +``3.16.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``3.17.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``3.17.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.18.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.18.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +============== ================== =================================================== .. _list_software_ASHS_303: @@ -1529,7 +1564,7 @@ version toolchain *astropy* +++++++++ -The Astropy Project is a community effort to develop a core package for astronomy using the Python programming language and improve usability, interoperability, and collaboration between astronomy Python packages. The core astropy package contains functionality aimed at professional astronomers and astrophysicists, but may be useful to anyone developing astronomy software. The Astropy Project also includes "affiliated packages," Python packages that are not necessarily developed by the core development team, but share the goals of Astropy, and often build from the core package's code and infrastructure. +The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages. *homepage*: https://www.astropy.org/ @@ -1539,6 +1574,7 @@ version versionsuffix toolchain ``2.0.12`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.0.14`` ``foss/2019a`` ``4.0.1`` ``-Python-3.7.4`` ``foss/2019b`` +``4.0.1`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================== =============================== @@ -1939,7 +1975,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_Biopython_956` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` +:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` .. _list_software_Bader_478: @@ -2267,6 +2303,7 @@ version toolchain ``0.29.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``1.1.0`` ``GCCcore/8.3.0`` ``2.0.0`` ``GCCcore/8.3.0`` +``3.4.1`` ``GCCcore/8.3.0`` ========== ==================================== @@ -2518,6 +2555,7 @@ version versionsuffix toolchain ``4.7.1`` ``-Python-3.6.6`` ``intel/2018b`` ``4.8.0`` ``GCCcore/8.2.0`` ``4.9.1`` ``GCCcore/8.3.0`` +``4.9.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ================= ================= @@ -2702,6 +2740,7 @@ version toolchain ``2.31.1`` ``GCCcore/7.4.0``, ``GCCcore/8.2.0``, ``system`` ``2.32`` ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` ``2.34`` ``GCCcore/10.1.0``, ``GCCcore/9.3.0``, ``system`` +``2.35`` ``GCCcore/10.2.0``, ``system`` ========== ======================================================================================================================================================================================== @@ -2830,6 +2869,22 @@ version versionsuffix toolchain =========== ================ =============================== +.. _list_software_BioPP_442: + +*BioPP* ++++++++ + +Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools. + +*homepage*: https://github.com/BioPP/bpp-core + +========= ============= +version toolchain +========= ============= +``2.4.1`` ``GCC/9.3.0`` +========= ============= + + .. _list_software_Biopython_956: *Biopython* @@ -2899,7 +2954,7 @@ version toolchain *Bison* +++++++ -Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. +Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. *homepage*: https://www.gnu.org/software/bison @@ -2916,6 +2971,7 @@ version toolchain ``3.5.2`` ``system`` ``3.5.3`` ``GCCcore/9.3.0``, ``system`` ``3.6.1`` ``GCCcore/10.1.0`` +``3.7.1`` ``GCCcore/10.2.0``, ``system`` ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -3194,17 +3250,17 @@ Statistical and novel interactive HTML plots for Python *homepage*: https://github.com/bokeh/bokeh -=========== ================== ================================== -version versionsuffix toolchain -=========== ================== ================================== -``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` -``0.12.3`` ``-Python-3.5.2`` ``intel/2016b`` -``0.12.15`` ``-Python-3.6.4`` ``intel/2018a`` -``1.0.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.3.4`` ``-Python-3.7.2`` ``foss/2019a`` -``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``2.0.2`` ``-Python-3.8.2`` ``foss/2020a`` -=========== ================== ================================== +=========== ================== =================================================== +version versionsuffix toolchain +=========== ================== =================================================== +``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` +``0.12.3`` ``-Python-3.5.2`` ``intel/2016b`` +``0.12.15`` ``-Python-3.6.4`` ``intel/2018a`` +``1.0.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.3.4`` ``-Python-3.7.2`` ``foss/2019a`` +``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2.0.2`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +=========== ================== =================================================== .. _list_software_BoltzTraP_898: @@ -3238,6 +3294,7 @@ version versionsuffix toolchain ``0.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``0.1.4`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``0.2.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``0.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ================= ================================== @@ -3324,7 +3381,7 @@ version versionsuffix toolchain ``1.68.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.69.0`` ``intel/2019.01`` ``1.70.0`` ``gompi/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` -``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b`` +``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` ``1.72.0`` ``gompi/2020a``, ``iimpi/2020a`` ``1.72.0`` ``-no_mpi`` ``GCCcore/9.3.0`` ========== ================== ==================================================================== @@ -3339,19 +3396,19 @@ Boost.Python is a C++ library which enables seamless interoperability between C+ *homepage*: https://boostorg.github.io/python -========== ================== =================================================== -version versionsuffix toolchain -========== ================== =================================================== -``1.64.0`` ``gompi/2019a``, ``gompic/2019a`` -``1.65.1`` ``-Python-2.7.14`` ``intel/2017b`` -``1.66.0`` ``-Python-2.7.14`` ``intel/2018a`` -``1.66.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.67.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``1.67.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.70.0`` ``gompi/2019a``, ``iimpi/2019a`` -``1.71.0`` ``gompi/2019b`` -``1.72.0`` ``gompi/2020a``, ``iimpi/2020a`` -========== ================== =================================================== +========== ================== ==================================================================== +version versionsuffix toolchain +========== ================== ==================================================================== +``1.64.0`` ``gompi/2019a``, ``gompic/2019a`` +``1.65.1`` ``-Python-2.7.14`` ``intel/2017b`` +``1.66.0`` ``-Python-2.7.14`` ``intel/2018a`` +``1.66.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.67.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``1.67.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.70.0`` ``gompi/2019a``, ``iimpi/2019a`` +``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` +``1.72.0`` ``gompi/2020a``, ``iimpi/2020a`` +========== ================== ==================================================================== .. _list_software_Bottleneck_1035: @@ -3478,6 +3535,22 @@ version toolchain ========= ==================== +.. _list_software_Bracken_694: + +*Bracken* ++++++++++ + +Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length. + +*homepage*: https://ccb.jhu.edu/software/bracken/ + +========= ================= +version toolchain +========= ================= +``2.6.0`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_BRAKER_439: *BRAKER* @@ -3576,6 +3649,22 @@ version versionsuffix toolchain ========= ================== ====================================== +.. _list_software_BUFRLIB_518: + +*BUFRLIB* ++++++++++ + +NCEP BUFRLIB software to encode or decode BUFR messages. It is not intended to be a primer on the BUFR code form itself. + +*homepage*: https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB + +============ ======================= +version toolchain +============ ======================= +``11.3.0.2`` ``iccifort/2020.1.217`` +============ ======================= + + .. _list_software_buildenv_857: *buildenv* @@ -3805,7 +3894,7 @@ version toolchain --- -:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_charmm_632` - :ref:`list_software_CHARMM_440` - :ref:`list_software_CHASE_356` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_charmm_632` - :ref:`list_software_CHARMM_440` - :ref:`list_software_CHASE_356` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_C3D_186: @@ -3914,6 +4003,22 @@ version versionsuffix toolchain ========== ================= =============== +.. _list_software_Calib_475: + +*Calib* ++++++++ + +Calib clusters paired-end reads using their barcodes and sequences. Calib is suitable for amplicon sequencing where a molecule is tagged, then PCR amplified with high depth, also known as Unique Molecule Identifier (UMI) sequencing. + +*homepage*: https://github.com/vpc-ccg/calib + +========= ============= +version toolchain +========= ============= +``0.3.4`` ``GCC/9.3.0`` +========= ============= + + .. _list_software_Cantera_702: *Cantera* @@ -4035,6 +4140,7 @@ Cartopy is a Python package designed to make drawing maps for data analysis and version versionsuffix toolchain ========== ================= ============== ``0.18.0`` ``-Python-3.7.4`` ``foss/2019b`` +``0.18.0`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================= ============== @@ -4173,18 +4279,19 @@ version toolchain *ccache* ++++++++ -Cache for C/C++ compilers +Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again -*homepage*: http://ccache.samba.org/ +*homepage*: https://ccache.dev/ -========= ============= ========== -version versionsuffix toolchain -========= ============= ========== -``3.2.5`` ``system`` -``3.3.1`` ``system`` -``3.3.3`` ``system`` -``3.3.4`` ``-f90`` ``system`` -========= ============= ========== +========== ============= ========== +version versionsuffix toolchain +========== ============= ========== +``3.2.5`` ``system`` +``3.3.1`` ``system`` +``3.3.3`` ``system`` +``3.3.4`` ``-f90`` ``system`` +``3.7.11`` ``system`` +========== ============= ========== .. _list_software_CCL_210: @@ -4317,12 +4424,13 @@ Climate Data Store API *homepage*: https://pypi.org/project/cdsapi -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``0.1.4`` ``foss/2019a`` -``0.1.4`` ``-Python-3.6.6`` ``foss/2018b`` -========= ================= ============== +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``0.1.4`` ``foss/2019a`` +``0.1.4`` ``-Python-3.6.6`` ``foss/2018b`` +``0.3.0`` ``GCCcore/9.3.0`` +========= ================= ================= .. _list_software_CellMix_686: @@ -4356,6 +4464,23 @@ version toolchain ``3.0.0`` ``system`` ``3.0.2`` ``system`` ``3.1.0`` ``system`` +``4.0.0`` ``system`` +========= ========== + + +.. _list_software_CellRanger-ATAC_1317: + +*CellRanger-ATAC* ++++++++++++++++++ + +Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data. + +*homepage*: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac + +========= ========== +version toolchain +========= ========== +``1.2.0`` ``system`` ========= ========== @@ -4519,11 +4644,12 @@ The CGNS system is designed to facilitate the exchange of data between sites and *homepage*: https://cgns.github.io/ -========= ============== -version toolchain -========= ============== -``3.3.1`` ``foss/2016b`` -========= ============== +========= =================== +version toolchain +========= =================== +``3.3.1`` ``foss/2016b`` +``4.1.0`` ``intelcuda/2019b`` +========= =================== .. _list_software_CharLS_541: @@ -4746,6 +4872,7 @@ version versionsuffix toolchain ``0.69-5`` ``-Perl-5.24.0`` ``foss/2016b`` ``0.69-6`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` ``0.69-6`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``0.69-9`` ``GCCcore/9.3.0`` ========== ================ ================= @@ -4827,9 +4954,12 @@ version versionsuffix toolchain ``7.0.1`` ``GCC/7.3.0-2.30`` ``8.0.0`` ``GCCcore/8.2.0`` ``8.0.0`` ``-CUDA-10.1.105`` ``GCCcore/8.2.0`` +``8.0.1`` ``-CUDA-10.1.105`` ``GCC/8.2.0-2.31.1`` +``8.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` ``9.0.1`` ``GCCcore/8.3.0`` ``9.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` -``10.0.0`` ``GCCcore/8.3.0`` +``10.0.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``10.0.1`` ``GCCcore/9.3.0`` ========== ================== ====================================== @@ -5405,7 +5535,7 @@ version toolchain CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. -*homepage*: http://www.cp2k.org/ +*homepage*: https://www.cp2k.org/ ======= ============= ================================================================== version versionsuffix toolchain @@ -5416,6 +5546,7 @@ version versionsuffix toolchain ``4.1`` ``-psmp`` ``foss/2016b`` ``5.1`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``6.1`` ``foss/2019a``, ``intel/2018a`` +``7.1`` ``intel/2020a`` ======= ============= ================================================================== @@ -5644,6 +5775,7 @@ CRPropa is a publicly available code to study the propagation of ultra high ener version versionsuffix toolchain ========= ================= ============== ``3.1.5`` ``-Python-3.7.2`` ``foss/2019a`` +``3.1.6`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -5741,6 +5873,7 @@ Program for finding CTFs of electron micrographs. version toolchain ========== ====================================================== ``4.1.13`` ``foss/2019a``, ``fosscuda/2019a``, ``fosscuda/2019b`` +``4.1.14`` ``foss/2019b``, ``fosscuda/2019b`` ========== ====================================================== @@ -5878,12 +6011,12 @@ Transcript assembly, differential expression, and differential regulation for RN *homepage*: http://cole-trapnell-lab.github.io/cufflinks/ -============ ================================================================================ -version toolchain -============ ================================================================================ -``2.2.1`` ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` -``20190706`` ``gompi/2019a`` -============ ================================================================================ +============ ================================================================================================= +version toolchain +============ ================================================================================================= +``2.2.1`` ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``gompi/2019b``, ``intel/2017b``, ``intel/2018a`` +``20190706`` ``gompi/2019a`` +============ ================================================================================================= .. _list_software_CUnit_483: @@ -6254,8 +6387,8 @@ version versionsuffix toolchain ``1.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.1.4`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``2.3.0`` ``-Python-3.7.2`` ``foss/2019a`` -``2.8.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``2.18.1`` ``-Python-3.8.2`` ``foss/2020a`` +``2.8.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2.18.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ================== =================================================== @@ -6268,11 +6401,12 @@ GNU datamash performs basic numeric, textual and statistical operations on input *homepage*: https://www.gnu.org/software/datamash/ -======= ============== -version toolchain -======= ============== -``1.3`` ``foss/2018a`` -======= ============== +======= ==================================== +version toolchain +======= ==================================== +``1.3`` ``foss/2018a`` +``1.5`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +======= ==================================== .. _list_software_davix_540: @@ -7104,7 +7238,7 @@ version versionsuffix toolchain --- -:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_E-ANTIC_481: @@ -7242,6 +7376,7 @@ version toolchain ``4.1.2`` ``system`` ``4.2.0`` ``system`` ``4.2.1`` ``system`` +``4.2.2`` ``system`` ========== ========== @@ -7300,6 +7435,23 @@ version versionsuffix toolchain ============ ============= =============== +.. _list_software_edlib_512: + +*edlib* ++++++++ + +Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance. + +*homepage*: https://martinsos.github.io/edlib + +=============== ================= ======================= +version versionsuffix toolchain +=============== ================= ======================= +``1.3.8.post1`` ``-Python-3.7.4`` ``iccifort/2019.5.281`` +``1.3.8.post1`` ``-Python-3.8.2`` ``GCC/9.3.0`` +=============== ================= ======================= + + .. _list_software_EggLib_554: *EggLib* @@ -7368,14 +7520,14 @@ The EIGENSOFT package combines functionality from our population genetics method *homepage*: http://www.hsph.harvard.edu/alkes-price/software/ -========= =============================== -version toolchain -========= =============================== -``6.0.1`` ``foss/2016a`` -``6.1.1`` ``foss/2016a`` -``6.1.4`` ``foss/2016b`` -``7.2.1`` ``foss/2019a``, ``intel/2019a`` -========= =============================== +========= =============================================================== +version toolchain +========= =============================================================== +``6.0.1`` ``foss/2016a`` +``6.1.1`` ``foss/2016a`` +``6.1.4`` ``foss/2016b`` +``7.2.1`` ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``intel/2019a`` +========= =============================================================== .. _list_software_elastix_762: @@ -7431,6 +7583,7 @@ version toolchain ``2018.05.001`` ``foss/2018b``, ``intel/2018b`` ``2018.11.001`` ``intel/2019a`` ``2019.11.001`` ``foss/2019b``, ``intel/2019b`` +``2020.05.001`` ``intel/2020a`` =================== ================================================ @@ -7474,7 +7627,7 @@ version versionsuffix toolchain GNU Emacs is an extensible, customizable text editor--and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing. -*homepage*: http://www.gnu.org/software/emacs/ +*homepage*: https://www.gnu.org/software/emacs/ ======== ============= ======================================================= version versionsuffix toolchain @@ -7485,6 +7638,7 @@ version versionsuffix toolchain ``24.5`` ``GCC/4.9.3-2.25`` ``25.1`` ``foss/2016a`` ``25.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``26.3`` ``GCCcore/8.3.0`` ======== ============= ======================================================= @@ -7675,7 +7829,7 @@ version versionsuffix toolchain ``7.0.2`` ``intel/2017b`` ``7.1.0r`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``8.0.0`` ``intel/2019b`` -``8.0.1`` ``foss/2020a`` +``8.0.1`` ``foss/2020a``, ``intel/2020a`` ============ ================ ================================================================= @@ -7829,7 +7983,7 @@ version toolchain ``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.2.6`` ``GCCcore/8.2.0`` ``2.2.7`` ``GCCcore/8.3.0`` -``2.2.9`` ``GCCcore/9.3.0`` +``2.2.9`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= ========================================================================================================================= @@ -7838,15 +7992,15 @@ version toolchain *expect* ++++++++ -Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. Expect really makes this stuff trivial. Expect is also useful for testing these same applications. +Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. Expect really makes this stuff trivial. Expect is also useful for testing these same applications. *homepage*: https://core.tcl.tk/expect/index -========== ================= -version toolchain -========== ================= -``5.45.4`` ``GCCcore/7.3.0`` -========== ================= +========== ==================================== +version toolchain +========== ==================================== +``5.45.4`` ``GCCcore/7.3.0``, ``GCCcore/9.3.0`` +========== ==================================== .. _list_software_eXpress_746: @@ -7888,7 +8042,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FIAT_292` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FIAT_292` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -8737,6 +8891,7 @@ version versionsuffix toolchain ================ ================= ============== ``1.8.13`` ``-Python-3.7.4`` ``foss/2019b`` ``1.8.13.post1`` ``-Python-3.7.2`` ``foss/2019a`` +``1.8.16`` ``-Python-3.8.2`` ``foss/2020a`` ================ ================= ============== @@ -8871,6 +9026,22 @@ version versionsuffix toolchain ========= ================= ================= +.. _list_software_flatbuffers_1172: + +*flatbuffers* ++++++++++++++ + +FlatBuffers: Memory Efficient Serialization Library + +*homepage*: https://github.com/google/flatbuffers/ + +========== ================= +version toolchain +========== ================= +``1.12.0`` ``GCCcore/8.3.0`` +========== ================= + + .. _list_software_FLEUR_382: *FLEUR* @@ -8905,7 +9076,7 @@ version toolchain ``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``2.6.2`` ``intel/2016b`` ``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` -``2.6.4`` ``GCCcore/10.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` +``2.6.4`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` ========== ======================================================================================================================================================================================================================================================================================================================================================================================= @@ -8989,13 +9160,14 @@ Flye is a de novo assembler for long and noisy reads, such as those produced by *homepage*: https://github.com/fenderglass/Flye -======= ================== =============== -version versionsuffix toolchain -======= ================== =============== -``2.4`` ``-Python-2.7.15`` ``intel/2018b`` -``2.6`` ``-Python-3.7.2`` ``foss/2019a`` -``2.6`` ``-Python-3.7.4`` ``intel/2019b`` -======= ================== =============== +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``2.4`` ``-Python-2.7.15`` ``intel/2018b`` +``2.6`` ``-Python-3.7.2`` ``foss/2019a`` +``2.6`` ``-Python-3.7.4`` ``intel/2019b`` +``2.8.1`` ``-Python-3.8.2`` ``intel/2020a`` +========= ================== =============== .. _list_software_FMILibrary_945: @@ -9569,7 +9741,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gblocks_709` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_gtest_551` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gblocks_709` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -9581,11 +9753,11 @@ Library contains GRIB2 encoder/decoder ('C' version). *homepage*: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ -========= ===================================================================================================== -version toolchain -========= ===================================================================================================== -``1.6.0`` ``GCCcore/8.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -========= ===================================================================================================== +========= ======================================================================================================================== +version toolchain +========= ======================================================================================================================== +``1.6.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +========= ======================================================================================================================== .. _list_software_g2lib_464: @@ -9597,12 +9769,12 @@ Library contains GRIB2 encoder/decoder and search/indexing routines. *homepage*: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ -========= ================================================== -version toolchain -========= ================================================== -``1.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``3.1.0`` ``GCCcore/8.3.0``, ``foss/2018b``, ``intel/2018b`` -========= ================================================== +========= ===================================================================== +version toolchain +========= ===================================================================== +``1.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +``3.1.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2018b`` +========= ===================================================================== .. _list_software_g2log_475: @@ -9802,7 +9974,9 @@ version versionsuffix toolchain ``4.1.0.0`` ``-Python-3.6.6`` ``foss/2018b`` ``4.1.2.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` ``4.1.3.0`` ``-Java-1.8`` ``GCCcore/8.3.0`` +``4.1.4.1`` ``-Java-1.8`` ``GCCcore/8.3.0`` ``4.1.4.1`` ``-Java-11`` ``GCCcore/8.3.0`` +``4.1.5.0`` ``-Java-1.8`` ``GCCcore/9.3.0`` ``4.1.5.0`` ``-Java-11`` ``GCCcore/9.3.0`` ============ =================== ================= @@ -9846,7 +10020,7 @@ version versionsuffix toolchain The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. -*homepage*: http://hboehm.info/gc/ +*homepage*: https://hboehm.info/gc/ ========== ==================================== version toolchain @@ -9940,6 +10114,7 @@ version versionsuffix toolchain ``9.2.0`` ``-2.32`` ``system`` ``9.3.0`` ``system`` ``10.1.0`` ``system`` +``10.2.0`` ``system`` ``system`` ``system`` ``system`` ``-2.29`` ``system`` ========== =================== ========== @@ -9979,6 +10154,7 @@ version toolchain ``9.2.0`` ``system`` ``9.3.0`` ``system`` ``10.1.0`` ``system`` +``10.2.0`` ``system`` ``system`` ``system`` ========== ========== @@ -10051,6 +10227,7 @@ version versionsuffix toolchain ``2.66`` ``-Perl-5.24.0`` ``foss/2016b`` ``2.68`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` ``2.69`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``2.71`` ``GCCcore/9.3.0`` ======== ================ ================= @@ -10349,6 +10526,22 @@ version toolchain ======== ================= +.. _list_software_gengetopt_973: + +*gengetopt* ++++++++++++ + +Gengetopt is a tool to write command line option parsing code for C programs. + +*homepage*: https://www.gnu.org/software/gengetopt/gengetopt.html + +======== ================= +version toolchain +======== ================= +``2.23`` ``GCCcore/9.3.0`` +======== ================= + + .. _list_software_GenomeMapper_1216: *GenomeMapper* @@ -10840,24 +11033,24 @@ Git is a free and open source distributed version control system designed to han *homepage*: http://git-scm.com/ -=========== ============= ================= -version versionsuffix toolchain -=========== ============= ================= -``1.8.5.6`` ``GCC/4.9.2`` -``2.2.2`` ``GCC/4.9.2`` -``2.4.1`` ``GCC/4.9.2`` -``2.8.0`` ``foss/2016a`` -``2.12.2`` ``foss/2016b`` -``2.13.1`` ``foss/2016b`` -``2.14.1`` ``GCCcore/6.4.0`` -``2.16.1`` ``foss/2018a`` -``2.18.0`` ``GCCcore/7.3.0`` -``2.19.1`` ``GCCcore/7.3.0`` -``2.21.0`` ``GCCcore/8.2.0`` -``2.21.0`` ``-nodocs`` ``GCCcore/8.2.0`` -``2.23.0`` ``GCCcore/8.3.0`` -``2.23.0`` ``-nodocs`` ``GCCcore/8.3.0`` -=========== ============= ================= +=========== ============= ==================================== +version versionsuffix toolchain +=========== ============= ==================================== +``1.8.5.6`` ``GCC/4.9.2`` +``2.2.2`` ``GCC/4.9.2`` +``2.4.1`` ``GCC/4.9.2`` +``2.8.0`` ``foss/2016a`` +``2.12.2`` ``foss/2016b`` +``2.13.1`` ``foss/2016b`` +``2.14.1`` ``GCCcore/6.4.0`` +``2.16.1`` ``foss/2018a`` +``2.18.0`` ``GCCcore/7.3.0`` +``2.19.1`` ``GCCcore/7.3.0`` +``2.21.0`` ``GCCcore/8.2.0`` +``2.21.0`` ``-nodocs`` ``GCCcore/8.2.0`` +``2.23.0`` ``GCCcore/8.3.0`` +``2.23.0`` ``-nodocs`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +=========== ============= ==================================== .. _list_software_git-extras_1032: @@ -11327,6 +11520,7 @@ version versionsuffix toolchain ``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``2.1.0b4`` ``GCC/8.3.0`` +``2.1.0b5`` ``GCC/9.3.0`` =========== ================== =============================== @@ -11562,6 +11756,7 @@ version toolchain ========= ========== ``2018b`` ``system`` ``2019a`` ``system`` +``2020a`` ``system`` ========= ========== @@ -11636,15 +11831,17 @@ version versionsuffix toolchain *googletest* ++++++++++++ -Google's C++ test framework +Google's framework for writing C++ tests on a variety of platforms *homepage*: https://github.com/google/googletest -========= ===================================================================== -version toolchain -========= ===================================================================== -``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b`` -========= ===================================================================== +========== ===================================================================== +version toolchain +========== ===================================================================== +``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b`` +``1.8.1`` ``GCCcore/8.2.0`` +``1.10.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ===================================================================== .. _list_software_gotree_646: @@ -11889,6 +12086,22 @@ version toolchain ========== ================================ +.. _list_software_graphite2_902: + +*graphite2* ++++++++++++ + +Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world. + +*homepage*: https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home + +========== ================= +version toolchain +========== ================= +``1.3.14`` ``GCCcore/8.3.0`` +========== ================= + + .. _list_software_GraphMap2_834: *GraphMap2* @@ -11921,6 +12134,7 @@ version versionsuffix toolchain ``2.40.1`` ``foss/2018b``, ``intel/2018a`` ``2.40.1`` ``-Python-2.7.15`` ``foss/2018b`` ``2.42.2`` ``foss/2019b`` +``2.42.2`` ``-Java-11`` ``GCCcore/8.3.0`` ``2.42.2`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================== =============================== @@ -12310,24 +12524,6 @@ version versionsuffix toolchain ========= ================== =============================== -.. _list_software_gtest_551: - -*gtest* -+++++++ - -Google's framework for writing C++ tests on a variety of platforms - -*homepage*: https://github.com/google/googletest - -========== ==================================== -version toolchain -========== ==================================== -``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``1.8.1`` ``GCCcore/8.2.0`` -``1.10.0`` ``GCCcore/8.3.0`` -========== ==================================== - - .. _list_software_GTK+_273: *GTK+* @@ -12393,12 +12589,12 @@ GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free *homepage*: http://gts.sourceforge.net/ -============ ================================================================================================================================= -version toolchain -============ ================================================================================================================================= -``0.7.6`` ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` -``20121130`` ``foss/2017b`` -============ ================================================================================================================================= +============ ==================================================================================================================================================== +version toolchain +============ ==================================================================================================================================================== +``0.7.6`` ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` +``20121130`` ``foss/2017b`` +============ ==================================================================================================================================================== .. _list_software_gubbins_746: @@ -12517,7 +12713,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_hyperopt_891` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_hyperopt_891` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -12560,7 +12756,7 @@ version toolchain HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data. -*homepage*: http://www.h5py.org/ +*homepage*: https://www.h5py.org/ ========== ===================================== ==================================================================================== version versionsuffix toolchain @@ -12593,7 +12789,7 @@ version versionsuffix toolchain ``2.8.0`` ``-Python-2.7.15-serial`` ``intel/2018b`` ``2.8.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.9.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``2.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` ``2.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ===================================== ==================================================================================== @@ -12779,6 +12975,7 @@ version versionsuffix toolchain ``4.2.13`` ``GCCcore/6.4.0`` ``4.2.13`` ``-no-netcdf`` ``intel/2017a`` ``4.2.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``4.2.15`` ``GCCcore/9.3.0`` ========== ============== ========================================================================== @@ -12912,6 +13109,22 @@ version toolchain ========= ============== +.. _list_software_HeFFTe_498: + +*HeFFTe* +++++++++ + +Highly Efficient FFT for Exascale (HeFFTe) library + +*homepage*: https://icl.utk.edu/fft + +======= ============== +version toolchain +======= ============== +``1.0`` ``foss/2020a`` +======= ============== + + .. _list_software_Hello_500: *Hello* @@ -12948,6 +13161,7 @@ version toolchain ``1.47.10`` ``GCCcore/9.1.0``, ``GCCcore/9.2.0`` ``1.47.12`` ``GCCcore/9.3.0`` ``1.47.15`` ``GCCcore/10.1.0`` +``1.47.16`` ``GCCcore/10.2.0`` =========== ================================================================================================================================================================================== @@ -13000,6 +13214,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_hierfstat_970: + +*hierfstat* ++++++++++++ + +Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy. + +*homepage*: https://cran.r-project.org/package=hierfstat + +========= ========================= ============== +version versionsuffix toolchain +========= ========================= ============== +``0.5-7`` ``-R-4.0.0-Python-3.8.2`` ``foss/2020a`` +========= ========================= ============== + + .. _list_software_HIPS_308: *HIPS* @@ -13151,6 +13381,7 @@ version versionsuffix toolchain ``0.18.2`` ``-TensorFlow-1.15.2-Python-3.7.4`` ``fosscuda/2019b`` ``0.18.2`` ``-TensorFlow-2.0.0-Python-3.7.4`` ``fosscuda/2019b`` ``0.19.1`` ``-TensorFlow-2.1.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.19.5`` ``-TensorFlow-2.2.0-Python-3.7.4`` ``fosscuda/2019b`` ========== =================================== ================== @@ -13500,7 +13731,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_ITSTool_654` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -14023,12 +14254,13 @@ Imageio is a Python library that provides an easy interface to read and write a *homepage*: https://imageio.github.io -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``2.3.0`` ``-Python-3.6.4`` ``intel/2018a`` -``2.5.0`` ``foss/2019a`` -========= ================= =============== +========= ================= =============================== +version versionsuffix toolchain +========= ================= =============================== +``2.3.0`` ``-Python-3.6.4`` ``intel/2018a`` +``2.5.0`` ``foss/2019a`` +``2.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +========= ================= =============================== .. _list_software_ImageJ_557: @@ -14148,6 +14380,7 @@ This python library helps you with augmenting images for your machine learning p version versionsuffix toolchain ========= ================= ============== ``0.2.8`` ``-Python-3.6.6`` ``foss/2018b`` +``0.4.0`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -14184,7 +14417,7 @@ version toolchain ``2019.3.199`` ``iimpi/2019.03`` ``2019.5.281`` ``iimpi/2019b``, ``iimpic/2019b`` ``2020.0.166`` ``iimpi/2020.00`` -``2020.1.217`` ``iimpi/2020.06-impi-18.5``, ``iimpi/2020a`` +``2020.1.217`` ``gompi/2020a``, ``iimpi/2020.06-impi-18.5``, ``iimpi/2020a``, ``iompi/2020a`` ============== ====================================================================================================================================================================================================================================================================== @@ -14204,6 +14437,22 @@ version toolchain ========= ================= +.. _list_software_immunedeconv_1290: + +*immunedeconv* +++++++++++++++ + +immunedeconv is an R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data. + +*homepage*: https://github.com/icbi-lab/immunedeconv + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``2.0.2`` ``-R-4.0.0`` ``foss/2020a`` +========= ============= ============== + + .. _list_software_IMOD_297: *IMOD* @@ -14611,6 +14860,22 @@ version toolchain ========== ============== +.. _list_software_ioapi_530: + +*ioapi* ++++++++ + +The Models-3/EDSS Input/Output Applications Programming Interface (I/O API) provides the environmental model developer with an easy-to-learn, easy-to-use programming library for data storage and access, available from both Fortran and C. The same routines can be used for both file storage (using netCDF files) and model coupling (using PVM mailboxes). It is the standard data access library for both the NCSC/CMAS's EDSS project and EPA's Models-3, CMAQ, and SMOKE, as well as various other atmospheric and hydrological modeling systems. + +*homepage*: https://www.cmascenter.org/ioapi/ + +=============== ============= =============== +version versionsuffix toolchain +=============== ============= =============== +``3.2-2020111`` ``-nocpl`` ``gompi/2019b`` +=============== ============= =============== + + .. _list_software_iomkl_540: *iomkl* @@ -14618,7 +14883,7 @@ version toolchain Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI. -*homepage*: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ +*homepage*: https://software.intel.com/en-us/intel-cluster-toolkit-compiler/ ========================== ========== version toolchain @@ -14633,6 +14898,7 @@ version toolchain ``2018a`` ``system`` ``2018b`` ``system`` ``2019.01`` ``system`` +``2020a`` ``system`` ========================== ========== @@ -14643,7 +14909,7 @@ version toolchain Intel C/C++ and Fortran compilers, alongside Open MPI. -*homepage*: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ +*homepage*: https://software.intel.com/en-us/intel-cluster-toolkit-compiler/ ========================== ========== version toolchain @@ -14658,6 +14924,7 @@ version toolchain ``2018a`` ``system`` ``2018b`` ``system`` ``2019.01`` ``system`` +``2020a`` ``system`` ========================== ========== @@ -14949,6 +15216,22 @@ version versionsuffix toolchain ========== ================== ============== +.. _list_software_itpp_445: + +*itpp* +++++++ + +IT++ is a C++ library of mathematical, signal processing and communication classes and functions. Its main use is in simulation of communication systems and for performing research in the area of communications. + +*homepage*: https://sourceforge.net/projects/itpp/ + +========= ============== +version toolchain +========= ============== +``4.3.1`` ``foss/2019b`` +========= ============== + + .. _list_software_ITSTool_654: *ITSTool* @@ -15001,12 +15284,12 @@ JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian *homepage*: http://mcmc-jags.sourceforge.net/ -========= =============================================================================== -version toolchain -========= =============================================================================== -``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` -``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``intel/2017b`` -========= =============================================================================== +========= =============================================================================================== +version toolchain +========= =============================================================================================== +``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` +``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2017b`` +========= =============================================================================================== .. _list_software_Jansson_732: @@ -15100,6 +15383,7 @@ version versionsuffix toolchain ``11`` ``system`` ``11.0.2`` ``system`` ``11.0.6`` ``-ppc64le`` ``system`` +``11.0.8`` ``-aarch64`` ``system`` ``13`` ``system`` ``13.0.2`` ``system`` ======================= ============= ========== @@ -15128,13 +15412,13 @@ version toolchain JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents. -*homepage*: +*homepage*: https://www.cl.cam.ac.uk/~mgk25/jbigkit/ -======= ======================================================= -version toolchain -======= ======================================================= -``2.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -======= ======================================================= +======= ========================================================================== +version toolchain +======= ========================================================================== +``2.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ========================================================================== .. _list_software_Jellyfish_938: @@ -15166,18 +15450,18 @@ jemalloc is a general purpose malloc(3) implementation that emphasizes fragmenta *homepage*: http://jemalloc.net -========= =============================== -version toolchain -========= =============================== -``4.1.0`` ``intel/2016a`` -``4.2.0`` ``foss/2016a``, ``intel/2016a`` -``4.2.1`` ``intel/2016b`` -``4.5.0`` ``intel/2017a`` -``5.0.1`` ``GCCcore/6.4.0`` -``5.1.0`` ``GCCcore/7.3.0`` -``5.2.0`` ``GCCcore/8.2.0`` -``5.2.1`` ``GCCcore/8.3.0`` -========= =============================== +========= ==================================== +version toolchain +========= ==================================== +``4.1.0`` ``intel/2016a`` +``4.2.0`` ``foss/2016a``, ``intel/2016a`` +``4.2.1`` ``intel/2016b`` +``4.5.0`` ``intel/2017a`` +``5.0.1`` ``GCCcore/6.4.0`` +``5.1.0`` ``GCCcore/7.3.0`` +``5.2.0`` ``GCCcore/8.2.0`` +``5.2.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ==================================== .. _list_software_jhbuild_738: @@ -15268,12 +15552,13 @@ version toolchain JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. -*homepage*: http://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html +*homepage*: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html ========== ================= version toolchain ========== ================= ``0.10.7`` ``GCCcore/8.2.0`` +``1.9.3`` ``GCCcore/8.3.0`` ========== ================= @@ -15282,9 +15567,9 @@ version toolchain *JUBE* ++++++ -The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, run those sets on different computer systems and evaluate the results. +The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, run those sets on different computer systems and evaluate the results. -*homepage*: http://www.fz-juelich.de/jsc/jube +*homepage*: https://www.fz-juelich.de/jsc/jube ========= ========== version toolchain @@ -15292,6 +15577,7 @@ version toolchain ``2.0.3`` ``system`` ``2.0.4`` ``system`` ``2.0.5`` ``system`` +``2.4.0`` ``system`` ========= ========== @@ -15304,11 +15590,11 @@ A C library that implements a dynamic array. *homepage*: http://judy.sourceforge.net/ -========= ================= -version toolchain -========= ================= -``1.0.5`` ``GCCcore/8.2.0`` -========= ================= +========= ==================================== +version toolchain +========= ==================================== +``1.0.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ==================================== .. _list_software_Julia_501: @@ -15329,6 +15615,7 @@ version versionsuffix toolchain ``1.4.0`` ``-linux-x86_64`` ``system`` ``1.4.1`` ``-linux-x86_64`` ``system`` ``1.4.2`` ``-linux-x86_64`` ``system`` +``1.5.1`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -15502,18 +15789,19 @@ version toolchain *Kent_tools* ++++++++++++ -Kent tools: collection of tools used by the UCSC genome browser. +Kent utilities: collection of tools used by the UCSC genome browser. -*homepage*: http://genome.cse.ucsc.edu/ +*homepage*: https://genome.cse.ucsc.edu/ -============ ================= ========== -version versionsuffix toolchain -============ ================= ========== -``20130806`` ``-linux.x86_64`` ``system`` -``20171107`` ``-linux.x86_64`` ``system`` -``20180716`` ``-linux.x86_64`` ``system`` -``20190326`` ``-linux.x86_64`` ``system`` -============ ================= ========== +============ ================= =============== +version versionsuffix toolchain +============ ================= =============== +``401`` ``gompi/2019b`` +``20130806`` ``-linux.x86_64`` ``system`` +``20171107`` ``-linux.x86_64`` ``system`` +``20180716`` ``-linux.x86_64`` ``system`` +``20190326`` ``-linux.x86_64`` ``system`` +============ ================= =============== .. _list_software_Keras_502: @@ -15827,7 +16115,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libpsml_755` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libpsml_755` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_limix-bgen_1004` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -16073,11 +16361,11 @@ Asynchronous input/output library that uses the kernels native interface. *homepage*: https://pagure.io/libaio -=========== ================= -version toolchain -=========== ================= -``0.3.111`` ``GCCcore/8.2.0`` -=========== ================= +=========== ==================================== +version toolchain +=========== ==================================== +``0.3.111`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +=========== ==================================== .. _list_software_libarchive_1049: @@ -16265,6 +16553,7 @@ version versionsuffix toolchain ``3.19.1`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` ``3.20.3`` ``GCCcore/7.3.0`` ``3.20.4`` ``GCCcore/8.2.0`` +``3.20.6`` ``GCCcore/8.3.0`` ========== ================== ================================================== @@ -16744,12 +17033,12 @@ Libiconv converts from one character encoding to another through Unicode convers *homepage*: https://www.gnu.org/software/libiconv -======== ======================================================= -version toolchain -======== ======================================================= -``1.15`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.16`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -======== ======================================================= +======== ========================================================================== +version toolchain +======== ========================================================================== +``1.15`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``1.16`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======== ========================================================================== .. _list_software_libidn_626: @@ -16779,16 +17068,33 @@ Libint library is used to evaluate the traditional (electron repulsion) and cert *homepage*: https://github.com/evaleev/libint -========= ================================================================================================================================================================== -version toolchain -========= ================================================================================================================================================================== -``1.1.4`` ``intel/2016a`` -``1.1.6`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``2.0.3`` ``foss/2018b``, ``gompi/2019a``, ``intel/2018b`` -``2.1.0`` ``intel/2016b`` -``2.4.2`` ``intel/2018a`` -``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` -========= ================================================================================================================================================================== +========= ================ ================================================================================================================================================================== +version versionsuffix toolchain +========= ================ ================================================================================================================================================================== +``1.1.4`` ``intel/2016a`` +``1.1.6`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``2.0.3`` ``foss/2018b``, ``gompi/2019a``, ``intel/2018b`` +``2.1.0`` ``intel/2016b`` +``2.4.2`` ``intel/2018a`` +``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` +``2.6.0`` ``-lmax-6-cp2k`` ``iimpi/2020a`` +========= ================ ================================================================================================================================================================== + + +.. _list_software_LiBis_467: + +*LiBis* ++++++++ + +An ultrasensitive alignment method for low input bisulfite sequencing + +*homepage*: https://github.com/Dangertrip/LiBis + +============ ================= ============== +version versionsuffix toolchain +============ ================= ============== +``20200428`` ``-Python-3.7.4`` ``foss/2019b`` +============ ================= ============== .. _list_software_libjpeg-turbo_1334: @@ -16864,6 +17170,23 @@ version toolchain ========== ==================================== +.. _list_software_libosmium_977: + +*libosmium* ++++++++++++ + +A fast and flexible C++ library for working with OpenStreetMap data. The Osmium Library has extensive support for all types of OSM entities: nodes, ways, relations, and changesets. It allows reading from and writing to OSM files in XML and PBF formats, including change files and full history files. Osmium can store OSM data in memory and on disk in various formats and using various indexes. Its easy to use handler interface allows you to quickly write data filtering and conversion functions. Osmium can create WKT, WKB, OGR, GEOS and GeoJSON geometries for easy conversion into many GIS formats and it can assemble multipolygons from ways and relations. + +*homepage*: https://osmcode.org/libosmium/ + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``2.15.4`` ``-Python-3.6.6`` ``foss/2018b`` +``2.15.6`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_libpciaccess_1253: *libpciaccess* @@ -17025,7 +17348,7 @@ version toolchain ======= =================================================================================================================================================================================================================================================================================================================================================================================== ``6.3`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``7.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``8.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +``8.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ======= =================================================================================================================================================================================================================================================================================================================================================================================== @@ -17321,6 +17644,7 @@ Libtirpc is a port of Suns Transport-Independent RPC library to Linux. version toolchain ========= ==================================== ``1.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.2.6`` ``GCCcore/8.3.0`` ========= ==================================== @@ -17503,18 +17827,18 @@ Libxc is a library of exchange-correlation functionals for density-functional th *homepage*: https://www.tddft.org/programs/libxc -========= ======================================================================================================================================= -version toolchain -========= ======================================================================================================================================= -``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` -``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` -``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` -``4.0.1`` ``foss/2017b``, ``intel/2017b`` -``4.0.3`` ``foss/2016b``, ``foss/2017a`` -``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` -``4.3.4`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` -========= ======================================================================================================================================= +========= ============================================================================================================================================== +version toolchain +========= ============================================================================================================================================== +``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` +``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` +``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` +``4.0.1`` ``foss/2017b``, ``intel/2017b`` +``4.0.3`` ``foss/2016b``, ``foss/2017a`` +``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` +``4.3.4`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217`` +========= ============================================================================================================================================== .. _list_software_libxcb_628: @@ -17856,7 +18180,7 @@ version versionsuffix toolchain ``1.1.30`` ``GCCcore/6.3.0`` ``1.1.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.1.33`` ``GCCcore/8.2.0`` -``1.1.34`` ``GCCcore/8.3.0`` +``1.1.34`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ================== ================================================================= @@ -17869,16 +18193,17 @@ LIBXSMM is a library for small dense and small sparse matrix-matrix multiplicati *homepage*: https://github.com/hfp/libxsmm -========= =============================================================================== -version toolchain -========= =============================================================================== -``1.4`` ``intel/2016a`` -``1.4.4`` ``foss/2016b``, ``intel/2016b`` -``1.6.4`` ``foss/2016b``, ``intel/2016b`` -``1.8.2`` ``intel/2017b`` -``1.8.3`` ``foss/2018a``, ``intel/2018a`` -``1.10`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -========= =============================================================================== +========== =============================================================================== +version toolchain +========== =============================================================================== +``1.4`` ``intel/2016a`` +``1.4.4`` ``foss/2016b``, ``intel/2016b`` +``1.6.4`` ``foss/2016b``, ``intel/2016b`` +``1.8.2`` ``intel/2017b`` +``1.8.3`` ``foss/2018a``, ``intel/2018a`` +``1.10`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` +``1.16.1`` ``iccifort/2020.1.217`` +========== =============================================================================== .. _list_software_libXt_515: @@ -18001,6 +18326,22 @@ version toolchain ========= ===================================================================== +.. _list_software_limix-bgen_1004: + +*limix-bgen* +++++++++++++ + +A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3. + +*homepage*: https://github.com/limix/bgen + +========= ================= +version toolchain +========= ================= +``3.0.3`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_LinBox_588: *LinBox* @@ -18274,13 +18615,15 @@ LS-PrePost is an advanced pre and post-processor that is delivered free with LS- *homepage*: http://lstc.com/products/ls-prepost -========= ============= ========== -version versionsuffix toolchain -========= ============= ========== -``4.6`` ``-centos6`` ``system`` -``4.6`` ``-centos7`` ``system`` -``4.7.8`` ``system`` -========= ============= ========== +========== ============= ========== +version versionsuffix toolchain +========== ============= ========== +``4.6`` ``-centos6`` ``system`` +``4.6`` ``-centos7`` ``system`` +``4.6.24`` ``system`` +``4.7.8`` ``system`` +``4.7.15`` ``system`` +========== ============= ========== .. _list_software_LSMS_319: @@ -18439,6 +18782,7 @@ version versionsuffix toolchain ``4.2.5`` ``-Python-3.6.6`` ``foss/2018b`` ``4.3.3`` ``GCCcore/8.2.0`` ``4.4.2`` ``GCCcore/8.3.0`` +``4.5.2`` ``GCCcore/9.3.0`` ========= ================== =============================== @@ -18500,7 +18844,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_magma_515` - :ref:`list_software_MAGMA_355` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_magma_515` - :ref:`list_software_MAGMA_355` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -18517,7 +18861,7 @@ version toolchain ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.4.16`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.4.18`` ``GCCcore/10.1.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` +``1.4.18`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -18725,7 +19069,7 @@ The makedepend package contains a C-preprocessor like utility to determine build version toolchain ========= ======================================================================================= ``1.0.5`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``1.0.6`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +``1.0.6`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ======================================================================================= @@ -18784,6 +19128,7 @@ version versionsuffix toolchain ``1.1.1`` ``system`` ``1.6.0`` ``system`` ``1.6.0`` ``-Python-2.7.16`` ``gompi/2019b`` +``1.6.0`` ``-Python-2.7.18`` ``gompi/2020a`` ========= ================== =============== @@ -18842,7 +19187,7 @@ version toolchain *MariaDB* +++++++++ -MariaDB An enhanced, drop-in replacement for MySQL. +MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga. *homepage*: https://mariadb.org/ @@ -18858,6 +19203,7 @@ version toolchain ``10.3.7`` ``intel/2018a`` ``10.3.10`` ``foss/2018b`` ``10.3.14`` ``foss/2019a`` +``10.4.13`` ``gompi/2019b`` =========== =============================== @@ -19028,6 +19374,7 @@ version versionsuffix toolchain ========= ================== =============================== ``2018b`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2018b`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2019b`` ``GCCcore/8.3.0`` ========= ================== =============================== @@ -19071,7 +19418,7 @@ version versionsuffix toolchain ``2.2.3`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.2.3`` ``-Python-3.6.6`` ``intel/2018b`` ``2.2.4`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``2.2.4`` ``-Python-2.7.16`` ``foss/2019b``, ``intel/2019b`` +``2.2.4`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``2.2.5`` ``-Python-2.7.16`` ``foss/2019b`` ``3.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` @@ -19303,14 +19650,15 @@ version toolchain MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data. -*homepage*: http://mdsplus.org/ +*homepage*: https://mdsplus.org/ -========== ================================ ============== -version versionsuffix toolchain -========== ================================ ============== -``7.0.67`` ``-Java-1.7.0_79-Python-2.7.11`` ``foss/2016a`` -``7.46.1`` ``foss/2018a`` -========== ================================ ============== +========== ================================ ================= +version versionsuffix toolchain +========== ================================ ================= +``7.0.67`` ``-Java-1.7.0_79-Python-2.7.11`` ``foss/2016a`` +``7.46.1`` ``foss/2018a`` +``7.96.8`` ``GCCcore/9.3.0`` +========== ================================ ================= .. _list_software_mdtest_657: @@ -19344,6 +19692,7 @@ version versionsuffix toolchain ``1.9.1`` ``-Python-3.6.3`` ``intel/2017b`` ``1.9.2`` ``-Python-3.6.6`` ``intel/2018b`` ``1.9.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.9.4`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================= =============================== @@ -19663,6 +20012,7 @@ version versionsuffix toolchain ``0.51.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``0.53.1`` ``-Python-3.6.3`` ``intel/2017b`` ``0.53.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``0.55.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========== ================= ================================== @@ -19993,6 +20343,22 @@ version toolchain ======= ================= +.. _list_software_minibar_738: + +*minibar* ++++++++++ + +Dual barcode and primer demultiplexing for MinION sequenced reads + +*homepage*: https://github.com/calacademy-research/minibar + +============ ================= ======================= +version versionsuffix toolchain +============ ================= ======================= +``20200326`` ``-Python-3.7.4`` ``iccifort/2019.5.281`` +============ ================= ======================= + + .. _list_software_Miniconda2_964: *Miniconda2* @@ -20138,6 +20504,22 @@ version versionsuffix toolchain =========== ================= =============== +.. _list_software_misha_530: + +*misha* ++++++++ + +The misha package is intended to help users to efficiently analyze genomic data achieved from various experiments. + +*homepage*: https://github.com/tanaylab/misha + +========== ============= ============== +version versionsuffix toolchain +========== ============= ============== +``4.0.10`` ``-R-4.0.0`` ``foss/2020a`` +========== ============= ============== + + .. _list_software_MITObim_625: *MITObim* @@ -20305,6 +20687,22 @@ version toolchain ============ ================================ +.. _list_software_MOABS_370: + +*MOABS* ++++++++ + +MOABS: MOdel based Analysis of Bisulfite Sequencing data + +*homepage*: https://github.com/sunnyisgalaxy/moabs + +=========== =============== +version toolchain +=========== =============== +``1.3.9.6`` ``gompi/2019b`` +=========== =============== + + .. _list_software_modred_635: *modred* @@ -20457,6 +20855,22 @@ version versionsuffix toolchain ========= ========================= ============== +.. _list_software_moonjit_768: + +*moonjit* ++++++++++ + +Moonjit is a Just-In-Time Compiler (JIT) for the Lua programming language. Lua is a powerful, dynamic and light-weight programming language. It may be embedded or used as a general-purpose, stand-alone language. + +*homepage*: https://github.com/moonjit/moonjit + +========= ================= +version toolchain +========= ================= +``2.2.0`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_mordecai_836: *mordecai* @@ -20557,6 +20971,7 @@ version toolchain ========= ================= ``1.2.6`` ``GCCcore/8.2.0`` ``1.3.1`` ``GCCcore/8.3.0`` +``1.3.2`` ``GCCcore/8.3.0`` ========= ================= @@ -20606,7 +21021,7 @@ version versionsuffix toolchain ========= =============== =============================== ``1.0.3`` ``intel/2017a`` ``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` -``1.1.0`` ``GCC/8.3.0`` +``1.1.0`` ``GCC/8.3.0``, ``GCC/9.3.0`` ========= =============== =============================== @@ -20751,6 +21166,7 @@ version versionsuffix toolchain ``0.19`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``1.0.0`` ``-Python-2.7.14`` ``intel/2018a`` ``1.0.0`` ``-Python-2.7.15`` ``foss/2018b`` +``1.1.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ================== =============================== @@ -21007,7 +21423,7 @@ version versionsuffix toolchain MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks. -*homepage*: http://drive5.com/muscle/ +*homepage*: https://drive5.com/muscle/ ============ =============== ====================================================================================================================================== version versionsuffix toolchain @@ -21245,7 +21661,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -21288,7 +21704,7 @@ version toolchain NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. -*homepage*: http://www.ks.uiuc.edu/Research/namd/ +*homepage*: https://www.ks.uiuc.edu/Research/namd/ ======== ============= ================================================================ version versionsuffix toolchain @@ -21296,7 +21712,9 @@ version versionsuffix toolchain ``2.11`` ``-mpi`` ``intel/2016a`` ``2.12`` ``-mpi`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``2.13`` ``fosscuda/2018b`` -``2.13`` ``-mpi`` ``foss/2018b``, ``intel/2018b`` +``2.13`` ``-mpi`` ``foss/2018b``, ``foss/2019b``, ``intel/2018b`` +``2.14`` ``fosscuda/2019b`` +``2.14`` ``-mpi`` ``foss/2019b``, ``foss/2020a``, ``intel/2020a`` ======== ============= ================================================================ @@ -21574,12 +21992,13 @@ Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find *homepage*: https://dev.yorhel.nl/ncdu -======== ================= -version toolchain -======== ================= -``1.13`` ``GCCcore/7.3.0`` -``1.14`` ``GCCcore/7.3.0`` -======== ================= +========== ================= +version toolchain +========== ================= +``1.13`` ``GCCcore/7.3.0`` +``1.14`` ``GCCcore/7.3.0`` +``1.15.1`` ``GCCcore/9.3.0`` +========== ================= .. _list_software_NCIPLOT_537: @@ -21608,13 +22027,13 @@ NCL is an interpreted language designed specifically for scientific data analysi *homepage*: https://www.ncl.ucar.edu -========= ================================================= -version toolchain -========= ================================================= -``6.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``6.5.0`` ``intel/2018a`` -``6.6.2`` ``foss/2018b``, ``intel/2018b``, ``intel/2019b`` -========= ================================================= +========= ================================================================= +version toolchain +========= ================================================================= +``6.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +``6.5.0`` ``intel/2018a`` +``6.6.2`` ``foss/2018b``, ``intel/2018b``, ``intel/2019b``, ``intel/2020a`` +========= ================================================================= .. _list_software_ncl_317: @@ -21640,7 +22059,7 @@ version toolchain manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 -*homepage*: http://nco.sourceforge.net +*homepage*: https://nco.sourceforge.net ========= =============================== version toolchain @@ -21653,6 +22072,7 @@ version toolchain ``4.7.6`` ``intel/2018a`` ``4.7.9`` ``foss/2018b``, ``intel/2018b`` ``4.8.1`` ``foss/2019a`` +``4.9.3`` ``gompi/2019b`` ========= =============================== @@ -21687,7 +22107,7 @@ version toolchain ``5.9`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25``, ``gimkl/2.11.5``, ``system`` ``6.0`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``6.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` -``6.2`` ``GCCcore/9.3.0`` +``6.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ======= ============================================================================================================================================================================================================================================================================================================================================================================= @@ -21700,11 +22120,11 @@ Ncview is a visual browser for netCDF format files. Typically you would use ncvi *homepage*: http://meteora.ucsd.edu/~pierce/ncview_home_page.html -========= ====================================================================================================================================================== -version toolchain -========= ====================================================================================================================================================== -``2.1.7`` ``foss/2017b``, ``gompi/2019a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b``, ``iomkl/2018b`` -========= ====================================================================================================================================================== +========= ====================================================================================================================================================================================== +version toolchain +========= ====================================================================================================================================================================================== +``2.1.7`` ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``gompi/2019a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b``, ``iomkl/2018b`` +========= ====================================================================================================================================================================================== .. _list_software_nd2reader_887: @@ -21855,7 +22275,7 @@ version versionsuffix toolchain ``4.4.4`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.4.4`` ``-HDF5-1.8.19`` ``foss/2017b``, ``intel/2017b`` ``4.4.5`` ``gompi/2019a``, ``iimpi/2019a`` -``4.5.2`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a`` +``4.5.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` ========= ================ ==================================================================================================================================================================================================================================================================================================================================== @@ -21882,6 +22302,7 @@ version versionsuffix toolchain ``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` ``1.5.2`` ``intel/2019a`` ``1.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.5.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========= ============================= =============================== @@ -22116,6 +22537,22 @@ version toolchain ========= ============================== +.. _list_software_NGLess_556: + +*NGLess* +++++++++ + +NGLess is a domain-specific language for NGS (next-generation sequencing data) processing. + +*homepage*: https://ngless.embl.de/ + +========= =================== ========== +version versionsuffix toolchain +========= =================== ========== +``1.1.1`` ``-static-Linux64`` ``system`` +========= =================== ========== + + .. _list_software_nglview_764: *nglview* @@ -22575,6 +23012,22 @@ version toolchain ========== ==================================== +.. _list_software_nsync_555: + +*nsync* ++++++++ + +nsync is a C library that exports various synchronization primitives, such as mutexes + +*homepage*: https://github.com/google/nsync + +========== ================= +version toolchain +========== ================= +``1.24.0`` ``GCCcore/8.3.0`` +========== ================= + + .. _list_software_ntCard_604: *ntCard* @@ -22793,7 +23246,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_orca_421` - :ref:`list_software_ORCA_293` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_orca_421` - :ref:`list_software_ORCA_293` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -23021,6 +23474,22 @@ version versionsuffix toolchain ========== ================= ========================================================== +.. _list_software_openCARP_728: + +*openCARP* +++++++++++ + +openCARP is an open cardiac electrophysiology simulator for in-silico experiments. + +*homepage*: https://opencarp.org + +======= ================= ============== +version versionsuffix toolchain +======= ================= ============== +``3.2`` ``-Python-3.8.2`` ``foss/2020a`` +======= ================= ============== + + .. _list_software_OpenCoarrays_1238: *OpenCoarrays* @@ -23144,6 +23613,7 @@ version versionsuffix toolchain ``6`` ``foss/2018b``, ``foss/2019b``, ``intel/2018a`` ``7`` ``foss/2019b`` ``7`` ``-20200508`` ``foss/2019b`` +``8`` ``foss/2020a`` ``v1606+`` ``foss/2018b`` ``v1612+`` ``foss/2018b`` ``v1712`` ``foss/2017b``, ``intel/2017b`` @@ -23176,6 +23646,22 @@ version versionsuffix toolchain ================ ================== ================================= +.. _list_software_OpenForceField_1381: + +*OpenForceField* +++++++++++++++++ + +Simulation and Parameter Estimation in Geophysics - A python package for simulation and gradient based parameter estimation in the context of geophysical applications. + +*homepage*: https://github.com/openforcefield/openforcefield/releases + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.7.0`` ``-Python-3.8.2`` ``intel/2020a`` +========= ================= =============== + + .. _list_software_OpenImageIO_1037: *OpenImageIO* @@ -23260,9 +23746,26 @@ version versionsuffix toolchain ========= ================= =============================== ``7.1.1`` ``-Python-3.6.3`` ``intel/2017b`` ``7.4.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``7.4.2`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================= =============================== +.. _list_software_OpenMMTools_1085: + +*OpenMMTools* ++++++++++++++ + +A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine. openmmtools is a Python library layer that sits on top of OpenMM to provide access to a variety of useful tools for building full-featured molecular simulation packages. + +*homepage*: https://github.com/choderalab/openmmtools + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``0.20.0`` ``-Python-3.8.2`` ``intel/2020a`` +========== ================= =============== + + .. _list_software_OpenMolcas_1009: *OpenMolcas* @@ -23322,11 +23825,28 @@ version versionsuffix toolchain ``4.0.0`` ``-hpcx`` ``GCC/8.2.0-2.31.1`` ``4.0.1`` ``GCC/8.3.0-2.32`` ``4.0.2`` ``GCC/9.2.0-2.32`` -``4.0.3`` ``GCC/9.3.0`` +``4.0.3`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` +``4.0.5`` ``GCC/9.3.0`` ``system`` ``GCC/system-2.29`` ========== ============= ==================================================================================================================== +.. _list_software_OpenMS_562: + +*OpenMS* +++++++++ + +As part of the deNBI Center for integrative Bioinformatics, OpenMS offers an open-source software C++ library (+ python bindings) for LC/MS data management and analyses. It provides an infrastructure for the rapid development of mass spectrometry related software as well as a rich toolset built on top of it. + +*homepage*: https://www.openms.de/ + +========= ============== +version toolchain +========= ============== +``2.4.0`` ``foss/2018b`` +========= ============== + + .. _list_software_OpenNLP_636: *OpenNLP* @@ -23515,6 +24035,7 @@ version toolchain ========= ================== ``3.8.0`` ``GNU/4.9.3-2.25`` ``3.9.0`` ``GNU/4.9.3-2.25`` +``6.5.0`` ``system`` ========= ================== @@ -23713,7 +24234,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_pip_329` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-mpi_1052` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_pip_329` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -23889,6 +24410,7 @@ version toolchain ========= ========== ``2.1.3`` ``system`` ``2.5`` ``system`` +``2.10`` ``system`` ========= ========== @@ -24088,6 +24610,7 @@ version versionsuffix toolchain ========= ================= =============== ``2.7.3`` ``-Python-3.6.3`` ``intel/2017b`` ``3.2.0`` ``-Python-3.7.4`` ``intel/2019b`` +``3.2.0`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================= =============== @@ -24186,6 +24709,7 @@ version toolchain ``0.8`` ``GNU/4.9.3-2.25`` ``0.9`` ``GCCcore/6.4.0``, ``foss/2016a`` ``0.10`` ``GCCcore/7.2.0``, ``GCCcore/8.3.0`` +``0.12`` ``GCCcore/9.3.0`` ======== ==================================== @@ -24500,6 +25024,22 @@ version toolchain ========== ========================================================== +.. _list_software_PennCNV_632: + +*PennCNV* ++++++++++ + +A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. + +*homepage*: https://penncnv.openbioinformatics.org/ + +========= ================= +version toolchain +========= ================= +``1.0.5`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_Percolator_1051: *Percolator* @@ -24545,6 +25085,7 @@ version versionsuffix toolchain ``5.28.1`` ``GCCcore/8.2.0`` ``5.30.0`` ``GCCcore/8.3.0`` ``5.30.2`` ``GCCcore/9.3.0`` +``5.32.0`` ``GCCcore/10.2.0`` ========== ============= ========================================================================================= @@ -24599,9 +25140,9 @@ version versionsuffix toolchain ``3.9.1`` ``-downloaded-deps`` ``foss/2018a`` ``3.9.3`` ``foss/2018a``, ``intel/2018a`` ``3.11.0`` ``-downloaded-deps`` ``foss/2018b`` -``3.11.1`` ``foss/2019a``, ``intel/2019a`` -``3.12.3`` ``foss/2019b`` -``3.12.4`` ``foss/2019b``, ``intel/2019b`` +``3.11.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.12.4`` ``-Python-2.7.16`` ``intel/2019b`` +``3.12.4`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.12.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ==================== =============================== @@ -25284,6 +25825,22 @@ version versionsuffix toolchain ========= ================== =================================================== +.. _list_software_plantcv_760: + +*plantcv* ++++++++++ + +PlantCV: Plant phenotyping using computer vision. + +*homepage*: https://pypi.org/project/plantcv/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``3.8.0`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_PlaScope_791: *PlaScope* @@ -25300,6 +25857,22 @@ version toolchain ========= ============== +.. _list_software_PlasmaPy_807: + +*PlasmaPy* +++++++++++ + +Open source Python ecosystem for plasma research and education + +*homepage*: https://www.plasmapy.org + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.3.1`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_PLAST_388: *PLAST* @@ -25536,7 +26109,7 @@ version toolchain ``2.2.1`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.2.3`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``3.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``3.0.2`` ``GCCcore/8.2.0`` +``3.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``3.1.4`` ``GCCcore/8.3.0`` ``3.1.5`` ``GCCcore/9.3.0`` @@ -25568,15 +26141,16 @@ version toolchain Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard -*homepage*: http://portablecl.org +*homepage*: https://portablecl.org -======= ================================ -version toolchain -======= ================================ -``1.2`` ``GCC/7.3.0-2.30`` -``1.3`` ``GCC/8.2.0-2.31.1`` -``1.4`` ``GCC/8.3.0``, ``gcccuda/2019b`` -======= ================================ +======= ======================================= +version toolchain +======= ======================================= +``1.2`` ``GCC/7.3.0-2.30`` +``1.3`` ``GCC/8.2.0-2.31.1``, ``gcccuda/2019a`` +``1.4`` ``GCC/8.3.0``, ``gcccuda/2019b`` +``1.5`` ``GCC/9.3.0`` +======= ======================================= .. _list_software_poetry_675: @@ -25656,11 +26230,12 @@ Poppler is a PDF rendering library based on the xpdf-3.0 code base. *homepage*: https://poppler.freedesktop.org/ -========== ============== -version toolchain -========== ============== -``0.70.1`` ``foss/2018b`` -========== ============== +========== ================= +version toolchain +========== ================= +``0.70.1`` ``foss/2018b`` +``0.90.1`` ``GCCcore/8.3.0`` +========== ================= .. _list_software_popscle_758: @@ -25730,6 +26305,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_Portcullis_1073: + +*Portcullis* +++++++++++++ + +Portcullis stands for PORTable CULLing of Invalid Splice junctions from pre-aligned RNA-seq data. It is known that RNAseq mapping tools generate many invalid junction predictions, particularly in deep datasets with high coverage over splice sites. In order to address this, instead for creating a new RNAseq mapper, with a focus on SJ accuracy we created a tool that takes in a BAM file generated by an RNAseq mapper of the user's own choice (e.g. Tophat2, Gsnap, STAR2 or HISAT2) as input (i.e. it's portable). It then, analyses and quantifies all splice junctions in the file before, filtering (culling) those which are unlikely to be genuine. Portcullis output's junctions in a variety of formats making it suitable for downstream analysis (such as differential splicing analysis and gene modelling) without additional work. Portcullis can also filter the original BAM file removing alignments associated with bad junctions. + +*homepage*: https://github.com/maplesond/portcullis + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.2.2`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_Postgres-XL_1064: *Postgres-XL* @@ -25767,6 +26358,7 @@ version versionsuffix toolchain ``10.3`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``11.3`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``11.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``12.4`` ``GCCcore/9.3.0`` ========= ================== ================================================================ @@ -26196,7 +26788,7 @@ version toolchain ``3.6.1`` ``GCCcore/7.3.0`` ``3.6.1.2`` ``GCCcore/8.2.0`` ``3.7.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.10.0`` ``GCCcore/8.3.0`` +``3.10.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` =========== =================================================== @@ -26225,7 +26817,7 @@ version versionsuffix toolchain ``3.4.0`` ``-Python-3.6.3`` ``intel/2017b`` ``3.6.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``3.6.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``3.10.0`` ``-Python-3.7.4`` ``foss/2019b`` +``3.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========== ================== ================================== @@ -26242,6 +26834,7 @@ Minimalistic protocol buffer decoder and encoder in C++. version toolchain ========= ================= ``1.6.8`` ``GCCcore/7.3.0`` +``1.7.0`` ``GCCcore/8.3.0`` ========= ================= @@ -26737,11 +27330,12 @@ Tools for working with the MSCOCO dataset *homepage*: https://github.com/cocodataset/cocoapi -========= ================= ================== -version versionsuffix toolchain -========= ================= ================== -``2.0.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` -========= ================= ================== +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``2.0.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.0.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========= ================= ================================== .. _list_software_pycodestyle_1205: @@ -26785,15 +27379,32 @@ version versionsuffix toolchain PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python. -*homepage*: http://mathema.tician.de/software/pycuda +*homepage*: https://mathema.tician.de/software/pycuda + +============ ============================= ======================================= +version versionsuffix toolchain +============ ============================= ======================================= +``2016.1.2`` ``-Python-2.7.12`` ``intel/2016b`` +``2017.1.1`` ``-Python-2.7.14`` ``intel/2018a`` +``2018.1`` ``-Python-3.6.4-CUDA-9.1.85`` ``intel/2018a`` +``2019.1.2`` ``-Python-3.7.4`` ``fosscuda/2019b``, ``intelcuda/2019b`` +============ ============================= ======================================= + -============ ============================= =============== -version versionsuffix toolchain -============ ============================= =============== -``2016.1.2`` ``-Python-2.7.12`` ``intel/2016b`` -``2017.1.1`` ``-Python-2.7.14`` ``intel/2018a`` -``2018.1`` ``-Python-3.6.4-CUDA-9.1.85`` ``intel/2018a`` -============ ============================= =============== +.. _list_software_PycURL_543: + +*PycURL* +++++++++ + +PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of features. + +*homepage*: http://pycurl.io/ + +============ ================= ================= +version versionsuffix toolchain +============ ================= ================= +``7.43.0.5`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +============ ================= ================= .. _list_software_PyDatastream_1231: @@ -26968,13 +27579,14 @@ version versionsuffix toolchain PyFR is an open-source Python based framework for solving advection-diffusion type problems on streaming architectures using the Flux Reconstruction approach of Huynh. The framework is designed to solve a range of governing systems on mixed unstructured grids containing various element types. It is also designed to target a range of hardware platforms via use of an in-built domain specific language derived from the Mako templating engine. -*homepage*: http://http://www.pyfr.org +*homepage*: http://www.pyfr.org -========= ============================= =============== -version versionsuffix toolchain -========= ============================= =============== -``1.7.6`` ``-Python-3.6.4-CUDA-9.1.85`` ``intel/2018a`` -========= ============================= =============== +========= ============================= =================== +version versionsuffix toolchain +========= ============================= =================== +``1.7.6`` ``-Python-3.6.4-CUDA-9.1.85`` ``intel/2018a`` +``1.9.0`` ``-Python-3.7.4`` ``intelcuda/2019b`` +========= ============================= =================== .. _list_software_pygccxml_871: @@ -26994,6 +27606,22 @@ version versionsuffix toolchain ============ ================== ============== +.. _list_software_PyGEOS_503: + +*PyGEOS* +++++++++ + +PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance improvement when operating on arrays of geometries. + +*homepage*: https://pygeos.readthedocs.io + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.7.1`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_pyGIMLi_635: *pyGIMLi* @@ -27401,12 +28029,13 @@ Python interface to PROJ4 library for cartographic transformations *homepage*: https://pyproj4.github.io/pyproj -========= ================= ================= -version versionsuffix toolchain -========= ================= ================= -``2.1.3`` ``GCCcore/8.2.0`` -``2.4.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -========= ================= ================= +=============== ================= ================= +version versionsuffix toolchain +=============== ================= ================= +``2.1.3`` ``GCCcore/8.2.0`` +``2.4.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.6.1.post1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +=============== ================= ================= .. _list_software_pyqstem_787: @@ -27601,6 +28230,22 @@ version versionsuffix toolchain ========== ================== =============== +.. _list_software_pySCENIC_670: + +*pySCENIC* +++++++++++ + +pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data. + +*homepage*: https://github.com/aertslab/pySCENIC + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``0.10.3`` ``-Python-3.8.2`` ``intel/2020a`` +========== ================= =============== + + .. _list_software_PySCF_421: *PySCF* @@ -27772,22 +28417,6 @@ version versionsuffix toolchain ========= ================== =============================== -.. _list_software_pytest-mpi_1052: - -*pytest-mpi* -++++++++++++ - -pytest_mpi is a plugin for pytest providing some useful tools when running tests under MPI, and testing MPI-related code. - -*homepage*: https://pytest-mpi.readthedocs.io - -======= ================= ================= -version versionsuffix toolchain -======= ================= ================= -``0.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -======= ================= ================= - - .. _list_software_PYTHIA_463: *PYTHIA* @@ -27970,6 +28599,7 @@ version versionsuffix toolchain ``1.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``1.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.6.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ============================= ================================== @@ -28059,7 +28689,7 @@ version versionsuffix toolchain Python bindings for ZeroMQ -*homepage*: http://www.zeromq.org/bindings:python +*homepage*: https://www.zeromq.org/bindings:python ========== ======================= =============================== version versionsuffix toolchain @@ -28076,6 +28706,7 @@ version versionsuffix toolchain ``16.0.3`` ``-Python-2.7.14-zmq4`` ``intel/2017b`` ``17.0.0`` ``-Python-2.7.14-zmq4`` ``foss/2018a`` ``17.0.0`` ``-Python-3.6.4-zmq4`` ``foss/2018a`` +``18.1.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========== ======================= =============================== @@ -28518,6 +29149,7 @@ version versionsuffix toolchain ``6.3`` ``foss/2018b``, ``intel/2018b`` ``6.4.1`` ``intel/2019a`` ``6.5`` ``intel/2019a``, ``intel/2019b`` +``6.6`` ``intel/2019b`` ========= ============= ================================ @@ -28631,7 +29263,7 @@ version versionsuffix toolchain The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. -*homepage*: http://qwt.sourceforge.net/ +*homepage*: https://qwt.sourceforge.io/ ========= ==================================================== version toolchain @@ -28639,6 +29271,7 @@ version toolchain ``6.1.2`` ``intel/2016a`` ``6.1.3`` ``foss/2016b``, ``intel/2016b`` ``6.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` +``6.1.5`` ``GCCcore/9.3.0`` ========= ==================================================== @@ -28664,7 +29297,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray_300` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_rstudio_778` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray_300` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_rstudio_778` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -28774,7 +29407,7 @@ version toolchain ``1.3.2`` ``GCCcore/8.2.0`` ``1.4.7`` ``GCCcore/8.2.0``, ``gcccuda/2019b`` ``1.4.10`` ``GCC/7.3.0-2.30`` -``1.4.13`` ``GCCcore/8.3.0`` +``1.4.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ==================================== @@ -29052,12 +29685,13 @@ RDKit is a collection of cheminformatics and machine-learning software written i *homepage*: https://www.rdkit.org -============= ================= =============== -version versionsuffix toolchain -============= ================= =============== -``2018.09.3`` ``-Python-3.6.6`` ``intel/2018b`` -``2019.09.3`` ``-Python-3.7.4`` ``foss/2019b`` -============= ================= =============== +============= ================= =============================== +version versionsuffix toolchain +============= ================= =============================== +``2018.09.3`` ``-Python-3.6.6`` ``intel/2018b`` +``2019.09.3`` ``-Python-3.7.4`` ``foss/2019b`` +``2020.03.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +============= ================= =============================== .. _list_software_RDP-Classifier_1304: @@ -29111,6 +29745,22 @@ version toolchain ======= ========== +.. _list_software_Reapr_506: + +*Reapr* ++++++++ + +A tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. + +*homepage*: https://www.sanger.ac.uk/science/tools/reapr + +========== ============== +version toolchain +========== ============== +``1.0.18`` ``foss/2019a`` +========== ============== + + .. _list_software_Red_283: *Red* @@ -29295,15 +29945,16 @@ version versionsuffix toolchain Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the 'PROJ.4' library. -*homepage*: http://rgdal.r-forge.r-project.org/ +*homepage*: https://rgdal.r-forge.r-project.org/ -========= ============= ============== -version versionsuffix toolchain -========= ============= ============== -``1.4-4`` ``-R-3.6.0`` ``foss/2019a`` -``1.4-8`` ``-R-3.6.2`` ``foss/2019b`` -``1.4-8`` ``-R-4.0.0`` ``foss/2020a`` -========= ============= ============== +========== ============= ============== +version versionsuffix toolchain +========== ============= ============== +``1.4-4`` ``-R-3.6.0`` ``foss/2019a`` +``1.4-8`` ``-R-3.6.2`` ``foss/2019b`` +``1.4-8`` ``-R-4.0.0`` ``foss/2020a`` +``1.5-16`` ``-R-4.0.0`` ``foss/2020a`` +========== ============= ============== .. _list_software_rgeos_544: @@ -29321,6 +29972,7 @@ version versionsuffix toolchain ``0.3-17`` ``-R-3.2.3`` ``intel/2016a`` ``0.5-1`` ``-R-3.6.0`` ``foss/2019a`` ``0.5-2`` ``-R-3.6.2`` ``foss/2019b`` +``0.5-5`` ``-R-4.0.0`` ``foss/2020a`` ========== ============= =============== @@ -29350,11 +30002,12 @@ Running and Analyzing OpenMM Jobs *homepage*: https://gitlab.com/Olllom/rickflow -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``0.7.0`` ``-Python-3.7.4`` ``intel/2019b`` -========= ================= =============== +================== ================= =============== +version versionsuffix toolchain +================== ================= =============== +``0.7.0`` ``-Python-3.7.4`` ``intel/2019b`` +``0.7.0-20200529`` ``-Python-3.7.4`` ``intel/2019b`` +================== ================= =============== .. _list_software_rioxarray_993: @@ -29391,6 +30044,7 @@ version versionsuffix toolchain ``4-8`` ``-R-3.5.1`` ``foss/2018b`` ``4-9`` ``-R-3.6.0`` ``foss/2019a`` ``4-10`` ``foss/2019b`` +``4-10`` ``-R-4.0.0`` ``foss/2020a`` ======== ============= =============== @@ -29542,6 +30196,22 @@ version toolchain ======= ============================== +.. _list_software_RnBeads_671: + +*RnBeads* ++++++++++ + +RnBeads is an R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution. + +*homepage*: https://rnbeads.org + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``2.6.0`` ``-R-4.0.0`` ``foss/2020a`` +========= ============= ============== + + .. _list_software_Roary_525: *Roary* @@ -29896,7 +30566,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDSL_310` - :ref:`list_software_sdsl-lite_913` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_Stata_509` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_Sumo_420` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -29986,9 +30656,9 @@ version versionsuffix toolchain *Salmon* ++++++++ -Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves its accuracy and speed via a number of different innovations, including the use of selective-alignment, and massively-parallel stochastic collapsed variational inference. +Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. -*homepage*: https://salmon.readthedocs.io +*homepage*: https://github.com/COMBINE-lab/salmon ========== ================== ================================ version versionsuffix toolchain @@ -30002,6 +30672,7 @@ version versionsuffix toolchain ``1.0.0`` ``gompi/2019a``, ``gompi/2019b`` ``1.1.0`` ``gompi/2019b`` ``1.2.0`` ``gompi/2019b`` +``1.3.0`` ``gompi/2020a`` ========== ================== ================================ @@ -30332,7 +31003,8 @@ version versionsuffix toolchain ``0.14.0`` ``-Python-3.6.4`` ``intel/2018a`` ``0.14.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``0.15.0`` ``-Python-3.7.2`` ``foss/2019a`` -``0.16.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``0.16.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``0.17.1`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================== =================================================== @@ -30372,7 +31044,7 @@ version versionsuffix toolchain ``0.20.3`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``0.20.4`` ``-Python-2.7.16`` ``intel/2019b`` ``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``0.23.1`` ``-Python-3.8.2`` ``foss/2020a`` +``0.23.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ================================= ======================================================================== @@ -30432,15 +31104,16 @@ version toolchain SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python. -*homepage*: http://www.scipy.org +*homepage*: https://www.scipy.org -========== ================== =============== -version versionsuffix toolchain -========== ================== =============== -``0.16.0`` ``-Python-2.7.12`` ``intel/2016b`` -``0.17.0`` ``-Python-2.7.11`` ``intel/2016a`` -``0.19.0`` ``-Python-3.5.2`` ``intel/2016b`` -========== ================== =============== +========== ================== ================================== +version versionsuffix toolchain +========== ================== ================================== +``0.16.0`` ``-Python-2.7.12`` ``intel/2016b`` +``0.17.0`` ``-Python-2.7.11`` ``intel/2016a`` +``0.19.0`` ``-Python-3.5.2`` ``intel/2016b`` +``1.4.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========== ================== ================================== .. _list_software_SciPy-bundle_1167: @@ -30456,8 +31129,8 @@ Bundle of Python packages for scientific software version versionsuffix toolchain =========== ================== ======================================================================== ``2019.03`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``2019.10`` ``-Python-2.7.16`` ``foss/2019b``, ``intel/2019b`` -``2019.10`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2019.10`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2019.10`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` ``2020.03`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` =========== ================== ======================================================================== @@ -30578,7 +31251,7 @@ version versionsuffix toolchain ``6.0.4`` ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``6.0.4`` ``-64bitint`` ``foss/2017b`` ``6.0.6`` ``foss/2018a``, ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2018a`` -``6.0.9`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a`` +``6.0.9`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` =================== ============= ===================================================================================================================================================== @@ -30692,27 +31365,11 @@ The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 libr *homepage*: https://github.com/simongog/sdsl-lite -================== ============= -version toolchain -================== ============= -``2.1.1-20191211`` ``GCC/8.3.0`` -================== ============= - - -.. _list_software_sdsl-lite_913: - -*sdsl-lite* -+++++++++++ - -Succinct Data Structure Library 2.0 - -*homepage*: https://github.com/simongog/sdsl-lite - -========= ================= -version toolchain -========= ================= -``2.1.1`` ``GCCcore/8.3.0`` -========= ================= +================== ================= +version toolchain +================== ================= +``2.1.1-20191211`` ``GCCcore/8.3.0`` +================== ================= .. _list_software_Seaborn_714: @@ -30786,7 +31443,7 @@ segemehl is a software to map short sequencer reads to reference genomes. Unli version toolchain ========= ================================================ ``0.2.0`` ``foss/2016b``, ``intel/2017b``, ``intel/2018a`` -``0.3.4`` ``foss/2018b`` +``0.3.4`` ``GCC/8.3.0``, ``foss/2018b`` ========= ================================================ @@ -31040,6 +31697,22 @@ version versionsuffix toolchain ============ ============= =============== +.. _list_software_sf_217: + +*sf* +++++ + +Support for simple features, a standardized way to encode spatial vector data. Binds to GDAL for reading and writing data, to GEOS for geometrical operations, and to PROJ for projection conversions and datum transformations. + +*homepage*: https://cran.r-project.org/package=sf + +========= ========================= ============== +version versionsuffix toolchain +========= ========================= ============== +``0.9-5`` ``-R-4.0.0-Python-3.8.2`` ``foss/2020a`` +========= ========================= ============== + + .. _list_software_Shannon_725: *Shannon* @@ -31135,6 +31808,7 @@ version versionsuffix toolchain ========= ================= ====================================== ``1.7.0`` ``-Python-3.7.2`` ``foss/2019a`` ``1.7.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``1.7.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` ========= ================= ====================================== @@ -31543,14 +32217,15 @@ SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software libra *homepage*: https://www.grycap.upv.es/slepc/ -========== =============================== -version toolchain -========== =============================== -``3.8.3`` ``foss/2017b`` -``3.9.2`` ``foss/2018a`` -``3.11.0`` ``foss/2018b`` -``3.12.2`` ``foss/2019b``, ``intel/2019b`` -========== =============================== +========== ================== =============================== +version versionsuffix toolchain +========== ================== =============================== +``3.8.3`` ``foss/2017b`` +``3.9.2`` ``foss/2018a`` +``3.11.0`` ``foss/2018b`` +``3.12.2`` ``-Python-2.7.16`` ``intel/2019b`` +``3.12.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +========== ================== =============================== .. _list_software_slepc4py_820: @@ -31603,6 +32278,22 @@ version versionsuffix toolchain ========== ================== =============== +.. _list_software_SLiM_341: + +*SLiM* +++++++ + +SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. + +*homepage*: https://messerlab.org/slim + +======= ============= +version toolchain +======= ============= +``3.4`` ``GCC/9.3.0`` +======= ============= + + .. _list_software_smafa_520: *smafa* @@ -31794,7 +32485,7 @@ version versionsuffix toolchain SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). -*homepage*: http://sourceforge.net/projects/snpeff/ +*homepage*: https://pcingola.github.io/SnpEff/ ======== ================== ========== version versionsuffix toolchain @@ -31802,6 +32493,7 @@ version versionsuffix toolchain ``3.6`` ``-Java-1.7.0_80`` ``system`` ``4.1d`` ``-Java-1.7.0_80`` ``system`` ``4.3t`` ``-Java-1.8`` ``system`` +``5.0`` ``-Java-13`` ``system`` ======== ================== ========== @@ -32055,6 +32747,7 @@ version versionsuffix toolchain ``2.4.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.4.0`` ``-Python-3.6.6`` ``intel/2018b`` ``2.4.5`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` +``3.0.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ========= =========================================== =============================== @@ -32063,7 +32756,7 @@ version versionsuffix toolchain *sparsehash* ++++++++++++ -An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. +An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. *homepage*: https://github.com/sparsehash/sparsehash @@ -32072,6 +32765,7 @@ version toolchain ========= ============================================================================================================================== ``2.0.2`` ``foss/2016a`` ``2.0.3`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``intel/2017a`` +``2.0.4`` ``GCCcore/9.3.0`` ========= ============================================================================================================================== @@ -32586,6 +33280,22 @@ version versionsuffix toolchain ========= ============================= ==================== +.. _list_software_stars_557: + +*stars* ++++++++ + +Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in R, using GDAL bindings provided by sf, and NetCDF bindings by ncmeta and RNetCDF. + +*homepage*: https://cran.r-project.org/package=stars + +========= ========================= ============== +version versionsuffix toolchain +========= ========================= ============== +``0.4-3`` ``-R-4.0.0-Python-3.8.2`` ``foss/2020a`` +========= ========================= ============== + + .. _list_software_Stata_509: *Stata* @@ -32624,6 +33334,7 @@ version versionsuffix toolchain ``0.9.0`` ``-Python-3.6.6`` ``intel/2018b`` ``0.10.1`` ``foss/2019a`` ``0.11.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.11.1`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================== =============================== @@ -32685,11 +33396,11 @@ The STREAM benchmark is a simple synthetic benchmark program that measures susta *homepage*: https://www.cs.virginia.edu/stream/ -======== ========================================================================== -version toolchain -======== ========================================================================== -``5.10`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``intel/2016b``, ``intel/2018b`` -======== ========================================================================== +======== ================================================================================================================== +version toolchain +======== ================================================================================================================== +``5.10`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``intel/2016b``, ``intel/2018b`` +======== ================================================================================================================== .. _list_software_strelka_758: @@ -32862,6 +33573,22 @@ version toolchain ========== ============== +.. _list_software_Sumo_420: + +*Sumo* +++++++ + +Sumo is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large road networks. + +*homepage*: https://sumo.sourceforge.net/ + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``1.3.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= + + .. _list_software_SUNDIALS_611: *SUNDIALS* @@ -33126,6 +33853,7 @@ version versionsuffix toolchain ``1.3`` ``-Python-3.6.6`` ``foss/2018b`` ``1.4`` ``foss/2019a``, ``intel/2019a`` ``1.5.1`` ``-Python-3.7.4`` ``foss/2019b`` +``1.6.2`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== =============================== @@ -33152,7 +33880,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` +:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_Trycycler_961` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` .. _list_software_tabix_536: @@ -33393,6 +34121,22 @@ version toolchain =========== ========== +.. _list_software_Telescope_932: + +*Telescope* ++++++++++++ + +Single locus resolution of Transposable ELEment expression using next-generation sequencing. + +*homepage*: https://github.com/mlbendall/telescope + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.0.3`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_tensorboardX_1275: *tensorboardX* @@ -33463,6 +34207,22 @@ version versionsuffix toolchain ========== ============================= =================================================== +.. _list_software_tensorflow-probability_2337: + +*tensorflow-probability* +++++++++++++++++++++++++ + +TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis. + +*homepage*: https://www.tensorflow.org/probability + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.9.0`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_TensorRT_801: *TensorRT* @@ -33596,10 +34356,26 @@ version toolchain ``6.4`` ``GCCcore/5.4.0`` ``6.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``6.6`` ``GCCcore/8.2.0`` -``6.7`` ``GCCcore/8.3.0`` +``6.7`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ==================================== +.. _list_software_texlive_769: + +*texlive* ++++++++++ + +TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to be a representation of the final typeset output, and so can be easily edited and manipulated. + +*homepage*: https://tug.org + +============ ================= +version toolchain +============ ================= +``20200406`` ``GCCcore/8.3.0`` +============ ================= + + .. _list_software_Text-CSV_702: *Text-CSV* @@ -33645,6 +34421,7 @@ version versionsuffix toolchain ``1.0.4`` ``-Python-3.6.4`` ``foss/2018a`` ``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` ``1.0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``1.0.4`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== =================================================== @@ -33697,6 +34474,22 @@ version toolchain ======== ================================ +.. _list_software_tidymodels_1086: + +*tidymodels* +++++++++++++ + +The tidy modeling "verse" is a collection of packages for modeling and statistical analysis that share the underlying design philosophy, grammar, and data structures of the tidyverse. + +*homepage*: https://cran.r-project.org/package=tidymodels + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``0.1.0`` ``-R-4.0.0`` ``foss/2020a`` +========= ============= ============== + + .. _list_software_Tika_393: *Tika* @@ -33754,12 +34547,13 @@ version toolchain The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. -*homepage*: http://dasher.wustl.edu/tinker +*homepage*: https://dasher.wustl.edu/tinker ========= ============== version toolchain ========= ============== ``8.6.1`` ``foss/2018b`` +``8.7.2`` ``foss/2019b`` ========= ============== @@ -34012,7 +34806,7 @@ version versionsuffix toolchain *tqdm* ++++++ -Instantly make your loops show a smart progress meter. +A fast, extensible progress bar for Python and CLI *homepage*: https://github.com/tqdm/tqdm @@ -34025,6 +34819,7 @@ version versionsuffix toolchain ``4.32.1`` ``GCCcore/8.2.0`` ``4.41.1`` ``GCCcore/8.3.0`` ``4.41.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``4.47.0`` ``GCCcore/9.3.0`` ========== ================== =============================== @@ -34345,6 +35140,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_Trycycler_961: + +*Trycycler* ++++++++++++ + +Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes. + +*homepage*: https://github.com/rrwick/Trycycler + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.3.3`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_TurboVNC_755: *TurboVNC* @@ -34451,7 +35262,7 @@ version versionsuffix toolchain --- -:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` +:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` .. _list_software_UCLUST_480: @@ -34561,6 +35372,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_umi4cPackage_1166: + +*umi4cPackage* +++++++++++++++ + +umi4cPackage is a processing and analysis pipeline for UMI-4C experiment. + +*homepage*: https://github.com/tanaylab/umi4cpackage + +============ ============= ============== +version versionsuffix toolchain +============ ============= ============== +``20200116`` ``-R-4.0.0`` ``foss/2020a`` +============ ============= ============== + + .. _list_software_umis_446: *umis* @@ -34600,13 +35427,14 @@ version versionsuffix toolchain Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. -*homepage*: +*homepage*: https://github.com/rrwick/Unicycler -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``0.4.7`` ``-Python-3.7.2`` ``foss/2019a`` -========= ================= ============== +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.4.7`` ``-Python-3.7.2`` ``foss/2019a`` +``0.4.8`` ``-Python-3.8.2`` ``gompi/2020a`` +========= ================= =============== .. _list_software_Unidecode_912: @@ -34793,7 +35621,7 @@ version toolchain --- -:ref:`list_software_V8_142` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_VarDict_685` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VMD_231` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` +:ref:`list_software_V8_142` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VMD_231` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` .. _list_software_V8_142: @@ -34864,6 +35692,22 @@ version versionsuffix toolchain ========= ================ ============== +.. _list_software_variant_tools_1413: + +*variant_tools* ++++++++++++++++ + +Variant tools is a software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analysis. Unlike some other tools used for Next-Gen sequencing analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants. + +*homepage*: https://vatlab.github.io/vat-docs/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``3.1.3`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_VariantMetaCaller_1711: *VariantMetaCaller* @@ -35162,15 +36006,16 @@ version toolchain VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. -*homepage*: http://www.ks.uiuc.edu/Research/vmd +*homepage*: https://www.ks.uiuc.edu/Research/vmd -========= ================== =============================== -version versionsuffix toolchain -========= ================== =============================== -``1.9.3`` ``-Python-2.7.12`` ``intel/2016b`` -``1.9.3`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2018a`` -``1.9.3`` ``-Python-2.7.15`` ``intel/2018b`` -========= ================== =============================== +============ ================== =============================== +version versionsuffix toolchain +============ ================== =============================== +``1.9.3`` ``-Python-2.7.12`` ``intel/2016b`` +``1.9.3`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2018a`` +``1.9.3`` ``-Python-2.7.15`` ``intel/2018b`` +``1.9.4a43`` ``-Python-3.7.4`` ``fosscuda/2019b`` +============ ================== =============================== .. _list_software_Voro++_508: @@ -35748,7 +36593,7 @@ version versionsuffix toolchain ``3.8.0`` ``-dmpar`` ``intel/2016a``, ``intel/2016b`` ``4.0.1`` ``-dmpar`` ``intel/2018b`` ``4.0.2`` ``-dmpar`` ``foss/2018b`` -``4.1.3`` ``-dmpar`` ``intel/2019b`` +``4.1.3`` ``-dmpar`` ``foss/2019b``, ``intel/2019b`` ========= ============= ================================ @@ -36156,13 +37001,13 @@ Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerce *homepage*: https://xerces.apache.org/xerces-c/ -========= ================= -version toolchain -========= ================= -``3.1.4`` ``GCCcore/6.4.0`` -``3.2.0`` ``GCCcore/7.3.0`` -``3.2.2`` ``GCCcore/8.2.0`` -========= ================= +========= ==================================== +version toolchain +========= ==================================== +``3.1.4`` ``GCCcore/6.4.0`` +``3.2.0`` ``GCCcore/7.3.0`` +``3.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ==================================== .. _list_software_xextproto_1021: @@ -36438,13 +37283,13 @@ X protocol and ancillary headers *homepage*: https://www.freedesktop.org/wiki/Software/xlibs -========== ========================================================================== -version toolchain -========== ========================================================================== -``7.0.28`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``7.0.29`` ``intel/2016a`` -``7.0.31`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` -========== ========================================================================== +========== ============================================================================================= +version toolchain +========== ============================================================================================= +``7.0.28`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``7.0.29`` ``intel/2016a`` +``7.0.31`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ============================================================================================= .. _list_software_XSD_239: @@ -36743,11 +37588,11 @@ Zip is a compression and file packaging/archive utility. Although highly compati *homepage*: http://www.info-zip.org/Zip.html -======= ==================================== -version toolchain -======= ==================================== -``3.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -======= ==================================== +======= ======================================================= +version toolchain +======= ======================================================= +``3.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ======================================================= .. _list_software_zlib_433: @@ -36765,7 +37610,7 @@ version toolchain ``1.2.7`` ``GCC/4.8.1``, ``GCC/4.8.2`` ``1.2.8`` ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.2.10`` ``system`` -``1.2.11`` ``GCCcore/10.1.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` +``1.2.11`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index 9566efcf..dc2d1a68 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -59,6 +59,7 @@ * CMakePythonPackage * EB_DOLFIN + * EB_pybind11 * EB_UFC * EB_Armadillo @@ -246,6 +247,7 @@ * CMakePythonPackage * EB_DOLFIN + * EB_pybind11 * EB_UFC * ConfigureMakePythonPackage @@ -258,6 +260,7 @@ * EB_numexpr * EB_PyQuante * EB_python_minus_meep + * EB_PyTorch * EB_PyZMQ * EB_SEPP * EB_TensorFlow @@ -371,6 +374,7 @@ * CMakePythonPackage * EB_DOLFIN + * EB_pybind11 * EB_UFC * ConfigureMakePythonPackage @@ -383,6 +387,7 @@ * EB_numexpr * EB_PyQuante * EB_python_minus_meep + * EB_PyTorch * EB_PyZMQ * EB_SEPP * EB_TensorFlow diff --git a/docs/version-specific/easyconfig_parameters.rst b/docs/version-specific/easyconfig_parameters.rst index bcb981c5..c7bf2d89 100644 --- a/docs/version-specific/easyconfig_parameters.rst +++ b/docs/version-specific/easyconfig_parameters.rst @@ -38,44 +38,45 @@ toolchain parameters build parameters ---------------- -========================== ===================================================================================================================== ================= -**Parameter name** **Description** **Default value** -========================== ===================================================================================================================== ================= -``bitbucket_account`` Bitbucket account name to be used to resolve template values in source URLs "%(namelower)s" -``buildopts`` Extra options passed to make step (default already has -j X) "" -``checksums`` Checksums for sources and patches [] -``configopts`` Extra options passed to configure (default already has --prefix) "" -``easyblock`` EasyBlock to use for building; if set to None, an easyblock is selected based on the software name None -``easybuild_version`` EasyBuild-version this spec-file was written for None -``enhance_sanity_check`` Indicate that additional sanity check commands & paths should enhance the existin sanity check, not replace it False -``fix_perl_shebang_for`` List of files for which Perl shebang should be fixed to '#!/usr/bin/env perl' (glob patterns supported) None -``fix_python_shebang_for`` List of files for which Python shebang should be fixed to '#!/usr/bin/env python' (glob patterns supported) None -``github_account`` GitHub account name to be used to resolve template values in source URLs "%(namelower)s" -``hidden`` Install module file as 'hidden' by prefixing its version with '.' False -``installopts`` Extra options for installation "" -``maxparallel`` Max degree of parallelism None -``parallel`` Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit) None -``patches`` List of patches to apply [] -``postinstallcmds`` Commands to run after the install step. [] -``prebuildopts`` Extra options pre-passed to build command. "" -``preconfigopts`` Extra options pre-passed to configure. "" -``preinstallopts`` Extra prefix options for installation. "" -``pretestopts`` Extra prefix options for test. "" -``runtest`` Indicates if a test should be run after make; should specify argument after make (for e.g.,"test" for make test) None -``sanity_check_commands`` format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h') [] -``sanity_check_paths`` List of files and directories to check (format: {'files':, 'dirs':}) {} -``skip`` Skip existing software False -``skipsteps`` Skip these steps [] -``source_urls`` List of URLs for source files [] -``sources`` List of source files [] -``stop`` Keyword to halt the build process after a certain step. None -``testopts`` Extra options for test. "" -``tests`` List of test-scripts to run after install. A test script should return a non-zero exit status to fail [] -``unpack_options`` Extra options for unpacking source "" -``unwanted_env_vars`` List of environment variables that shouldn't be set during build [] -``versionprefix`` Additional prefix for software version (placed before version and toolchain name) "" -``versionsuffix`` Additional suffix for software version (placed after toolchain name) "" -========================== ===================================================================================================================== ================= +============================= ===================================================================================================================== ================= +**Parameter name** **Description** **Default value** +============================= ===================================================================================================================== ================= +``bitbucket_account`` Bitbucket account name to be used to resolve template values in source URLs "%(namelower)s" +``buildopts`` Extra options passed to make step (default already has -j X) "" +``checksums`` Checksums for sources and patches [] +``configopts`` Extra options passed to configure (default already has --prefix) "" +``cuda_compute_capabilities`` List of CUDA compute capabilities to build with (if supported) [] +``easyblock`` EasyBlock to use for building; if set to None, an easyblock is selected based on the software name None +``easybuild_version`` EasyBuild-version this spec-file was written for None +``enhance_sanity_check`` Indicate that additional sanity check commands & paths should enhance the existin sanity check, not replace it False +``fix_perl_shebang_for`` List of files for which Perl shebang should be fixed to '#!/usr/bin/env perl' (glob patterns supported) None +``fix_python_shebang_for`` List of files for which Python shebang should be fixed to '#!/usr/bin/env python' (glob patterns supported) None +``github_account`` GitHub account name to be used to resolve template values in source URLs "%(namelower)s" +``hidden`` Install module file as 'hidden' by prefixing its version with '.' False +``installopts`` Extra options for installation "" +``maxparallel`` Max degree of parallelism None +``parallel`` Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit) None +``patches`` List of patches to apply [] +``postinstallcmds`` Commands to run after the install step. [] +``prebuildopts`` Extra options pre-passed to build command. "" +``preconfigopts`` Extra options pre-passed to configure. "" +``preinstallopts`` Extra prefix options for installation. "" +``pretestopts`` Extra prefix options for test. "" +``runtest`` Indicates if a test should be run after make; should specify argument after make (for e.g.,"test" for make test) None +``sanity_check_commands`` format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h') [] +``sanity_check_paths`` List of files and directories to check (format: {'files':, 'dirs':}) {} +``skip`` Skip existing software False +``skipsteps`` Skip these steps [] +``source_urls`` List of URLs for source files [] +``sources`` List of source files [] +``stop`` Keyword to halt the build process after a certain step. None +``testopts`` Extra options for test. "" +``tests`` List of test-scripts to run after install. A test script should return a non-zero exit status to fail [] +``unpack_options`` Extra options for unpacking source "" +``unwanted_env_vars`` List of environment variables that shouldn't be set during build [] +``versionprefix`` Additional prefix for software version (placed before version and toolchain name) "" +``versionsuffix`` Additional suffix for software version (placed after toolchain name) "" +============================= ===================================================================================================================== ================= file-management parameters diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index ff0d7f4f..f13ff7d6 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -187,6 +187,7 @@ easyconfig parameter description ``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``configure_cmd`` Configure command to use ``"cmake"`` ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``generator`` Build file generator to use. None to use CMakes default ``None`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``install_cmd`` Build command to use ``"make install"`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` @@ -262,6 +263,7 @@ easyconfig parameter description ``configure_cmd`` Configure command to use ``"cmake"`` ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``files_to_copy`` List of files or dirs to copy ``None`` +``generator`` Build file generator to use. None to use CMakes default ``None`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``install_cmd`` Build command to use ``"make install"`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` @@ -298,6 +300,7 @@ easyconfig parameter description ``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``configure_cmd`` Configure command to use ``"cmake"`` ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``generator`` Build file generator to use. None to use CMakes default ``"Ninja"`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``install_cmd`` Build command to use ``"make install"`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` @@ -324,7 +327,7 @@ Build a Python package and module with cmake. Some packages use cmake to first build and install C Python packages and then put the Python package in lib/pythonX.Y/site-packages. - We install this in a seperate location and generate a module file + We install this in a seperate location and generate a module file which sets the PYTHONPATH. We use the default CMake implementation, and use make_module_extra from PythonPackage. @@ -345,6 +348,7 @@ easyconfig parameter description ``configure_cmd`` Configure command to use ``"cmake"`` ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``generator`` Build file generator to use. None to use CMakes default ``None`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``install_cmd`` Build command to use ``"make install"`` ``install_target`` Option to pass to setup.py ``"install"`` @@ -364,6 +368,7 @@ easyconfig parameter description ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` ======================== ================================================================================================================================================================================================== ================== @@ -554,6 +559,7 @@ easyconfig parameter description ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` ======================== =================================================================================================================================================================================================== ================== @@ -653,6 +659,7 @@ easyconfig parameter description ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` ======================== ========================================================================================================= ============= @@ -948,6 +955,7 @@ easyconfig parameter description ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` =========================== ========================================================================================================= ============= @@ -983,6 +991,7 @@ easyconfig parameter description ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` ======================== ========================================================================================================= ============= @@ -1281,6 +1290,7 @@ easyconfig parameter description ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` ======================== ========================================================================================================= ============= @@ -1316,6 +1326,7 @@ easyconfig parameter description ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` ``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` ``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` ======================== ========================================================================================================= ============= diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index 40e86b30..642bc91d 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -275,6 +275,7 @@ Option flag Opt ``--filter-env-vars=FILTER-ENV-VARS`` List of names of environment variables that should *not* be defined/updated by module files generated by EasyBuild (type comma-separated list) ``--fixed-installdir-naming-scheme`` Use fixed naming scheme for installation directories (default: True; disable with --disable-fixed-installdir-naming-scheme) ``--force-download=FORCE-DOWNLOAD`` Force re-downloading of sources and/or patches, even if they are available already in source path (type choice; default: sources) (choices: all, patches, sources) +``--generate-devel-module`` Generate a develop module file, implies --force if disabled (default: True; disable with --disable-generate-devel-module) ``--group=GROUP`` Group to be used for software installations (only verified, not set) ``--group-writable-installdir`` Enable group write permissions on installation directory after installation (default: False) ``--hidden`` Install 'hidden' module file(s) by prefixing their version with '.' (default: False) @@ -284,7 +285,9 @@ Option flag Opt ``--ignore-osdeps`` Ignore any listed OS dependencies (default: False) ``--install-latest-eb-release`` Install latest known version of easybuild (default: False) ``--lib64-fallback-sanity-check`` Fallback in sanity check to lib64/ equivalent for missing libraries (default: True; disable with --disable-lib64-fallback-sanity-check) +``--lib64-lib-symlink`` Automatically create symlinks for lib64/ pointing to lib/ if the former is missing (default: True; disable with --disable-lib64-lib-symlink) ``--max-fail-ratio-adjust-permissions=MAX-FAIL-RATIO-ADJUST-PERMISSIONS`` Maximum ratio for failures to allow when adjusting permissions (type float; default: 0.5) +``--minimal-build-env=MINIMAL-BUILD-ENV`` Minimal build environment to define when using system toolchain, specified as a comma-separated list that defines a mapping between name of environment variable and its value separated by a colon (':') (default: CC:gcc,CXX:g++) ``--minimal-toolchains`` Use minimal toolchain when resolving dependencies (default: False) ``--module-only`` Only generate module file(s); skip all steps except for module, prepare, ready, postiter, sanitycheck (default: False) ``--modules-tool-version-check`` Check version of modules tool being used (default: True; disable with --disable-modules-tool-version-check) @@ -304,6 +307,7 @@ Option flag Opt ``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` Silence specified deprecation warnings (type comma-separated list) ``-t, --skip-test-cases`` Skip running test cases (default: False) ``--sticky-bit`` Set sticky bit on newly created directories (default: False) +``--sysroot=SYSROOT`` Location root directory of system, prefix for standard paths like /usr/lib and /usr/include ``-T, --trace`` Provide more information in output to stdout on progress (default: False) ``--umask=UMASK`` umask to use (e.g. '022'); non-user write permissions on install directories are removed ``--update-modules-tool-cache`` Update modules tool cache file(s) after generating module file (default: False) From 28c694c198475affecdf1b98e33ece5d712ebdca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Sep 2020 10:24:38 +0200 Subject: [PATCH 077/286] fix easyblock/easyconfig/software counts in EasyBuild v4.3.0 release notes --- docs/Release_notes.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 12f439fe..98d9b5d9 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,9 +3,9 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,013** different software packages, -including 31 different (compiler) toolchains. It contains 222 software-specific easyblocks and 37 generic easyblocks, -alongside 10,147 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,059** different software packages, +including 31 different (compiler) toolchains. It contains 224 software-specific easyblocks and 37 generic easyblocks, +alongside 10,384 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. From cf8671c51cf9e905f7beb1a76007881a842353f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Sep 2020 10:55:25 +0200 Subject: [PATCH 078/286] add missing links for new software supported in EasyBuild v4.3.0 --- docs/Release_notes.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 98d9b5d9..1e793f6e 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -131,12 +131,12 @@ feature release * added example easyconfig files for 49 new software packages: * almosthere (`#11152 `_), arcasHLA (`#10867 `_), BioPP (`#11113 `_), Bracken (`#10829 `_), BUFRLIB (`#11140 `_), Calib (`#11111 `_), - CellRanger-ATAC (`#11186 `_), edlib (#10470, `#11246 `_), flatbuffers (`#11109 `_), gengetopt (`#11117 `_), graphite2 (`#11168 `_), + CellRanger-ATAC (`#11186 `_), edlib (`#10470 `_, `#11246 `_), flatbuffers (`#11109 `_), gengetopt (`#11117 `_), graphite2 (`#11168 `_), HeFFTe (`#10990 `_), hierfstat (`#11249 `_), immunedeconv (`#11136 `_), ioapi (`#10959 `_), itpp (`#10958 `_), LiBis (`#11059 `_), - libosmium (`#11024 `_), limix-bgen (`#11152 `_), minibar (#10470, `#11246 `_), misha (`#11127 `_), MOABS (`#10747 `_), moonjit (`#11163 `_), + libosmium (`#11024 `_), limix-bgen (`#11152 `_), minibar (`#10470 `_, `#11246 `_), misha (`#11127 `_), MOABS (`#10747 `_), moonjit (`#11163 `_), NGLess (`#11128 `_), nsync (`#11109 `_), openCARP (`#11117 `_), OpenForceField (`#11048 `_), OpenMMTools (`#11046 `_), OpenMS (`#10994 `_), PennCNV (`#10986 `_), plantcv (`#10968 `_), PlasmaPy (`#10732 `_), Portcullis (`#11038 `_), PycURL (`#11169 `_), PyGEOS (`#11110 `_), - pySCENIC (`#11115 `_), Reapr (`#9296 `_), RnBeads (`#11142 `_), sf (`#11248 `_), SLiM (`#11172 `_), stars (#11215, `#11248 `_), Sumo (`#11071 `_), + pySCENIC (`#11115 `_), Reapr (`#9296 `_), RnBeads (`#11142 `_), sf (`#11248 `_), SLiM (`#11172 `_), stars (`#11215 `_, `#11248 `_), Sumo (`#11071 `_), Telescope (`#10943 `_), tensorflow-probability (`#10312 `_), texlive (`#11168 `_), tidymodels (`#11010 `_), Trycycler (`#11207 `_), umi4cPackage (`#11127 `_), variant_tools (`#11169 `_) From d7473649f51810eb19cc2f8e3f0c385e11d5aae6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Sep 2020 11:13:02 +0200 Subject: [PATCH 079/286] add more missing links + minor formatting fixes in EasyBuild v4.3.0 release notes --- docs/Release_notes.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 1e793f6e..5efd9df8 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -193,15 +193,15 @@ feature release * add missing pkg-config build dependency in recent R-bundle-Bioconductor easyconfigs (`#11104 `_) * add patch to h5py 2.8.0 (`#11119 `_) and 2.9.0 (`#11118 `_) easyconfigs to avoid MPI_Init on ``import h5py`` * add patch to support libbfd 2.34 API change in Score-P 6.0 (`#11123 `_) - * use pip to install protobuf-python in 2019b toolchain (requires re-downloading source tarball!) (#11143, `#11260 `_) - * add missing Keras-Applications extension to TensorFlow 2.2.0 easyconfigs with foss*/2019b toolchain (`#11156 `_) + * use pip to install protobuf-python in 2019b toolchain (requires re-downloading source tarball!) (`#11143 `_, `#11260 `_) + * add missing Keras-Applications extension to TensorFlow 2.2.0 easyconfigs with ``foss*/2019b`` toolchain (`#11156 `_) * add missing pocl dependency in R 3.6.0 (`#11157 `_) * update Meson build dep to 0.55.1 for GLib, X11, Mesa & co to fix aggressive RPATH stripping (`#11178 `_) * disable generating of man pages in recent libdrm easyconfigs to avoid installation failure if docbook-xsl is not installed (`#11182 `_) - * add fontconfig and bzip2 as direct dependencies for Qt5 to fix installation with --rpath (`#11183 `_) + * add fontconfig and bzip2 as direct dependencies for Qt5 to fix installation with ``--rpath`` (`#11183 `_) * fix failing ``make check`` for MPFR 4.x (`#11187 `_) and GMP (`#11188 `_) when installing with ``eb --rpath`` * add pkg-config as a build dependency for libglvnd (`#11189 `_) - * add missing libiconv build dep in recent Doxygen easyconfigs (`#11191 `_, `#11257 `_) + * add missing libiconv dep in recent Doxygen easyconfigs (`#11191 `_, `#11257 `_) * enhance Java/11 wrapper to also support for aarch64/Arm (`#11192 `_) * add pkg-config as a build dependency to Ghostscript 9.52, needed on aarch64/arm (`#11194 `_) * add patch for pycrypto extension in recent Python easyconfigs to remove hardcoded ``/usr/include`` which causes problems when ``eb --sysroot`` is used (`#11202 `_) @@ -210,7 +210,7 @@ feature release * other changes: - * don't require custom sanity_check_paths for CUDA bundle easyconfigs (`#10936 `_) + * don't require custom ``sanity_check_paths`` for CUDA bundle easyconfigs (`#10936 `_) * move intervaltree and sortedcontainers to main Python easyconfigs (`#10969 `_, `#10970 `_) * disable qtwayland in Qt5 v5.14.1 (`#11107 `_) * remove mklml (small MKL) from PyTorch 1.3.1 and 1.4.0 easyconfigs (`#11019 `_) From 8e7b2f8c2b375f1ab4447c47705b89357890c883 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Sep 2020 11:35:51 +0200 Subject: [PATCH 080/286] bump version to 4.3.0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 8218c5c2..b09fdf57 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.2.2' +VERSION = '4.3.0' # Utility function to read README file From d8d6ff5342beb73300a8687f10505aca158e08a9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 23 Oct 2020 17:31:04 +0200 Subject: [PATCH 081/286] Fix order of index arguments --- docs/Easyconfigs_index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Easyconfigs_index.rst b/docs/Easyconfigs_index.rst index 333c9dd0..3d131b40 100644 --- a/docs/Easyconfigs_index.rst +++ b/docs/Easyconfigs_index.rst @@ -137,7 +137,7 @@ By default, EasyBuild will consider index files to remain valid for 1 week (7 * To create an index that *always* remains valid (never expires), use zero (``0``) as value for ``--index-max-age``:: - $ eb --create-index --index-max-age=0 $HOME/easybuild-easyconfigs/easybuild/easyconfigs + $ eb --index-max-age=0 --create-index $HOME/easybuild-easyconfigs/easybuild/easyconfigs $ head -n 2 $HOME/easybuild-easyconfigs/easybuild/easyconfigs/.eb-path-index # created at: 2020-04-13 15:10:07.173191 From 842af8fcd24fc33f7ad076d9874e4914fd082db7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Oct 2020 22:03:18 +0100 Subject: [PATCH 082/286] auto-update docs for EasyBuild v4.3.1 --- docs/version-specific/Supported_software.rst | 3105 ++++++++++++----- .../config_file_constants.rst | 2 +- docs/version-specific/easyblocks.rst | 6 +- .../version-specific/easyconfig_constants.rst | 4 +- docs/version-specific/generic_easyblocks.rst | 11 +- docs/version-specific/help.rst | 2 +- docs/version-specific/toolchain_opts.rst | 39 +- docs/version-specific/toolchains.rst | 1 + 8 files changed, 2292 insertions(+), 878 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index a5abf6b4..0c7f0b63 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2059 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2133 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -93,9 +93,9 @@ version versionsuffix toolchain *ABINIT* ++++++++ -ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. +ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. -*homepage*: http://www.abinit.org/ +*homepage*: https://www.abinit.org/ ========== ======================== =============================== version versionsuffix toolchain @@ -112,6 +112,7 @@ version versionsuffix toolchain ``8.6.3`` ``intel/2018a`` ``8.10.2`` ``intel/2018b`` ``8.10.3`` ``intel/2018b`` +``9.2.1`` ``intel/2020a`` ========== ======================== =============================== @@ -128,6 +129,7 @@ Assembly Based ReAligner version toolchain ======== ======================= ``2.22`` ``iccifort/2019.5.281`` +``2.23`` ``GCC/9.3.0`` ======== ======================= @@ -209,11 +211,11 @@ ACTC converts independent triangles into triangle strips or fans. *homepage*: https://sourceforge.net/projects/actc -======= ======================================================================== -version toolchain -======= ======================================================================== -``1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``intel/2016b`` -======= ======================================================================== +======= =========================================================================================== +version toolchain +======= =========================================================================================== +``1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2016b`` +======= =========================================================================================== .. _list_software_ada_294: @@ -654,11 +656,12 @@ AmberTools consists of several independently developed packages that work well b *homepage*: http://ambermd.org/ -======= ================================ -version toolchain -======= ================================ -``17`` ``intel/2017b``, ``intel/2018a`` -======= ================================ +======= ================== ================================ +version versionsuffix toolchain +======= ================== ================================ +``17`` ``intel/2017b``, ``intel/2018a`` +``17`` ``-Python-2.7.14`` ``foss/2018a`` +======= ================== ================================ .. _list_software_AMD-LibM_611: @@ -805,6 +808,7 @@ version toolchain ``2019.07`` ``system`` ``2019.10`` ``system`` ``2020.02`` ``system`` +``2020.07`` ``system`` =========== ========== @@ -1074,14 +1078,14 @@ version versionsuffix toolchain Apache Portable Runtime (APR) libraries. -*homepage*: http://apr.apache.org/ +*homepage*: https://apr.apache.org/ -========= ===================================================== -version toolchain -========= ===================================================== -``1.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``iomkl/2018a`` -``1.7.0`` ``GCCcore/8.2.0`` -========= ===================================================== +========= ======================================================== +version toolchain +========= ======================================================== +``1.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``iomkl/2018a`` +``1.7.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +========= ======================================================== .. _list_software_APR-util_718: @@ -1093,11 +1097,11 @@ Apache Portable Runtime (APR) util libraries. *homepage*: http://apr.apache.org/ -========= ======================================================================== -version toolchain -========= ======================================================================== -``1.6.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``iomkl/2018a`` -========= ======================================================================== +========= =============================================================================================================== +version toolchain +========= =============================================================================================================== +``1.6.1`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``iomkl/2018a`` +========= =============================================================================================================== .. _list_software_ARAGORN_522: @@ -1474,6 +1478,8 @@ version versionsuffix toolchain ``3.18.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``3.19.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``3.20.1`` ``-Python-3.8.2`` ``intel/2020a`` ============== ================== =================================================== @@ -1574,7 +1580,7 @@ version versionsuffix toolchain ``2.0.12`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.0.14`` ``foss/2019a`` ``4.0.1`` ``-Python-3.7.4`` ``foss/2019b`` -``4.0.1`` ``-Python-3.8.2`` ``foss/2020a`` +``4.0.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ================== =============================== @@ -1594,6 +1600,7 @@ version toolchain ``2.32.0`` ``GCCcore/8.2.0`` ``2.34.1`` ``GCCcore/8.3.0`` ``2.34.2`` ``GCCcore/9.3.0`` +``2.38.0`` ``GCCcore/10.2.0`` ========== ================== @@ -1613,6 +1620,7 @@ version toolchain ``2.32.0`` ``GCCcore/8.2.0`` ``2.34.0`` ``GCCcore/8.3.0`` ``2.36.0`` ``GCCcore/9.3.0`` +``2.38.0`` ``GCCcore/10.2.0`` ========== ================== @@ -1637,7 +1645,7 @@ version toolchain ``2.28.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a`` ``2.32.0`` ``GCCcore/8.2.0`` ``2.34.1`` ``GCCcore/8.3.0`` -``2.36.0`` ``GCCcore/9.3.0`` +``2.36.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========== =================================================================== @@ -1805,12 +1813,12 @@ Autoconf is an extensible package of M4 macros that produce shell scripts to au *homepage*: http://www.gnu.org/software/autoconf/ -======== ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= -version toolchain -======== ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= -``2.68`` ``foss/2016b`` -``2.69`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -======== ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +version toolchain +======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +``2.68`` ``foss/2016b`` +``2.69`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= .. _list_software_Autoconf-archive_1614: @@ -1893,8 +1901,9 @@ version toolchain ``1.14`` ``GCC/4.8.2``, ``intel/2016a`` ``1.14.1`` ``GCC/4.8.2`` ``1.15`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.15.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` +``1.15.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ``1.16.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``1.16.2`` ``GCCcore/10.2.0`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -1946,6 +1955,7 @@ version toolchain ``20150215`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``20170619`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` ``20180311`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``20200321`` ``GCCcore/10.2.0`` ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -1966,6 +1976,7 @@ version versionsuffix toolchain ``1.16.290`` ``-Python-3.6.6`` ``foss/2018b`` ``1.17.7`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``1.18.89`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``2.0.55`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ============ ================== ================= @@ -1975,7 +1986,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` +:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` .. _list_software_Bader_478: @@ -2020,11 +2031,11 @@ Count DNA sequence reads in BAM files *homepage*: https://github.com/genome/bam-readcount -========= ============== -version toolchain -========= ============== -``0.8.0`` ``foss/2018b`` -========= ============== +========= ============================= +version toolchain +========= ============================= +``0.8.0`` ``GCC/9.3.0``, ``foss/2018b`` +========= ============================= .. _list_software_BAMM_285: @@ -2304,6 +2315,7 @@ version toolchain ``1.1.0`` ``GCCcore/8.3.0`` ``2.0.0`` ``GCCcore/8.3.0`` ``3.4.1`` ``GCCcore/8.3.0`` +``3.6.0`` ``GCCcore/9.3.0`` ========== ==================================== @@ -2421,7 +2433,9 @@ Samtools is a suite of programs for interacting with high-throughput sequencing version toolchain ========== ========================================================================================= ``1.3`` ``foss/2016a``, ``intel/2016a`` +``1.3.1`` ``foss/2016b`` ``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` +``1.8`` ``GCC/6.4.0-2.28`` ``1.9`` ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ========== ========================================================================================= @@ -2492,6 +2506,7 @@ The bdbag utilities are a collection of software programs for working with BagIt version versionsuffix toolchain ========= ================== =============== ``1.4.1`` ``-Python-2.7.14`` ``intel/2018a`` +``1.4.1`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================== =============== @@ -2913,6 +2928,7 @@ version versionsuffix toolchain ``1.74`` ``foss/2019a`` ``1.75`` ``-Python-2.7.16`` ``foss/2019b`` ``1.75`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``1.78`` ``-Python-3.8.2`` ``intel/2020a`` ======== ================== =================================================== @@ -3057,6 +3073,7 @@ version versionsuffix toolchain ``2.2.26`` ``-Linux_x86_64`` ``system`` ``2.8.1`` ``-Linux_x86_64`` ``system`` ``2.10.0`` ``-Linux_x86_64`` ``system`` +``2.10.1`` ``-Linux_x86_64`` ``system`` ========== ================= ========== @@ -3081,7 +3098,7 @@ version versionsuffix toolchain ``2.7.1`` ``-Python-2.7.14`` ``intel/2017b`` ``2.8.1`` ``foss/2018b`` ``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a``, ``iimpi/2019b`` -``2.10.1`` ``gompi/2020a`` +``2.10.1`` ``gompi/2020a``, ``iimpi/2020a`` ========== ================== ================================================================== @@ -3094,11 +3111,11 @@ BLAT on DNA is designed to quickly find sequences of 95% and greater similarity *homepage*: http://genome.ucsc.edu/FAQ/FAQblat.html -======= ===================================================================================================== -version toolchain -======= ===================================================================================================== -``3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a`` -======= ===================================================================================================== +======= ==================================================================================================================== +version toolchain +======= ==================================================================================================================== +``3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a`` +======= ==================================================================================================================== .. _list_software_Blender_700: @@ -3400,7 +3417,7 @@ Boost.Python is a C++ library which enables seamless interoperability between C+ version versionsuffix toolchain ========== ================== ==================================================================== ``1.64.0`` ``gompi/2019a``, ``gompic/2019a`` -``1.65.1`` ``-Python-2.7.14`` ``intel/2017b`` +``1.65.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.66.0`` ``-Python-2.7.14`` ``intel/2018a`` ``1.66.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.67.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` @@ -3424,6 +3441,7 @@ Fast NumPy array functions written in C version versionsuffix toolchain ========= ================= =============== ``1.2.1`` ``-Python-3.6.4`` ``intel/2018a`` +``1.3.2`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= =============== @@ -3597,6 +3615,7 @@ breseq is a computational pipeline for the analysis of short-read re-sequencing version versionsuffix toolchain ========== ============= =============== ``0.35.0`` ``-R-3.6.0`` ``intel/2019a`` +``0.35.4`` ``-R-4.0.0`` ``foss/2020a`` ========== ============= =============== @@ -3633,6 +3652,23 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_Bsoft_510: + +*Bsoft* ++++++++ + +Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages. + +*homepage*: https://lsbr.niams.nih.gov/bsoft/ + +========= ============== +version toolchain +========= ============== +``2.0.2`` ``foss/2017b`` +``2.0.7`` ``GCC/9.3.0`` +========= ============== + + .. _list_software_BSseeker2_838: *BSseeker2* @@ -3834,6 +3870,7 @@ version versionsuffix toolchain ``0.8.1`` ``-Python-2.7.14`` ``intel/2018a`` ``0.8.2`` ``-Python-3.6.6`` ``foss/2018b`` ``0.8.4`` ``foss/2019a`` +``0.8.8`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== =============== @@ -3884,7 +3921,7 @@ bzip2 is a freely available, patent free, high-quality data compressor. It typi version toolchain ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.0.6`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.0.8`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -3894,7 +3931,7 @@ version toolchain --- -:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_charmm_632` - :ref:`list_software_CHARMM_440` - :ref:`list_software_CHASE_356` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_C3D_186: @@ -3957,16 +3994,16 @@ Cairo is a 2D graphics library with support for multiple output devices. Curren *homepage*: https://cairographics.org -=========== ================ ================================================================ -version versionsuffix toolchain -=========== ================ ================================================================ -``1.14.6`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``1.14.6`` ``-GLib-2.48.0`` ``foss/2016a``, ``intel/2016a`` -``1.14.8`` ``intel/2017a`` -``1.14.10`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017b`` -``1.14.12`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.16.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -=========== ================ ================================================================ +=========== ================ =========================================================================== +version versionsuffix toolchain +=========== ================ =========================================================================== +``1.14.6`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``1.14.6`` ``-GLib-2.48.0`` ``foss/2016a``, ``intel/2016a`` +``1.14.8`` ``intel/2017a`` +``1.14.10`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017b`` +``1.14.12`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.16.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +=========== ================ =========================================================================== .. _list_software_cairomm_744: @@ -4210,6 +4247,22 @@ version versionsuffix toolchain ============ ================== =============== +.. _list_software_causallift_1064: + +*causallift* +++++++++++++ + +CausalLift: Python package for Uplift Modeling in real-world business; applicable for both A/B testing and observational data + +*homepage*: https://github.com/Minyus/causallift + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.0.6`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_causalml_850: *causalml* @@ -4242,6 +4295,22 @@ version toolchain ========== ============== +.. _list_software_CAVIAR_438: + +*CAVIAR* +++++++++ + +CAusal Variants Identication in Associated Regions. A statistical framework that quantifies the probability of each variant to be causal while allowing an arbitrary number of causal variants. + +*homepage*: https://github.com/fhormoz/caviar + +================ ============== +version toolchain +================ ============== +``2.2-20190419`` ``foss/2019b`` +================ ============== + + .. _list_software_Cbc_264: *Cbc* @@ -4265,13 +4334,13 @@ version toolchain C interface to the BLAS -*homepage*: http://www.netlib.org/blas/ +*homepage*: https://www.netlib.org/blas/ -============ ============== -version toolchain -============ ============== -``20110120`` ``foss/2016b`` -============ ============== +============ ================================================ +version toolchain +============ ================================================ +``20110120`` ``foss/2016b``, ``intel/2019b``, ``intel/2020a`` +============ ================================================ .. _list_software_ccache_599: @@ -4294,6 +4363,22 @@ version versionsuffix toolchain ========== ============= ========== +.. _list_software_CCfits_572: + +*CCfits* +++++++++ + +CCfits is an object oriented interface to the cfitsio library. It is designed to make the capabilities of cfitsio available to programmers working in C++. + +*homepage*: https://heasarc.gsfc.nasa.gov/fitsio/CCfits/ + +======= ================= +version toolchain +======= ================= +``2.5`` ``GCCcore/9.3.0`` +======= ================= + + .. _list_software_CCL_210: *CCL* @@ -4303,11 +4388,12 @@ Clozure CL (often called CCL for short) is a free Common Lisp implementation wi *homepage*: https://ccl.clozure.com/ -========== ========== -version toolchain -========== ========== -``1.11.5`` ``system`` -========== ========== +========== ================= +version toolchain +========== ================= +``1.11.5`` ``system`` +``1.12`` ``GCCcore/9.3.0`` +========== ================= .. _list_software_cclib_509: @@ -4332,18 +4418,18 @@ version versionsuffix toolchain *CD-HIT* ++++++++ -CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. +CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. -*homepage*: http://weizhong-lab.ucsd.edu/cd-hit/ +*homepage*: https://github.com/weizhongli/cdhit -========= ============== ================================================ -version versionsuffix toolchain -========= ============== ================================================ -``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` -``4.6.6`` ``foss/2016b`` -``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` -``4.8.1`` ``GCC/9.3.0``, ``foss/2018b`` -========= ============== ================================================ +========= ============== ====================================================== +version versionsuffix toolchain +========= ============== ====================================================== +``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` +``4.6.6`` ``foss/2016b`` +``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` +``4.8.1`` ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` +========= ============== ====================================================== .. _list_software_cdbfasta_824: @@ -4501,6 +4587,22 @@ version toolchain ============== =============================== +.. _list_software_Cereal_588: + +*Cereal* +++++++++ + +cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. + +*homepage*: https://uscilab.github.io/cereal/ + +========= ========== +version toolchain +========= ========== +``1.3.0`` ``system`` +========= ========== + + .. _list_software_CESM-deps_769: *CESM-deps* @@ -4517,6 +4619,22 @@ version toolchain ======= ================================================ +.. _list_software_CFDEMcoupling_1216: + +*CFDEMcoupling* ++++++++++++++++ + +CFDEMcoupling is an open source CFD-DEM engine. It provides the possibility to couple the DEM engine LIGGGHTS to a CFD framework. + +*homepage*: https://www.cfdem.com/cfdemrcoupling-open-source-cfd-dem-framework + +========= ============== +version toolchain +========= ============== +``3.8.0`` ``foss/2018a`` +========= ============== + + .. _list_software_CFITSIO_529: *CFITSIO* @@ -4566,25 +4684,25 @@ The goal of the CGAL Open Source Project is to provide easy access to efficient *homepage*: http://www.cgal.org/ -========== ================== =============================== -version versionsuffix toolchain -========== ================== =============================== -``4.8`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``4.8.1`` ``foss/2016b``, ``intel/2016b`` -``4.8.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``4.9`` ``-Python-2.7.12`` ``intel/2016b`` -``4.9`` ``-Python-2.7.13`` ``intel/2017a`` -``4.11`` ``-Python-2.7.13`` ``intel/2017a`` -``4.11`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``4.11`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``4.11.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``4.11.1`` ``-Python-2.7.15`` ``foss/2018b`` -``4.11.1`` ``-Python-3.6.4`` ``foss/2018a`` -``4.11.1`` ``-Python-3.6.6`` ``foss/2018b`` -``4.14`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``4.14.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``4.14.3`` ``-Python-3.8.2`` ``gompi/2020a`` -========== ================== =============================== +========== ================== ================================ +version versionsuffix toolchain +========== ================== ================================ +``4.8`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``4.8.1`` ``foss/2016b``, ``intel/2016b`` +``4.8.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``4.9`` ``-Python-2.7.12`` ``intel/2016b`` +``4.9`` ``-Python-2.7.13`` ``intel/2017a`` +``4.11`` ``-Python-2.7.13`` ``intel/2017a`` +``4.11`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``4.11`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``4.11.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``4.11.1`` ``-Python-2.7.15`` ``foss/2018b`` +``4.11.1`` ``-Python-3.6.4`` ``foss/2018a`` +``4.11.1`` ``-Python-3.6.6`` ``foss/2018b`` +``4.14`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``4.14.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``4.14.3`` ``-Python-3.8.2`` ``gompi/2020a``, ``iimpi/2020a`` +========== ================== ================================ .. _list_software_cget_419: @@ -4669,35 +4787,35 @@ version toolchain ========= ==================================== -.. _list_software_charmm_632: +.. _list_software_CHARMM_440: -*charmm* +*CHARMM* ++++++++ -CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. charmm provides all the functionality of CHARMM except its performance enhancements. +CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. *homepage*: http://www.charmm.org ======== =============================== version toolchain ======== =============================== -``43b2`` ``foss/2017b``, ``intel/2017b`` +``37b2`` ``foss/2016a``, ``intel/2016a`` ======== =============================== -.. _list_software_CHARMM_440: +.. _list_software_charmm_632: -*CHARMM* +*charmm* ++++++++ -CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. +CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. charmm provides all the functionality of CHARMM except its performance enhancements. *homepage*: http://www.charmm.org ======== =============================== version toolchain ======== =============================== -``37b2`` ``foss/2016a``, ``intel/2016a`` +``43b2`` ``foss/2017b``, ``intel/2017b`` ======== =============================== @@ -4717,6 +4835,38 @@ version toolchain ============ ========== +.. _list_software_Check_478: + +*Check* ++++++++ + +Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format. + +*homepage*: https://libcheck.github.io/check/ + +========== ================= +version toolchain +========== ================= +``0.15.2`` ``GCCcore/9.3.0`` +========== ================= + + +.. _list_software_check_510: + +*check* ++++++++ + +Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format. + +*homepage*: https://libcheck.github.io/check/ + +========== ================= +version toolchain +========== ================= +``0.12.0`` ``GCCcore/6.4.0`` +========== ================= + + .. _list_software_CheckM_555: *CheckM* @@ -4762,17 +4912,33 @@ CheMPS2 is a scientific library which contains a spin-adapted implementation of *homepage*: https://github.com/SebWouters/CheMPS2 -=========== ================================================================ -version toolchain -=========== ================================================================ -``1.6`` ``intel/2016a`` -``1.7.1`` ``intel/2016a`` -``1.7.2`` ``intel/2016a`` -``1.7-rc2`` ``intel/2016a`` -``1.8`` ``intel/2016b`` -``1.8.8`` ``intel/2018b`` -``1.8.9`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` -=========== ================================================================ +=========== ================================================================================= +version toolchain +=========== ================================================================================= +``1.6`` ``intel/2016a`` +``1.7-rc2`` ``intel/2016a`` +``1.7.1`` ``intel/2016a`` +``1.7.2`` ``intel/2016a`` +``1.8`` ``intel/2016b`` +``1.8.8`` ``intel/2018b`` +``1.8.9`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b`` +=========== ================================================================================= + + +.. _list_software_chewBBACA_752: + +*chewBBACA* ++++++++++++ + +chewBBACA stands for "BSR-Based Allele Calling Algorithm". chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci. + +*homepage*: https://github.com/B-UMMI/chewBBACA + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``2.5.5`` ``-Python-3.8.2`` ``intel/2020a`` +========= ================= =============== .. _list_software_Chimera_697: @@ -4972,11 +5138,12 @@ Python bindings for libclang *homepage*: https://clang.llvm.org -========= ================== ================= -version versionsuffix toolchain -========= ================== ================= -``8.0.0`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` -========= ================== ================= +========== ================== ================= +version versionsuffix toolchain +========== ================== ================= +``8.0.0`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``10.0.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +========== ================== ================= .. _list_software_CLAPACK_495: @@ -5106,13 +5273,13 @@ version toolchain ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. -*homepage*: http://www.ebi.ac.uk/Tools/msa/clustalw2/ +*homepage*: https://www.ebi.ac.uk/Tools/msa/clustalw2/ -======= ========================================================================================================== -version toolchain -======= ========================================================================================================== -``2.1`` ``foss/2016b``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b`` -======= ========================================================================================================== +======= =========================================================================================================================== +version toolchain +======= =========================================================================================================================== +``2.1`` ``foss/2016b``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b``, ``intel/2020a`` +======= =========================================================================================================================== .. _list_software_Cluster-Buster_1412: @@ -5192,6 +5359,7 @@ version toolchain ``3.13.3`` ``GCCcore/8.2.0`` ``3.15.3`` ``GCCcore/8.3.0`` ``3.16.4`` ``GCCcore/9.3.0`` +``3.18.4`` ``GCCcore/10.2.0`` ========== ================================================================================================================================================= @@ -5308,6 +5476,22 @@ version versionsuffix toolchain ============ ================== ============== +.. _list_software_COMSOL_461: + +*COMSOL* +++++++++ + +COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. + +*homepage*: https://www.comsol.com + +============= ========== +version toolchain +============= ========== +``5.4.0.225`` ``system`` +============= ========== + + .. _list_software_Con3F_409: *Con3F* @@ -5371,12 +5555,13 @@ HTTP proxy for node.js including a REST API for updating the routing table. Dev *homepage*: https://github.com/jupyterhub/configurable-http-proxy -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``1.3.0`` ``-nodejs-4.4.7`` ``foss/2016a`` -``3.1.1`` ``-nodejs-8.9.4`` ``foss/2017a`` -========= ================= ============== +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``1.3.0`` ``-nodejs-4.4.7`` ``foss/2016a`` +``3.1.1`` ``-nodejs-8.9.4`` ``foss/2017a`` +``4.2.1`` ``GCCcore/10.2.0`` +========= ================= ================== .. _list_software_ConnectomeWorkbench_1966: @@ -5970,9 +6155,26 @@ version toolchain ``10.1.168`` ``system`` ``10.1.243`` ``GCC/8.3.0``, ``iccifort/2019.5.281``, ``system`` ``10.2.89`` ``GCC/8.3.0`` +``11.0.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` ================= ========================================================================== +.. _list_software_CUDAcore_710: + +*CUDAcore* +++++++++++ + +CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. + +*homepage*: https://developer.nvidia.com/cuda-toolkit + +========== ========== +version toolchain +========== ========== +``11.0.2`` ``system`` +========== ========== + + .. _list_software_cuDNN_440: *cuDNN* @@ -5990,7 +6192,11 @@ version versionsuffix toolchain ``5.0-rc`` ``system`` ``5.1`` ``-CUDA-8.0.44`` ``system`` ``6.0`` ``-CUDA-8.0.61`` ``system`` +``6.0.21`` ``-CUDA-7.5.18`` ``system`` +``6.0.21`` ``-CUDA-8.0.44`` ``system`` ``7.0.2`` ``-CUDA-9.0.176`` ``system`` +``7.0.5`` ``-CUDA-8.0.44`` ``system`` +``7.0.5`` ``-CUDA-9.0.176`` ``system`` ``7.0.5`` ``-CUDA-9.1.85`` ``system`` ``7.0.5.15`` ``fosscuda/2017b``, ``fosscuda/2018a``, ``intelcuda/2017b`` ``7.1.4.18`` ``fosscuda/2018b`` @@ -6065,6 +6271,7 @@ version toolchain ``7.63.0`` ``GCCcore/8.2.0`` ``7.66.0`` ``GCCcore/8.3.0`` ``7.69.1`` ``GCCcore/9.3.0`` +``7.72.0`` ``GCCcore/10.2.0`` ========== =================================================================================== @@ -6260,7 +6467,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` .. _list_software_dadi_402: @@ -6295,6 +6502,22 @@ version versionsuffix toolchain ========= ============= ============== +.. _list_software_Dalton_610: + +*Dalton* +++++++++ + +The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory. Any published work arising from use of one of the Dalton2016 programs must acknowledge that by a proper reference, https://www.daltonprogram.org/www/citation.html. + +*homepage*: https://daltonprogram.org/ + +======== ============= =============== +version versionsuffix toolchain +======== ============= =============== +``2016`` ``-i8`` ``intel/2017b`` +======== ============= =============== + + .. _list_software_damageproto_1171: *damageproto* @@ -6443,6 +6666,7 @@ version toolchain ``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` ``18.1.25`` ``GCCcore/7.3.0`` ``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``18.1.40`` ``GCCcore/10.2.0`` =========== ======================================================= @@ -6523,6 +6747,7 @@ version toolchain ``1.13.6`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.13.8`` ``GCCcore/8.2.0`` ``1.13.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.13.18`` ``GCCcore/10.2.0`` =========== ==================================== @@ -6657,6 +6882,7 @@ version versionsuffix toolchain ``3.3.0`` ``-Python-2.7.15`` ``intel/2018b`` ``3.3.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``4.0.6`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``5.0.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========= ================== =============================== @@ -6736,12 +6962,12 @@ A Python library for phylogenetics and phylogenetic computing: reading, writing *homepage*: https://pypi.python.org/pypi/DendroPy/ -========= ================== ===================================================== -version versionsuffix toolchain -========= ================== ===================================================== -``4.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2019a`` -``4.4.0`` ``-Python-2.7.15`` ``intel/2018b`` -========= ================== ===================================================== +========= ================== ======================================================================== +version versionsuffix toolchain +========= ================== ======================================================================== +``4.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2019a`` +``4.4.0`` ``-Python-2.7.15`` ``intel/2018b`` +========= ================== ======================================================================== .. _list_software_destiny_768: @@ -6909,6 +7135,23 @@ version toolchain ========= ================= +.. _list_software_DIRAC_355: + +*DIRAC* ++++++++ + +DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations + +*homepage*: http://www.diracprogram.org + +======== ============================ =============== +version versionsuffix toolchain +======== ============================ =============== +``19.0`` ``-Python-2.7.18-int64`` ``intel/2020a`` +``19.0`` ``-Python-2.7.18-mpi-int64`` ``intel/2020a`` +======== ============================ =============== + + .. _list_software_distributed_1187: *distributed* @@ -7055,13 +7298,13 @@ Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles *homepage*: https://github.com/google/double-conversion -========= ==================================== -version toolchain -========= ==================================== -``3.0.3`` ``foss/2018a`` -``3.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.1.5`` ``GCCcore/9.3.0`` -========= ==================================== +========= ===================================== +version toolchain +========= ===================================== +``3.0.3`` ``foss/2018a`` +``3.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========= ===================================== .. _list_software_DoubletFinder_1319: @@ -7238,7 +7481,7 @@ version versionsuffix toolchain --- -:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExifTool_810` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_E-ANTIC_481: @@ -7377,6 +7620,7 @@ version toolchain ``4.2.0`` ``system`` ``4.2.1`` ``system`` ``4.2.2`` ``system`` +``4.3.0`` ``system`` ========== ========== @@ -7405,17 +7649,18 @@ ecCodes is a package developed by ECMWF which provides an application programmin *homepage*: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home -========== ================= ================================ -version versionsuffix toolchain -========== ================= ================================ -``2.7.3`` ``intel/2018a`` -``2.8.2`` ``intel/2018a`` -``2.9.2`` ``intel/2018b``, ``iomkl/2018b`` -``2.12.5`` ``gompi/2019a`` -``2.15.0`` ``iimpi/2019b`` -``2.17.0`` ``-Python-3.6.6`` ``foss/2018b`` -``2.17.0`` ``-Python-3.7.4`` ``foss/2019b`` -========== ================= ================================ +========== ================== ================================ +version versionsuffix toolchain +========== ================== ================================ +``2.7.3`` ``intel/2018a`` +``2.7.3`` ``-Python-2.7.14`` ``intel/2017b`` +``2.8.2`` ``intel/2018a`` +``2.9.2`` ``intel/2018b``, ``iomkl/2018b`` +``2.12.5`` ``gompi/2019a`` +``2.15.0`` ``iimpi/2019b`` +``2.17.0`` ``-Python-3.6.6`` ``foss/2018b`` +``2.17.0`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================== ================================ .. _list_software_ED2_187: @@ -7444,12 +7689,12 @@ Lightweight, super fast library for sequence alignment using edit (Levenshtein) *homepage*: https://martinsos.github.io/edlib -=============== ================= ======================= -version versionsuffix toolchain -=============== ================= ======================= -``1.3.8.post1`` ``-Python-3.7.4`` ``iccifort/2019.5.281`` -``1.3.8.post1`` ``-Python-3.8.2`` ``GCC/9.3.0`` -=============== ================= ======================= +=============== ================= ====================================== +version versionsuffix toolchain +=============== ================= ====================================== +``1.3.8.post1`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``1.3.8.post1`` ``-Python-3.8.2`` ``GCC/9.3.0`` +=============== ================= ====================================== .. _list_software_EggLib_554: @@ -7573,18 +7818,18 @@ Eigenvalue SoLvers for Petaflop-Applications . *homepage*: https://elpa.rzg.mpg.de -=================== ================================================ -version toolchain -=================== ================================================ -``2015.02.002`` ``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` -``2016.05.004`` ``intel/2016b``, ``intel/2017a`` -``2016.11.001.pre`` ``foss/2018b``, ``intel/2018b`` -``2017.11.001`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -``2018.05.001`` ``foss/2018b``, ``intel/2018b`` -``2018.11.001`` ``intel/2019a`` -``2019.11.001`` ``foss/2019b``, ``intel/2019b`` -``2020.05.001`` ``intel/2020a`` -=================== ================================================ +=================== ================================================================ +version toolchain +=================== ================================================================ +``2015.02.002`` ``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` +``2016.05.004`` ``intel/2016b``, ``intel/2017a`` +``2016.11.001.pre`` ``foss/2018b``, ``intel/2018b`` +``2017.11.001`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +``2018.05.001`` ``foss/2018b``, ``intel/2018b`` +``2018.11.001`` ``intel/2019a`` +``2019.11.001`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` +``2020.05.001`` ``intel/2020a`` +=================== ================================================================ .. _list_software_ELPH_297: @@ -7833,6 +8078,38 @@ version versionsuffix toolchain ============ ================ ================================================================= +.. _list_software_ESMValTool_934: + +*ESMValTool* +++++++++++++ + +The Earth System Model eValuation Tool (ESMValTool) is a community diagnostics and performance metrics tool for the evaluation of Earth System Models (ESMs) that allows for routine comparison of single or multiple models, either against predecessor versions or against observations. + +*homepage*: https://www.esmvaltool.org/ + +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``1.1.0`` ``-Python-2.7.14`` ``intel/2017b`` +========= ================== =============== + + +.. _list_software_eSpeak-NG_795: + +*eSpeak-NG* ++++++++++++ + +The eSpeak NG is a compact open source software text-to-speech synthesizer for Linux, Windows, Android and other operating systems. It supports more than 100 languages and accents. It is based on the eSpeak engine created by Jonathan Duddington. + +*homepage*: https://github.com/espeak-ng/espeak-ng + +======== =============== +version toolchain +======== =============== +``1.50`` ``gompi/2020a`` +======== =============== + + .. _list_software_Essentia_828: *Essentia* @@ -7948,6 +8225,22 @@ version toolchain ======= ============== +.. _list_software_ExifTool_810: + +*ExifTool* +++++++++++ + +Perl module (Image::ExifTool) and program (exiftool) to read EXIF information from images + +*homepage*: https://owl.phy.queensu.ca/~phil/exiftool/ + +========= ================= +version toolchain +========= ================= +``12.00`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_Exonerate_939: *Exonerate* @@ -8042,7 +8335,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FIAT_292` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -8077,6 +8370,22 @@ version toolchain ======= ================= +.. _list_software_FabIO_417: + +*FabIO* ++++++++ + +FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers (as a python dictionary) and datasets (as a numpy ndarray of integers or floats). + +*homepage*: http://www.silx.org + +========== ================= ================================== +version versionsuffix toolchain +========== ================= ================================== +``0.10.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========== ================= ================================== + + .. _list_software_faceswap_842: *faceswap* @@ -8181,15 +8490,16 @@ version versionsuffix toolchain FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. -*homepage*: https://www.iodbc.org/ +*homepage*: https://github.com/ParBLiSS/FastANI -======= ============================================================== -version toolchain -======= ============================================================== -``1.1`` ``foss/2018b``, ``intel/2018b`` -``1.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``1.3`` ``iccifort/2019.5.281`` -======= ============================================================== +======== ============================================================== +version toolchain +======== ============================================================== +``1.1`` ``foss/2018b``, ``intel/2018b`` +``1.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``1.3`` ``iccifort/2019.5.281`` +``1.31`` ``iccifort/2020.1.217`` +======== ============================================================== .. _list_software_FastME_544: @@ -8446,11 +8756,11 @@ The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/ *homepage*: http://hannonlab.cshl.edu/fastx_toolkit/ -========== ================================================================== -version toolchain -========== ================================================================== -``0.0.14`` ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2018a`` -========== ================================================================== +========== ================================================================================= +version toolchain +========== ================================================================================= +``0.0.14`` ``GCC/9.3.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2018a`` +========== ================================================================================= .. _list_software_fatslim_752: @@ -8589,6 +8899,38 @@ version toolchain ========= =============== +.. _list_software_festival_862: + +*festival* +++++++++++ + +University of Edinburgh's Festival Speech Synthesis Systems is a free software multi-lingual speech synthesis workbench that runs on multiple-platforms offering black box text to speech, as well as an open architecture for research in speech synthesis. It designed as a component of large speech technology systems. + +*homepage*: ['http://festvox.org/festival/'] + +========= ================= +version toolchain +========= ================= +``2.5.0`` ``GCCcore/9.3.0`` +========= ================= + + +.. _list_software_fetchMG_670: + +*fetchMG* ++++++++++ + +The program “fetchMG” was written to extract the 40 MGs from genomes and metagenomes in an easy and accurate manner. + +*homepage*: http://vm-lux.embl.de/~mende/fetchMG/about.html + +======= ==================================== +version toolchain +======= ==================================== +``1.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ==================================== + + .. _list_software_FFC_207: *FFC* @@ -8679,18 +9021,18 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: http://www.fftw.org -========= ============= ================================================================================================================================================================================================================================ -version versionsuffix toolchain -========= ============= ================================================================================================================================================================================================================================ -``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` -``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` -``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` -``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` -``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` -``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` -``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``iomkl/2018b`` -``3.3.8`` ``-serial`` ``GCC/9.3.0`` -========= ============= ================================================================================================================================================================================================================================ +========= ============= ================================================================================================================================================================================================================================================== +version versionsuffix toolchain +========= ============= ================================================================================================================================================================================================================================================== +``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` +``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` +``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` +``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` +``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` +``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` +``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``iomkl/2018b`` +``3.3.8`` ``-serial`` ``GCC/9.3.0`` +========= ============= ================================================================================================================================================================================================================================================== .. _list_software_FGSL_300: @@ -8709,6 +9051,22 @@ version toolchain ========= =============== +.. _list_software_FHI-aims_686: + +*FHI-aims* +++++++++++ + +FHI-aims is an efficient, accurate all-electron, full-potential electronic structure code package for computational molecular and materials science (non-periodic and periodic systems). The code supports DFT (semilocal and hybrid) and many-body perturbation theory. FHI-aims is particularly efficient for molecular systems and nanostructures, while maintaining high numerical accuracy for all production tasks. Production calculations handle up to several thousand atoms and can efficiently use (ten) thousands of cores. + +*homepage*: https://aimsclub.fhi-berlin.mpg.de/ + +============ =============== +version toolchain +============ =============== +``200112_2`` ``intel/2019b`` +============ =============== + + .. _list_software_FIAT_292: *FIAT* @@ -8886,13 +9244,13 @@ Fiona is designed to be simple and dependable. It focuses on reading and writing *homepage*: https://github.com/Toblerity/Fiona -================ ================= ============== -version versionsuffix toolchain -================ ================= ============== -``1.8.13`` ``-Python-3.7.4`` ``foss/2019b`` -``1.8.13.post1`` ``-Python-3.7.2`` ``foss/2019a`` -``1.8.16`` ``-Python-3.8.2`` ``foss/2020a`` -================ ================= ============== +================ ================= ================================== +version versionsuffix toolchain +================ ================= ================================== +``1.8.13`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.8.13.post1`` ``-Python-3.7.2`` ``foss/2019a`` +``1.8.16`` ``-Python-3.8.2`` ``foss/2020a`` +================ ================= ================================== .. _list_software_Firefox_723: @@ -9035,11 +9393,11 @@ FlatBuffers: Memory Efficient Serialization Library *homepage*: https://github.com/google/flatbuffers/ -========== ================= -version toolchain -========== ================= -``1.12.0`` ``GCCcore/8.3.0`` -========== ================= +========== ==================================== +version toolchain +========== ==================================== +``1.12.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ==================================== .. _list_software_FLEUR_382: @@ -9080,6 +9438,22 @@ version toolchain ========== ======================================================================================================================================================================================================================================================================================================================================================================================= +.. _list_software_Flexbar_708: + +*Flexbar* ++++++++++ + +The program Flexbar preprocesses high-throughput sequencing data efficiently + +*homepage*: https://github.com/seqan/flexbar + +========= ============== +version toolchain +========= ============== +``3.5.0`` ``foss/2018b`` +========= ============== + + .. _list_software_FlexiDot_799: *FlexiDot* @@ -9126,7 +9500,7 @@ version toolchain ========= =================================================================================================================================================================================================== ``1.3.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.3.4`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b`` -``1.3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` +``1.3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/9.3.0`` ========= =================================================================================================================================================================================================== @@ -9137,7 +9511,7 @@ version toolchain ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. -*homepage*: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent +*homepage*: https://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent ========== ========== version toolchain @@ -9148,6 +9522,7 @@ version toolchain ``17.1`` ``system`` ``18.0`` ``system`` ``18.1`` ``system`` +``18.2`` ``system`` ========== ========== @@ -9217,6 +9592,8 @@ version toolchain ``3.0.1`` ``foss/2016b``, ``intel/2016b`` ``3.0.2`` ``GCCcore/6.4.0``, ``intel/2017a`` ``5.3.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``6.2.1`` ``GCCcore/9.3.0`` +``7.0.3`` ``GCCcore/9.3.0`` ========= ==================================== @@ -9259,7 +9636,7 @@ version versionsuffix toolchain ``2.12.6`` ``GCCcore/6.4.0`` ``2.13.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.13.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2.13.92`` ``GCCcore/9.3.0`` +``2.13.92`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` =========== ================== ====================================================================================== @@ -9325,6 +9702,7 @@ version toolchain ``2018b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` +``2020a`` ``system`` ========= ========== @@ -9337,11 +9715,11 @@ FoX is an XML library written in Fortran 95. It allows software developers to re *homepage*: http://homepages.see.leeds.ac.uk/~earawa/FoX/ -========= ================================ -version toolchain -========= ================================ -``4.1.2`` ``intel/2017b``, ``intel/2018a`` -========= ================================ +========= =============================================== +version toolchain +========= =============================================== +``4.1.2`` ``GCC/9.3.0``, ``intel/2017b``, ``intel/2018a`` +========= =============================================== .. _list_software_FPM_227: @@ -9519,6 +9897,7 @@ version versionsuffix toolchain ``2.9`` ``GCCcore/6.4.0`` ``2.9.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.10.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.10.3`` ``GCCcore/10.2.0`` ========== ================== ====================================================================== @@ -9549,14 +9928,47 @@ The Free Implementation of the Unicode Bidirectional Algorithm. *homepage*: https://github.com/fribidi/fribidi -========= ======================================================= -version toolchain -========= ======================================================= -``1.0.1`` ``foss/2018a``, ``intel/2018a`` -``1.0.2`` ``GCCcore/6.4.0`` -``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``1.0.9`` ``GCCcore/9.3.0`` -========= ======================================================= +========== ======================================================= +version toolchain +========== ======================================================= +``1.0.1`` ``foss/2018a``, ``intel/2018a`` +``1.0.2`` ``GCCcore/6.4.0`` +``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.0.9`` ``GCCcore/9.3.0`` +``1.0.10`` ``GCCcore/10.2.0`` +========== ======================================================= + + +.. _list_software_FRUIT_394: + +*FRUIT* ++++++++ + +FORTRAN Unit Test Framework (FRUIT) + +*homepage*: https://fortranxunit.sourceforge.io + +========= =============== =============================== +version versionsuffix toolchain +========= =============== =============================== +``3.4.3`` ``-Ruby-2.5.1`` ``foss/2018a``, ``intel/2018a`` +========= =============== =============================== + + +.. _list_software_FRUIT_processor_1481: + +*FRUIT_processor* ++++++++++++++++++ + +FORTRAN Unit Test Framework (FRUIT) + +*homepage*: https://fortranxunit.sourceforge.io + +========= =============== =============================== +version versionsuffix toolchain +========= =============== =============================== +``3.4.3`` ``-Ruby-2.5.1`` ``foss/2018a``, ``intel/2018a`` +========= =============== =============================== .. _list_software_FSL_229: @@ -9741,7 +10153,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gblocks_709` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -9978,9 +10390,27 @@ version versionsuffix toolchain ``4.1.4.1`` ``-Java-11`` ``GCCcore/8.3.0`` ``4.1.5.0`` ``-Java-1.8`` ``GCCcore/9.3.0`` ``4.1.5.0`` ``-Java-11`` ``GCCcore/9.3.0`` +``4.1.8.1`` ``-Java-1.8`` ``GCCcore/9.3.0`` ============ =================== ================= +.. _list_software_Gaussian_827: + +*Gaussian* +++++++++++ + +Gaussian provides state-of-the-art capabilities for electronic structure modeling. Gaussian 09 is licensed for a wide variety of computer systems. All versions of Gaussian 09 contain every scientific/modeling feature, and none imposes any artificial limitations on calculations other than your computing resources and patience. This is the official gaussian AVX2 build. + +*homepage*: https://www.gaussian.com/ + +=========== ============= ========== +version versionsuffix toolchain +=========== ============= ========== +``09.e.01`` ``-AVX`` ``system`` +``16.A.03`` ``-AVX2`` ``system`` +=========== ============= ========== + + .. _list_software_Gblocks_709: *Gblocks* @@ -9997,6 +10427,22 @@ version toolchain ========= ========== +.. _list_software_GBprocesS_872: + +*GBprocesS* ++++++++++++ + +GBprocesS allows for the extraction of genomic inserts from NGS data for GBS experiments. Preprocessing is performed in different stages that are part of a linear pipeline where the steps are performed in order. GBprocesS provides a flexible way to adjust the functionality to your needs, as the operations required and the execution order vary depending on the GBS protocol used. + +*homepage*: https://gbprocess.readthedocs.io/ + +======= ================= =============== +version versionsuffix toolchain +======= ================= =============== +``2.3`` ``-Python-3.8.2`` ``intel/2020a`` +======= ================= =============== + + .. _list_software_gbs2ploidy_1023: *gbs2ploidy* @@ -10177,6 +10623,7 @@ version toolchain ``2018b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` +``2020a`` ``system`` =========== ========== @@ -10417,10 +10864,26 @@ version toolchain ``2.36.12`` ``foss/2018b``, ``fosscuda/2018b`` ``2.38.1`` ``GCCcore/8.2.0`` ``2.38.2`` ``GCCcore/8.3.0`` -``2.40.0`` ``GCCcore/9.3.0`` +``2.40.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` =========== ==================================================================================== +.. _list_software_GDRCopy_632: + +*GDRCopy* ++++++++++ + +A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. + +*homepage*: https://github.com/NVIDIA/gdrcopy + +======= ================ ================= +version versionsuffix toolchain +======= ================ ================= +``2.1`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` +======= ================ ================= + + .. _list_software_Geant4_547: *Geant4* @@ -10542,6 +11005,22 @@ version toolchain ======== ================= +.. _list_software_Genome_Profiler_1533: + +*Genome_Profiler* ++++++++++++++++++ + +Genome Profiler (GeP) is a program to perform whole-genome multilocus sequence typing (wgMLST) analysis for bacterial isolates + +*homepage*: https://sourceforge.net/projects/genomeprofiler/ + +======= ================ ============== +version versionsuffix toolchain +======= ================ ============== +``2.1`` ``-Perl-5.24.0`` ``foss/2016b`` +======= ================ ============== + + .. _list_software_GenomeMapper_1216: *GenomeMapper* @@ -10651,12 +11130,13 @@ GeoPandas is a project to add support for geographic data to pandas objects. It *homepage*: https://github.com/geopandas/geopandas -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``0.7.0`` ``-Python-3.7.4`` ``foss/2019b`` -``0.8.0`` ``-Python-3.7.2`` ``foss/2019a`` -========= ================= ============== +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``0.7.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``0.8.0`` ``-Python-3.7.2`` ``foss/2019a`` +``0.8.1`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ================================== .. _list_software_geopy_548: @@ -10757,6 +11237,7 @@ version versionsuffix toolchain ``0.19.8.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` ``0.19.8.1`` ``-libxml2-2.9.7`` ``GCCcore/6.4.0`` ``0.20.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +``0.21`` ``GCCcore/10.2.0``, ``system`` ============ ================== =================================================================================================== @@ -10884,7 +11365,7 @@ giflib is a library for reading and writing gif images. It is API and ABI compat version toolchain ========= ==================================== ``5.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``5.2.1`` ``GCCcore/8.3.0`` +``5.2.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ==================================== @@ -11050,6 +11531,7 @@ version versionsuffix toolchain ``2.21.0`` ``-nodocs`` ``GCCcore/8.2.0`` ``2.23.0`` ``GCCcore/8.3.0`` ``2.23.0`` ``-nodocs`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.28.0`` ``-nodocs`` ``GCCcore/10.2.0`` =========== ============= ==================================== @@ -11100,6 +11582,7 @@ GitPython is a python library used to interact with Git repositories version versionsuffix toolchain ========== ================= =============================== ``2.1.11`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``2.1.15`` ``system`` ``3.0.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``3.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========== ================= =============================== @@ -11144,7 +11627,7 @@ version toolchain GL2PS: an OpenGL to PostScript printing library -*homepage*: http://www.geuz.org/gl2ps/ +*homepage*: https://www.geuz.org/gl2ps/ ========= ================ ==================================================================================================================================== version versionsuffix toolchain @@ -11152,6 +11635,7 @@ version versionsuffix toolchain ``1.3.9`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.3.9`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` ``1.4.0`` ``GCCcore/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +``1.4.2`` ``GCCcore/9.3.0`` ========= ================ ==================================================================================================================================== @@ -11231,6 +11715,7 @@ version toolchain ``2.60.1`` ``GCCcore/8.2.0`` ``2.62.0`` ``GCCcore/8.3.0`` ``2.64.1`` ``GCCcore/9.3.0`` +``2.66.1`` ``GCCcore/10.2.0`` ========== ================================================= @@ -11464,7 +11949,7 @@ version toolchain ``6.1.0`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``6.1.1`` ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``6.1.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b`` -``6.2.0`` ``GCCcore/9.3.0`` +``6.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========== ===================================================================================================================================================== @@ -11722,6 +12207,7 @@ version versionsuffix toolchain ``1.60.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``1.63.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``1.64.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``1.66.1`` ``GCCcore/10.2.0`` ========== ================== ================================== @@ -11807,6 +12293,7 @@ version toolchain ``2018b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` +``2020a`` ``system`` ========= ========== @@ -11927,7 +12414,7 @@ GNU gperf is a perfect hash function generator. For a given list of strings, it version toolchain ========= ========================================================================================================================= ``3.0.4`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``3.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``3.1`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ========================================================================================================================= @@ -12291,6 +12778,22 @@ version versionsuffix toolchain ============ =================== =============== +.. _list_software_groff_532: + +*groff* ++++++++ + +Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. + +*homepage*: https://www.gnu.org/software/groff + +========== ================= +version toolchain +========== ================= +``1.22.4`` ``GCCcore/9.3.0`` +========== ================= + + .. _list_software_GroIMP_526: *GroIMP* @@ -12341,8 +12844,10 @@ version versionsuffix toolchain ``2019.2`` ``fosscuda/2019a`` ``2019.3`` ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019a``, ``fosscuda/2019b`` ``2019.4`` ``foss/2019b`` +``2019.6`` ``fosscuda/2019b`` ``2020`` ``foss/2019b``, ``fosscuda/2019b`` ``2020.1`` ``-Python-3.8.2`` ``foss/2020a`` +``2020.3`` ``fosscuda/2019b`` ========== ================= ============================================================================================================ @@ -12521,6 +13026,7 @@ version versionsuffix toolchain ``0.2.2`` ``-Python-2.7.15`` ``intel/2018b`` ``0.3.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ``1.0.2`` ``-Python-3.7.4`` ``intel/2019b`` +``1.3.0`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================== =============================== @@ -12544,6 +13050,7 @@ version toolchain ``3.24.8`` ``GCCcore/8.2.0`` ``3.24.13`` ``GCCcore/8.3.0`` ``3.24.17`` ``GCCcore/9.3.0`` +``3.24.23`` ``GCCcore/10.2.0`` =========== ================================================================================ @@ -12644,7 +13151,7 @@ version toolchain ``1.8.8`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b`` ``2.0.11`` ``GCC/4.9.3-2.25``, ``foss/2016a`` ``2.2.2`` ``GCCcore/6.4.0`` -``2.2.4`` ``GCCcore/7.3.0`` +``2.2.4`` ``GCCcore/7.3.0``, ``GCCcore/9.3.0`` ========== ====================================================================================================================================================================================================================== @@ -12698,13 +13205,13 @@ gzip (GNU zip) is a popular data compression program as a replacement for compre *homepage*: http://www.gnu.org/software/gzip/ -======== ======================================================= -version toolchain -======== ======================================================= -``1.8`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``1.9`` ``GCCcore/7.3.0`` -``1.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======== ======================================================= +======== =========================================================================== +version toolchain +======== =========================================================================== +``1.8`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``1.9`` ``GCCcore/7.3.0`` +``1.10`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======== =========================================================================== .. _list_software_letter_h: @@ -12713,7 +13220,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_hyperopt_891` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -12889,6 +13396,7 @@ version toolchain ``2.2.0`` ``foss/2018b``, ``fosscuda/2018b`` ``2.4.0`` ``GCCcore/8.2.0`` ``2.6.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.6.7`` ``GCCcore/10.2.0`` ========= ================================================ @@ -12899,13 +13407,14 @@ version toolchain Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids. -*homepage*: http://ab-initio.mit.edu/wiki/index.php/Harminv +*homepage*: https://github.com/stevengj/harminv -======= ============== -version toolchain -======= ============== -``1.4`` ``foss/2016a`` -======= ============== +========= =============== +version toolchain +========= =============== +``1.4`` ``foss/2016a`` +``1.4.1`` ``intel/2020a`` +========= =============== .. _list_software_harmony_766: @@ -13312,6 +13821,7 @@ version toolchain ========= ============================================================================================================================================ ``3.1b2`` ``GCC/6.4.0-2.28``, ``foss/2016a``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a``, ``intel/2018a`` ``3.2.1`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iimpi/2019b``, ``intel/2018b`` +``3.3.1`` ``iimpi/2020a`` ========= ============================================================================================================================================ @@ -13382,6 +13892,7 @@ version versionsuffix toolchain ``0.18.2`` ``-TensorFlow-2.0.0-Python-3.7.4`` ``fosscuda/2019b`` ``0.19.1`` ``-TensorFlow-2.1.0-Python-3.7.4`` ``fosscuda/2019b`` ``0.19.5`` ``-TensorFlow-2.2.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.20.3`` ``-TensorFlow-2.3.1-Python-3.7.4`` ``fosscuda/2019b`` ========== =================================== ================== @@ -13464,7 +13975,7 @@ version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``fosscuda/2019b``, ``gomkl/2019a``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020a``, ``intelcuda/2019b``, ``iomkl/2019.01`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gomkl/2019a``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= @@ -13507,6 +14018,7 @@ version versionsuffix toolchain ``0.11.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.11.2`` ``-Python-3.6.6`` ``foss/2018b`` ``0.11.2`` ``-Python-3.7.2`` ``foss/2019a`` +``0.11.2`` ``-Python-3.7.4`` ``foss/2019b`` =========== ================== ================================================ @@ -13530,7 +14042,7 @@ version versionsuffix toolchain ``1.4.1`` ``foss/2016a``, ``intel/2017a`` ``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` ``1.7`` ``intel/2018a`` -``1.8`` ``foss/2018a``, ``intel/2018a`` +``1.8`` ``GCC/6.4.0-2.28``, ``foss/2018a``, ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ``20160107`` ``-PacBio`` ``intel/2017a`` @@ -13602,26 +14114,10 @@ version toolchain ``2.0.2`` ``GCCcore/8.2.0`` ``2.0.3`` ``GCCcore/8.3.0`` ``2.1.0`` ``GCCcore/9.2.0`` -``2.2.0`` ``GCCcore/9.3.0`` +``2.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` =========== ===================================================================================================================================================================================================================================================== -.. _list_software_hyperopt_891: - -*hyperopt* -++++++++++ - -Distributed Asynchronous Hyperparameter Optimization in Python - -*homepage*: https://github.com/hyperopt/hyperopt - -========= ========================== =============== -version versionsuffix toolchain -========= ========================== =============== -``0.2.4`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` -========= ========================== =============== - - .. _list_software_Hyperopt_859: *Hyperopt* @@ -13639,6 +14135,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_hyperopt_891: + +*hyperopt* +++++++++++ + +Distributed Asynchronous Hyperparameter Optimization in Python + +*homepage*: https://github.com/hyperopt/hyperopt + +========= ========================== =============== +version versionsuffix toolchain +========= ========================== =============== +``0.2.4`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` +========= ========================== =============== + + .. _list_software_hyperspy_900: *hyperspy* @@ -13664,11 +14176,12 @@ HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package *homepage*: https://veg.github.io/hyphy-site/ -========= =============== -version toolchain -========= =============== -``2.5.1`` ``gompi/2019a`` -========= =============== +========== =============== +version toolchain +========== =============== +``2.3.13`` ``foss/2016b`` +``2.5.1`` ``gompi/2019a`` +========== =============== .. _list_software_HyPo_384: @@ -13701,6 +14214,7 @@ version versionsuffix toolchain ========== ================= ================================== ``4.5.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``4.23.4`` ``GCCcore/8.2.0`` +``4.39.3`` ``-Python-3.6.4`` ``intel/2018a`` ``4.44.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``5.6.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========== ================= ================================== @@ -13731,7 +14245,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -13901,6 +14415,7 @@ version versionsuffix toolchain ``2017.4.196`` ``-GCC-6.4.0-2.28`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` +``2020a`` ``system`` ============== =================== ========== @@ -13913,11 +14428,12 @@ ichorCNA is a tool for estimating the fraction of tumor in cell-free DNA from ul *homepage*: https://github.com/broadinstitute/ichorCNA/wiki -========= ============== -version toolchain -========= ============== -``0.2.0`` ``foss/2019b`` -========= ============== +================== ============== +version toolchain +================== ============== +``0.2.0`` ``foss/2019b`` +``0.3.2-20191219`` ``foss/2020a`` +================== ============== .. _list_software_icmake_618: @@ -13968,6 +14484,7 @@ version toolchain ``64.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``65.1`` ``GCCcore/8.3.0`` ``66.1`` ``GCCcore/9.3.0`` +``67.1`` ``GCCcore/10.2.0`` ======== ==================================== @@ -13980,11 +14497,11 @@ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequen *homepage*: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/ -========= ==================================================== -version toolchain -========= ==================================================== -``1.1.3`` ``GCC/8.2.0-2.31.1``, ``foss/2018a``, ``foss/2018b`` -========= ==================================================== +========= =================================================================== +version toolchain +========= =================================================================== +``1.1.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2018a``, ``foss/2018b`` +========= =================================================================== .. _list_software_ieeg-cli_767: @@ -14090,6 +14607,7 @@ version toolchain ========= ================================================ ``0.7.1`` ``foss/2018b``, ``intel/2016b``, ``intel/2017b`` ``0.8.0`` ``foss/2019b`` +``0.8.2`` ``foss/2020a`` ========= ================================================ @@ -14209,9 +14727,26 @@ version toolchain ``2017b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` +``2020a`` ``system`` =========== ========== +.. _list_software_ILAMB_357: + +*ILAMB* ++++++++ + +The International Land Model Benchmarking (ILAMB) project is a model-data intercomparison and integration project designed to improve the performance of land models and, in parallel, improve the design of new measurement campaigns to reduce uncertainties associated with key land surface processes. + +*homepage*: https://www.ilamb.org/ + +======= ================= ============== +version versionsuffix toolchain +======= ================= ============== +``2.5`` ``-Python-3.8.2`` ``foss/2020a`` +======= ================= ============== + + .. _list_software_IMa2_297: *IMa2* @@ -14417,7 +14952,7 @@ version toolchain ``2019.3.199`` ``iimpi/2019.03`` ``2019.5.281`` ``iimpi/2019b``, ``iimpic/2019b`` ``2020.0.166`` ``iimpi/2020.00`` -``2020.1.217`` ``gompi/2020a``, ``iimpi/2020.06-impi-18.5``, ``iimpi/2020a``, ``iompi/2020a`` +``2020.1.217`` ``gompi/2020a``, ``iimpi/2020.06-impi-18.5``, ``iimpi/2020a``, ``iimpic/2020a``, ``iompi/2020a`` ============== ====================================================================================================================================================================================================================================================================== @@ -14511,7 +15046,7 @@ version versionsuffix toolchain ``2019.2.187`` ``iccifort/2019.2.187-GCC-8.2.0-2.31.1`` ``2019.3.199`` ``iccifort/2019.3.199-GCC-8.3.0-2.32`` ``2019.6.166`` ``iccifort/2020.0.166-GCC-9.2.0`` -``2019.7.217`` ``iccifort/2020.1.217`` +``2019.7.217`` ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` ``system`` ``iccifort/system-GCC-system-2.29`` ============== ============= ================================================================================================================================================================================================================================ @@ -14767,6 +15302,7 @@ version toolchain ``2017b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` +``2020a`` ``system`` =========== ========== @@ -14833,7 +15369,7 @@ intltool is a set of tools to centralize translation of many different file for ========== ================ ====================================================================================== version versionsuffix toolchain ========== ================ ====================================================================================== -``0.51.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.51.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.51.0`` ``-Perl-5.20.3`` ``intel/2016a`` ``0.51.0`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` ``0.51.0`` ``-Perl-5.24.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` @@ -15076,7 +15612,8 @@ version versionsuffix toolchain ``7.7.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``7.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``7.13.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``7.15.0`` ``-Python-3.8.2`` ``foss/2020a`` +``7.15.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``7.18.1`` ``GCCcore/10.2.0`` ========== ================== ======================================================================================= @@ -15112,6 +15649,7 @@ version versionsuffix toolchain ========== ========================== ================================== ``0.8.15`` ``-R-3.4.3-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.1`` ``-R-3.6.2-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.1`` ``-R-3.6.3-Python-3.8.2`` ``foss/2020a`` ========== ========================== ================================== @@ -15272,7 +15810,7 @@ version toolchain --- -:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyterhub_1106` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` +:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` .. _list_software_JAGS_293: @@ -15323,7 +15861,7 @@ version toolchain ``1.900.1`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``2.0.10`` ``intel/2016b`` ``2.0.12`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` -``2.0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.0.14`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` =========== ========================================================================================================================================================== @@ -15336,57 +15874,58 @@ Java Platform, Standard Edition (Java SE) lets you develop and deploy Java appl *homepage*: https://java.com/ -======================= ============= ========== -version versionsuffix toolchain -======================= ============= ========== -``1.6.0_24`` ``system`` -``1.7.0_10`` ``system`` -``1.7.0_15`` ``system`` -``1.7.0_21`` ``system`` -``1.7.0_40`` ``system`` -``1.7.0_45`` ``system`` -``1.7.0_60`` ``system`` -``1.7.0_75`` ``system`` -``1.7.0_76`` ``system`` -``1.7.0_79`` ``system`` -``1.7.0_80`` ``system`` -``1.8`` ``system`` -``1.8.0_20`` ``system`` -``1.8.0_25`` ``system`` -``1.8.0_31`` ``system`` -``1.8.0_40`` ``system`` -``1.8.0_45`` ``system`` -``1.8.0_60`` ``system`` -``1.8.0_65`` ``system`` -``1.8.0_66`` ``system`` -``1.8.0_72`` ``system`` -``1.8.0_74`` ``system`` -``1.8.0_77`` ``system`` -``1.8.0_92`` ``system`` -``1.8.0_112`` ``system`` -``1.8.0_121`` ``system`` -``1.8.0_131`` ``system`` -``1.8.0_141`` ``system`` -``1.8.0_144`` ``system`` -``1.8.0_152`` ``system`` -``1.8.0_162`` ``system`` -``1.8.0_172`` ``system`` -``1.8.0_181`` ``system`` -``1.8.0_192`` ``system`` -``1.8.0_202`` ``system`` -``1.8.0_212`` ``system`` -``1.8.0_221`` ``system`` -``1.8.0_231`` ``system`` -``1.8.0_241`` ``system`` -``1.8_191-b26-OpenJDK`` ``system`` -``1.9.0.4`` ``system`` -``11`` ``system`` -``11.0.2`` ``system`` -``11.0.6`` ``-ppc64le`` ``system`` -``11.0.8`` ``-aarch64`` ``system`` -``13`` ``system`` -``13.0.2`` ``system`` -======================= ============= ========== +============= ======================== ========== +version versionsuffix toolchain +============= ======================== ========== +``1.6.0_24`` ``system`` +``1.7.0_10`` ``system`` +``1.7.0_15`` ``system`` +``1.7.0_21`` ``system`` +``1.7.0_40`` ``system`` +``1.7.0_45`` ``system`` +``1.7.0_60`` ``system`` +``1.7.0_75`` ``system`` +``1.7.0_76`` ``system`` +``1.7.0_79`` ``system`` +``1.7.0_80`` ``system`` +``1.8`` ``system`` +``1.8.0_20`` ``system`` +``1.8.0_25`` ``system`` +``1.8.0_31`` ``system`` +``1.8.0_40`` ``system`` +``1.8.0_45`` ``system`` +``1.8.0_60`` ``system`` +``1.8.0_65`` ``system`` +``1.8.0_66`` ``system`` +``1.8.0_72`` ``system`` +``1.8.0_74`` ``system`` +``1.8.0_77`` ``system`` +``1.8.0_92`` ``system`` +``1.8.0_112`` ``system`` +``1.8.0_121`` ``system`` +``1.8.0_131`` ``system`` +``1.8.0_141`` ``system`` +``1.8.0_144`` ``system`` +``1.8.0_152`` ``system`` +``1.8.0_162`` ``system`` +``1.8.0_172`` ``system`` +``1.8.0_181`` ``system`` +``1.8.0_192`` ``system`` +``1.8.0_202`` ``system`` +``1.8.0_212`` ``system`` +``1.8.0_221`` ``system`` +``1.8.0_231`` ``system`` +``1.8.0_241`` ``system`` +``1.8_191`` ``-b26-OpenJDK`` ``system`` +``1.8_265`` ``-b01-OpenJDK-aarch64`` ``system`` +``1.9.0.4`` ``system`` +``11`` ``system`` +``11.0.2`` ``system`` +``11.0.6`` ``-ppc64le`` ``system`` +``11.0.8`` ``-aarch64`` ``system`` +``13`` ``system`` +``13.0.2`` ``system`` +============= ======================== ========== .. _list_software_JAXFrontCE_884: @@ -15559,6 +16098,7 @@ version toolchain ========== ================= ``0.10.7`` ``GCCcore/8.2.0`` ``1.9.3`` ``GCCcore/8.3.0`` +``1.9.4`` ``GCCcore/9.3.0`` ========== ================= @@ -15652,21 +16192,22 @@ version versionsuffix toolchain ======== =================== ========== -.. _list_software_jupyterhub_1106: +.. _list_software_JupyterHub_1042: -*jupyterhub* +*JupyterHub* ++++++++++++ JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs. -*homepage*: http://jupyter.org +*homepage*: https://jupyter.org -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``0.6.1`` ``-Python-3.5.1`` ``foss/2016a`` -``0.8.1`` ``-Python-3.6.4`` ``foss/2017a`` -========= ================= ============== +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``0.6.1`` ``-Python-3.5.1`` ``foss/2016a`` +``0.8.1`` ``-Python-3.6.4`` ``foss/2017a`` +``1.1.0`` ``GCCcore/10.2.0`` +========= ================= ================== .. _list_software_JupyterLab_1026: @@ -15682,6 +16223,7 @@ JupyterLab is the next-generation user interface for Project Jupyter offering al version versionsuffix toolchain ========= ================= ================================== ``1.2.5`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.2.8`` ``GCCcore/10.2.0`` ========= ================= ================================== @@ -15707,7 +16249,7 @@ version toolchain --- -:ref:`list_software_Kaiju_500` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_king_425` - :ref:`list_software_kma_313` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` +:ref:`list_software_Kaiju_500` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_kedro_533` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_king_425` - :ref:`list_software_kma_313` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` .. _list_software_Kaiju_500: @@ -15784,6 +16326,22 @@ version toolchain ========= ================================================================== +.. _list_software_kedro_533: + +*kedro* ++++++++ + +Kedro is an open-source Python framework that applies software engineering best-practice to data and machine-learning pipelines. + +*homepage*: https://github.com/quantumblacklabs/kedro + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.16.5`` ``-Python-3.8.2`` ``foss/2020a`` +========== ================= ============== + + .. _list_software_Kent_tools_1058: *Kent_tools* @@ -16019,13 +16577,13 @@ version versionsuffix toolchain Kratos Multiphysics (A.K.A Kratos) is a framework for building parallel multi-disciplinary simulation software. -*homepage*: http://www.cimne.com/kratos +*homepage*: https://www.cimne.com/kratos -======= ================= ============== -version versionsuffix toolchain -======= ================= ============== -``6.0`` ``-Python-3.6.4`` ``foss/2018a`` -======= ================= ============== +======= ================= =============================== +version versionsuffix toolchain +======= ================= =============================== +``6.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +======= ================= =============================== .. _list_software_KronaTools_1036: @@ -16115,7 +16673,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libpsml_755` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_limix-bgen_1004` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_limix-bgen_1004` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -16160,13 +16718,14 @@ LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale At *homepage*: https://lammps.sandia.gov/ -============ ======================== =============================== -version versionsuffix toolchain -============ ======================== =============================== -``3Mar2020`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` -``3Mar2020`` ``-Python-3.8.2-kokkos`` ``foss/2020a``, ``intel/2020a`` -``7Aug2019`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` -============ ======================== =============================== +============ ============================= =============================== +version versionsuffix toolchain +============ ============================= =============================== +``3Mar2020`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` +``3Mar2020`` ``-Python-3.8.2-kokkos`` ``foss/2020a``, ``intel/2020a`` +``7Aug2019`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` +``7Aug2019`` ``-Python-3.7.4-kokkos-OCTP`` ``intel/2019b`` +============ ============================= =============================== .. _list_software_lancet_631: @@ -16229,11 +16788,12 @@ lavaan is a free, open source R package for latent variable analysis *homepage*: http://lavaan.org -============== ============= ============== -version versionsuffix toolchain -============== ============= ============== -``0.6-4.1433`` ``-R-3.6.0`` ``foss/2019a`` -============== ============= ============== +============== ============= =============== +version versionsuffix toolchain +============== ============= =============== +``0.6-2`` ``-R-3.4.4`` ``intel/2018a`` +``0.6-4.1433`` ``-R-3.6.0`` ``foss/2019a`` +============== ============= =============== .. _list_software_LCov_372: @@ -16268,6 +16828,22 @@ version toolchain ========= ========== +.. _list_software_leidenalg_933: + +*leidenalg* ++++++++++++ + +Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python. + +*homepage*: https://github.com/vtraag/leidenalg + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.8.2`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_LEMON_379: *LEMON* @@ -16377,11 +16953,28 @@ Multi-format archive and compression library *homepage*: https://www.libarchive.org/ +========= ================== +version toolchain +========= ================== +``3.4.0`` ``GCCcore/8.2.0`` +``3.4.2`` ``GCCcore/9.3.0`` +``3.4.3`` ``GCCcore/10.2.0`` +========= ================== + + +.. _list_software_libav_526: + +*libav* ++++++++ + +Libav is a friendly and community-driven effort to provide its users with a set of portable, functional and high-performance libraries for dealing with multimedia formats of all sorts. + +*homepage*: https://libav.org/ + ========= ================= version toolchain ========= ================= -``3.4.0`` ``GCCcore/8.2.0`` -``3.4.2`` ``GCCcore/9.3.0`` +``11.10`` ``GCCcore/6.4.0`` ========= ================= @@ -16450,6 +17043,7 @@ An API to provide an efficient distributed queue on a cluster. libcircle is an version toolchain ============== ================================ ``0.2.1-rc.1`` ``gompi/2019a``, ``iimpi/2019a`` +``0.3`` ``gompi/2020a``, ``iimpi/2020a`` ============== ================================ @@ -16595,6 +17189,7 @@ version toolchain ``2.4.97`` ``GCCcore/8.2.0`` ``2.4.99`` ``GCCcore/8.3.0`` ``2.4.100`` ``GCCcore/9.3.0`` +``2.4.102`` ``GCCcore/10.2.0`` =========== ================================================== @@ -16658,12 +17253,13 @@ Epoxy is a library for handling OpenGL function pointer management for you *homepage*: https://github.com/anholt/libepoxy -========= ===================================== -version toolchain -========= ===================================== -``1.5.3`` ``GCCcore/8.2.0``, ``fosscuda/2018b`` -``1.5.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ===================================== +========= ======================================================== +version toolchain +========= ======================================================== +``1.5.2`` ``foss/2018a`` +``1.5.3`` ``GCCcore/8.2.0``, ``fosscuda/2018b`` +``1.5.4`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================== .. _list_software_libevent_857: @@ -16681,6 +17277,7 @@ version toolchain ``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` ``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` ``2.1.11`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.1.12`` ``GCCcore/10.2.0`` ========== ====================================================================================== @@ -16693,12 +17290,13 @@ Libfabric is a core component of OFI. It is the library that defines and exports *homepage*: https://ofiwg.github.io/libfabric/ -========== ================= -version toolchain -========== ================= -``1.9.1`` ``GCCcore/9.3.0`` -``1.10.1`` ``GCCcore/9.3.0`` -========== ================= +========== ===================================== +version toolchain +========== ===================================== +``1.9.1`` ``GCCcore/9.3.0`` +``1.10.1`` ``GCCcore/9.3.0`` +``1.11.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========== ===================================== .. _list_software_libffcall_927: @@ -16731,7 +17329,7 @@ The libffi library provides a portable, high level programming interface to var version toolchain ========= ============================================================================================================================================================================================================================================================================================================= ``3.2.1`` ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``system`` -``3.3`` ``GCCcore/9.3.0`` +``3.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================================================================================================================================================================================================================= @@ -16868,7 +17466,7 @@ version versionsuffix toolchain ========= ================ =========================================================================================================================================================================================================================================================================================================================================== ``9.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b``, ``iomkl/2018a`` ``9.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` -``9.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``9.0.1`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ================ =========================================================================================================================================================================================================================================================================================================================================== @@ -16879,12 +17477,13 @@ version versionsuffix toolchain libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. -*homepage*: https://github.com/NVIDIA/libglvnd +*homepage*: https://gitlab.freedesktop.org/glvnd/libglvnd ========= ======================================================= version toolchain ========= ======================================================= ``1.2.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.3.2`` ``GCCcore/10.2.0`` ========= ======================================================= @@ -17077,7 +17676,7 @@ version versionsuffix toolchain ``2.1.0`` ``intel/2016b`` ``2.4.2`` ``intel/2018a`` ``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` -``2.6.0`` ``-lmax-6-cp2k`` ``iimpi/2020a`` +``2.6.0`` ``-lmax-6-cp2k`` ``gompi/2020a``, ``iimpi/2020a`` ========= ================ ================================================================================================================================================================== @@ -17119,6 +17718,7 @@ version versionsuffix toolchain ``2.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.0.3`` ``GCCcore/8.3.0`` ``2.0.4`` ``GCCcore/9.3.0`` +``2.0.5`` ``GCCcore/10.2.0`` ========= ================= ================================================================== @@ -17170,6 +17770,38 @@ version toolchain ========== ==================================== +.. _list_software_libmo_unpack_1268: + +*libmo_unpack* +++++++++++++++ + +A library for handling the WGDOS and RLE compression schemes used in UM files. + +*homepage*: https://github.com/SciTools/libmo_unpack + +========= ================= +version toolchain +========= ================= +``3.1.2`` ``GCCcore/6.4.0`` +========= ================= + + +.. _list_software_libobjcryst_1191: + +*libobjcryst* ++++++++++++++ + +ObjCryst++ is Object-Oriented Crystallographic Library for C++ + +*homepage*: https://github.com/diffpy/libobjcryst + +============ =============== +version toolchain +============ =============== +``2017.2.3`` ``intel/2020a`` +============ =============== + + .. _list_software_libosmium_977: *libosmium* @@ -17201,7 +17833,7 @@ version toolchain ========== ============================================================================================= ``0.13.4`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.16`` ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``0.16`` ``GCCcore/10.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ========== ============================================================================================= @@ -17229,7 +17861,7 @@ version toolchain ``1.6.32`` ``GCCcore/6.4.0`` ``1.6.34`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.6.36`` ``GCCcore/8.2.0`` -``1.6.37`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.6.37`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ===================================================================== @@ -17250,22 +17882,6 @@ version toolchain ========== ==================================== -.. _list_software_libpsml_755: - -*libpsml* -+++++++++ - -LibPSML provides a Fortran API to parse files in the PSeudopotential Markup Language (PSML) format. - -*homepage*: https://launchpad.net/libpsml - -========= ============================== -version toolchain -========= ============================== -``1.1.7`` ``foss/2016b``, ``foss/2017a`` -========= ============================== - - .. _list_software_libPSML_627: *libPSML* @@ -17282,6 +17898,22 @@ version toolchain ========= ======================= +.. _list_software_libpsml_755: + +*libpsml* ++++++++++ + +LibPSML provides a Fortran API to parse files in the PSeudopotential Markup Language (PSML) format. + +*homepage*: https://launchpad.net/libpsml + +========= ============================== +version toolchain +========= ============================== +``1.1.7`` ``foss/2016b``, ``foss/2017a`` +========= ============================== + + .. _list_software_libpsortb_977: *libpsortb* @@ -17477,18 +18109,18 @@ Sodium is a modern, easy-to-use software library for encryption, decryption, sig *homepage*: https://doc.libsodium.org/ -========== ==================================== -version toolchain -========== ==================================== -``1.0.6`` ``intel/2016a`` -``1.0.8`` ``foss/2016a`` -``1.0.11`` ``foss/2016b``, ``intel/2016b`` -``1.0.12`` ``GCCcore/6.4.0``, ``intel/2017a`` -``1.0.13`` ``GCCcore/6.4.0``, ``foss/2017a`` -``1.0.16`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.0.17`` ``GCCcore/8.2.0`` -``1.0.18`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ==================================== +========== ======================================================== +version toolchain +========== ======================================================== +``1.0.6`` ``intel/2016a`` +``1.0.8`` ``foss/2016a`` +``1.0.11`` ``foss/2016b``, ``intel/2016b`` +``1.0.12`` ``GCCcore/6.4.0``, ``intel/2017a`` +``1.0.13`` ``GCCcore/6.4.0``, ``foss/2017a`` +``1.0.16`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.0.17`` ``GCCcore/8.2.0`` +``1.0.18`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ======================================================== .. _list_software_LibSoup_702: @@ -17627,7 +18259,7 @@ version toolchain ``4.0.8`` ``intel/2017a``, ``intel/2017b`` ``4.0.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018b`` ``4.0.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``4.1.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ========================================================================================================= @@ -17644,7 +18276,7 @@ Libtirpc is a port of Suns Transport-Independent RPC library to Linux. version toolchain ========= ==================================== ``1.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.2.6`` ``GCCcore/8.3.0`` +``1.2.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ==================================== @@ -17657,13 +18289,13 @@ GNU libtool is a generic library support script. Libtool hides the complexity of *homepage*: http://www.gnu.org/software/libtool -========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain -========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` -``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` -``2.4.6`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +version toolchain +========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` +``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``2.4.6`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_libunistring_1306: @@ -17700,6 +18332,7 @@ version toolchain ``1.1`` ``GCC/4.9.2``, ``foss/2016a``, ``intel/2016b`` ``1.2.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016b`` ``1.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.4.0`` ``GCCcore/10.2.0`` ========= ======================================================================= @@ -17811,11 +18444,11 @@ The libXau package contains a library implementing the X11 Authorization Protoco *homepage*: http://www.freedesktop.org/wiki/Software/xlibs -========= ================================================= -version toolchain -========= ================================================= -``1.0.8`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -========= ================================================= +========= ==================================================================== +version toolchain +========= ==================================================================== +``1.0.8`` ``GCCcore/6.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +========= ==================================================================== .. _list_software_libxc_530: @@ -17848,12 +18481,13 @@ version toolchain The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. -*homepage*: http://xcb.freedesktop.org/ +*homepage*: https://xcb.freedesktop.org/ ========== ================================================= version toolchain ========== ================================================= ``1.11.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``1.13`` ``GCCcore/6.4.0`` ========== ================================================= @@ -17898,11 +18532,11 @@ The libXdmcp package contains a library implementing the X Display Manager Contr *homepage*: http://www.freedesktop.org/wiki/Software/xlibs -========= ================================================= -version toolchain -========= ================================================= -``1.1.2`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -========= ================================================= +========= ==================================================================== +version toolchain +========= ==================================================================== +``1.1.2`` ``GCCcore/6.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +========= ==================================================================== .. _list_software_libXext_736: @@ -18060,7 +18694,7 @@ version versionsuffix toolchain ``2.9.7`` ``GCCcore/6.4.0`` ``2.9.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.9.9`` ``GCCcore/8.3.0`` -``2.9.10`` ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``2.9.10`` ``GCCcore/10.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ========== ================== ================================================================================================================================================================================== @@ -18202,7 +18836,7 @@ version toolchain ``1.8.2`` ``intel/2017b`` ``1.8.3`` ``foss/2018a``, ``intel/2018a`` ``1.10`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``1.16.1`` ``iccifort/2020.1.217`` +``1.16.1`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` ========== =============================================================================== @@ -18404,6 +19038,7 @@ version toolchain ``9.0.0`` ``GCCcore/8.3.0`` ``9.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``10.0.0`` ``GCCcore/8.3.0`` +``11.0.0`` ``GCCcore/10.2.0`` ========== ======================================================================== @@ -18565,12 +19200,12 @@ Longshot is a variant calling tool for diploid genomes using long error prone re *homepage*: https://github.com/pjedge/longshot -========= ================== -version toolchain -========= ================== -``0.3.4`` ``GCCcore/8.2.0`` -``0.4.1`` ``GCC/7.3.0-2.30`` -========= ================== +========= ===================================== +version toolchain +========= ===================================== +``0.3.4`` ``GCCcore/8.2.0`` +``0.4.1`` ``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` +========= ===================================== .. _list_software_lpsolve_773: @@ -18811,14 +19446,14 @@ LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s p *homepage*: https://lz4.github.io/lz4/ -========= ==================================== -version toolchain -========= ==================================== -``1.8.2`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0`` -``1.9.0`` ``GCCcore/7.3.0`` -``1.9.1`` ``GCCcore/8.2.0`` -``1.9.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ==================================== +========= ======================================================== +version toolchain +========= ======================================================== +``1.8.2`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0`` +``1.9.0`` ``GCCcore/7.3.0`` +``1.9.1`` ``GCCcore/8.2.0`` +``1.9.2`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================== .. _list_software_LZO_245: @@ -18830,12 +19465,12 @@ Portable lossless data compression library *homepage*: http://www.oberhumer.com/opensource/lzo/ -======== ================================================================================================================================================================================================================== -version toolchain -======== ================================================================================================================================================================================================================== -``2.09`` ``intel/2016b``, ``intel/2017b`` -``2.10`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` -======== ================================================================================================================================================================================================================== +======== ====================================================================================================================================================================================================================================== +version toolchain +======== ====================================================================================================================================================================================================================================== +``2.09`` ``intel/2016b``, ``intel/2017b`` +``2.10`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` +======== ====================================================================================================================================================================================================================================== .. _list_software_letter_m: @@ -18844,7 +19479,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_magma_515` - :ref:`list_software_MAGMA_355` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -18925,16 +19560,17 @@ MAFFT is a multiple sequence alignment program for unix-like operating systems. *homepage*: https://mafft.cbrc.jp/alignment/software/source.html -========= ==================== ====================================================================== -version versionsuffix toolchain -========= ==================== ====================================================================== -``7.305`` ``-with-extensions`` ``foss/2016b`` -``7.397`` ``-with-extensions`` ``intel/2018a`` -``7.427`` ``-with-extensions`` ``foss/2018b``, ``intel/2018b`` -``7.429`` ``-with-extensions`` ``GCC/8.2.0-2.31.1`` -``7.453`` ``-with-extensions`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``gompi/2020a``, ``iccifort/2019.5.281`` -``7.470`` ``-with-extensions`` ``GCC/9.3.0``, ``gompi/2020a`` -========= ==================== ====================================================================== +========= ==================== ======================================================================================= +version versionsuffix toolchain +========= ==================== ======================================================================================= +``7.305`` ``-with-extensions`` ``foss/2016b`` +``7.397`` ``-with-extensions`` ``intel/2018a`` +``7.427`` ``-with-extensions`` ``foss/2018b``, ``intel/2018b`` +``7.429`` ``-with-extensions`` ``GCC/8.2.0-2.31.1`` +``7.453`` ``-with-extensions`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``gompi/2020a``, ``iccifort/2019.5.281``, ``iimpi/2020a`` +``7.470`` ``-with-extensions`` ``GCC/9.3.0``, ``gompi/2020a`` +``7.471`` ``-with-extensions`` ``iimpi/2020a`` +========= ==================== ======================================================================================= .. _list_software_magick_620: @@ -18953,6 +19589,23 @@ version versionsuffix toolchain ======= ============= ============== +.. _list_software_MAGMA_355: + +*MAGMA* ++++++++ + +MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis. + +*homepage*: https://ctg.cncr.nl/software/magma + +========== ============== +version toolchain +========== ============== +``1.07b`` ``foss/2018b`` +``1.07bb`` ``GCC/8.3.0`` +========== ============== + + .. _list_software_magma_515: *magma* @@ -18973,23 +19626,6 @@ version versionsuffix toolchain ========= ================ ======================================= -.. _list_software_MAGMA_355: - -*MAGMA* -+++++++ - -MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis. - -*homepage*: https://ctg.cncr.nl/software/magma - -========== ============== -version toolchain -========== ============== -``1.07b`` ``foss/2018b`` -``1.07bb`` ``GCC/8.3.0`` -========== ============== - - .. _list_software_MagresPython_1249: *MagresPython* @@ -19089,6 +19725,22 @@ version toolchain ========= ============== +.. _list_software_makeinfo_842: + +*makeinfo* +++++++++++ + +makeinfo is part of the Texinfo project, the official documentation format of the GNU project. + +*homepage*: https://www.gnu.org/software/texinfo/ + +======= ==================================== +version toolchain +======= ==================================== +``6.7`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ==================================== + + .. _list_software_Mako_392: *Mako* @@ -19110,6 +19762,7 @@ version versionsuffix toolchain ``1.0.8`` ``GCCcore/8.2.0`` ``1.1.0`` ``GCCcore/8.3.0`` ``1.1.2`` ``GCCcore/9.3.0`` +``1.1.3`` ``GCCcore/10.2.0`` ========= ================== ================================================================================================================================================================= @@ -19444,6 +20097,22 @@ version versionsuffix toolchain ========= =================== =============== +.. _list_software_mauveAligner_1248: + +*mauveAligner* +++++++++++++++ + +Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research into comparative genomics and the study of genome-wide evolutionary dynamics. This version was built without Graphical User Interface. + +*homepage*: https://darlinglab.org/mauve/mauve.html + +======== =============== +version toolchain +======== =============== +``4736`` ``gompi/2020a`` +======== =============== + + .. _list_software_Maven_503: *Maven* @@ -19534,6 +20203,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_MBROLA_445: + +*MBROLA* +++++++++ + +MBROLA is a speech synthesizer based on the concatenation of diphones. It takes a list of phonemes as input, together with prosodic information (duration of phonemes and a piecewise linear description of pitch), and produces speech samples on 16 bits (linear), at the sampling frequency of the diphone database. MBROLA voices project provides list of MBROLA speech synthesizer voices. It is intended to provide easier collaboration and automatic updates for individual users and packagers. + +*homepage*: ['https://github.com/numediart/MBROLA', 'https://github.com/numediart/MBROLA-voices'] + +======= ==================== ================= +version versionsuffix toolchain +======= ==================== ================= +``3.3`` ``-voices-20200330`` ``GCCcore/9.3.0`` +======= ==================== ================= + + .. _list_software_mbuffer_743: *mbuffer* @@ -19652,13 +20337,46 @@ MDSplus is a set of software tools for data acquisition and storage and a method *homepage*: https://mdsplus.org/ -========== ================================ ================= -version versionsuffix toolchain -========== ================================ ================= -``7.0.67`` ``-Java-1.7.0_79-Python-2.7.11`` ``foss/2016a`` -``7.46.1`` ``foss/2018a`` -``7.96.8`` ``GCCcore/9.3.0`` -========== ================================ ================= +=========== ================================ ================= +version versionsuffix toolchain +=========== ================================ ================= +``7.0.67`` ``-Java-1.7.0_79-Python-2.7.11`` ``foss/2016a`` +``7.46.1`` ``foss/2018a`` +``7.96.8`` ``GCCcore/9.3.0`` +``7.96.12`` ``GCCcore/9.3.0`` +=========== ================================ ================= + + +.. _list_software_MDSplus-Java_1111: + +*MDSplus-Java* +++++++++++++++ + +MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data. + +*homepage*: https://mdsplus.org + +=========== ============= ================= +version versionsuffix toolchain +=========== ============= ================= +``7.96.12`` ``-Java-13`` ``GCCcore/9.3.0`` +=========== ============= ================= + + +.. _list_software_MDSplus-Python_1367: + +*MDSplus-Python* +++++++++++++++++ + +MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data. + +*homepage*: https://mdsplus.org + +=========== ================= ============== +version versionsuffix toolchain +=========== ================= ============== +``7.96.12`` ``-Python-3.8.2`` ``foss/2020a`` +=========== ================= ============== .. _list_software_mdtest_657: @@ -19692,7 +20410,7 @@ version versionsuffix toolchain ``1.9.1`` ``-Python-3.6.3`` ``intel/2017b`` ``1.9.2`` ``-Python-3.6.6`` ``intel/2018b`` ``1.9.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.9.4`` ``-Python-3.8.2`` ``intel/2020a`` +``1.9.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========= ================= =============================== @@ -19701,9 +20419,9 @@ version versionsuffix toolchain *medaka* ++++++++ -medaka is a tool to create a consensus sequence of nanopore sequencing data. +medaka is a tool to create a consensus sequence from nanopore sequencing data. -*homepage*: https://nanoporetech.github.io/medaka +*homepage*: https://github.com/nanoporetech/medaka ========== ================= ============== version versionsuffix toolchain @@ -19711,6 +20429,8 @@ version versionsuffix toolchain ``0.4.3`` ``-Python-3.6.6`` ``foss/2018b`` ``0.11.4`` ``-Python-3.6.6`` ``foss/2018b`` ``0.12.0`` ``-Python-3.6.6`` ``foss/2018b`` +``1.1.1`` ``-Python-3.7.4`` ``foss/2019b`` +``1.1.3`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================= ============== @@ -19812,6 +20532,7 @@ version versionsuffix toolchain ``1.1.4`` ``-Python-2.7.15`` ``foss/2018b`` ``1.1.4`` ``-Python-3.6.6`` ``foss/2018b`` ``1.2.8`` ``GCCcore/8.2.0`` +``1.2.9`` ``GCCcore/9.3.0`` ========= ================== ============================== @@ -19971,6 +20692,7 @@ version toolchain ``19.1.7`` ``GCCcore/8.3.0`` ``19.2.1`` ``GCCcore/8.3.0`` ``20.0.2`` ``GCCcore/9.3.0`` +``20.2.1`` ``GCCcore/10.2.0`` ========== ==================================================================== @@ -20013,6 +20735,7 @@ version versionsuffix toolchain ``0.53.1`` ``-Python-3.6.3`` ``intel/2017b`` ``0.53.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``0.55.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``0.55.3`` ``GCCcore/10.2.0`` ========== ================= ================================== @@ -20684,6 +21407,7 @@ version toolchain ``5-9375b`` ``intel/2018a`` ``8-fac81`` ``intel/2018b`` ``10-6d92c`` ``gompi/2019b``, ``iimpi/2019b`` +``11-e1a1c`` ``iimpi/2019b`` ============ ================================ @@ -21112,11 +21836,13 @@ MPI-Based File Utilities For Distributed Systems *homepage*: https://hpc.github.io/mpifileutils/ -========= ================================ -version toolchain -========= ================================ -``0.9.1`` ``gompi/2019a``, ``iimpi/2019a`` -========= ================================ +========== ================================ +version toolchain +========== ================================ +``0.9.1`` ``gompi/2019a``, ``iimpi/2019a`` +``0.10`` ``gompi/2020a``, ``iimpi/2020a`` +``0.10.1`` ``gompi/2020a`` +========== ================================ .. _list_software_mpiP_406: @@ -21217,9 +21943,9 @@ version versionsuffix toolchain =================== ================== =============== ``0.3.14`` ``-Python-2.7.11`` ``intel/2016a`` ``0.3.15`` ``-Python-2.7.12`` ``intel/2016b`` -``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` ``3.0-rc-20191217`` ``-Python-2.7.16`` ``foss/2019b`` ``3.0-rc-20191217`` ``-Python-3.7.4`` ``foss/2019b`` +``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` ``3.0_RC2`` ``-Python-2.7.13`` ``foss/2017a`` ``3.0_RC3`` ``-Python-2.7.14`` ``intel/2018a`` =================== ================== =============== @@ -21358,12 +22084,12 @@ MUMmer is a system for rapidly aligning entire genomes, whether in complete or *homepage*: http://mummer.sourceforge.net/ -============== ============== -version toolchain -============== ============== -``3.23`` ``foss/2016b`` -``4.0.0beta2`` ``foss/2018b`` -============== ============== +============== ================================= +version toolchain +============== ================================= +``3.23`` ``GCCcore/9.3.0``, ``foss/2016b`` +``4.0.0beta2`` ``GCCcore/9.3.0``, ``foss/2018b`` +============== ================================= .. _list_software_MUMPS_402: @@ -21535,6 +22261,22 @@ version versionsuffix toolchain ========= ========================== ============== +.. _list_software_MyCC_332: + +*MyCC* +++++++ + +MyCC is built and delivered as a tailored solution for metagenomics sequencesclassfication. + +*homepage*: https://sourceforge.net/projects/sb2nhri/files/MyCC/ + +============== ================== =============== +version versionsuffix toolchain +============== ================== =============== +``2017-03-01`` ``-Python-2.7.16`` ``intel/2019b`` +============== ================== =============== + + .. _list_software_mygene_645: *mygene* @@ -21661,7 +22403,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -21706,16 +22448,17 @@ NAMD is a parallel molecular dynamics code designed for high-performance simulat *homepage*: https://www.ks.uiuc.edu/Research/namd/ -======== ============= ================================================================ -version versionsuffix toolchain -======== ============= ================================================================ -``2.11`` ``-mpi`` ``intel/2016a`` -``2.12`` ``-mpi`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``2.13`` ``fosscuda/2018b`` -``2.13`` ``-mpi`` ``foss/2018b``, ``foss/2019b``, ``intel/2018b`` -``2.14`` ``fosscuda/2019b`` -``2.14`` ``-mpi`` ``foss/2019b``, ``foss/2020a``, ``intel/2020a`` -======== ============= ================================================================ +======== ================ ================================================================ +version versionsuffix toolchain +======== ================ ================================================================ +``2.11`` ``-mpi`` ``intel/2016a`` +``2.12`` ``-CUDA-8.0.61`` ``foss/2016b`` +``2.12`` ``-mpi`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``2.13`` ``fosscuda/2018b`` +``2.13`` ``-mpi`` ``foss/2018b``, ``foss/2019b``, ``intel/2018b`` +``2.14`` ``fosscuda/2019b`` +``2.14`` ``-mpi`` ``foss/2019b``, ``foss/2020a``, ``intel/2020a`` +======== ================ ================================================================ .. _list_software_NanoComp_795: @@ -21734,22 +22477,6 @@ version versionsuffix toolchain ========== ================= =============== -.. _list_software_nanofilt_859: - -*nanofilt* -++++++++++ - -Filtering and trimming of long read sequencing data. - -*homepage*: https://github.com/wdecoster/nanofilt - -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``2.5.0`` ``-Python-3.6.6`` ``foss/2018b`` -========= ================= ============== - - .. _list_software_NanoFilt_795: *NanoFilt* @@ -21766,6 +22493,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_nanofilt_859: + +*nanofilt* +++++++++++ + +Filtering and trimming of long read sequencing data. + +*homepage*: https://github.com/wdecoster/nanofilt + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``2.5.0`` ``-Python-3.6.6`` ``foss/2018b`` +========= ================= ============== + + .. _list_software_nanoget_748: *nanoget* @@ -21798,6 +22541,22 @@ version versionsuffix toolchain ========== ================= =============== +.. _list_software_nanomax-analysis-utils_2273: + +*nanomax-analysis-utils* +++++++++++++++++++++++++ + +A set of tools for handling and analysing data at the NanoMAX beamline. + +*homepage*: https://github.com/maxiv-science/nanomax-analysis-utils + +======= ================= ================================== +version versionsuffix toolchain +======= ================= ================================== +``0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +======= ================= ================================== + + .. _list_software_nanonet_755: *nanonet* @@ -21866,6 +22625,7 @@ version toolchain ``2.13.01`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``2.13.03`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.14.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.15.05`` ``GCCcore/10.2.0`` =========== ==================================================================================== @@ -22097,7 +22857,7 @@ version toolchain *ncurses* +++++++++ -The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. +The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. *homepage*: https://www.gnu.org/software/ncurses/ @@ -22107,7 +22867,7 @@ version toolchain ``5.9`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25``, ``gimkl/2.11.5``, ``system`` ``6.0`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``6.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` -``6.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``6.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0``, ``system`` ======= ============================================================================================================================================================================================================================================================================================================================================================================= @@ -22175,6 +22935,22 @@ version versionsuffix toolchain ======= ============== ========== +.. _list_software_Nek5000_483: + +*Nek5000* ++++++++++ + +a fast and scalable high-order solver for computational fluid dynamics + +*homepage*: https://nek5000.mcs.anl.gov/ + +======== =============== +version toolchain +======== =============== +``17.0`` ``intel/2018a`` +======== =============== + + .. _list_software_Net-core_765: *Net-core* @@ -22410,7 +23186,7 @@ version toolchain Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. -*homepage*: http://www.lysator.liu.se/~nisse/nettle/ +*homepage*: https://www.lysator.liu.se/~nisse/nettle/ ========= =========================================================================================================================================== version toolchain @@ -22421,6 +23197,7 @@ version toolchain ``3.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018a`` ``3.4.1`` ``GCCcore/8.2.0`` ``3.5.1`` ``GCCcore/8.3.0`` +``3.6`` ``GCCcore/9.3.0`` ========= =========================================================================================================================================== @@ -22433,23 +23210,23 @@ NetworkX is a Python package for the creation, manipulation, and study of the st *homepage*: https://pypi.python.org/pypi/networkx -======== ================== =============================================== -version versionsuffix toolchain -======== ================== =============================================== -``1.1`` ``-Python-2.7.12`` ``intel/2016b`` -``1.11`` ``-Python-2.7.11`` ``foss/2016a`` -``1.11`` ``-Python-2.7.14`` ``intel/2017b`` -``1.11`` ``-Python-3.5.1`` ``foss/2016a`` -``2.0`` ``-Python-2.7.14`` ``intel/2017b`` -``2.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b`` -``2.2`` ``-Python-2.7.16`` ``foss/2019b`` -``2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``2.4`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``2.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -======== ================== =============================================== +======== ================== =================================================== +version versionsuffix toolchain +======== ================== =================================================== +``1.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.11`` ``-Python-2.7.11`` ``foss/2016a`` +``1.11`` ``-Python-2.7.14`` ``intel/2017b`` +``1.11`` ``-Python-3.5.1`` ``foss/2016a`` +``2.0`` ``-Python-2.7.14`` ``intel/2017b`` +``2.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b`` +``2.2`` ``-Python-2.7.16`` ``foss/2019b`` +``2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``2.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +======== ================== =================================================== .. _list_software_NeuroKit_817: @@ -22534,6 +23311,7 @@ The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transf version toolchain ========= ============================== ``3.5.1`` ``foss/2018b``, ``foss/2019a`` +``3.5.2`` ``foss/2020a`` ========= ============================== @@ -22566,6 +23344,7 @@ IPython widget to interactively view molecular structures and trajectories. version versionsuffix toolchain ========= ================= =============== ``2.7.0`` ``-Python-3.7.2`` ``intel/2019a`` +``2.7.7`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================= =============== @@ -22766,6 +23545,7 @@ version toolchain ``1.8.2`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017b``, ``intel/2018a`` ``1.9.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` ``1.10.0`` ``GCCcore/9.3.0`` +``1.10.1`` ``GCCcore/10.2.0`` ========== ==================================================================================== @@ -22871,6 +23651,7 @@ version toolchain ``10.15.1`` ``foss/2018b`` ``10.15.3`` ``GCCcore/8.2.0`` ``12.16.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``12.19.0`` ``GCCcore/10.2.0`` =========== ======================================================= @@ -22990,6 +23771,7 @@ version toolchain ``4.20`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``4.21`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``4.25`` ``GCCcore/9.3.0`` +``4.29`` ``GCCcore/10.2.0`` ======== ==================================== @@ -23009,6 +23791,7 @@ version toolchain ``3.42.1`` ``GCCcore/8.2.0`` ``3.45`` ``GCCcore/8.3.0`` ``3.51`` ``GCCcore/9.3.0`` +``3.57`` ``GCCcore/10.2.0`` ========== ==================================== @@ -23021,11 +23804,11 @@ nsync is a C library that exports various synchronization primitives, such as mu *homepage*: https://github.com/google/nsync -========== ================= -version toolchain -========== ================= -``1.24.0`` ``GCCcore/8.3.0`` -========== ================= +========== ==================================== +version toolchain +========== ==================================== +``1.24.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ==================================== .. _list_software_ntCard_604: @@ -23108,7 +23891,7 @@ version toolchain ``2.0.10`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25`` ``2.0.11`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.3.0-2.26``, ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``GCC/6.2.0-2.27``, ``GCC/6.3.0-2.27``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` ``2.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2.0.13`` ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``2.0.13`` ``GCCcore/10.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ========== ============================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -23246,7 +24029,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_orca_421` - :ref:`list_software_ORCA_293` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_orca_421` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -23550,6 +24333,7 @@ version versionsuffix toolchain ``4.0.1`` ``-Python-2.7.15`` ``foss/2018b`` ``4.0.1`` ``-Python-3.6.6`` ``foss/2018b`` ``4.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``4.2.0`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================== ================================================================ @@ -23597,32 +24381,32 @@ OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive *homepage*: https://www.openfoam.com/ -================ ============= ================================================ -version versionsuffix toolchain -================ ============= ================================================ -``2.2.2`` ``intel/2016a``, ``intel/2017a`` -``2.2.x`` ``intel/2019a`` -``2.3.1`` ``intel/2017a``, ``intel/2019b`` -``2.4.0`` ``intel/2017a``, ``intel/2019a`` -``3.0.0`` ``foss/2016a`` -``3.0.1`` ``intel/2016b``, ``intel/2018a`` -``4.0`` ``foss/2016b``, ``intel/2016b`` -``4.1`` ``foss/2016b``, ``intel/2017a`` -``5.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``5.0-20180108`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``6`` ``foss/2018b``, ``foss/2019b``, ``intel/2018a`` -``7`` ``foss/2019b`` -``7`` ``-20200508`` ``foss/2019b`` -``8`` ``foss/2020a`` -``v1606+`` ``foss/2018b`` -``v1612+`` ``foss/2018b`` -``v1712`` ``foss/2017b``, ``intel/2017b`` -``v1806`` ``foss/2018b`` -``v1812`` ``foss/2018b`` -``v1906`` ``foss/2019b`` -``v1912`` ``foss/2019b``, ``intel/2019b`` -``v2006`` ``foss/2020a`` -================ ============= ================================================ +================ ============= ================================================= +version versionsuffix toolchain +================ ============= ================================================= +``2.2.2`` ``intel/2016a``, ``intel/2017a``, ``intel/2018a`` +``2.2.x`` ``intel/2019a`` +``2.3.1`` ``intel/2017a``, ``intel/2019b`` +``2.4.0`` ``intel/2017a``, ``intel/2019a`` +``3.0.0`` ``foss/2016a`` +``3.0.1`` ``intel/2016b``, ``intel/2018a`` +``4.0`` ``foss/2016b``, ``intel/2016b`` +``4.1`` ``foss/2016b``, ``intel/2017a`` +``5.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``5.0-20180108`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``6`` ``foss/2018b``, ``foss/2019b``, ``intel/2018a`` +``7`` ``foss/2019b`` +``7`` ``-20200508`` ``foss/2019b`` +``8`` ``foss/2020a`` +``v1606+`` ``foss/2018b`` +``v1612+`` ``foss/2018b`` +``v1712`` ``foss/2017b``, ``intel/2017b`` +``v1806`` ``foss/2018b`` +``v1812`` ``foss/2018b`` +``v1906`` ``foss/2019b`` +``v1912`` ``foss/2019b``, ``intel/2019b`` +``v2006`` ``foss/2020a`` +================ ============= ================================================= .. _list_software_OpenFOAM-Extend_1354: @@ -23671,14 +24455,15 @@ OpenImageIO is a library for reading and writing images, and a bunch of related *homepage*: https://openimageio.org/ -========== ================================ -version toolchain -========== ================================ -``1.6.17`` ``intel/2016b`` -``1.7.17`` ``intel/2017a`` -``1.8.16`` ``foss/2018b``, ``intel/2018b`` -``2.0.12`` ``gompi/2019b``, ``iimpi/2019b`` -========== ================================ +============ ================================ +version toolchain +============ ================================ +``1.6.17`` ``intel/2016b`` +``1.7.17`` ``intel/2017a`` +``1.8.16`` ``foss/2018b``, ``intel/2018b`` +``2.0.12`` ``gompi/2019b``, ``iimpi/2019b`` +``2.1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` +============ ================================ .. _list_software_OpenJPEG_696: @@ -23825,8 +24610,8 @@ version versionsuffix toolchain ``4.0.0`` ``-hpcx`` ``GCC/8.2.0-2.31.1`` ``4.0.1`` ``GCC/8.3.0-2.32`` ``4.0.2`` ``GCC/9.2.0-2.32`` -``4.0.3`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` -``4.0.5`` ``GCC/9.3.0`` +``4.0.3`` ``GCC/9.3.0``, ``gcccuda/2020a``, ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` +``4.0.5`` ``GCC/10.2.0``, ``GCC/9.3.0`` ``system`` ``GCC/system-2.29`` ========== ============= ==================================================================================================================== @@ -23872,11 +24657,11 @@ OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM *homepage*: http://code.google.com/p/openpgm/ -=========== ================================================================================================================================================================================================ -version toolchain -=========== ================================================================================================================================================================================================ -``5.2.122`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -=========== ================================================================================================================================================================================================ +=========== ==================================================================================================================================================================================================================== +version toolchain +=========== ==================================================================================================================================================================================================================== +``5.2.122`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +=========== ==================================================================================================================================================================================================================== .. _list_software_OpenPIV_641: @@ -23922,11 +24707,12 @@ OpenRefine is a power tool that allows you to load data, understand it, clean it *homepage*: https://github.com/OpenRefine/OpenRefine -======= =================== ========== -version versionsuffix toolchain -======= =================== ========== -``2.7`` ``-Java-1.8.0_144`` ``system`` -======= =================== ========== +========= =================== ========== +version versionsuffix toolchain +========= =================== ========== +``2.7`` ``-Java-1.8.0_144`` ``system`` +``3.4.1`` ``-Java-11`` ``system`` +========= =================== ========== .. _list_software_OpenSlide_899: @@ -23985,6 +24771,7 @@ version toolchain ``1.1.1b`` ``GCCcore/8.2.0`` ``1.1.1d`` ``GCCcore/8.3.0`` ``1.1.1e`` ``GCCcore/9.3.0`` +``1.1.1h`` ``GCCcore/10.2.0`` ========== ===================================================================== @@ -24004,6 +24791,22 @@ version versionsuffix toolchain ========= ================ =============================== +.. _list_software_OPERA-MS_580: + +*OPERA-MS* +++++++++++ + +OPERA-MS is a hybrid metagenomic assembler which combines the advantages of short and long-read technologies to provide high quality assemblies, addressing issues of low contiguity for short-read only assemblies, and low base-pair quality for long-read only assemblies. + +*homepage*: https://github.com/CSB5/OPERA-MS + +================== ================= ============== +version versionsuffix toolchain +================== ================= ============== +``0.9.0-20200802`` ``-Python-3.8.2`` ``foss/2020a`` +================== ================= ============== + + .. _list_software_OptiType_830: *OptiType* @@ -24055,6 +24858,27 @@ version versionsuffix toolchain ======= ================= ============== +.. _list_software_ORCA_293: + +*ORCA* +++++++ + +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. + +*homepage*: https://orcaforum.kofo.mpg.de + +====================== ================== =============== +version versionsuffix toolchain +====================== ================== =============== +``3_0_2-linux_x86-64`` ``-OpenMPI-1.8.1`` ``system`` +``4.0.0.2`` ``-OpenMPI-2.0.2`` ``system`` +``4.0.1`` ``-OpenMPI-2.0.2`` ``system`` +``4.1.0`` ``-OpenMPI-3.1.3`` ``system`` +``4.2.0`` ``gompi/2019b`` +``4.2.1`` ``gompi/2019b`` +====================== ================== =============== + + .. _list_software_orca_421: *orca* @@ -24071,25 +24895,20 @@ version toolchain ========= ================= -.. _list_software_ORCA_293: +.. _list_software_ORFfinder_863: -*ORCA* -++++++ +*ORFfinder* ++++++++++++ -ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. +ORF finder searches for open reading frames (ORFs) in the DNA sequence you enter. The program returns the range of each ORF, along with its protein translation. Use ORF finder to search newly sequenced DNA for potential protein encoding segments, verify predicted protein using newly developed SMART BLAST or regular BLASTP. -*homepage*: https://orcaforum.kofo.mpg.de +*homepage*: https://www.ncbi.nlm.nih.gov/orffinder/ -====================== ================== =============== -version versionsuffix toolchain -====================== ================== =============== -``3_0_2-linux_x86-64`` ``-OpenMPI-1.8.1`` ``system`` -``4.0.0.2`` ``-OpenMPI-2.0.2`` ``system`` -``4.0.1`` ``-OpenMPI-2.0.2`` ``system`` -``4.1.0`` ``-OpenMPI-3.1.3`` ``system`` -``4.2.0`` ``gompi/2019b`` -``4.2.1`` ``gompi/2019b`` -====================== ================== =============== +========= ========== +version toolchain +========= ========== +``0.4.3`` ``system`` +========= ========== .. _list_software_OrfM_372: @@ -24168,14 +24987,15 @@ version toolchain OSU Micro-Benchmarks -*homepage*: http://mvapich.cse.ohio-state.edu/benchmarks/ +*homepage*: https://mvapich.cse.ohio-state.edu/benchmarks/ -========= ============================== -version toolchain -========= ============================== -``5.3.2`` ``foss/2016a``, ``foss/2017a`` -``5.6.2`` ``gompi/2019a`` -========= ============================== +========= ========================================================================================================================= +version toolchain +========= ========================================================================================================================= +``5.3.2`` ``foss/2016a``, ``foss/2017a`` +``5.6.2`` ``gompi/2019a`` +``5.6.3`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpic/2019b``, ``iimpic/2020a`` +========= ========================================================================================================================= .. _list_software_OTF2_283: @@ -24234,7 +25054,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_pip_329` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -24334,6 +25154,7 @@ PAML is a package of programs for phylogenetic analyses of DNA or protein sequ version toolchain ======== ========================================================== ``4.9i`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +``4.9j`` ``GCCcore/9.3.0`` ======== ========================================================== @@ -24360,6 +25181,7 @@ version versionsuffix toolchain ``0.20.1`` ``-Python-3.6.1`` ``intel/2017a`` ``0.21.0`` ``-Python-2.7.13`` ``intel/2017a`` ``0.21.0`` ``-Python-3.6.3`` ``intel/2017b`` +``1.1.2`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================== =============================== @@ -24437,6 +25259,7 @@ version toolchain ``1.42.4`` ``foss/2018b``, ``fosscuda/2018b`` ``1.43.0`` ``GCCcore/8.2.0`` ``1.44.7`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.47.0`` ``GCCcore/10.2.0`` =========== ==================================== @@ -24623,11 +25446,11 @@ ParMETIS is an MPI-based parallel library that implements a variety of algorithm *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview -========= ========================================================================================================================================================================================================================================================================================== -version toolchain -========= ========================================================================================================================================================================================================================================================================================== -``4.0.3`` ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -========= ========================================================================================================================================================================================================================================================================================== +========= ============================================================================================================================================================================================================================================================================================================================ +version toolchain +========= ============================================================================================================================================================================================================================================================================================================================ +``4.0.3`` ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +========= ============================================================================================================================================================================================================================================================================================================================ .. _list_software_ParMGridGen_1040: @@ -24845,6 +25668,7 @@ version versionsuffix toolchain ``4.6.0`` ``system`` ``4.6.0`` ``-Python-2.7.11`` ``intel/2016a`` ``4.6.0`` ``-Python-2.7.12`` ``intel/2016b`` +``4.6.0`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== @@ -24928,6 +25752,7 @@ version versionsuffix toolchain ``1.1.4`` ``-Python-2.7.11`` ``intel/2016a`` ``1.2.3`` ``-Python-3.6.6`` ``foss/2018b`` ``1.2.3`` ``-Python-3.7.2`` ``gompi/2019a`` +``1.2.3`` ``-Python-3.7.4`` ``iimpi/2019b`` ``20160205`` ``-Python-2.7.11`` ``intel/2016a`` ============ ================== =============== @@ -24964,8 +25789,9 @@ version toolchain ``8.39`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` ``8.40`` ``GCCcore/6.3.0``, ``gimkl/2017a``, ``intel/2016b``, ``intel/2017a`` ``8.41`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``8.42`` ``GCCcore/6.4.0`` ``8.43`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``8.44`` ``GCCcore/9.3.0`` +``8.44`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ======== ================================================================================== @@ -24985,6 +25811,7 @@ version toolchain ``10.31`` ``foss/2018b`` ``10.33`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``10.34`` ``GCCcore/9.3.0`` +``10.35`` ``GCCcore/10.2.0`` ========= ==================================== @@ -25328,6 +26155,22 @@ version versionsuffix toolchain ======= ================== ============== +.. _list_software_phonemizer_1089: + +*phonemizer* +++++++++++++ + +The phonemizer allows simple phonemization of words and texts in many languages. Provides both the phonemize command-line tool and the Python function phonemizer.phonemize. It is using four backends: espeak, espeak-mbrola, festival and segments. + +*homepage*: https://github.com/bootphon/phonemizer + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``2.2.1`` ``-Python-3.8.2`` ``gompi/2020a`` +========= ================= =============== + + .. _list_software_phono3py_832: *phono3py* @@ -25352,7 +26195,7 @@ version versionsuffix toolchain Phonopy is an open source package of phonon calculations based on the supercell approach. -*homepage*: http://atztogo.github.io/phonopy/ +*homepage*: https://atztogo.github.io/phonopy/ ============= ================== =============================== version versionsuffix toolchain @@ -25364,6 +26207,7 @@ version versionsuffix toolchain ``1.14.2`` ``-Python-2.7.15`` ``intel/2018b`` ``2.0.0`` ``-Python-2.7.14`` ``intel/2018a`` ``2.2.0`` ``-Python-3.7.2`` ``intel/2019a`` +``2.7.1`` ``-Python-3.8.2`` ``intel/2020a`` ============= ================== =============================== @@ -25499,6 +26343,7 @@ version versionsuffix toolchain ``2.20.6`` ``-Java-1.8`` ``system`` ``2.21.1`` ``-Java-11`` ``system`` ``2.21.6`` ``-Java-11`` ``system`` +``2.22.1`` ``-Java-11`` ``system`` =========== =================== ========== @@ -25511,13 +26356,13 @@ pigz, which stands for parallel implementation of gzip, is a fully functional *homepage*: https://zlib.net/pigz/ -========= ========================================================================================== -version toolchain -========= ========================================================================================== -``2.3.3`` ``foss/2016b`` -``2.3.4`` ``GCCcore/6.4.0`` -``2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018a`` -========= ========================================================================================== +========= ================================================================================================================================= +version toolchain +========= ================================================================================================================================= +``2.3.3`` ``foss/2016b`` +``2.3.4`` ``GCCcore/6.4.0`` +``2.4`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` +========= ================================================================================================================================= .. _list_software_PIL_229: @@ -25660,6 +26505,38 @@ version toolchain ==================== ================== +.. _list_software_Pingouin_841: + +*Pingouin* +++++++++++ + +Pingouin is an open-source statistical package written in Python 3 and based mostly on Pandas and NumPy. + +*homepage*: https://pingouin-stats.org/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.3.8`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + +.. _list_software_Pint_411: + +*Pint* +++++++ + +Pint is a Python package to define, operate and manipulate physical quantities: the product of a numerical value and a unit of measurement. It allows arithmetic operations between them and conversions from and to different units. + +*homepage*: https://github.com/hgrecco/pint + +======== ================= ================= +version versionsuffix toolchain +======== ================= ================= +``0.14`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +======== ================= ================= + + .. _list_software_pip_329: *pip* @@ -25757,6 +26634,7 @@ version toolchain ``0.34.0`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``0.38.0`` ``GCCcore/8.2.0`` ``0.38.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.40.0`` ``GCCcore/10.2.0`` ========== ============================================================================================================================================ @@ -25785,14 +26663,14 @@ pkg-config is a helper tool used when compiling applications and libraries. It *homepage*: http://www.freedesktop.org/wiki/Software/pkg-config/ -========== =========================================================================================================================================================================== -version toolchain -========== =========================================================================================================================================================================== -``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` -``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``0.29.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a``, ``system`` -========== =========================================================================================================================================================================== +========== ==================================================================================================================================================================================== +version toolchain +========== ==================================================================================================================================================================================== +``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` +``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``0.29.2`` ``GCCcore/10.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a``, ``system`` +========== ==================================================================================================================================================================================== .. _list_software_pkgconfig_952: @@ -25952,6 +26830,7 @@ version toolchain =========================== ============================== ``1.07`` ``foss/2016a``, ``foss/2016b`` ``1.07-x86_64`` ``system`` +``1.9b5`` ``golf/2020a`` ``1.9b_4.1-x86_64`` ``system`` ``1.9b_6.17-x86_64`` ``system`` ``2.00-alpha1-x86_64`` ``system`` @@ -26112,7 +26991,7 @@ version toolchain ``3.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``3.1.4`` ``GCCcore/8.3.0`` -``3.1.5`` ``GCCcore/9.3.0`` +``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= ======================================================= @@ -26522,6 +27401,7 @@ PyYAML-based python module to produce pretty and readable YAML-serialized data. version toolchain =========== ================= ``19.12.0`` ``GCCcore/8.3.0`` +``20.4.0`` ``GCCcore/9.3.0`` =========== ================= @@ -26615,12 +27495,12 @@ Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbi *homepage*: https://github.com/hyattpd/Prodigal/ -========= ========================================================================== -version toolchain -========= ========================================================================== -``2.6.2`` ``GCC/4.9.3-binutils-2.25`` -``2.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= ========================================================================== +========= ============================================================================================= +version toolchain +========= ============================================================================================= +``2.6.2`` ``GCC/4.9.3-binutils-2.25`` +``2.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ============================================================================================= .. _list_software_PROJ_315: @@ -26789,6 +27669,7 @@ version toolchain ``3.6.1.2`` ``GCCcore/8.2.0`` ``3.7.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.10.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``3.13.0`` ``GCCcore/9.3.0`` =========== =================================================== @@ -26818,6 +27699,7 @@ version versionsuffix toolchain ``3.6.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``3.6.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``3.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``3.13.0`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================== ================================== @@ -26905,6 +27787,8 @@ version versionsuffix toolchain ``1.0`` ``-mt-Python-2.7.11`` ``intel/2016a`` ``1.2.1`` ``-Python-2.7.15`` ``intel/2018b`` ``1.2.1`` ``-Python-2.7.15-maxam8`` ``intel/2018b`` +``1.3.1`` ``-Python-3.7.2`` ``foss/2019a`` +``1.3.2`` ``-Python-3.7.4`` ``intel/2019b`` ========= ========================= =============== @@ -27274,18 +28158,18 @@ Python bindings for the cairo library *homepage*: https://pycairo.readthedocs.io/ -========== ================== ================= -version versionsuffix toolchain -========== ================== ================= -``1.10.0`` ``-Python-2.7.11`` ``intel/2016a`` -``1.16.1`` ``-Python-3.6.3`` ``foss/2017b`` -``1.16.2`` ``-Python-2.7.14`` ``intel/2017b`` -``1.18.0`` ``-Python-2.7.14`` ``intel/2018a`` -``1.18.0`` ``-Python-2.7.15`` ``foss/2018b`` -``1.18.0`` ``-Python-3.6.6`` ``foss/2018b`` -``1.18.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``1.18.2`` ``GCCcore/8.3.0`` -========== ================== ================= +========== ================== ==================================== +version versionsuffix toolchain +========== ================== ==================================== +``1.10.0`` ``-Python-2.7.11`` ``intel/2016a`` +``1.16.1`` ``-Python-3.6.3`` ``foss/2017b`` +``1.16.2`` ``-Python-2.7.14`` ``intel/2017b`` +``1.18.0`` ``-Python-2.7.14`` ``intel/2018a`` +``1.18.0`` ``-Python-2.7.15`` ``foss/2018b`` +``1.18.0`` ``-Python-3.6.6`` ``foss/2018b`` +``1.18.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``1.18.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ================== ==================================== .. _list_software_PyCharm_692: @@ -27381,14 +28265,15 @@ PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python. *homepage*: https://mathema.tician.de/software/pycuda -============ ============================= ======================================= -version versionsuffix toolchain -============ ============================= ======================================= -``2016.1.2`` ``-Python-2.7.12`` ``intel/2016b`` -``2017.1.1`` ``-Python-2.7.14`` ``intel/2018a`` -``2018.1`` ``-Python-3.6.4-CUDA-9.1.85`` ``intel/2018a`` -``2019.1.2`` ``-Python-3.7.4`` ``fosscuda/2019b``, ``intelcuda/2019b`` -============ ============================= ======================================= +============ =============================== ======================================= +version versionsuffix toolchain +============ =============================== ======================================= +``2016.1.2`` ``-Python-2.7.12`` ``intel/2016b`` +``2017.1.1`` ``-CUDA-9.0.176-Python-2.7.14`` ``foss/2017b`` +``2017.1.1`` ``-Python-2.7.14`` ``intel/2018a`` +``2018.1`` ``-Python-3.6.4-CUDA-9.1.85`` ``intel/2018a`` +``2019.1.2`` ``-Python-3.7.4`` ``fosscuda/2019b``, ``intelcuda/2019b`` +============ =============================== ======================================= .. _list_software_PycURL_543: @@ -27407,6 +28292,22 @@ version versionsuffix toolchain ============ ================= ================= +.. _list_software_pydantic_860: + +*pydantic* +++++++++++ + +Data validation and settings management using Python type hinting. + +*homepage*: https://github.com/samuelcolvin/pydantic + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``1.6.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= + + .. _list_software_PyDatastream_1231: *PyDatastream* @@ -27487,6 +28388,8 @@ A basic Python-based EGA download client version versionsuffix toolchain ========== ================= ================= ``3.0.33`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``3.4.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``3.4.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========== ================= ================= @@ -27619,6 +28522,7 @@ PyGEOS is a C/Python library with vectorized geometry functions. The geometry op version versionsuffix toolchain ========= ================= ============== ``0.7.1`` ``-Python-3.7.4`` ``foss/2019b`` +``0.8`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -27828,6 +28732,7 @@ pylift is an uplift library that provides, primarily: (1) Fast uplift modeling version versionsuffix toolchain ========= ================= ============== ``0.1.5`` ``-Python-3.7.4`` ``foss/2019b`` +``0.1.5`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -27949,6 +28854,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_pyobjcryst_1113: + +*pyobjcryst* +++++++++++++ + +Python bindings to ObjCryst++, the Object-Oriented Crystallographic Library. + +*homepage*: https://github.com/diffpy/pyobjcryst + +=============== ================= =============== +version versionsuffix toolchain +=============== ================= =============== +``2.1.0.post2`` ``-Python-3.8.2`` ``intel/2020a`` +=============== ================= =============== + + .. _list_software_Pyomo_532: *Pyomo* @@ -27966,6 +28887,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_PyOpenCL_746: + +*PyOpenCL* +++++++++++ + +PyOpenCL lets you access GPUs and other massively parallel compute devices from Python. + +*homepage*: https://mathema.tician.de/software/pyopencl/ + +============ ================= ================== +version versionsuffix toolchain +============ ================= ================== +``2020.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` +============ ================= ================== + + .. _list_software_PyOpenGL_750: *PyOpenGL* @@ -27984,6 +28921,7 @@ version versionsuffix toolchain ``3.1.1a1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` ``3.1.3b2`` ``-Python-2.7.14`` ``intel/2018a`` ``3.1.3b2`` ``-Python-2.7.15`` ``foss/2018b`` +``3.1.5`` ``GCCcore/8.3.0`` =========== ================== =============================== @@ -28096,6 +29034,7 @@ version versionsuffix toolchain ``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``5.13.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``5.15.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========== ================== =============================== @@ -28104,7 +29043,7 @@ version versionsuffix toolchain *PyQtGraph* +++++++++++ -PyQtGraph is a pure-python graphics and GUI library built on PyQt4/PySide and numpy. +PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and numpy. *homepage*: http://www.pyqtgraph.org/ @@ -28114,6 +29053,7 @@ version versionsuffix toolchain ``0.10.0`` ``-Python-3.6.4`` ``intel/2018a`` ``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``0.10.0`` ``-Python-3.7.2`` ``intel/2019a`` +``0.11.0`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================= =============================== @@ -28142,11 +29082,12 @@ PyRETIS is a Python library for rare event molecular simulations with emphasis o *homepage*: http://www.pyretis.org -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``2.1.0`` ``-Python-3.6.6`` ``intel/2018b`` -========= ================= =============== +========= ================= =============================== +version versionsuffix toolchain +========= ================= =============================== +``2.1.0`` ``-Python-3.6.6`` ``intel/2018b`` +``2.5.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +========= ================= =============================== .. _list_software_pyringe_766: @@ -28210,7 +29151,7 @@ version versionsuffix toolchain ``0.15.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``0.15.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``0.15.3`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``0.16.0.1`` ``GCC/9.3.0`` +``0.16.0.1`` ``GCC/8.3.0``, ``GCC/9.3.0`` ============ ================== ============================================================== @@ -28313,6 +29254,22 @@ version versionsuffix toolchain ======= ================= ================= +.. _list_software_pyspoa_668: + +*pyspoa* +++++++++ + +Python bindings to spoa. + +*homepage*: https://github.com/nanoporetech/pyspoa + +========= ================= ============= +version versionsuffix toolchain +========= ================= ============= +``0.0.4`` ``-Python-3.7.4`` ``GCC/8.3.0`` +========= ================= ============= + + .. _list_software_pysqlite_891: *pysqlite* @@ -28399,7 +29356,7 @@ version versionsuffix toolchain pytest: simple powerful testing with Python -*homepage*: http://pytest.org +*homepage*: https://pytest.org ========= ================== =============================== version versionsuffix toolchain @@ -28414,6 +29371,7 @@ version versionsuffix toolchain ``4.3.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``4.4.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``4.4.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``6.0.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========= ================== =============================== @@ -28460,7 +29418,7 @@ version versionsuffix toolchain ``2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``2.7.15`` ``-bare`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``2.7.16`` ``GCCcore/8.3.0`` -``2.7.18`` ``GCCcore/9.3.0`` +``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``3.5.1`` ``foss/2016a``, ``intel/2016a`` ``3.5.2`` ``foss/2016.04``, ``foss/2016b``, ``intel/2016b`` ``3.5.2`` ``-bare`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` @@ -28473,6 +29431,7 @@ version versionsuffix toolchain ``3.7.2`` ``GCCcore/8.2.0`` ``3.7.4`` ``GCCcore/8.3.0`` ``3.8.2`` ``GCCcore/9.3.0`` +``3.8.6`` ``GCCcore/10.2.0`` ========== ================= ================================================================================================================================================================= @@ -28501,13 +29460,13 @@ Python interface to the igraph high performance graph library, primarily aimed a *homepage*: https://igraph.org/python -=============== ================== =============== -version versionsuffix toolchain -=============== ================== =============== -``0.7.1.post6`` ``-Python-2.7.14`` ``intel/2017b`` -``0.7.1.post6`` ``-Python-3.6.6`` ``foss/2018b`` -``0.8.0`` ``foss/2019b`` -=============== ================== =============== +=============== ================== ============================== +version versionsuffix toolchain +=============== ================== ============================== +``0.7.1.post6`` ``-Python-2.7.14`` ``intel/2017b`` +``0.7.1.post6`` ``-Python-3.6.6`` ``foss/2018b`` +``0.8.0`` ``foss/2019b``, ``foss/2020a`` +=============== ================== ============================== .. _list_software_python-Levenshtein_1876: @@ -28599,7 +29558,7 @@ version versionsuffix toolchain ``1.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``1.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``1.6.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.6.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========= ============================= ================================== @@ -28629,11 +29588,11 @@ A Variant Call Format reader for Python. *homepage*: https://github.com/jamescasbon/PyVCF -========= ============= -version toolchain -========= ============= -``0.6.8`` ``GCC/8.3.0`` -========= ============= +========= ================== ============= +version versionsuffix toolchain +========= ================== ============= +``0.6.8`` ``-Python-2.7.16`` ``GCC/8.3.0`` +========= ================== ============= .. _list_software_PyWavelets_1044: @@ -28716,7 +29675,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcat_425` - :ref:`list_software_qcint_543` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` +:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcat_425` - :ref:`list_software_qcint_543` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_Qtconsole_952` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_QtPy_398` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` .. _list_software_Q6_135: @@ -29046,6 +30005,22 @@ version toolchain ================== ================= +.. _list_software_Qtconsole_952: + +*Qtconsole* ++++++++++++ + +A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. The Qtconsole is a very lightweight application that largely feels like a terminal, but provides a number of enhancements only possible in a GUI, such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and more. + +*homepage*: https://jupyter.org/ + +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``4.7.7`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========= ================= ================================== + + .. _list_software_QtKeychain_1009: *QtKeychain* @@ -29094,6 +30069,22 @@ version versionsuffix toolchain ======= ============= ========== +.. _list_software_QtPy_398: + +*QtPy* +++++++ + +QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide. + +*homepage*: https://github.com/spyder-ide/qtpy + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``1.9.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= + + .. _list_software_Qualimap_826: *Qualimap* @@ -29204,6 +30195,7 @@ version versionsuffix toolchain ``2.1.4`` ``-Python-2.7.12`` ``intel/2016b`` ``2.2.0`` ``-Python-2.7.14`` ``intel/2017b`` ``2.2.4`` ``-Python-3.7.2`` ``intel/2019a`` +``2.2.4`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================== =============== @@ -29297,7 +30289,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray_300` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_rstudio_778` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray_300` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_rstudio_778` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -29309,27 +30301,29 @@ R is a free software environment for statistical computing and graphics. *homepage*: https://www.r-project.org/ -========= ================== =================================================== -version versionsuffix toolchain -========= ================== =================================================== -``3.2.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` -``3.2.3`` ``-bare`` ``foss/2016a``, ``intel/2016a`` -``3.2.3`` ``-libX11-1.6.3`` ``intel/2016a`` -``3.3.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``3.3.3`` ``-X11-20160819`` ``foss/2016b``, ``intel/2016b`` -``3.3.3`` ``-X11-20170314`` ``intel/2017a`` -``3.4.0`` ``-X11-20170314`` ``intel/2017a`` -``3.4.1`` ``-X11-20160819`` ``foss/2016b`` -``3.4.3`` ``-X11-20171023`` ``foss/2017b``, ``intel/2017b`` -``3.4.4`` ``-X11-20180131`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` -``3.5.0`` ``-X11-20180131`` ``iomkl/2018a`` -``3.5.1`` ``foss/2018b``, ``intel/2018b`` -``3.5.1`` ``-Python-2.7.15`` ``foss/2018b`` -``3.6.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` -``3.6.2`` ``foss/2019b``, ``fosscuda/2019b`` -``3.6.3`` ``foss/2020a`` -``4.0.0`` ``foss/2020a`` -========= ================== =================================================== +========= ============================= =================================================== +version versionsuffix toolchain +========= ============================= =================================================== +``3.2.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` +``3.2.3`` ``-bare`` ``foss/2016a``, ``intel/2016a`` +``3.2.3`` ``-libX11-1.6.3`` ``intel/2016a`` +``3.3.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` +``3.3.3`` ``-X11-20160819`` ``foss/2016b``, ``intel/2016b`` +``3.3.3`` ``-X11-20170314`` ``intel/2017a`` +``3.4.0`` ``-X11-20170314`` ``intel/2017a`` +``3.4.1`` ``-X11-20160819`` ``foss/2016b`` +``3.4.3`` ``-X11-20171023`` ``foss/2017b``, ``intel/2017b`` +``3.4.3`` ``-X11-20171023-HDF5-1.8.19`` ``intel/2017b`` +``3.4.4`` ``-X11-20180131`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` +``3.5.0`` ``-X11-20180131`` ``iomkl/2018a`` +``3.5.1`` ``foss/2018b``, ``intel/2018b`` +``3.5.1`` ``-Python-2.7.15`` ``foss/2018b`` +``3.5.1`` ``-bare`` ``foss/2018b`` +``3.6.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` +``3.6.2`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``3.6.3`` ``foss/2020a`` +``4.0.0`` ``foss/2020a`` +========= ============================= =================================================== .. _list_software_R-bundle-Bioconductor_2065: @@ -29539,6 +30533,38 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_rasterio_873: + +*rasterio* +++++++++++ + +Rasterio reads and writes geospatial raster data. + +*homepage*: https://github.com/mapbox/rasterio + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.1.7`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + +.. _list_software_rasterstats_1216: + +*rasterstats* ++++++++++++++ + +rasterstats is a Python module for summarizing geospatial raster datasets based on vector geometries. + +*homepage*: https://github.com/perrygeo/python-rasterstats + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.15.0`` ``-Python-3.8.2`` ``foss/2020a`` +========== ================= ============== + + .. _list_software_RAxML_420: *RAxML* @@ -29720,13 +30746,14 @@ re2c is a free and open-source lexer generator for C and C++. Its main goal is g *homepage*: https://re2c.org/ -========= ================= -version toolchain -========= ================= -``1.1.1`` ``GCCcore/8.2.0`` -``1.2.1`` ``GCCcore/8.3.0`` -``1.3`` ``GCCcore/9.3.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``1.1.1`` ``GCCcore/8.2.0`` +``1.2.1`` ``GCCcore/8.3.0`` +``1.3`` ``GCCcore/9.3.0`` +``2.0.3`` ``GCCcore/10.2.0`` +========= ================== .. _list_software_Reads2snp_882: @@ -29810,6 +30837,7 @@ version toolchain ``2.20`` ``system`` ``2.21`` ``system`` ``3.0`` ``system`` +``3.2`` ``system`` ======== ========== @@ -29835,6 +30863,22 @@ version versionsuffix toolchain ======================= ================ ============================================================================================================ +.. _list_software_ReMatCh_644: + +*ReMatCh* ++++++++++ + +Reads mapping against target sequences, checking mapping and consensus sequences production + +*homepage*: https://github.com/B-UMMI/ReMatCh + +======= ================== ============== +version versionsuffix toolchain +======= ================== ============== +``3.2`` ``-Python-2.7.12`` ``foss/2016b`` +======= ================== ============== + + .. _list_software_REMORA_454: *REMORA* @@ -30527,13 +31571,29 @@ version toolchain ``2.3.4`` ``system`` ``2.4.2`` ``foss/2017b`` ``2.5.0`` ``foss/2018a``, ``intel/2017a``, ``intel/2017b`` -``2.5.1`` ``intel/2018a`` +``2.5.1`` ``foss/2018a``, ``intel/2018a`` ``2.6.1`` ``GCCcore/7.3.0`` ``2.6.3`` ``GCCcore/8.2.0`` ``2.7.1`` ``GCCcore/8.3.0`` ========= ================================================ +.. _list_software_Ruby-Tk_654: + +*Ruby-Tk* ++++++++++ + +Ruby Tk interface module using tcltklib + +*homepage*: https://github.com/ruby/tk + +========= =============== =============================== +version versionsuffix toolchain +========= =============== =============================== +``0.2.0`` ``-Ruby-2.5.1`` ``foss/2018a``, ``intel/2018a`` +========= =============== =============================== + + .. _list_software_Rust_430: *Rust* @@ -30543,21 +31603,21 @@ Rust is a systems programming language that runs blazingly fast, prevents segfau *homepage*: https://www.rust-lang.org -========== ======================================================= -version toolchain -========== ======================================================= -``1.8.0`` ``foss/2016a`` -``1.12.0`` ``foss/2016b`` -``1.12.1`` ``foss/2016b`` -``1.18.0`` ``foss/2017a`` -``1.21.0`` ``foss/2017b`` -``1.22.1`` ``GCCcore/6.4.0`` -``1.29.2`` ``GCCcore/7.3.0`` -``1.30.1`` ``GCCcore/6.4.0`` -``1.35.0`` ``GCCcore/8.2.0`` -``1.37.0`` ``GCCcore/8.3.0`` -``1.42.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` -========== ======================================================= +========== ========================================================================== +version toolchain +========== ========================================================================== +``1.8.0`` ``foss/2016a`` +``1.12.0`` ``foss/2016b`` +``1.12.1`` ``foss/2016b`` +``1.18.0`` ``foss/2017a`` +``1.21.0`` ``foss/2017b`` +``1.22.1`` ``GCCcore/6.4.0`` +``1.29.2`` ``GCCcore/7.3.0`` +``1.30.1`` ``GCCcore/6.4.0`` +``1.35.0`` ``GCCcore/8.2.0`` +``1.37.0`` ``GCCcore/8.3.0`` +``1.42.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ========================================================================== .. _list_software_letter_s: @@ -30566,7 +31626,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_Sumo_420` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_Sumo_420` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -30768,6 +31828,7 @@ version versionsuffix toolchain ``1.8`` ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.10`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` +``1.11`` ``GCC/9.3.0`` ========== ================= ======================================================================================================================================= @@ -30821,6 +31882,22 @@ version versionsuffix toolchain ============ =================== ========== +.. _list_software_SBCL_292: + +*SBCL* +++++++ + +Steel Bank Common Lisp (SBCL) is a high performance Common Lisp compiler. It is open source / free software, with a permissive license. In addition to the compiler and runtime system for ANSI Common Lisp, it provides an interactive environment including a debugger, a statistical profiler, a code coverage tool, and many other extensions. + +*homepage*: http://sbcl.sourceforge.net/ + +========= ================= +version toolchain +========= ================= +``2.0.9`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_sbt_329: *sbt* @@ -30830,11 +31907,12 @@ sbt is a build tool for Scala, Java, and more. *homepage*: http://www.scala-sbt.org/ -========= =================== ========== -version versionsuffix toolchain -========= =================== ========== -``1.0.2`` ``-Java-1.8.0_152`` ``system`` -========= =================== ========== +========== =================== ========== +version versionsuffix toolchain +========== =================== ========== +``1.0.2`` ``-Java-1.8.0_152`` ``system`` +``1.3.13`` ``-Java-1.8`` ``system`` +========== =================== ========== .. _list_software_ScaFaCoS_707: @@ -30876,7 +31954,7 @@ version versionsuffix toolchain ``2.0.2`` ``-OpenBLAS-0.3.1`` ``gompi/2018b``, ``gompic/2018b`` ``2.0.2`` ``-OpenBLAS-0.3.3`` ``gompi/2018.08`` ``2.0.2`` ``-OpenBLAS-0.3.5`` ``gompi/2019a``, ``gompic/2019a`` -``2.1.0`` ``gompi/2020a`` +``2.1.0`` ``gompi/2020a``, ``gompic/2020a`` ========= ================================= ============================================================================================================================================ @@ -31078,9 +32156,26 @@ version versionsuffix toolchain ========= ================= =============== ``0.5.2`` ``-Python-3.6.6`` ``intel/2018b`` ``0.7.4`` ``-Python-3.7.4`` ``foss/2019b`` +``0.8.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= =============== +.. _list_software_scikit-uplift_1352: + +*scikit-uplift* ++++++++++++++++ + +scikit-uplift is a Python module for classic approaches for uplift modeling built on top of scikit-learn. Uplift prediction aims to estimate the causal impact of a treatment at the individual level. + +*homepage*: https://github.com/maks-sh/scikit-uplift + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.2.0`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_SCIPhI_480: *SCIPhI* @@ -31130,6 +32225,7 @@ version versionsuffix toolchain =========== ================== ======================================================================== ``2019.03`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` ``2019.10`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2019.10`` ``-Python-3.7.2`` ``intel/2019a`` ``2019.10`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` ``2020.03`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` =========== ================== ======================================================================== @@ -31195,6 +32291,7 @@ version versionsuffix toolchain ``3.0.5`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``3.1.1`` ``GCCcore/8.3.0`` ``3.1.2`` ``GCCcore/9.3.0`` +``4.0.1`` ``GCCcore/10.2.0`` ========= ======================= ================================================================================= @@ -31337,6 +32434,22 @@ version toolchain ========= ========== +.. _list_software_SDL_227: + +*SDL* ++++++ + +SDL: Simple DirectMedia Layer, a cross-platform multimedia library + +*homepage*: https://www.libsdl.org/ + +========== ================= +version toolchain +========== ================= +``1.2.15`` ``GCCcore/6.4.0`` +========== ================= + + .. _list_software_SDL2_277: *SDL2* @@ -31350,12 +32463,44 @@ SDL: Simple DirectMedia Layer, a cross-platform multimedia library version toolchain ========== ====================================================================== ``2.0.4`` ``intel/2016b`` -``2.0.8`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``2.0.8`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``2.0.9`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.0.10`` ``GCCcore/8.3.0`` ========== ====================================================================== +.. _list_software_SDL2_image_887: + +*SDL2_image* +++++++++++++ + +SDL_image is an image file loading library. + +*homepage*: https://www.libsdl.org/projects/SDL_image/ + +========= ================= +version toolchain +========= ================= +``2.0.3`` ``GCCcore/6.4.0`` +========= ================= + + +.. _list_software_SDL_image_837: + +*SDL_image* ++++++++++++ + +SDL_image is an image file loading library. + +*homepage*: https://www.libsdl.org/projects/SDL_image/release-1.2.html + +========== ================= +version toolchain +========== ================= +``1.2.12`` ``GCCcore/6.4.0`` +========== ================= + + .. _list_software_SDSL_310: *SDSL* @@ -31548,7 +32693,7 @@ version toolchain *seq2HLA* +++++++++ -In-silico method written in Python and R to determine HLA genotypes of a sample. +In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class. *homepage*: https://github.com/TRON-Bioinformatics/seq2HLA @@ -31594,6 +32739,23 @@ version toolchain ========= ========== +.. _list_software_SeqKit_593: + +*SeqKit* +++++++++ + +SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation + +*homepage*: https://bioinf.shenwei.me/seqkit/ + +========== ========== +version toolchain +========== ========== +``0.8.1`` ``system`` +``0.13.2`` ``system`` +========== ========== + + .. _list_software_Seqmagick_917: *Seqmagick* @@ -31653,11 +32815,11 @@ The serf library is a high performance C-based HTTP client library built upon t *homepage*: http://serf.apache.org/ -========= ====================================================================================== -version toolchain -========= ====================================================================================== -``1.3.9`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``intel/2017b``, ``iomkl/2018a`` -========= ====================================================================================== +========= ============================================================================================================================= +version toolchain +========= ============================================================================================================================= +``1.3.9`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``intel/2017b``, ``iomkl/2018a`` +========= ============================================================================================================================= .. _list_software_setuptools_1122: @@ -31954,7 +33116,7 @@ SIESTA is both a method and its computer program implementation, to perform effi =============== ============= =============================== version versionsuffix toolchain =============== ============= =============================== -``4.0`` ``intel/2017a`` +``4.0`` ``foss/2017b``, ``intel/2017a`` ``4.0.1`` ``intel/2017a`` ``4.1-b2`` ``intel/2017a`` ``4.1-b3`` ``intel/2017a`` @@ -31964,6 +33126,22 @@ version versionsuffix toolchain =============== ============= =============================== +.. _list_software_silx_448: + +*silx* +++++++ + +The silx project provides a collection of Python packages to support the development of data assessment, reduction and analysis applications at synchrotron radiation facilities. + +*homepage*: http://www.silx.org/ + +========== ================= ================================== +version versionsuffix toolchain +========== ================= ================================== +``0.13.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========== ================= ================================== + + .. _list_software_SimPEG_517: *SimPEG* @@ -32099,6 +33277,22 @@ version toolchain ========= ================================ +.. _list_software_SiNVICT_576: + +*SiNVICT* ++++++++++ + +SiNVICT is a tool for the detection of SNVs and indels from cfDNA/ctDNA samples obtained by ultra-deep sequencing. + +*homepage*: https://github.com/sfu-compbio/sinvict + +================ ============= +version toolchain +================ ============= +``1.0-20180817`` ``GCC/9.3.0`` +================ ============= + + .. _list_software_SIONlib_624: *SIONlib* @@ -32458,7 +33652,7 @@ version toolchain ``1.1.3`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25`` ``1.1.6`` ``system`` ``1.1.7`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``intel/2017b`` -``1.1.8`` ``GCCcore/9.3.0`` +``1.1.8`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================ @@ -32628,6 +33822,22 @@ version toolchain ========= ============== +.. _list_software_sonic_540: + +*sonic* ++++++++ + +Sonic is a simple algorithm for speeding up or slowing down speech. However, it's optimized for speed ups of over 2X, unlike previous algorithms for changing speech rate. The Sonic library is a very simple ANSI C library that is designed to easily be integrated into streaming voice applications, like TTS back ends. + +*homepage*: https://github.com/espeak-ng/sonic + +============ =============== +version toolchain +============ =============== +``20180202`` ``gompi/2020a`` +============ =============== + + .. _list_software_SortMeRNA_827: *SortMeRNA* @@ -32802,6 +34012,22 @@ version versionsuffix toolchain ============= ============= =============== +.. _list_software_speech_tools_1288: + +*speech_tools* +++++++++++++++ + +The Edinburgh Speech Tools Library is a collection of C++ class, functions and related programs for manipulating the sorts of objects used in speech processing. It includes support for reading and writing waveforms, parameter files (LPC, Ceptra, F0) in various formats and converting between them. It also includes support for linguistic type objects and support for various label files and ngrams (with smoothing). + +*homepage*: ['http://festvox.org/festival/'] + +========= ================= +version toolchain +========= ================= +``2.5.0`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_spglib_641: *spglib* @@ -32837,6 +34063,7 @@ version versionsuffix toolchain ``1.10.0.2`` ``-Python-2.7.14`` ``intel/2017b`` ``1.10.0.2`` ``-Python-3.6.3`` ``intel/2017b`` ``1.14.1.post0`` ``-Python-3.7.2`` ``intel/2019a`` +``1.16.0`` ``-Python-3.8.2`` ``intel/2020a`` ================ ================== =============== @@ -32976,6 +34203,7 @@ Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) alg version toolchain ========= ================== ``3.0.1`` ``GCC/7.3.0-2.30`` +``4.0.0`` ``GCC/8.3.0`` ========= ================== @@ -33010,6 +34238,8 @@ version versionsuffix toolchain ``3.1.4`` ``-Python-2.7.13`` ``intel/2017a`` ``3.3.1`` ``-Python-3.6.4`` ``foss/2018a`` ``3.3.2`` ``-Python-3.6.6`` ``foss/2018b`` +``4.1.5`` ``-Python-3.7.2`` ``foss/2019a`` +``4.1.5`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== =============== @@ -33039,6 +34269,7 @@ version toolchain ``3.27.2`` ``GCCcore/8.2.0`` ``3.29.0`` ``GCCcore/8.3.0`` ``3.31.1`` ``GCCcore/9.3.0`` +``3.33.0`` ``GCCcore/10.2.0`` ============ ==================================================================================================================================================================== @@ -33313,6 +34544,22 @@ version versionsuffix toolchain ======= ============= ========== +.. _list_software_Statistics-R_1194: + +*Statistics-R* +++++++++++++++ + +Perl interface with the R statistical program + +*homepage*: https://metacpan.org/pod/Statistics::R + +======== ============== +version toolchain +======== ============== +``0.34`` ``foss/2020a`` +======== ============== + + .. _list_software_statsmodels_1203: *statsmodels* @@ -33384,6 +34631,7 @@ version versionsuffix toolchain ========= ================== ============== ``1.7.3`` ``-Python-2.7.15`` ``foss/2018b`` ``1.7.6`` ``-Python-3.7.2`` ``foss/2019a`` +``1.7.6`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== ============== @@ -33453,11 +34701,11 @@ The program structure is a free software package for using multi-locus genotype *homepage*: https://web.stanford.edu/group/pritchardlab/structure.html -========= ============================================================ -version toolchain -========= ============================================================ -``2.3.4`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.3.199-GCC-8.3.0-2.32`` -========= ============================================================ +========= ===================================================================================== +version toolchain +========= ===================================================================================== +``2.3.4`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.3.199-GCC-8.3.0-2.32``, ``iccifort/2019.5.281`` +========= ===================================================================================== .. _list_software_Subread_710: @@ -33488,14 +34736,15 @@ Subversion is an open source version control system. *homepage*: http://subversion.apache.org/ -========== =============================== -version toolchain -========== =============================== -``1.9.7`` ``iomkl/2018a`` -``1.9.9`` ``GCCcore/7.3.0`` -``1.10.0`` ``foss/2017b``, ``intel/2017b`` -``1.12.0`` ``GCCcore/8.2.0`` -========== =============================== +========== ===================================== +version toolchain +========== ===================================== +``1.9.7`` ``iomkl/2018a`` +``1.9.9`` ``GCCcore/7.3.0`` +``1.10.0`` ``foss/2017b``, ``intel/2017b`` +``1.12.0`` ``GCCcore/8.2.0`` +``1.14.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========== ===================================== .. _list_software_suds_447: @@ -33573,6 +34822,22 @@ version toolchain ========== ============== +.. _list_software_SUMO_324: + +*SUMO* +++++++ + +"Simulation of Urban MObility" (SUMO) is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a large set of tools for scenario creation. + +*homepage*: https://sumo.dlr.de/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.7.0`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_Sumo_420: *Sumo* @@ -33870,7 +35135,7 @@ Szip compression software, providing lossless compression of scientific data version toolchain ========= ========================================================================================================================================================================================================================================================================= ``2.1`` ``GCC/4.8.1``, ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``2.1.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ========================================================================================================================================================================================================================================================================= @@ -33880,7 +35145,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_Trycycler_961` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` +:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` .. _list_software_tabix_536: @@ -33940,11 +35205,11 @@ Taiyaki is research software for training models for basecalling Oxford Nanopore *homepage*: https://github.com/nanoporetech/taiyaki -================== ================= ================================== -version versionsuffix toolchain -================== ================= ================================== -``5.0.1-20200316`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -================== ================= ================================== +================== =============================== ================================== +version versionsuffix toolchain +================== =============================== ================================== +``5.1.0-20200617`` ``-Python-3.7.2-PyTorch-1.2.0`` ``foss/2019a``, ``fosscuda/2019a`` +================== =============================== ================================== .. _list_software_TAMkin_548: @@ -33962,6 +35227,7 @@ version versionsuffix toolchain ``1.0.9`` ``-Python-2.7.11`` ``intel/2016a`` ``1.2.4`` ``-Python-2.7.14`` ``intel/2017b`` ``1.2.6`` ``-Python-3.7.2`` ``intel/2019a`` +``1.2.6`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================== =============== @@ -34067,7 +35333,7 @@ version toolchain ``8.6.7`` ``GCCcore/6.4.0`` ``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``8.6.10`` ``GCCcore/9.3.0`` +``8.6.10`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========== ========================================================================================================================================================================= @@ -34204,6 +35470,8 @@ version versionsuffix toolchain ``2.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.3.1`` ``-Python-3.8.2`` ``foss/2020a`` ========== ============================= =================================================== @@ -34474,6 +35742,22 @@ version toolchain ======== ================================ +.. _list_software_tidybayes_974: + +*tidybayes* ++++++++++++ + +Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models ('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. + +*homepage*: https://cran.r-project.org/package=tidybayes + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``2.1.1`` ``-R-4.0.0`` ``foss/2020a`` +========= ============= ============== + + .. _list_software_tidymodels_1086: *tidymodels* @@ -34554,6 +35838,7 @@ version toolchain ========= ============== ``8.6.1`` ``foss/2018b`` ``8.7.2`` ``foss/2019b`` +``8.8.1`` ``foss/2020a`` ========= ============== @@ -34594,7 +35879,7 @@ version versionsuffix toolchain ``8.6.7`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2018a``, ``iomkl/2018a`` ``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``8.6.10`` ``GCCcore/9.3.0`` +``8.6.10`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========== ================= ================================================================================================================================================ @@ -34615,6 +35900,7 @@ version versionsuffix toolchain ``2.7.15`` ``GCCcore/8.2.0`` ``2.7.15`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.7.16`` ``GCCcore/8.3.0`` +``2.7.18`` ``GCCcore/9.3.0`` ``3.6.1`` ``-Python-3.6.1`` ``foss/2017a``, ``intel/2017a`` ``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` ``3.6.3`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` @@ -34623,6 +35909,7 @@ version versionsuffix toolchain ``3.7.2`` ``GCCcore/8.2.0`` ``3.7.4`` ``GCCcore/8.3.0`` ``3.8.2`` ``GCCcore/9.3.0`` +``3.8.6`` ``GCCcore/10.2.0`` ========== ================== ========================================================================================================= @@ -34780,6 +36067,7 @@ version versionsuffix toolchain ``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` ``0.4.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``0.5.0`` ``-Python-3.7.4-PyTorch-1.4.0`` ``fosscuda/2019b`` +``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``fosscuda/2019b`` ========= =============================== ================================== @@ -34888,6 +36176,22 @@ version versionsuffix toolchain ========= =============== ========== +.. _list_software_treatSens_953: + +*treatSens* ++++++++++++ + +Utilities to investigate sensitivity to unmeasured confounding in parametric models with either binary or continuous treatment. + +*homepage*: https://github.com/vdorie/treatSens + +================ ============= ============== +version versionsuffix toolchain +================ ============= ============== +``3.0-20201002`` ``-R-4.0.0`` ``foss/2020a`` +================ ============= ============== + + .. _list_software_TreeMix_702: *TreeMix* @@ -34994,6 +36298,7 @@ version versionsuffix toolchain ``0.6.2`` ``-Python-2.7.15`` ``foss/2018b`` ``0.6.2`` ``-Python-3.6.6`` ``foss/2018b`` ``0.6.5`` ``-Java-11-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.6.6`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ========================= =============================== @@ -35002,15 +36307,15 @@ version versionsuffix toolchain *trimAl* ++++++++ -EVB, FEP and LIE simulator. +A tool for automated alignment trimming in large-scale phylogenetic analyses -*homepage*: https://github.com/scapella/trimal +*homepage*: http://trimal.cgenomics.org/ -========= ==================== -version toolchain -========= ==================== -``1.4.1`` ``GCC/8.2.0-2.31.1`` -========= ==================== +========= ===================================== +version toolchain +========= ===================================== +``1.4.1`` ``GCC/8.2.0-2.31.1``, ``intel/2018a`` +========= ===================================== .. _list_software_Trimmomatic_1158: @@ -35073,6 +36378,7 @@ version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ``2.2.1`` ``-Python-2.7.15`` ``foss/2019a`` +``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ============== @@ -35089,6 +36395,7 @@ TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific pro version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` +``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ============== @@ -35097,14 +36404,15 @@ version versionsuffix toolchain *TRIQS-dft_tools* +++++++++++++++++ -TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. This TRIQS-based-based application is aimed at ab-initio calculations for correlated materials, combining realistic DFT band-structure calculations with the dynamical mean-field theory. Together with the necessary tools to perform the DMFT self-consistency loop for realistic multi-band problems, the package provides a full-fledged charge self-consistent interface to the Wien2K package. In addition, if Wien2k is not available, it provides a generic interface for one-shot DFT+DMFT calculations, where only the single-particle Hamiltonian in orbital space has to be provided. +TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. This TRIQS-based-based application is aimed at ab-initio calculations for correlated materials, combining realistic DFT band-structure calculation with the dynamical mean-field theory. Together with the necessary tools to perform the DMFT self-consistency loop for realistic multi-band problems, the package provides a full-fledged charge self-consistent interface to the Wien2K package. In addition, if Wien2k is not available, it provides a generic interface for one-shot DFT+DMFT calculations, where only the single-particle Hamiltonian in orbital space has to be provided. -*homepage*: https://triqs.github.io/dft_tools +*homepage*: https://triqs.github.io/dft_tools/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` +``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ============== @@ -35121,6 +36429,7 @@ TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific pro version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` +``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ============== @@ -35156,6 +36465,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_tsne_442: + +*tsne* +++++++ + +Python library containing T-SNE algorithms. + +*homepage*: https://github.com/danielfrg/tsne + +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``0.1.8`` ``-Python-2.7.16`` ``intel/2019b`` +========= ================== =============== + + .. _list_software_TurboVNC_755: *TurboVNC* @@ -35290,16 +36615,18 @@ Unified Communication X An open-source production grade communication framework *homepage*: http://www.openucx.org/ -============ ============= ======================================================= -version versionsuffix toolchain -============ ============= ======================================================= -``1.3.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.5.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.5.0rc1`` ``-hpcx`` ``GCCcore/8.2.0`` -``1.5.1`` ``GCCcore/8.2.0`` -``1.6.1`` ``GCCcore/8.3.0`` -``1.8.0`` ``GCCcore/9.3.0`` -============ ============= ======================================================= +============ ================ ======================================================= +version versionsuffix toolchain +============ ================ ======================================================= +``1.3.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.5.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.5.0rc1`` ``-hpcx`` ``GCCcore/8.2.0`` +``1.5.1`` ``GCCcore/8.2.0`` +``1.6.1`` ``GCCcore/8.3.0`` +``1.8.0`` ``GCCcore/9.3.0`` +``1.8.0`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` +``1.9.0`` ``GCCcore/10.2.0`` +============ ================ ======================================================= .. _list_software_udocker_749: @@ -35328,14 +36655,14 @@ UDUNITS supports conversion of unit specifications between formatted and binary *homepage*: https://www.unidata.ucar.edu/software/udunits/ -========== =========================================================================================================================================================== -version toolchain -========== =========================================================================================================================================================== -``2.2.20`` ``foss/2016a``, ``intel/2016b`` -``2.2.24`` ``intel/2017a`` -``2.2.25`` ``foss/2017b``, ``intel/2017b`` -``2.2.26`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -========== =========================================================================================================================================================== +========== =========================================================================================================================================================================== +version toolchain +========== =========================================================================================================================================================================== +``2.2.20`` ``foss/2016a``, ``intel/2016b`` +``2.2.24`` ``intel/2017a`` +``2.2.25`` ``foss/2017b``, ``intel/2017b`` +``2.2.26`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +========== =========================================================================================================================================================================== .. _list_software_UFL_231: @@ -35511,11 +36838,11 @@ UnZip is an extraction utility for archives compressed in .zip format (also call *homepage*: http://www.info-zip.org/UnZip.html -======= ========================================================================== -version toolchain -======= ========================================================================== -``6.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -======= ========================================================================== +======= ================================================================================================================= +version toolchain +======= ================================================================================================================= +``6.0`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ================================================================================================================= .. _list_software_UQTk_357: @@ -35577,13 +36904,13 @@ utf8proc is a small, clean C library that provides Unicode normalization, case-f *homepage*: https://github.com/JuliaStrings/utf8proc -========= ================= -version toolchain -========= ================= -``2.2.0`` ``GCCcore/6.4.0`` -``2.3.0`` ``GCCcore/8.2.0`` -``2.5.0`` ``GCCcore/8.3.0`` -========= ================= +========= ======================================================== +version toolchain +========= ======================================================== +``2.2.0`` ``GCCcore/6.4.0`` +``2.3.0`` ``GCCcore/8.2.0`` +``2.5.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================== .. _list_software_util-linux_1051: @@ -35612,6 +36939,7 @@ version toolchain ``2.33`` ``GCCcore/8.2.0`` ``2.34`` ``GCCcore/8.3.0`` ``2.35`` ``GCCcore/9.3.0`` +``2.36`` ``GCCcore/10.2.0`` ========== ==================================== @@ -35633,11 +36961,13 @@ R interface to Google's open source JavaScript engine *homepage*: https://cran.r-project.org/web/packages/V8/ -======= ============= ============== -version versionsuffix toolchain -======= ============= ============== -``2.2`` ``-R-3.5.1`` ``foss/2018b`` -======= ============= ============== +========= ============= =============================== +version versionsuffix toolchain +========= ============= =============================== +``2.2`` ``-R-3.5.1`` ``foss/2018b`` +``2.3`` ``-R-3.6.0`` ``foss/2019a``, ``intel/2019a`` +``3.2.0`` ``-R-3.6.2`` ``foss/2019b`` +========= ============= =============================== .. _list_software_Valgrind_823: @@ -35655,7 +36985,7 @@ version toolchain ``3.11.0`` ``foss/2016a``, ``intel/2016a`` ``3.13.0`` ``foss/2017b``, ``foss/2018a``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.14.0`` ``foss/2018b`` -``3.16.1`` ``gompi/2019b`` +``3.16.1`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2020a`` ========== ================================================================================= @@ -35992,11 +37322,12 @@ VirtualGL is an open source toolkit that gives any Linux or Unix remote display *homepage*: https://virtualgl.org/ -========= ============== -version toolchain -========= ============== -``2.6.1`` ``foss/2018b`` -========= ============== +========= ================= +version toolchain +========= ================= +``2.6.1`` ``foss/2018b`` +``2.6.2`` ``GCCcore/9.3.0`` +========= ================= .. _list_software_VMD_231: @@ -36115,6 +37446,7 @@ version versionsuffix toolchain ``4.1.8`` ``system`` ``4.1.9`` ``system`` ``5.1.0`` ``system`` +``5.2.0`` ``system`` =========== ================================== =============== @@ -36284,7 +37616,23 @@ version toolchain --- -:ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_WHAM_301` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` +:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_WHAM_301` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` + + +.. _list_software_wandb_524: + +*wandb* ++++++++ + +CLI and Python API for Weights and Biases (wandb), a tool for visualizing and tracking your machine learning experiments. + +*homepage*: https://www.wandb.com/ + +========== ================= ================= +version versionsuffix toolchain +========== ================= ================= +``0.8.30`` ``-Python-3.7.4`` ``gcccuda/2019b`` +========== ================= ================= .. _list_software_Wannier90_829: @@ -36502,6 +37850,22 @@ version toolchain ======= ============= +.. _list_software_WisecondorX_1141: + +*WisecondorX* ++++++++++++++ + +WisecondorX -- an evolved WISECONDOR + +*homepage*: https://github.com/CenterForMedicalGeneticsGhent/WisecondorX + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.1.6`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_WISExome_753: *WISExome* @@ -36554,7 +37918,7 @@ version versionsuffix toolchain ``1.6.7`` ``-intel-2017b`` ``system`` ``1.6.8`` ``-intel-2018a`` ``system`` ``1.6.8`` ``-intel-2018b`` ``system`` -``1.6.11`` ``-intel-2019b`` ``system`` +``1.6.11`` ``intel/2019b`` ``1.6.12`` ``-foss-2019a`` ``system`` ========== ================ =============== @@ -36593,6 +37957,7 @@ version versionsuffix toolchain ``3.8.0`` ``-dmpar`` ``intel/2016a``, ``intel/2016b`` ``4.0.1`` ``-dmpar`` ``intel/2018b`` ``4.0.2`` ``-dmpar`` ``foss/2018b`` +``4.1.3`` ``-dm+sm`` ``intel/2019b`` ``4.1.3`` ``-dmpar`` ``foss/2019b``, ``intel/2019b`` ========= ============= ================================ @@ -36733,6 +38098,7 @@ version toolchain ``20190311`` ``GCCcore/8.2.0`` ``20190717`` ``GCCcore/8.3.0`` ``20200222`` ``GCCcore/9.3.0`` +``20201008`` ``GCCcore/10.2.0`` ============ ================================================== @@ -36826,6 +38192,7 @@ version versionsuffix toolchain ``0.12.1`` ``-Python-3.6.6`` ``intel/2018b`` ``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` ``0.15.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.16.1`` ``-Python-3.8.2`` ``intel/2020a`` ========== ================== =============================== @@ -36853,12 +38220,13 @@ version toolchain The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. -*homepage*: http://xcb.freedesktop.org/ +*homepage*: https://xcb.freedesktop.org/ ======== ========== version toolchain ======== ========== ``1.11`` ``system`` +``1.13`` ``system`` ======== ========== @@ -37007,6 +38375,7 @@ version toolchain ``3.1.4`` ``GCCcore/6.4.0`` ``3.2.0`` ``GCCcore/7.3.0`` ``3.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.2.3`` ``GCCcore/9.3.0`` ========= ==================================== @@ -37059,6 +38428,7 @@ version versionsuffix toolchain ``0.6a2`` ``-Python-3.6.1`` ``intel/2017a`` ``0.72.1`` ``-Python-2.7.14`` ``intel/2017b`` ``0.90`` ``-Python-3.7.4`` ``foss/2019b`` +``1.2.0`` ``-Python-3.8.2`` ``foss/2020a`` ``20171120`` ``-Java-1.8.0_152`` ``intel/2017b`` ============ =================== =============== @@ -37246,13 +38616,13 @@ X.org macros utilities. *homepage*: https://cgit.freedesktop.org/xorg/util/macros -========== ================================================================================================================ -version toolchain -========== ================================================================================================================ -``1.19.0`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` -``1.19.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``1.19.2`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -========== ================================================================================================================ +========== ==================================================================================================================================== +version toolchain +========== ==================================================================================================================================== +``1.19.0`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` +``1.19.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``1.19.2`` ``GCCcore/10.2.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +========== ==================================================================================================================================== .. _list_software_xprop_569: @@ -37270,7 +38640,7 @@ version versionsuffix toolchain ``1.2.2`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``1.2.2`` ``-X11-20180131`` ``GCCcore/6.4.0`` ``1.2.3`` ``GCCcore/7.3.0`` -``1.2.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.2.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ================= ======================================================================================================================= @@ -37370,6 +38740,7 @@ Xvfb is an X server that can run on machines with no display hardware and no phy version toolchain ========== ==================================== ``1.20.8`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.20.9`` ``GCCcore/9.3.0`` ========== ==================================== @@ -37391,7 +38762,7 @@ version versionsuffix toolchain ``5.2.2`` ``-gettext-0.19.7`` ``foss/2016a``, ``intel/2016a`` ``5.2.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``gimkl/2017a`` ``5.2.4`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` -``5.2.5`` ``GCCcore/10.1.0``, ``GCCcore/9.3.0`` +``5.2.5`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= =================== =========================================================================================================================================================== @@ -37560,6 +38931,7 @@ version toolchain ``4.2.2`` ``foss/2017a``, ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` ``4.2.5`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` ``4.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.3.3`` ``GCCcore/10.2.0`` ========= ========================================================================================================= @@ -37588,11 +38960,11 @@ Zip is a compression and file packaging/archive utility. Although highly compati *homepage*: http://www.info-zip.org/Zip.html -======= ======================================================= -version toolchain -======= ======================================================= -``3.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ======================================================= +======= =========================================================================== +version toolchain +======= =========================================================================== +``3.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= =========================================================================== .. _list_software_zlib_433: @@ -37680,5 +39052,6 @@ version toolchain ``1.3.4`` ``foss/2016b`` ``1.4.0`` ``GCCcore/8.2.0``, ``foss/2018b`` ``1.4.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.4.5`` ``GCCcore/10.2.0`` ========= ==================================== diff --git a/docs/version-specific/config_file_constants.rst b/docs/version-specific/config_file_constants.rst index 43437312..967995c4 100644 --- a/docs/version-specific/config_file_constants.rst +++ b/docs/version-specific/config_file_constants.rst @@ -12,8 +12,8 @@ only in 'DEFAULT' section: ========================== =================================================== =================================================================== Constant name Constant help Constant value ========================== =================================================== =================================================================== -``DEFAULT_ROBOT_PATHS`` List of default robot paths (':'-separated) ``/home/example/work/easybuild-easyconfigs/easybuild/easyconfigs`` ``DEFAULT_REPOSITORYPATH`` Default easyconfigs repository path ``/home/example/.local/easybuild/ebfiles_repo`` +``DEFAULT_ROBOT_PATHS`` List of default robot paths (':'-separated) ``/home/example/work/easybuild-easyconfigs/easybuild/easyconfigs`` ``USER`` Current username, translated uid from password file ``example`` ``HOME`` Current user's home directory, expanded '~' ``/home/example`` ========================== =================================================== =================================================================== diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index dc2d1a68..45d262ec 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -30,6 +30,7 @@ * EB_Java * EB_MATLAB * EB_MCR + * EB_NVHPC * EB_PGI * EB_Samcef * EB_Stata @@ -67,7 +68,6 @@ * EB_Blender * EB_CGAL * EB_Clang - * EB_DIRAC * EB_Doxygen * EB_Eigen * EB_ELSI @@ -81,6 +81,7 @@ * EB_OpenCV * EB_PSI * EB_ROOT + * EB_ScaLAPACK * EB_SuperLU * EB_Trilinos @@ -170,7 +171,6 @@ * EB_R * EB_Ruby * EB_SAMtools - * EB_ScaLAPACK * EB_Scalasca1 * EB_Score_minus_P * EB_SHRiMP @@ -210,6 +210,7 @@ * EB_ALADIN * EB_Bazel * EB_Boost + * EB_CFDEMcoupling * EB_CHARMM * EB_CP2K * EB_FSL @@ -337,6 +338,7 @@ * EB_Java * EB_MATLAB * EB_MCR + * EB_NVHPC * EB_PGI * EB_Samcef * EB_Stata diff --git a/docs/version-specific/easyconfig_constants.rst b/docs/version-specific/easyconfig_constants.rst index 61682839..223bdc23 100644 --- a/docs/version-specific/easyconfig_constants.rst +++ b/docs/version-specific/easyconfig_constants.rst @@ -18,7 +18,7 @@ Constant name Constant value ``OS_PKG_PAM_DEV`` ``('pam-devel', 'libpam0g-dev')`` OS packages providing Pluggable Authentication Module (PAM) developement support ``OS_TYPE`` ``Darwin`` System type (e.g. 'Linux' or 'Darwin') ``OS_VERSION`` ``UNKNOWN`` System version -``SYSTEM`` ``{'version': 'system', 'name': 'system'}`` System toolchain -``SYS_PYTHON_VERSION`` ``2.7.16`` System Python version (platform.python_version()) +``SYSTEM`` ``{'name': 'system', 'version': 'system'}`` System toolchain +``SYS_PYTHON_VERSION`` ``3.8.5`` System Python version (platform.python_version()) ====================== ============================================================= ================================================================================ diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index f13ff7d6..3d860914 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -1072,11 +1072,12 @@ Builds and installs Ruby Gems. Extra easyconfig parameters specific to ``RubyGem`` easyblock ------------------------------------------------------------- -==================== ================================== ============= -easyconfig parameter description default value -==================== ================================== ============= -``options`` Dictionary with extension options. ``{}`` -==================== ================================== ============= +==================== ==================================== ============= +easyconfig parameter description default value +==================== ==================================== ============= +``gem_file`` Path to gem file in unpacked sources ``None`` +``options`` Dictionary with extension options. ``{}`` +==================== ==================================== ============= Customised steps in ``RubyGem`` easyblock ----------------------------------------- diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index 642bc91d..f3d02352 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -166,7 +166,7 @@ Option flag Option description ``--git-working-dirs-path=GIT-WORKING-DIRS-PATH`` Path to Git working directories for EasyBuild repositories (type ) ``--github-org=GITHUB-ORG`` GitHub organization (type ) ``--github-user=GITHUB-USER`` GitHub username (type ) -``--include-easyblocks-from-pr=PR#`` Include easyblocks from specified PR (type ) +``--include-easyblocks-from-pr=PR#`` Include easyblocks from specified PR (type comma-separated list; default: ) ``--install-github-token`` Install GitHub token (requires --github-user) (default: False) ``--list-prs=STATE,ORDER,DIRECTION`` List pull requests (type ; default: open,created,desc) ``--merge-pr=PR#`` Merge pull request (type ) diff --git a/docs/version-specific/toolchain_opts.rst b/docs/version-specific/toolchain_opts.rst index b515c15a..e3b55763 100644 --- a/docs/version-specific/toolchain_opts.rst +++ b/docs/version-specific/toolchain_opts.rst @@ -5,7 +5,7 @@ Available toolchain options (by toolchain) *(see also* ``eb --avail-toolchain-opts `` *)* -ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - GCC_ - GCCcore_ - GNU_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - goblf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ +ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - goblf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ .. _ClangGCC: @@ -326,6 +326,43 @@ option description ========================= ======================================================================= ========= +.. _NVHPC: + +Available options for NVHPC toolchain +------------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + .. _PGI: Available options for PGI toolchain diff --git a/docs/version-specific/toolchains.rst b/docs/version-specific/toolchains.rst index 1a7b6ced..f1e87f54 100644 --- a/docs/version-specific/toolchains.rst +++ b/docs/version-specific/toolchains.rst @@ -71,6 +71,7 @@ Name Compiler(s) MPI Linear algebra **ipsmpi** icc, ifort psmpi *(none)* *(none)* **iqacml** icc, ifort QLogicMPI ACML, ScaLAPACK FFTW **ismkl** icc, ifort MPICH2 imkl imkl +**NVHPC** NVHPC *(none)* *(none)* *(none)* **PGI** PGI *(none)* *(none)* *(none)* **pmkl** PGI *(none)* imkl imkl **pomkl** PGI OpenMPI imkl imkl From b26a66f656e5d0cdf21063168c5e7185a8915004 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 29 Oct 2020 11:04:53 +0800 Subject: [PATCH 083/286] update release notes for EasyBuild v4.3.1 --- docs/Release_notes.rst | 192 ++++++++++++++++++++++++++++++++++++++++- 1 file changed, 188 insertions(+), 4 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 5efd9df8..1d87cc0b 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,196 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,059** different software packages, -including 31 different (compiler) toolchains. It contains 224 software-specific easyblocks and 37 generic easyblocks, -alongside 10,384 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,134** different software packages, +including 31 different (compiler) toolchains. It contains 225 software-specific easyblocks and 37 generic easyblocks, +alongside 10,794 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb431: + +EasyBuild v4.3.1 (October 29th 2020) +------------------------------------ + +bugfix/update release + +**framework** + +* various enhancements, including: + + * further GCC toolchain fixes for aarch64 (`#3433 `_) + * take into account ``--include-easyblocks-from-pr`` when uploading test reports (`#3446 `_) + * add path to pkg-config files in sysroot to ``$PKG_CONFIG_PATH`` when ``--sysroot`` is specified (`#3451 `_) + * add support for NVHPC compiler + toolchain (based on PGI) (`#3454 `_) + * check for _VERSION and _PREFIX Cray environment variables with both software and module name (`#3460 `_) + * allow including easyblocks from multiple PRs (`#3480 `_, `#3481 `_) + +* various bug fixes, including: + + * avoid ``UnicodeDecodeError`` in ``apply_regex_substitutions`` when patching files that include non-UTF-8 characters (`#3450 `_) + * avoid appending lib stubs pattern to RPATH filter over and over again (`#3452 `_) + * fix missing string template on error for incorrect extension ``sources`` value (`#3461 `_) + * fix compatibility with Python 3.9 by renaming fancy root logger (`#3465 `_) + * also remove empty checksums list specified in easyconfig file when using ``--inject-checksums`` (`#3466 `_) + * avoid confusing error log message when determining impi version while trying to define value for ``%(mpi_cmd_prefix)s`` template (`#3474 `_) + * unset ``$LD_LIBRARY_PATH`` when checking for OS dependencies with ``rpm`` & co (`#3477 `_) + * don't change directory in ``download_repo`` function in ``tools.github`` (`#3486 `_) + * take ``source_urls``, ``checksums``, ``patches`` into account when extension source is specified via ``sources`` (`#3487 `_) + +* other changes: + + * consider ``$EB_INSTALLPYTHON`` in ``eb`` command to specify ``python`` command to use for running EasyBuild (`#3428 `_) + * use only the sub folder name for ``createSubmoduleDeps`` script (`#3464 `_) + +**easyblocks** + +* 2 new software-specific easyblocks: + + * CFDEMcoupling (`#1439 `_), NVHPC (`#2190 `_) + +* minor enhancements, including: + + * support having PyQt5 installed as part of Qt5 in QScintilla easyblock (`#2040 `_) + * update TensorFlow easyblock to put Bazel build files in build directory + avoid unnecessary runtime patching (`#2166 `_) + * update CBLAS easyblock for toolchains that include imkl (`#2175 `_) + * add workaround for duplicate prefix path in Eigen CMake config (`#2176 `_) + * enable ``CTEST_OUTPUT_ON_FAILURE`` for CMakeMake test step (`#2181 `_) + * add XLA build support to TensorFlow easyblock (`#2182 `_) + * also consider libfabric dep (``--with-ofi``) when setting default OpenMPI configure options (`#2184 `_) + * make easyblock for installing CMake aware of ``--sysroot`` (`#2187 `_) + * make OpenBLAS respect the parallelism set by easybuild (`#2191 `_) + * handle option of building Michigan State University CCT3 & CCSD3A methods in GAMESS_US easyblock (`#2194 `_) + * add support to RubyGem easyblock for installing zipped gems (`#2203 `_) + * update ScaLAPACK easyblock to support installation with CMake for recent versions (>= v2.1.0) (`#2205 `_) + * update Score-P easyblock to add support for NVHPC toolchain (`#2206 `_) + +* various bug fixes, including: + + * add ``torch/lib`` subdirectory in Python lib dir to ``$LD_LIBRARY_PATH`` for PyTorch installations (`#2183 `_) + * update MUMmer easyblock to use ``apply_regex_substitutions`` and ``copy_file`` functions (`#2185 `_) + * configure OpenMPI 4.x with ``--without-verbs`` when using UCX (`#2188 `_) + * take into account that zlib may be listed in ``--filter-deps`` in custom easyblock for XML R package (`#2189 `_) + * add sanity check commands to Clang easyblock and print warning for missing ncurses (`#2193 `_) + * enhance OpenFOAM easyblock to add symlinks for libraries to ensure ``mpi`` versions have preference over ``dummy`` versions (`#2196 `_) + * leverage installed OpenSSL/BoringSSL when cURL is used as a dependency for TensorFlow (`#2197 `_) + * add ``-ffree-line-length-none`` to gfortran flags in Siesta easyblock (`#2204 `_) + * respect ``--disable-mpi-tests`` in Siesta easyblock (`#2207 `_) + +* other changes, including: + + * set ``$EB_INSTALLPYTHON`` in module generated for EasyBuild rather than setting ``$EB_PYTHON``, to allow overriding Python command to be used for running EasyBuild with ``$EB_PYTHON`` (`#2109 `_) + * remove unused custom easyblock for DIRAC (`#2192 `_, `#2198 `_) + +**easyconfigs** + +* added easyconfigs for 2 new toolchains: + + * fosscuda/2020a (`#11424 `_) and intelcuda/2020a (`#11425 `_) + +* added example easyconfig files for 75 new software packages: + + * Bsoft (`#6551 `_, `#11537 `_), causallift (`#11436 `_), CAVIAR (`#11158 `_), CCfits (`#11505 `_), Cereal (`#11506 `_), + CFDEMcoupling (`#6465 `_), Check (`#11295 `_), chewBBACA (`#11418 `_), COMSOL (`#11513 `_), CUDAcore (`#11295 `_), Dalton (`#5808 `_), + DIRAC (`#11414 `_), ESMValTool (`#6329 `_), eSpeak-NG (`#11236 `_), ExifTool (`#11521 `_), FabIO (`#11517 `_), festival (`#11236 `_), + fetchMG (`#11283 `_), FHI-aims (`#11198 `_), Flexbar (`#11305 `_), FRUIT (`#6613 `_), FRUIT_processor (`#6631 `_), Gaussian (`#4247 `_), + GBprocesS (`#11512 `_), GDRCopy (`#11295 `_), Genome_Profiler (`#6066 `_), groff (`#11200 `_), ILAMB (`#11309 `_), kedro (`#11436 `_), + leidenalg (`#11407 `_), libav (`#6194 `_), libmo_unpack (`#6329 `_), libobjcryst (`#11321 `_), makeinfo (`#11368 `_), + mauveAligner (`#11395 `_), MBROLA (`#11236 `_), MDSplus-Java (`#10705 `_), MDSplus-Python (`#10705 `_), MyCC (`#11283 `_), + nanomax-analysis-utils (`#11517 `_), Nek5000 (`#6408 `_), NVHPC (`#11391 `_), OPERA-MS (`#11410 `_), ORFfinder (`#7031 `_), + phonemizer (`#11236 `_), Pingouin (`#11280 `_), Pint (`#11151 `_), pydantic (`#11151 `_), pyobjcryst (`#11321 `_), PyOpenCL (`#11517 `_), + pyspoa (`#11438 `_), QtPy (`#11517 `_), Qtconsole (`#11517 `_), rasterio (`#11468 `_), rasterstats (`#11468 `_), ReMatCh (`#6067 `_), + Ruby-Tk (`#6613 `_), SBCL (`#11413 `_), scikit-uplift (`#11432 `_), SDL (`#6202 `_), SDL2 (`#6203 `_), SDL2_image (`#6203 `_), + SDL_image (`#6202 `_), SeqKit (`#11538 `_), silx (`#11517 `_), SiNVICT (`#11404 `_), sonic (`#11236 `_), speech_tools (`#11236 `_), + Statistics-R (`#11274 `_), SUMO (`#11435 `_), tidybayes (`#11335 `_), treatSens (`#11431 `_), tsne (`#11283 `_), wandb (`#11450 `_), + WisecondorX (`#11399 `_) + +* added additional easyconfigs for various supported software packages, including: + + * ABINIT 9.2.1, ASE 3.20.1, Autotools 20200321, Bazel 3.6.0, Biopython 1.78, CCL 1.12, CMake 3.18.4, CUDA 11.0.2, + cURL 7.72.0, deepdiff 5.0.2, fmt 7.0.3, GATK 4.1.8.1, GLib 2.66.1, GROMACS 2020.3, GTK+ 3.24.23, git 2.28.0, + HMMER 3.3.1, Horovod 0.20.3, ICU 67.1, IPython 7.18.1, ichorCNA 0.3.2, JupyterHub 1.1.0, JupyterLab 2.2.8, + LLVM 11.0.0, libarchive 3.4.3, libcircle 0.3, libevent 2.1.12, libfabric 1.11.0, libglvnd 1.3.2, libunwind 1.4.0, + libxcb 1.13, MAFFT 7.471, MDSplus 7.96.12, MEGAHIT 1.2.9, MMseqs2 11-e1a1c, Mako 1.1.3, Mesa 20.2.1, Meson 0.55.3, + medaka 1.1.3, mpifileutils 0.10.1, NASM 2.15.05, NSPR 4.29, NSS 3.57, Ninja 1.10.1, nettle 3.6, nglview 2.7.7, + nodejs 12.19.0, OpenImageIO 2.1.12.0, OpenRefine 3.4.1, OpenSSL 1.1.1h, PCRE2 10.35, PSI4 1.3.2, Pango 1.47.0, + PyGEOS 0.8, PyOpenGL 3.1.5, PyQt5 5.15.1, PyQtGraph 0.11.0, PyRETIS 2.5.0, Python 3.8.6, pandas 1.1.2, + phonopy 2.7.1, picard 2.22.1, pixman 0.40.0, protobuf 3.13.0, pyEGA3 3.4.0, pytest 6.0.1, ReFrame 3.2. re2c 2.0.3, + SAMtools 1.11, SCons 4.0.1, SQLite 3.33.0, Spyder 4.1.5, Subversion 1.14.0, sbt 1.3.13, spglib-python 1.16.0, + spoa 4.0.0, TINKER 8.8.1, TRIQS 3.0.0, Taiyaki 5.1.0, TensorFlow 2.3.1, Tkinter 2.7.18 + 3.8.6, torchvision 0.7.0, + UCX 1.9.0, V8 3.2.0, VirtualGL 2.6.2, vsc mympirun 5.2.0 X11 20201008, XGBoost 1.2.0, + XZ 5.2.5, Xerces-C++ 3.2.3, xarray 0.16.1, ZeroMQ 4.3.3, zstd 1.4.5 + +* minor enhancements, including: + + * use more EasyBuild installed dependencies for TensorFlow 2.2.0 (`#11224 `_) + * add additional extensions to R 4.0.0 easyconfig (`#11340 `_, `#11430 `_, `#11487 `_) + * add additional extensions to Bioconductor 3.11 bundle (`#11341 `_, `#11488 `_) + * make libtirpc easier to use as replacement of rpc in glibc (for RHEL8) (`#11355 `_) + * add libevent, libfabric and PMIx dependencies to OpenMPI 4.0.3 (for foss/2020a & iomkl/2020a) (`#11387 `_, `#11568 `_) + * build LibTIFF with ``-fPIC`` (`#11527 `_) + * update Java/1.8 wrapper to also support aarch64 (`#11545 `_) + +* various bug fixes, including: + + * add Python 3 as build dep for Xvfb 1.20.8 easyconfigs (`#10745 `_) + * patch out bug in collective primitive in TensorFlow 2.2.0 (`#11175 `_) + * add missing groff build dependency for Perl (provides nroff tool requires to install man pages) (`#11200 `_) + * add pocl dependency to GDAL easyconfig using fosscuda/2019b toolchain to make sure it builds on POWER (`#11273 `_) + * add libtirpc as a build dep for HDF to fix installation on RHEL8 (`#11279 `_) + * fix build problems with make 4.2.1 on RHEL8 (`#11282 `_, `#11371 `_) + * change ``$LIBS`` in Ghostscript 9.27 easyconfig to include location of zlib library to link with (`#11291 `_) + * remove ``--no-dist-info`` configuration option for SIP in recent PyQt5 easyconfigs (`#11307 `_) + * make sure correct zlib is used in recent Ghostscript easyconfigs (`#11319 `_) + * remove GLog and GFlags from PyTorch 1.2.0 (`#11327 `_), 1.3.1 (`#11325 `_), 1.4.0 (`#11322 `_) and 1.6.0 (`#11323 `_) + * use PyTorch easyblock for PyTorch 1.3.1 (`#11325 `_) + * add missing git build dependency for OpenImageIO 2.0.12 (`#11328 `_) + * fix HDF 4.2.14 easyconfigs for RHEL8 (`#11330 `_) + * add patch to fix installation of LAMMPS 7Aug2019 on AMD Epyc systems (`#11334 `_) + * fix dependency on Bowtie of v0.x in seq2HLA easyconfigs (`#11339 `_) + * fix installation of Hadoop v2.10.0 on RHEL8 (`#11358 `_) + * add patch to fix installation of Sailfish v0.10.1 on RHEL8 (`#11364 `_) + * add patch to fix installation of FuSeq v1.1.2 on RHEL8 (`#11365 `_) + * fix installation of Qt5 5.14.1 on top of zlib provided by Gentoo + stick to Python 2 as build dep (`#11385 `_, `#11386 `_) + * add patch for LAME configure script to make it check for correct ncurses symbol (`#11388 `_) + * add protobuf-python as a dependency and corresponding sanity check to PyTorch 1.6 (`#11390 `_) + * fix Multiwfn 3.6 installation on RHEL8 (`#11402 `_) + * fix OpenFOAM 2.3.1 installation with intel/2019b on RHEL8 (`#11409 `_) + * fix broken worker easyconfigs (`#11412 `_) + * add ncurses runtime dependency to Clang easyconfigs (`#11415 `_, `#11416 `_, `#11419 `_, `#11472 `_) + * fix installation of Bioconductor 3.11 bundle on aarch64 (`#11417 `_) + * add patch to libunwind fixing a failure on POWER (`#11421 `_) + * fix infinite loop build bug on ppc64le for R 4.0.0 (`#11428 `_) + * fix compilation of Qt5 v5.12.3 and v5.13.1 on Ubuntu 20.04 (`#11434 `_) + * fix PyVCF easyconfig, only supports Python 2 (`#11437 `_) + * add patches to fix miscomputation (on POWER) and performance issues for OpenBLAS (`#11443 `_, `#11444 `_, `#11445 `_) + * add missing DB dependency (required for DB_File) to easyconfigs for Perl (`#11451 `_, `#11452 `_) + * fix dbarts extension in R v4.0.0 easyconfigs for non-x86_64 (`#11453 `_) + * use Homebrew source mirror to auto-download sources for DB v18.1.25 and v18.1.32 (`#11454 `_) + * add missing UnZip dependency for Python 3.8.2 (`#11458 `_) + * add support for building OpenBLAS on ARM TSV110 with GCC 8.3 (`#11464 `_) + * allow Kent_tools to build when MySQL installed at the OS level (`#11471 `_) + * add missing ``moduleclass`` to easyconfigs for: + + * Arlequin 3.5.2.2 (`#11473 `_), MEGAHIT 1.2.8 (`#11474 `_) and 1.2.9 (`#11475 `_), PyCUDA 2019.1.2 (`#11476 `_) + + * fix source for SQLite 3.31.1 (`#11483 `_) + * fix installation of worker 1.6.11 with intel/2019b on RHEL 8.2 (`#11498 `_) + * fix checksum in NAMD 2.12 easyconfigs + add source URL (`#11515 `_) + * add BLAS/LAPACK check to GPAW patch adding EasyBuild configuration files (`#11523 `_) + * backport fixes for Score-P v6.0 (`#11540 `_) + * add XZ build dep to easyconfigs for libarchive v3.4.0 and v3.4.2 (`#11561 `_) + * add patch for OpenMPI 3.1.4 adding device parameters for ConnectX-6 (`#11575 `_) + +* other changes: + + * update README on constructing source file for MATLAB (`#6341 `_) + * remove easyconfigs for Taiyaki that depend on PyTorch 1.3.1, since latest version still requires PyTorch 1.2.0 (`#11301 `_) + * make CI error messages less confusing ("is" -> "should be") (`#11314 `_) + * remove extensions from R-bundle-Bioconductor 3.11 easyconfigs that are also included in R 4.0.0 (`#11429 `_) + * cache M4 source tarball to avoid test failures because of download problems (`#11469 `_) + * rename jupyterhub to JupyterHub (`#11571 `_) + + .. _release_notes_eb430: EasyBuild v4.3.0 (September 13th 2020) @@ -111,7 +295,7 @@ feature release * solve issue where pybind11 picks up on the system Python instead of one provided by a module (`#2158 `_) * fix Qt5 easyblock to support installation on Arm/aarch64 (requires platform to be ``linux-g++``) (`#2160 `_) * fix OpenFOAM easyblock to support installation on Arm/aarch64 systems (`#2162 `_) - * explicitely enable/disable CUDA options in PyTorch easyblock + fix download check in sanity check + fix for disabling of *NNPACK on POWER systems (`#2164 `_) + * explicitly enable/disable CUDA options in PyTorch easyblock + fix download check in sanity check + fix for disabling of *NNPACK on POWER systems (`#2164 `_) * fix sanity check in Mathematica easyblock for 11.x versions older than 11.3 (`#2168 `_) * unset ``$COLUMNS`` if it is set to ``0`` before running Perl's configure script (`#2169 `_) From 10b452989dbfe2d48646659bfbd541b3b702b347 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 29 Oct 2020 17:05:40 +0800 Subject: [PATCH 084/286] bump version to 4.3.1 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index b09fdf57..4666f46a 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.3.0' +VERSION = '4.3.1' # Utility function to read README file From 47f87de1e55d1060abd9c33c1cc5af287cb32854 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Oct 2020 11:33:02 +0100 Subject: [PATCH 085/286] bump EasyBuild version in docs + bump docs release --- docs/Changelog.rst | 1 + docs/conf.py | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index f2c22ea4..a4c4f2fa 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20200913.01** (`Oct 29th 2020`): update release notes for EasyBuild v4.3.1 (see :ref:`release_notes_eb431`) * **release 20200913.01** (`Sep 13th 2020`): update release notes for EasyBuild v4.3.0 (see :ref:`release_notes_eb430`) * **release 20200708.01** (`July 8th 2020`): update release notes for EasyBuild v4.2.2 (see :ref:`release_notes_eb422`) * **release 20200520.01** (`May 20th 2020`): update release notes for EasyBuild v4.2.1 (see :ref:`release_notes_eb421`) diff --git a/docs/conf.py b/docs/conf.py index b325ea80..2acb5cba 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.3.0' # this is meant to reference the version of EasyBuild +version = '4.3.1' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20200913.0' # this is meant to reference the version of the documentation itself +release = '20201029.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 746f506961420636dbf95f359de3504e6690501c Mon Sep 17 00:00:00 2001 From: Denis Kristak Date: Wed, 11 Nov 2020 12:32:20 +0100 Subject: [PATCH 086/286] docs for Building with easystack - includes devel notes --- docs/Building_with_easystack.rst | 143 +++++++++++++++++++++++++++++++ 1 file changed, 143 insertions(+) create mode 100644 docs/Building_with_easystack.rst diff --git a/docs/Building_with_easystack.rst b/docs/Building_with_easystack.rst new file mode 100644 index 00000000..5078fff0 --- /dev/null +++ b/docs/Building_with_easystack.rst @@ -0,0 +1,143 @@ +.. building_with_easystack: + +Building with Easystack +======================= + +This documentation covers aspects of using Easybuild with *Easystack*. + +*Note: this is an experimental feature. Some of the mentioned functionality may be subject to change or be prone to errors.* + +.. contents:: + :depth: 3 + :backlinks: none + + +.. building_with_easystack_basics: + +The Basics +---------- + +Building with *Easystack* lets user create a file that specifies all the software they want to build, and call EasyBuild with that file as argument. +EasyBuild then loops over the software specified in the spec file to build it. + + +.. building_with_easystack_usage: + +Usage +------------------------- + +To build software with *Easystack*, type: + +.. code:: + + eb --easystack yourEasystackFile.yaml + +where yourEasystackFile.yaml is the file with specifications that you just created (more about this in the next chapter). + +.. building_with_easystack_structure: + +Structure of an Easystack file +------------------------- + +Easystack file can currently be of type YAML. + +General options, which should be applied to each software (i.e. *robot*), are defined at the top of the file. + +Afterwards, particular software specifications follow. + +It is mandatory to specify basic software-related keywords - *software name*, *toolchain* and *versions*. + +*software name*: Name of software. + +*toolchain*: A group of development related utilities (eg compiler) and libraries. +(see :ref:`toolchains` for more details). + +*versions*: Version of software. If multiple entries are provided, EB will install all of them. +Can be in form of a list or consecutive line entries (see example). + +**General structure of YAML-formatted *easystack*:** + +.. code:: + + software: + software_name: + toolchain: + toolchain_name (incl. version): + software_version: + versionsuffix: + +**Use-case example of YAML-formatted *easystack*:** + +.. code:: + + software: + Bioconductor: + toolchains: + foss-2020a: + versions: + 3.11: + EasyBuild: + toolchains: + SYSTEM: + versions: [4.3.1] + GROMACS: + toolchains: + foss-2020a: + versions: + 2020.1: + 2020.3: + fosscuda-2020a: + versions: [2020.1] + OpenFOAM: + toolchains: + foss-2020a: + versions: [8, v2006] + R: + toolchains: + foss-2020a: + versions: [4.0.0] + +Installation using this *easystack* called 'myeasystack.yaml' with command + +.. code:: + + eb --easystack myeasystack.yaml; + +is an equivalent of running: + +.. code:: + + eb Bioconductor-3.11-foss-2020a.eb; + eb EasyBuild-4.3.1-SYSTEM.eb; + eb GROMACS-2020.1-foss-2020a.eb; + eb GROMACS-2020.3-foss-2020a.eb; + eb GROMACS-2020.1-fosscuda-2020a.eb; + eb OpenFOAM-8-foss-2020a.eb; + eb OpenFOAM-v2006-foss-2020a.eb; + eb R-4.0.0-foss-2020a.eb; + + +to be developed: + + +**Optionally, more advanced keywords can be specified:** +*easybuild_version*, *robot*, *from_pr*, *versionsuffix*, *include-labels*, *exclude-labels*. + +*easybuild_version:* if present, EB framework will check if the Easystack file was intended for the current version of the EB framework. + +*robot:* enables dependency resolution. (see :ref:`Using_the_EasyBuild_command_line` for more details). + +*from_pr:* easyconfig files that are added or modified by a +particular pull request to the easybuild-easyconfigs GitHub repository +can be used (regardless of whether the pull request is merged or not). +(see :ref:`Integration_with_GitHub` for more details). + +*versionsuffix:* additional suffix for software version (placed after toolchain name) +(see :ref:`easyconfig_parameters` for more details). + +*include-labels:* + + +*exclude-labels:* + + From 721a58b3f962bc717cc041c78ad691394cf725f2 Mon Sep 17 00:00:00 2001 From: Denis Kristak Date: Wed, 11 Nov 2020 12:46:27 +0100 Subject: [PATCH 087/286] restructured code --- docs/Building_with_easystack.rst | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/docs/Building_with_easystack.rst b/docs/Building_with_easystack.rst index 5078fff0..54433941 100644 --- a/docs/Building_with_easystack.rst +++ b/docs/Building_with_easystack.rst @@ -101,21 +101,13 @@ Installation using this *easystack* called 'myeasystack.yaml' with command .. code:: - eb --easystack myeasystack.yaml; + eb --easystack myeasystack.yaml is an equivalent of running: .. code:: - eb Bioconductor-3.11-foss-2020a.eb; - eb EasyBuild-4.3.1-SYSTEM.eb; - eb GROMACS-2020.1-foss-2020a.eb; - eb GROMACS-2020.3-foss-2020a.eb; - eb GROMACS-2020.1-fosscuda-2020a.eb; - eb OpenFOAM-8-foss-2020a.eb; - eb OpenFOAM-v2006-foss-2020a.eb; - eb R-4.0.0-foss-2020a.eb; - + eb Bioconductor-3.11-foss-2020a.eb EasyBuild-4.3.1-SYSTEM.eb GROMACS-2020.1-foss-2020a.eb GROMACS-2020.3-foss-2020a.eb GROMACS-2020.1-fosscuda-2020a.eb OpenFOAM-8-foss-2020a.eb OpenFOAM-v2006-foss-2020a.eb R-4.0.0-foss-2020a.eb to be developed: From 38995c2ce1ececf0a4171f7c4e2171a07c67665e Mon Sep 17 00:00:00 2001 From: Denis Kristak Date: Mon, 30 Nov 2020 15:55:59 +0100 Subject: [PATCH 088/286] changes after review --- docs/Building_with_easystack.rst | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/Building_with_easystack.rst b/docs/Building_with_easystack.rst index 54433941..a03b6f2c 100644 --- a/docs/Building_with_easystack.rst +++ b/docs/Building_with_easystack.rst @@ -30,26 +30,26 @@ To build software with *Easystack*, type: .. code:: - eb --easystack yourEasystackFile.yaml + eb --easystack example.yaml -where yourEasystackFile.yaml is the file with specifications that you just created (more about this in the next chapter). +where example.yaml is the file with specifications that you just created (more about this in the next chapter). .. building_with_easystack_structure: Structure of an Easystack file ------------------------- -Easystack file can currently be of type YAML. +Easystack files are written in YAML syntax. ( YAML guide: https://learnxinyminutes.com/docs/yaml ) General options, which should be applied to each software (i.e. *robot*), are defined at the top of the file. Afterwards, particular software specifications follow. -It is mandatory to specify basic software-related keywords - *software name*, *toolchain* and *versions*. +It is mandatory to specify basic software-related keywords - *software name*, *toolchains* and *versions*. *software name*: Name of software. -*toolchain*: A group of development related utilities (eg compiler) and libraries. +*toolchains*: A group of development related utilities (eg compiler) and libraries. (see :ref:`toolchains` for more details). *versions*: Version of software. If multiple entries are provided, EB will install all of them. @@ -61,7 +61,7 @@ Can be in form of a list or consecutive line entries (see example). software: software_name: - toolchain: + toolchains: toolchain_name (incl. version): software_version: versionsuffix: @@ -109,8 +109,8 @@ is an equivalent of running: eb Bioconductor-3.11-foss-2020a.eb EasyBuild-4.3.1-SYSTEM.eb GROMACS-2020.1-foss-2020a.eb GROMACS-2020.3-foss-2020a.eb GROMACS-2020.1-fosscuda-2020a.eb OpenFOAM-8-foss-2020a.eb OpenFOAM-v2006-foss-2020a.eb R-4.0.0-foss-2020a.eb -to be developed: - +To be developed +--------------- **Optionally, more advanced keywords can be specified:** *easybuild_version*, *robot*, *from_pr*, *versionsuffix*, *include-labels*, *exclude-labels*. From 5b0cb677d86e6c9252366e2cf38a423969e626a0 Mon Sep 17 00:00:00 2001 From: Denis Kristak Date: Mon, 30 Nov 2020 16:02:12 +0100 Subject: [PATCH 089/286] repaired formatting --- docs/Building_with_easystack.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Building_with_easystack.rst b/docs/Building_with_easystack.rst index a03b6f2c..a2432735 100644 --- a/docs/Building_with_easystack.rst +++ b/docs/Building_with_easystack.rst @@ -55,7 +55,7 @@ It is mandatory to specify basic software-related keywords - *software name*, *t *versions*: Version of software. If multiple entries are provided, EB will install all of them. Can be in form of a list or consecutive line entries (see example). -**General structure of YAML-formatted *easystack*:** +**General structure of YAML-formatted easystack:** .. code:: @@ -66,7 +66,7 @@ Can be in form of a list or consecutive line entries (see example). software_version: versionsuffix: -**Use-case example of YAML-formatted *easystack*:** +**Use-case example of YAML-formatted easystack:** .. code:: From 8b32fc6a1a16ceb9849434fccd77ff60c3730068 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Nov 2020 16:38:47 +0100 Subject: [PATCH 090/286] small tweaks in doc page for easystack files --- docs/Building_with_easystack.rst | 135 ------------------------------- docs/Easystack-files.rst | 121 +++++++++++++++++++++++++++ docs/Experimental_features.rst | 1 + 3 files changed, 122 insertions(+), 135 deletions(-) delete mode 100644 docs/Building_with_easystack.rst create mode 100644 docs/Easystack-files.rst diff --git a/docs/Building_with_easystack.rst b/docs/Building_with_easystack.rst deleted file mode 100644 index a2432735..00000000 --- a/docs/Building_with_easystack.rst +++ /dev/null @@ -1,135 +0,0 @@ -.. building_with_easystack: - -Building with Easystack -======================= - -This documentation covers aspects of using Easybuild with *Easystack*. - -*Note: this is an experimental feature. Some of the mentioned functionality may be subject to change or be prone to errors.* - -.. contents:: - :depth: 3 - :backlinks: none - - -.. building_with_easystack_basics: - -The Basics ----------- - -Building with *Easystack* lets user create a file that specifies all the software they want to build, and call EasyBuild with that file as argument. -EasyBuild then loops over the software specified in the spec file to build it. - - -.. building_with_easystack_usage: - -Usage -------------------------- - -To build software with *Easystack*, type: - -.. code:: - - eb --easystack example.yaml - -where example.yaml is the file with specifications that you just created (more about this in the next chapter). - -.. building_with_easystack_structure: - -Structure of an Easystack file -------------------------- - -Easystack files are written in YAML syntax. ( YAML guide: https://learnxinyminutes.com/docs/yaml ) - -General options, which should be applied to each software (i.e. *robot*), are defined at the top of the file. - -Afterwards, particular software specifications follow. - -It is mandatory to specify basic software-related keywords - *software name*, *toolchains* and *versions*. - -*software name*: Name of software. - -*toolchains*: A group of development related utilities (eg compiler) and libraries. -(see :ref:`toolchains` for more details). - -*versions*: Version of software. If multiple entries are provided, EB will install all of them. -Can be in form of a list or consecutive line entries (see example). - -**General structure of YAML-formatted easystack:** - -.. code:: - - software: - software_name: - toolchains: - toolchain_name (incl. version): - software_version: - versionsuffix: - -**Use-case example of YAML-formatted easystack:** - -.. code:: - - software: - Bioconductor: - toolchains: - foss-2020a: - versions: - 3.11: - EasyBuild: - toolchains: - SYSTEM: - versions: [4.3.1] - GROMACS: - toolchains: - foss-2020a: - versions: - 2020.1: - 2020.3: - fosscuda-2020a: - versions: [2020.1] - OpenFOAM: - toolchains: - foss-2020a: - versions: [8, v2006] - R: - toolchains: - foss-2020a: - versions: [4.0.0] - -Installation using this *easystack* called 'myeasystack.yaml' with command - -.. code:: - - eb --easystack myeasystack.yaml - -is an equivalent of running: - -.. code:: - - eb Bioconductor-3.11-foss-2020a.eb EasyBuild-4.3.1-SYSTEM.eb GROMACS-2020.1-foss-2020a.eb GROMACS-2020.3-foss-2020a.eb GROMACS-2020.1-fosscuda-2020a.eb OpenFOAM-8-foss-2020a.eb OpenFOAM-v2006-foss-2020a.eb R-4.0.0-foss-2020a.eb - -To be developed ---------------- - -**Optionally, more advanced keywords can be specified:** -*easybuild_version*, *robot*, *from_pr*, *versionsuffix*, *include-labels*, *exclude-labels*. - -*easybuild_version:* if present, EB framework will check if the Easystack file was intended for the current version of the EB framework. - -*robot:* enables dependency resolution. (see :ref:`Using_the_EasyBuild_command_line` for more details). - -*from_pr:* easyconfig files that are added or modified by a -particular pull request to the easybuild-easyconfigs GitHub repository -can be used (regardless of whether the pull request is merged or not). -(see :ref:`Integration_with_GitHub` for more details). - -*versionsuffix:* additional suffix for software version (placed after toolchain name) -(see :ref:`easyconfig_parameters` for more details). - -*include-labels:* - - -*exclude-labels:* - - diff --git a/docs/Easystack-files.rst b/docs/Easystack-files.rst new file mode 100644 index 00000000..29503454 --- /dev/null +++ b/docs/Easystack-files.rst @@ -0,0 +1,121 @@ +.. easystack: + +Easystack files +=============== + +This documentation covers aspects of specifying a software stack to instlal with Easybuild with *easystack files*. + +*Note: this is an experimental feature. Some of the mentioned functionality may be subject to change or be prone to errors.* + +.. contents:: + :depth: 3 + :backlinks: none + + +.. easystack_basics: + +The basics +---------- + +*Easystack files* describe an entire software stack, and can be used to specify to EasyBuild what to install. + +.. easystack_usage: + +Usage +----- + +To build software with *Easystack*, type: + +.. code:: + + eb --easystack example.yaml --experimental + +where ``example.yaml`` is the file with specifications that you just created (more about this in the next section). + +.. easystack_structure: + +Structure of an easystack file +------------------------------ + +Easystack files are written in `YAML syntax `_. + +General options, which should be applied to each software (for example ``robot``), are defined at the top of the file. + +Afterwards, particular software specifications follow. + +It is mandatory to specify basic software-related keywords: *software name*, *toolchains* and *versions*. + +- *software name*: Name of the software. +- *toolchains*: Names and versions of compiler :ref:`toolchains`. +- *versions*: Versions of software. If multiple entries are provided, EasyBuild will install all of them. +Can be in form of a list or consecutive line entries (see example). + +**General structure of YAML-formatted easystack:** + +.. code:: + + software: + : + toolchains: + : + : + versionsuffix: '<-example>' + +**Example of YAML-formatted easystack:** + +.. code:: + + software: + Bioconductor: + toolchains: + foss-2020a: + versions: + 3.11: + EasyBuild: + toolchains: + SYSTEM: + versions: [4.3.1] + GROMACS: + toolchains: + foss-2020a: + versions: + 2020.1: + 2020.3: + fosscuda-2020a: + versions: [2020.1] + OpenFOAM: + toolchains: + foss-2020a: + versions: [8, v2006] + R: + toolchains: + foss-2020a: + versions: [4.0.0] + +To install the software specified in this *easystack file* named '``myeasystack.yaml``', run: + +.. code:: + + eb --easystack myeasystack.yaml + +This is equivalent to running: + +.. code:: + + eb Bioconductor-3.11-foss-2020a.eb EasyBuild-4.3.1-SYSTEM.eb GROMACS-2020.1-foss-2020a.eb GROMACS-2020.3-foss-2020a.eb GROMACS-2020.1-fosscuda-2020a.eb OpenFOAM-8-foss-2020a.eb OpenFOAM-v2006-foss-2020a.eb R-4.0.0-foss-2020a.eb + +To be developed +--------------- + +- **Optionally, more advanced keywords can be specified:** + *easybuild_version*, *robot*, *from_pr*, *versionsuffix*, *include-labels*, *exclude-labels*. +- *easybuild_version:* if present, EasyBuild will check if the easystack file was intended for the current version of EasyBuild. +- *robot:* enables dependency resolution; see :ref:`Using_the_EasyBuild_command_line` for more details. +- *from_pr:* easyconfig files that are added or modified by a + particular pull request to the easybuild-easyconfigs GitHub repository + can be used (regardless of whether the pull request is merged or not). + (see :ref:`Integration_with_GitHub` for more details). +- *versionsuffix:* additional suffix for software version (placed after toolchain name) + (see :ref:`easyconfig_parameters` for more details). +- *include-labels:* +- *exclude-labels:* diff --git a/docs/Experimental_features.rst b/docs/Experimental_features.rst index f26118c5..dbca8a87 100644 --- a/docs/Experimental_features.rst +++ b/docs/Experimental_features.rst @@ -13,3 +13,4 @@ Currently enabled experimental features include: * support for easyconfig files in YAML syntax (see :ref:`easyconfig_yeb_format`) * support for generating container recipes & images (see :ref:`containers`) + * support for using easystack files (see :ref:`easystack`) From a84d41cf1704e6d5a678491abbe9ef87d8156dcc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Nov 2020 16:45:43 +0100 Subject: [PATCH 091/286] fix typos in docs --- docs/Contributing.rst | 2 +- docs/Release_notes.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Contributing.rst b/docs/Contributing.rst index ff1469b6..4bb59f33 100644 --- a/docs/Contributing.rst +++ b/docs/Contributing.rst @@ -497,7 +497,7 @@ Some aspects of this are automated, others require human intervention. Requirements for pull requests ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -**Only pull requests (PRs) that fullfil these requirements are eligible to be merged:** +**Only pull requests (PRs) that fulfill these requirements are eligible to be merged:** (i) *the PR must target the* ``develop`` *branch of the repository*; see :ref:`contributing_review_process_develop_branch` diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 5efd9df8..d1c5a061 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -111,7 +111,7 @@ feature release * solve issue where pybind11 picks up on the system Python instead of one provided by a module (`#2158 `_) * fix Qt5 easyblock to support installation on Arm/aarch64 (requires platform to be ``linux-g++``) (`#2160 `_) * fix OpenFOAM easyblock to support installation on Arm/aarch64 systems (`#2162 `_) - * explicitely enable/disable CUDA options in PyTorch easyblock + fix download check in sanity check + fix for disabling of *NNPACK on POWER systems (`#2164 `_) + * explicitly enable/disable CUDA options in PyTorch easyblock + fix download check in sanity check + fix for disabling of *NNPACK on POWER systems (`#2164 `_) * fix sanity check in Mathematica easyblock for 11.x versions older than 11.3 (`#2168 `_) * unset ``$COLUMNS`` if it is set to ``0`` before running Perl's configure script (`#2169 `_) From 7eae2e108f35affa1854560d17a502d55f78fe76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Nov 2020 17:10:00 +0100 Subject: [PATCH 092/286] fix links, add link to easystack files doc page on index page --- docs/Easystack-files.rst | 14 +++++++------- docs/index.rst | 1 + 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/docs/Easystack-files.rst b/docs/Easystack-files.rst index 29503454..322ef428 100644 --- a/docs/Easystack-files.rst +++ b/docs/Easystack-files.rst @@ -1,25 +1,25 @@ -.. easystack: +.. _easystack: Easystack files =============== This documentation covers aspects of specifying a software stack to instlal with Easybuild with *easystack files*. -*Note: this is an experimental feature. Some of the mentioned functionality may be subject to change or be prone to errors.* +*Note: this is an `experimental feature `. Some of the mentioned functionality may be subject to change or be prone to errors.* .. contents:: :depth: 3 :backlinks: none -.. easystack_basics: +.. _easystack_basics: The basics ---------- *Easystack files* describe an entire software stack, and can be used to specify to EasyBuild what to install. -.. easystack_usage: +.. _easystack_usage: Usage ----- @@ -32,7 +32,7 @@ To build software with *Easystack*, type: where ``example.yaml`` is the file with specifications that you just created (more about this in the next section). -.. easystack_structure: +.. _easystack_structure: Structure of an easystack file ------------------------------ @@ -107,8 +107,8 @@ This is equivalent to running: To be developed --------------- -- **Optionally, more advanced keywords can be specified:** - *easybuild_version*, *robot*, *from_pr*, *versionsuffix*, *include-labels*, *exclude-labels*. +Optionally, more advanced keywords can be specified: *easybuild_version*, *robot*, *from_pr*, *versionsuffix*, *include-labels*, *exclude-labels*. + - *easybuild_version:* if present, EasyBuild will check if the easystack file was intended for the current version of EasyBuild. - *robot:* enables dependency resolution; see :ref:`Using_the_EasyBuild_command_line` for more details. - *from_pr:* easyconfig files that are added or modified by a diff --git a/docs/index.rst b/docs/index.rst index 50f51df0..1996ca18 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -65,6 +65,7 @@ Advanced usage topics Detecting_loaded_modules Easyconfig-files-local-variables Easyconfigs_index + Easystack-files Experimental_features Extended_dry_run Hooks From 4934ca27231b5efc2077e017914c24f863a39138 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Nov 2020 17:38:22 +0100 Subject: [PATCH 093/286] fix ref back to Experimental features page --- docs/Easystack-files.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Easystack-files.rst b/docs/Easystack-files.rst index 322ef428..23bb905f 100644 --- a/docs/Easystack-files.rst +++ b/docs/Easystack-files.rst @@ -5,7 +5,7 @@ Easystack files This documentation covers aspects of specifying a software stack to instlal with Easybuild with *easystack files*. -*Note: this is an `experimental feature `. Some of the mentioned functionality may be subject to change or be prone to errors.* +*Note: this is an* :ref:`experimental feature `. *Some of the mentioned functionality may be subject to change or be prone to errors.* .. contents:: :depth: 3 From 47fa9fce97b2eac529461811c0771641bef4b076 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Nov 2020 18:05:33 +0100 Subject: [PATCH 094/286] make note about experimental feature bold --- docs/Easystack-files.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Easystack-files.rst b/docs/Easystack-files.rst index 23bb905f..ab34b132 100644 --- a/docs/Easystack-files.rst +++ b/docs/Easystack-files.rst @@ -5,7 +5,7 @@ Easystack files This documentation covers aspects of specifying a software stack to instlal with Easybuild with *easystack files*. -*Note: this is an* :ref:`experimental feature `. *Some of the mentioned functionality may be subject to change or be prone to errors.* +**Note: this is an* :ref:`experimental feature `. *Some of the mentioned functionality may be subject to change or be prone to errors.** .. contents:: :depth: 3 From 31c4ea18bc4271ea287ecb532ac3f1adc3420264 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Dec 2020 19:39:16 +0100 Subject: [PATCH 095/286] add definition for 2020b common toolchains --- docs/Common-toolchains.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/Common-toolchains.rst b/docs/Common-toolchains.rst index f95ea1cf..a2a203d5 100644 --- a/docs/Common-toolchains.rst +++ b/docs/Common-toolchains.rst @@ -176,6 +176,8 @@ Component versions in ``foss`` toolchain +----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ | ``2020a`` | May '20 | 2.34 | 9.3.0 | 4.0.3 | 0.3.9 | (incl. with OpenBLAS) | 2.1.0 | 3.3.8 | +----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ +| ``2020b`` | Nov '20 | 2.35 | 10.2.0 | 4.0.5 | 0.3.12 | (incl. with OpenBLAS) | 2.1.0 | 3.3.8 | ++----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ *(components marked with* * *were patched)* @@ -212,6 +214,8 @@ Component versions in ``intel`` toolchain +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ | ``2020a`` | May'20 | 2.34 | 9.3.0 | 2020.1.217 | 2019.7.217 | 2020.1.217 | +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ +| ``2020b`` | Nov'20 | 2.35 | 10.2.0 | 2020.4.304 | 2019.9.304 | 2020.4.304 | ++----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ ``(*)``: This toolchain is deprecated, see :ref:`deprecated_easyconfigs_toolchains` for more information. From a215c179335c1066f1bd5a7112d193fbe0d7a794 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Dec 2020 22:48:15 +0100 Subject: [PATCH 096/286] auto-update docs for EasyBuild v4.3.2 --- docs/version-specific/Supported_software.rst | 1583 +++++++++++++---- docs/version-specific/easyblocks.rst | 5 + .../version-specific/easyconfig_templates.rst | 3 +- docs/version-specific/generic_easyblocks.rst | 1 + docs/version-specific/help.rst | 242 +-- docs/version-specific/toolchain_opts.rst | 428 ++++- docs/version-specific/toolchains.rst | 161 +- 7 files changed, 1827 insertions(+), 596 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 0c7f0b63..71800a44 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2133 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2176 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -574,6 +574,22 @@ version versionsuffix toolchain ========== ================== =============== +.. _list_software_alsa-lib_773: + +*alsa-lib* +++++++++++ + +The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system. + +*homepage*: https://www.alsa-project.org + +========= ================= +version toolchain +========= ================= +``1.2.4`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_Amara_482: *Amara* @@ -1289,7 +1305,7 @@ version toolchain ``3.4.0`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b``, ``intel/2017a`` ``3.5.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b`` ``3.6.2`` ``intel/2018a`` -``3.7.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019b`` +``3.7.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` ========= ================================================================================ @@ -1479,6 +1495,7 @@ version versionsuffix toolchain ``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``3.19.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``3.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.20.1`` ``-Python-3.8.2`` ``intel/2020a`` ============== ================== =================================================== @@ -1506,13 +1523,14 @@ version toolchain IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows. -*homepage*: http://asperasoft.com +*homepage*: https://asperasoft.com ========= ================= ========== version versionsuffix toolchain ========= ================= ========== ``3.7.2`` ``.354.010c3b8`` ``system`` ``3.9.0`` ``.1326.6985b21`` ``system`` +``3.9.6`` ``.1467.159c5b1`` ``system`` ========= ================= ========== @@ -1533,6 +1551,22 @@ version toolchain ========= ========== +.. _list_software_assimp_653: + +*assimp* +++++++++ + +Open Asset Import Library (assimp) is a library to import and export various 3d-model-formats including scene-post-processing to generate missing render data. + +*homepage*: https://github.com/assimp/assimp + +========= ================= +version toolchain +========= ================= +``5.0.1`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_Assimulo_845: *Assimulo* @@ -1986,7 +2020,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` +:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` .. _list_software_Bader_478: @@ -2369,6 +2403,7 @@ version versionsuffix toolchain ``38.50b`` ``GCC/8.2.0-2.31.1`` ``38.76`` ``GCC/8.2.0-2.31.1`` ``38.79`` ``GCC/8.3.0`` +``38.87`` ``iccifort/2020.1.217`` ========== =================== =============================== @@ -2411,13 +2446,14 @@ version toolchain The Byte Code Engineering Library (Apache Commons BCEL™) is intended to give users a convenient way to analyze, create, and manipulate (binary) Java class files (those ending with .class). -*homepage*: http://commons.apache.org/proper/commons-bcel/ +*homepage*: https://commons.apache.org/proper/commons-bcel/ -======= ============= ========== -version versionsuffix toolchain -======= ============= ========== -``5.2`` ``-Java-1.8`` ``system`` -======= ============= ========== +========= ============= ========== +version versionsuffix toolchain +========= ============= ========== +``5.2`` ``-Java-1.8`` ``system`` +``6.5.0`` ``-Java-1.8`` ``system`` +========= ============= ========== .. _list_software_BCFtools_764: @@ -2466,14 +2502,14 @@ bcl2fastq Conversion Software both demultiplexes data and converts BCL files gen *homepage*: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html -========== ================== ============================================== -version versionsuffix toolchain -========== ================== ============================================== -``2.19.1`` ``-Python-2.7.12`` ``foss/2016b`` -``2.20.0`` ``GCC/8.3.0``, ``foss/2018b``, ``intel/2019a`` -``2.20.0`` ``-Python-2.7.12`` ``foss/2016b`` -``2.20.0`` ``-Python-2.7.14`` ``intel/2017b`` -========== ================== ============================================== +========== ================== ============================================================= +version versionsuffix toolchain +========== ================== ============================================================= +``2.19.1`` ``-Python-2.7.12`` ``foss/2016b`` +``2.20.0`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``intel/2019a`` +``2.20.0`` ``-Python-2.7.12`` ``foss/2016b`` +``2.20.0`` ``-Python-2.7.14`` ``intel/2017b`` +========== ================== ============================================================= .. _list_software_bcolz_538: @@ -2932,6 +2968,22 @@ version versionsuffix toolchain ======== ================== =================================================== +.. _list_software_BioServices_1118: + +*BioServices* ++++++++++++++ + +Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols). + +*homepage*: http://bioservices.readthedocs.io/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.7.9`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_biscuit_755: *biscuit* @@ -3143,7 +3195,7 @@ version versionsuffix toolchain *BLIS* ++++++ -AMD fork of BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. +AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. *homepage*: https://developer.amd.com/amd-cpu-libraries/blas-library/ @@ -3152,7 +3204,9 @@ version versionsuffix toolchain ========= ============= ================== ``0.3.2`` ``GCC/7.3.0-2.30`` ``0.6.0`` ``GCC/8.3.0-2.32`` +``0.8.0`` ``GCC/9.3.0`` ``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` +``2.2`` ``-amd`` ``GCC/9.3.0`` ========= ============= ================== @@ -3401,6 +3455,7 @@ version versionsuffix toolchain ``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` ``1.72.0`` ``gompi/2020a``, ``iimpi/2020a`` ``1.72.0`` ``-no_mpi`` ``GCCcore/9.3.0`` +``1.74.0`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` ========== ================== ==================================================================== @@ -3829,12 +3884,12 @@ The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl *homepage*: https://core.tcl-lang.org/bwidget/home -========== ================= -version toolchain -========== ================= -``1.9.13`` ``GCCcore/8.2.0`` -``1.9.14`` ``GCCcore/8.3.0`` -========== ================= +========== ==================================== +version toolchain +========== ==================================== +``1.9.13`` ``GCCcore/8.2.0`` +``1.9.14`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ==================================== .. _list_software_BWISE_378: @@ -3871,6 +3926,7 @@ version versionsuffix toolchain ``0.8.2`` ``-Python-3.6.6`` ``foss/2018b`` ``0.8.4`` ``foss/2019a`` ``0.8.8`` ``-Python-3.7.4`` ``foss/2019b`` +``0.8.9`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== =============== @@ -3931,7 +3987,7 @@ version toolchain --- -:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_C3D_186: @@ -4164,6 +4220,22 @@ version toolchain ========== ============== +.. _list_software_carputils_983: + +*carputils* ++++++++++++ + +carputils is a Python framework for generating and running openCARP examples. + +*homepage*: https://git.opencarp.org/openCARP/carputils + +============ ================= ============== +version versionsuffix toolchain +============ ================= ============== +``20200915`` ``-Python-3.8.2`` ``foss/2020a`` +============ ================= ============== + + .. _list_software_Cartopy_738: *Cartopy* @@ -4413,6 +4485,22 @@ version versionsuffix toolchain ========= ================= =============================== +.. _list_software_cctools_759: + +*cctools* ++++++++++ + +The Cooperating Computing Tools (CCTools) help you to design and deploy scalable applications that run on hundreds or thousands of machines at once. + +*homepage*: https://ccl.cse.nd.edu/ + +========== ================= +version toolchain +========== ================= +``7.0.22`` ``GCCcore/8.3.0`` +========== ================= + + .. _list_software_CD-HIT_409: *CD-HIT* @@ -4551,6 +4639,7 @@ version toolchain ``3.0.2`` ``system`` ``3.1.0`` ``system`` ``4.0.0`` ``system`` +``5.0.0`` ``system`` ========= ========== @@ -4844,11 +4933,11 @@ Check is a unit testing framework for C. It features a simple interface for defi *homepage*: https://libcheck.github.io/check/ -========== ================= -version toolchain -========== ================= -``0.15.2`` ``GCCcore/9.3.0`` -========== ================= +========== ===================================== +version toolchain +========== ===================================== +``0.15.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========== ===================================== .. _list_software_check_510: @@ -4884,6 +4973,7 @@ version versionsuffix toolchain ``1.0.13`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.0.18`` ``-Python-2.7.15`` ``foss/2019a`` ``1.1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.1.3`` ``-Python-3.8.2`` ``intel/2020a`` ========== ================== =============================== @@ -5126,6 +5216,7 @@ version versionsuffix toolchain ``9.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` ``10.0.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``10.0.1`` ``GCCcore/9.3.0`` +``11.0.0`` ``GCCcore/9.3.0`` ========== ================== ====================================== @@ -5181,7 +5272,7 @@ version toolchain ``2.3.4.3`` ``foss/2017b``, ``intel/2017b`` ``2.4.0.0`` ``intel/2017b`` ``2.4.1.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018b`` -``2.4.1.3`` ``foss/2019b`` +``2.4.1.3`` ``foss/2019b``, ``foss/2020a`` =========== ================================================================ @@ -5428,6 +5519,22 @@ version toolchain =========== ==================== +.. _list_software_code-server_1119: + +*code-server* ++++++++++++++ + +Run VS Code on any machine anywhere and access it in the browser. + +*homepage*: https://github.com/cdr/code-server + +========= ========== +version toolchain +========= ========== +``3.7.3`` ``system`` +========= ========== + + .. _list_software_CODEX2_421: *CODEX2* @@ -5729,8 +5836,8 @@ version versionsuffix toolchain ``3.0`` ``-psmp`` ``intel/2016b`` ``4.1`` ``intel/2016b`` ``4.1`` ``-psmp`` ``foss/2016b`` -``5.1`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``6.1`` ``foss/2019a``, ``intel/2018a`` +``5.1`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a``, ``intel/2020a`` +``6.1`` ``foss/2019a``, ``intel/2018a``, ``intel/2020a`` ``7.1`` ``intel/2020a`` ======= ============= ================================================================== @@ -5915,6 +6022,22 @@ version toolchain ======== ========================================================= +.. _list_software_CRISPResso2_959: + +*CRISPResso2* ++++++++++++++ + +CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. + +*homepage*: https://github.com/pinellolab/CRISPResso2 + +========== ================== ============== +version versionsuffix toolchain +========== ================== ============== +``2.0.44`` ``-Python-2.7.16`` ``foss/2019b`` +========== ================== ============== + + .. _list_software_CrossMap_808: *CrossMap* @@ -6156,6 +6279,7 @@ version toolchain ``10.1.243`` ``GCC/8.3.0``, ``iccifort/2019.5.281``, ``system`` ``10.2.89`` ``GCC/8.3.0`` ``11.0.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` +``11.1.1`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` ================= ========================================================================== @@ -6172,6 +6296,7 @@ CUDA (formerly Compute Unified Device Architecture) is a parallel computing pla version toolchain ========== ========== ``11.0.2`` ``system`` +``11.1.1`` ``system`` ========== ========== @@ -6180,7 +6305,7 @@ version toolchain *cuDNN* +++++++ -The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. +The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. *homepage*: https://developer.nvidia.com/cudnn @@ -6205,6 +6330,8 @@ version versionsuffix toolchain ``7.6.2.24`` ``-CUDA-10.1.243`` ``system`` ``7.6.4.38`` ``gcccuda/2019a``, ``gcccuda/2019b`` ``7.6.4.38`` ``-CUDA-10.0.130`` ``system`` +``8.0.4.30`` ``-CUDA-11.0.2`` ``system`` +``8.0.4.30`` ``-CUDA-11.1.1`` ``system`` ============ ================== =========================================================== @@ -7211,7 +7338,7 @@ version toolchain DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications. It operates directly on the user binary executable, without any Linux kernel modules or other kernel modifications. -*homepage*: https://github.com/dmtcp/dmtcp +*homepage*: http://dmtcp.sourceforge.net/index.html ========= ================================================= version toolchain @@ -7220,6 +7347,7 @@ version toolchain ``2.5.0`` ``foss/2016a`` ``2.5.1`` ``system`` ``2.5.2`` ``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2018b`` +``2.6.0`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` ========= ================================================= @@ -7343,6 +7471,7 @@ version toolchain ``1.8.15`` ``GCCcore/8.2.0`` ``1.8.16`` ``GCCcore/8.3.0`` ``1.8.17`` ``GCCcore/9.3.0`` +``1.8.20`` ``GCCcore/10.2.0`` =========== ======================================================================================================================================================= @@ -7481,7 +7610,7 @@ version versionsuffix toolchain --- -:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExifTool_810` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExifTool_810` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_E-ANTIC_481: @@ -7621,6 +7750,7 @@ version toolchain ``4.2.1`` ``system`` ``4.2.2`` ``system`` ``4.3.0`` ``system`` +``4.3.1`` ``system`` ========== ========== @@ -7753,6 +7883,7 @@ version toolchain ``3.3.4`` ``system`` ``3.3.5`` ``system`` ``3.3.7`` ``GCCcore/9.3.0``, ``system`` +``3.3.8`` ``GCCcore/10.2.0`` ========== =========================================== @@ -7791,6 +7922,22 @@ version toolchain ========= ============== +.. _list_software_elfutils_872: + +*elfutils* +++++++++++ + +The elfutils project provides libraries and tools for ELF files and DWARF data. + +*homepage*: https://elfutils.org/ + +========= ================= +version toolchain +========= ================= +``0.182`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_Elk_284: *Elk* @@ -7941,6 +8088,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_EMU_231: + +*EMU* ++++++ + +EMU infers population structure in the presence of missingness and works for both haploid, psuedo-haploid and diploid genotype datasets + +*homepage*: http://www.popgen.dk/software/index.php/EMU + +======== ================= ============== +version versionsuffix toolchain +======== ================= ============== +``0.66`` ``-Python-3.7.4`` ``foss/2019b`` +======== ================= ============== + + .. _list_software_enaBrowserTool_1462: *enaBrowserTool* @@ -8335,7 +8498,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -8828,6 +8991,7 @@ version versionsuffix toolchain ``6.5.3`` ``intel/2017a`` ``6.6.0`` ``intel/2017b``, ``intel/2018a`` ``6.7.0`` ``intel/2018a`` +``6.7.5`` ``intel/2020a`` ========= ============= ================================ @@ -8993,6 +9157,7 @@ version toolchain ``4.1.3`` ``GCCcore/8.2.0`` ``4.2.1`` ``GCCcore/8.3.0`` ``4.2.2`` ``GCCcore/9.3.0`` +``4.3.1`` ``GCCcore/10.2.0`` =========== =================================================== @@ -9021,18 +9186,35 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: http://www.fftw.org -========= ============= ================================================================================================================================================================================================================================================== -version versionsuffix toolchain -========= ============= ================================================================================================================================================================================================================================================== -``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` -``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` -``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` -``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` -``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` -``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` -``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``iomkl/2018b`` -``3.3.8`` ``-serial`` ``GCC/9.3.0`` -========= ============= ================================================================================================================================================================================================================================================== +========= ============= ====================================================================================================================================================================================================================================================================================================== +version versionsuffix toolchain +========= ============= ====================================================================================================================================================================================================================================================================================================== +``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` +``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` +``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` +``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` +``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` +``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` +``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``gompic/2020b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``iomkl/2018b`` +``3.3.8`` ``-amd`` ``gompi/2020a`` +``3.3.8`` ``-serial`` ``GCC/9.3.0`` +========= ============= ====================================================================================================================================================================================================================================================================================================== + + +.. _list_software_fgbio_519: + +*fgbio* ++++++++ + +A set of tools to analyze genomic data with a focus on Next Generation Sequencing. + +*homepage*: https://fulcrumgenomics.github.io/fgbio + +========= ========== +version toolchain +========= ========== +``1.3.0`` ``system`` +========= ========== .. _list_software_FGSL_300: @@ -9470,6 +9652,22 @@ version versionsuffix toolchain ======== ================== ============== +.. _list_software_Flink_500: + +*Flink* ++++++++ + +Apache Flink is a framework and distributed processing engine for stateful computations over unbounded and bounded data streams. Flink has been designed to run in all common cluster environments, perform computations at in-memory speed and at any scale. + +*homepage*: https://flink.apache.org/ + +========== =================== ========== +version versionsuffix toolchain +========== =================== ========== +``1.11.2`` ``-bin-scala_2.11`` ``system`` +========== =================== ========== + + .. _list_software_FLINT_381: *FLINT* @@ -9682,6 +9880,7 @@ version toolchain ``2019a`` ``system`` ``2019b`` ``system`` ``2020a`` ``system`` +``2020b`` ``system`` =========== ========== @@ -9703,6 +9902,7 @@ version toolchain ``2019a`` ``system`` ``2019b`` ``system`` ``2020a`` ``system`` +``2020b`` ``system`` ========= ========== @@ -9855,6 +10055,22 @@ version toolchain ========== ======================================================= +.. _list_software_FreeSASA_682: + +*FreeSASA* +++++++++++ + +FreeSASA is a command line tool, C-library and Python module for calculating solvent accessible surface areas (SASA). + +*homepage*: https://freesasa.github.io + +========= ============= +version toolchain +========= ============= +``2.0.3`` ``GCC/8.3.0`` +========= ============= + + .. _list_software_FreeSurfer_1017: *FreeSurfer* @@ -10153,7 +10369,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -10624,6 +10840,7 @@ version toolchain ``2019a`` ``system`` ``2019b`` ``system`` ``2020a`` ``system`` +``2020b`` ``system`` =========== ========== @@ -10877,11 +11094,12 @@ A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. *homepage*: https://github.com/NVIDIA/gdrcopy -======= ================ ================= -version versionsuffix toolchain -======= ================ ================= -``2.1`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` -======= ================ ================= +======= ================ ================== +version versionsuffix toolchain +======= ================ ================== +``2.1`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` +``2.1`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` +======= ================ ================== .. _list_software_Geant4_547: @@ -10891,7 +11109,7 @@ version versionsuffix toolchain Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. -*homepage*: http://geant4.cern.ch/ +*homepage*: https://geant4.cern.ch ============= ================================================================ version toolchain @@ -10904,9 +11122,26 @@ version toolchain ``10.04`` ``intel/2017b`` ``10.5`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018b`` ``10.6`` ``foss/2019b`` +``10.6.2`` ``foss/2020a`` ============= ================================================================ +.. _list_software_Geant4-data_1002: + +*Geant4-data* ++++++++++++++ + +Datasets for Geant4. + +*homepage*: https://geant4.cern.ch/ + +============ ========== +version toolchain +============ ========== +``20201103`` ``system`` +============ ========== + + .. _list_software_gearshifft_1059: *gearshifft* @@ -11121,6 +11356,22 @@ version versionsuffix toolchain ========== ================== ============== +.. _list_software_geocube_730: + +*geocube* ++++++++++ + +Tool to convert geopandas vector data into rasterized xarray data. + +*homepage*: https://corteva.github.io/geocube/latest/ + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.0.14`` ``-Python-3.8.2`` ``foss/2020a`` +========== ================= ============== + + .. _list_software_geopandas_946: *geopandas* @@ -11336,20 +11587,21 @@ Ghostscript is a versatile processor for PostScript data with the ability to ren *homepage*: https://ghostscript.com -======== ================== ================================================== -version versionsuffix toolchain -======== ================== ================================================== -``9.19`` ``intel/2016a``, ``intel/2016b`` -``9.20`` ``foss/2016b``, ``intel/2016b`` -``9.21`` ``intel/2017a`` -``9.22`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` -``9.22`` ``-cairo-1.14.12`` ``GCCcore/6.4.0`` -``9.23`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``9.23`` ``-cairo-1.14.12`` ``GCCcore/6.4.0`` -``9.27`` ``GCCcore/8.2.0`` -``9.50`` ``GCCcore/8.3.0`` -``9.52`` ``GCCcore/9.3.0`` -======== ================== ================================================== +========== ================== ================================================== +version versionsuffix toolchain +========== ================== ================================================== +``9.19`` ``intel/2016a``, ``intel/2016b`` +``9.20`` ``foss/2016b``, ``intel/2016b`` +``9.21`` ``intel/2017a`` +``9.22`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` +``9.22`` ``-cairo-1.14.12`` ``GCCcore/6.4.0`` +``9.23`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``9.23`` ``-cairo-1.14.12`` ``GCCcore/6.4.0`` +``9.27`` ``GCCcore/8.2.0`` +``9.50`` ``GCCcore/8.3.0`` +``9.52`` ``GCCcore/9.3.0`` +``9.53.3`` ``GCCcore/10.2.0`` +========== ================== ================================================== .. _list_software_giflib_621: @@ -11361,12 +11613,12 @@ giflib is a library for reading and writing gif images. It is API and ABI compat *homepage*: http://giflib.sourceforge.net/ -========= ==================================== -version toolchain -========= ==================================== -``5.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``5.2.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ==================================== +========= ======================================================== +version toolchain +========= ======================================================== +``5.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``5.2.1`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================== .. _list_software_gifsicle_838: @@ -11585,6 +11837,7 @@ version versionsuffix toolchain ``2.1.15`` ``system`` ``3.0.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``3.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``3.1.9`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========== ================= =============================== @@ -11821,6 +12074,7 @@ version versionsuffix toolchain ``5.7`` ``-peigs`` ``intel/2019a`` ``5.7.2`` ``intel/2019b`` ``5.7.2`` ``-peigs`` ``intel/2019b`` +``5.8`` ``intel/2020a`` ========= ============= =============== @@ -11883,14 +12137,14 @@ The GLPK (GNU Linear Programming Kit) package is intended for solving large-sca *homepage*: https://www.gnu.org/software/glpk/ -======== ============================================================================================= -version toolchain -======== ============================================================================================= -``4.58`` ``foss/2016a``, ``intel/2016a`` -``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` -``4.61`` ``intel/2017a`` -``4.65`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======== ============================================================================================= +======== ================================================================================================================= +version toolchain +======== ================================================================================================================= +``4.58`` ``foss/2016a``, ``intel/2016a`` +``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` +``4.61`` ``intel/2017a`` +``4.65`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======== ================================================================================================================= .. _list_software_glproto_775: @@ -12181,6 +12435,23 @@ version toolchain ========= ========== +.. _list_software_gobff_516: + +*gobff* ++++++++ + +GCC and GFortran based compiler toolchain with OpenMPI, BLIS, libFLAME, ScaLAPACK and FFTW. + +*homepage*: (none) + +=========== ============= ========== +version versionsuffix toolchain +=========== ============= ========== +``2020.06`` ``-amd`` ``system`` +``2020.11`` ``system`` +=========== ============= ========== + + .. _list_software_GObject-Introspection_2108: *GObject-Introspection* @@ -12272,6 +12543,7 @@ version versionsuffix toolchain ``2019a`` ``system`` ``2019b`` ``system`` ``2020a`` ``system`` +``2020b`` ``system`` ``system`` ``-2.29`` ``system`` =========== ============= ========== @@ -12294,6 +12566,7 @@ version toolchain ``2019a`` ``system`` ``2019b`` ``system`` ``2020a`` ``system`` +``2020b`` ``system`` ========= ========== @@ -12372,14 +12645,15 @@ GPAW is a density-functional theory (DFT) Python code based on the projector-aug *homepage*: https://wiki.fysik.dtu.dk/gpaw/ -========== ============================ =============================== -version versionsuffix toolchain -========== ============================ =============================== -``1.4.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``19.8.1`` ``-ASE-3.18.0-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``19.8.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``20.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -========== ============================ =============================== +=========== ============================ =============================== +version versionsuffix toolchain +=========== ============================ =============================== +``1.4.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``19.8.1`` ``-ASE-3.18.0-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``19.8.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``20.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``20.10.0`` ``-ASE-3.20.1-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +=========== ============================ =============================== .. _list_software_GPAW-setups_1024: @@ -12423,7 +12697,7 @@ version toolchain *gperftools* ++++++++++++ -gperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C++ with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. +gperftools is a collection of a high-performance multi-threaded malloc() implementation, plus some pretty nifty performance analysis tools. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. *homepage*: https://github.com/gperftools/gperftools @@ -12433,6 +12707,7 @@ version toolchain ``2.5`` ``foss/2016a``, ``intel/2016b`` ``2.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.7.90`` ``GCCcore/8.3.0`` +``2.8`` ``GCCcore/9.3.0`` ========== ==================================== @@ -12848,6 +13123,7 @@ version versionsuffix toolchain ``2020`` ``foss/2019b``, ``fosscuda/2019b`` ``2020.1`` ``-Python-3.8.2`` ``foss/2020a`` ``2020.3`` ``fosscuda/2019b`` +``2020.4`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================= ============================================================================================================ @@ -12933,7 +13209,7 @@ version toolchain ``2.3`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b``, ``intel/2017a`` ``2.4`` ``GCCcore/6.4.0`` ``2.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2.6`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217`` +``2.6`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` ========= ============================================================================================================================ @@ -13297,7 +13573,8 @@ version versionsuffix toolchain ``2.8.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.9.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` ``2.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` -``2.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``2.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` +``3.1.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ========== ===================================== ==================================================================================== @@ -13548,7 +13825,8 @@ version versionsuffix toolchain ``1.10.1`` ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2017b``, ``iomkl/2018a`` ``1.10.2`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``1.10.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompic/2019a``, ``gompic/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpic/2019a``, ``iimpic/2019b`` -``1.10.6`` ``gompi/2020a``, ``iimpi/2020a`` +``1.10.6`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpic/2020a`` +``1.10.7`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpic/2020b`` ``1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` ================= ============= ================================================================================================================================================================================================================== @@ -13772,6 +14050,7 @@ version toolchain ``2.0.5`` ``intel/2017a`` ``2.1.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``2.2.0`` ``foss/2018b`` +``2.2.1`` ``foss/2019b`` ============== ================================================================================= @@ -13821,7 +14100,7 @@ version toolchain ========= ============================================================================================================================================ ``3.1b2`` ``GCC/6.4.0-2.28``, ``foss/2016a``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a``, ``intel/2018a`` ``3.2.1`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iimpi/2019b``, ``intel/2018b`` -``3.3.1`` ``iimpi/2020a`` +``3.3.1`` ``gompi/2020a``, ``iimpi/2020a`` ========= ============================================================================================================================================ @@ -13975,7 +14254,7 @@ version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gomkl/2019a``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gomkl/2019a``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020a``, ``intel/2020b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= @@ -14217,6 +14496,8 @@ version versionsuffix toolchain ``4.39.3`` ``-Python-3.6.4`` ``intel/2018a`` ``4.44.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``5.6.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``5.41.2`` ``GCCcore/10.2.0`` +``5.41.5`` ``GCCcore/10.2.0`` ========== ================= ================================== @@ -14245,7 +14526,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -14395,6 +14676,7 @@ version versionsuffix toolchain ``2020.0.166`` ``system`` ``2020.0.166`` ``-GCC-9.2.0`` ``system`` ``2020.1.217`` ``system`` +``2020.4.304`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ============== ===================== ========== @@ -14416,6 +14698,7 @@ version versionsuffix toolchain ``2019a`` ``system`` ``2019b`` ``system`` ``2020a`` ``system`` +``2020b`` ``system`` ============== =================== ========== @@ -14707,6 +14990,7 @@ version versionsuffix toolchain ``2020.00`` ``system`` ``2020.06-impi-18.5`` ``system`` ``2020a`` ``system`` +``2020b`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ===================== ==================== ========== @@ -14728,6 +15012,7 @@ version toolchain ``2019a`` ``system`` ``2019b`` ``system`` ``2020a`` ``system`` +``2020b`` ``system`` =========== ========== @@ -14825,28 +15110,29 @@ ImageMagick is a software suite to create, edit, compose, or convert bitmap imag *homepage*: https://www.imagemagick.org/ -============ =================================== =============================== -version versionsuffix toolchain -============ =================================== =============================== -``6.9.4-8`` ``intel/2016a`` -``7.0.1-6`` ``intel/2016a`` -``7.0.1-9`` ``intel/2016a`` -``7.0.2-9`` ``intel/2016a`` -``7.0.3-1`` ``intel/2016b`` -``7.0.5-4`` ``intel/2017a`` -``7.0.5-10`` ``foss/2016b`` -``7.0.7-8`` ``-JasPer-1.900.1`` ``intel/2017a`` -``7.0.7-14`` ``foss/2017b``, ``intel/2017b`` -``7.0.7-15`` ``GCCcore/6.4.0`` -``7.0.7-26`` ``foss/2018a`` -``7.0.7-30`` ``GCCcore/6.4.0`` -``7.0.7-30`` ``-Ghostscript-9.22-cairo-1.14.12`` ``GCCcore/6.4.0`` -``7.0.7-39`` ``-Ghostscript-9.23-cairo-1.14.12`` ``GCCcore/6.4.0`` -``7.0.8-11`` ``GCCcore/7.3.0`` -``7.0.8-46`` ``GCCcore/8.2.0`` -``7.0.9-5`` ``GCCcore/8.3.0`` -``7.0.10-1`` ``GCCcore/9.3.0`` -============ =================================== =============================== +============= =================================== =============================== +version versionsuffix toolchain +============= =================================== =============================== +``6.9.4-8`` ``intel/2016a`` +``7.0.1-6`` ``intel/2016a`` +``7.0.1-9`` ``intel/2016a`` +``7.0.2-9`` ``intel/2016a`` +``7.0.3-1`` ``intel/2016b`` +``7.0.5-4`` ``intel/2017a`` +``7.0.5-10`` ``foss/2016b`` +``7.0.7-8`` ``-JasPer-1.900.1`` ``intel/2017a`` +``7.0.7-14`` ``foss/2017b``, ``intel/2017b`` +``7.0.7-15`` ``GCCcore/6.4.0`` +``7.0.7-26`` ``foss/2018a`` +``7.0.7-30`` ``GCCcore/6.4.0`` +``7.0.7-30`` ``-Ghostscript-9.22-cairo-1.14.12`` ``GCCcore/6.4.0`` +``7.0.7-39`` ``-Ghostscript-9.23-cairo-1.14.12`` ``GCCcore/6.4.0`` +``7.0.8-11`` ``GCCcore/7.3.0`` +``7.0.8-46`` ``GCCcore/8.2.0`` +``7.0.9-5`` ``GCCcore/8.3.0`` +``7.0.10-1`` ``GCCcore/9.3.0`` +``7.0.10-35`` ``GCCcore/10.2.0`` +============= =================================== =============================== .. _list_software_imake_519: @@ -14950,9 +15236,10 @@ version toolchain ``2019.1.144`` ``gompi/2019a``, ``iimpi/2019.01``, ``iimpi/2019a``, ``iimpic/2019a``, ``iompi/2019.01`` ``2019.2.187`` ``iimpi/2019.02`` ``2019.3.199`` ``iimpi/2019.03`` -``2019.5.281`` ``iimpi/2019b``, ``iimpic/2019b`` +``2019.5.281`` ``gompi/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` ``2020.0.166`` ``iimpi/2020.00`` ``2020.1.217`` ``gompi/2020a``, ``iimpi/2020.06-impi-18.5``, ``iimpi/2020a``, ``iimpic/2020a``, ``iompi/2020a`` +``2020.4.304`` ``iimpi/2020b``, ``iimpic/2020b`` ============== ====================================================================================================================================================================================================================================================================== @@ -15047,6 +15334,7 @@ version versionsuffix toolchain ``2019.3.199`` ``iccifort/2019.3.199-GCC-8.3.0-2.32`` ``2019.6.166`` ``iccifort/2020.0.166-GCC-9.2.0`` ``2019.7.217`` ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` +``2019.9.304`` ``iccifort/2020.4.304``, ``iccifortcuda/2020b`` ``system`` ``iccifort/system-GCC-system-2.29`` ============== ============= ================================================================================================================================================================================================================================ @@ -15267,6 +15555,7 @@ version versionsuffix toolchain ``2020.00`` ``system`` ``2020.06-impi-18.5`` ``system`` ``2020a`` ``system`` +``2020b`` ``system`` ===================== ============= ========== @@ -15303,6 +15592,7 @@ version toolchain ``2019a`` ``system`` ``2019b`` ``system`` ``2020a`` ``system`` +``2020b`` ``system`` =========== ========== @@ -15497,6 +15787,22 @@ version toolchain ========= ============== +.. _list_software_IPM_230: + +*IPM* ++++++ + +IPM is a portable profiling infrastructure for parallel codes. It provides a low-overhead profile of application performance and resource utilization in a parallel program. Communication, computation, and IO are the primary focus. + +*homepage*: https://github.com/nerscadmin/IPM + +========= =================================================================================== +version toolchain +========= =================================================================================== +``2.0.6`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iompi/2020a`` +========= =================================================================================== + + .. _list_software_Ipopt_524: *Ipopt* @@ -15626,13 +15932,13 @@ Efficient phylogenomic software by maximum likelihood *homepage*: http://www.iqtree.org/ -========== ============= =============================== -version versionsuffix toolchain -========== ============= =============================== -``1.5.5`` ``-omp-mpi`` ``foss/2016a`` -``1.6.6`` ``intel/2018a`` -``1.6.12`` ``foss/2018b``, ``intel/2019b`` -========== ============= =============================== +========== ============= =============================================== +version versionsuffix toolchain +========== ============= =============================================== +``1.5.5`` ``-omp-mpi`` ``foss/2016a`` +``1.6.6`` ``intel/2018a`` +``1.6.12`` ``foss/2018b``, ``foss/2020a``, ``intel/2019b`` +========== ============= =============================================== .. _list_software_IRkernel_796: @@ -15862,6 +16168,7 @@ version toolchain ``2.0.10`` ``intel/2016b`` ``2.0.12`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` ``2.0.14`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.0.16`` ``GCCcore/9.3.0`` =========== ========================================================================================================================================================== @@ -16093,13 +16400,13 @@ JsonCpp is a C++ library that allows manipulating JSON values, including serial *homepage*: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html -========== ================= -version toolchain -========== ================= -``0.10.7`` ``GCCcore/8.2.0`` -``1.9.3`` ``GCCcore/8.3.0`` -``1.9.4`` ``GCCcore/9.3.0`` -========== ================= +========== ===================================== +version toolchain +========== ===================================== +``0.10.7`` ``GCCcore/8.2.0`` +``1.9.3`` ``GCCcore/8.3.0`` +``1.9.4`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========== ===================================== .. _list_software_JUBE_294: @@ -16673,7 +16980,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_limix-bgen_1004` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_limix-bgen_1004` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -16701,12 +17008,12 @@ LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGP *homepage*: http://lame.sourceforge.net/ -========== ============================================================================================================== -version toolchain -========== ============================================================================================================== -``3.99.5`` ``foss/2016b``, ``intel/2017a`` -``3.100`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` -========== ============================================================================================================== +========== ================================================================================================================================== +version toolchain +========== ================================================================================================================================== +``3.99.5`` ``foss/2016b``, ``intel/2017a`` +``3.100`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` +========== ================================================================================================================================== .. _list_software_LAMMPS_458: @@ -17218,13 +17525,14 @@ version toolchain This BSD-style licensed command line editor library provides generic line editing, history, and tokenization functions, similar to those found in GNU Readline. -*homepage*: http://thrysoee.dk/editline/ +*homepage*: https://thrysoee.dk/editline/ ============ ================== version toolchain ============ ================== ``20150325`` ``GNU/4.9.3-2.25`` ``20180525`` ``GCCcore/6.4.0`` +``20191231`` ``GCCcore/9.3.0`` ============ ================== @@ -17338,15 +17646,17 @@ version toolchain *libFLAME* ++++++++++ -AMD fork of libFLAME. libFLAME is a portable library for dense matrix computations, providing much of the functionality present in LAPACK. +libFLAME is a portable library for dense matrix computations, providing much of the functionality present in LAPACK. *homepage*: https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame -======= ============= ================== -version versionsuffix toolchain -======= ============= ================== -``1.0`` ``-amd`` ``GCC/7.3.0-2.30`` -======= ============= ================== +========= ============= ================== +version versionsuffix toolchain +========= ============= ================== +``1.0`` ``-amd`` ``GCC/7.3.0-2.30`` +``2.2`` ``-amd`` ``GCC/9.3.0`` +``5.2.0`` ``GCC/9.3.0`` +========= ============= ================== .. _list_software_libfontenc_1060: @@ -17632,12 +17942,12 @@ Libiconv converts from one character encoding to another through Unicode convers *homepage*: https://www.gnu.org/software/libiconv -======== ========================================================================== -version toolchain -======== ========================================================================== -``1.15`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``1.16`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======== ========================================================================== +======== =========================================================================== +version toolchain +======== =========================================================================== +``1.15`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``1.16`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======== =========================================================================== .. _list_software_libidn_626: @@ -17655,6 +17965,7 @@ version toolchain ``1.32`` ``GCCcore/5.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` ``1.34`` ``GCCcore/6.4.0`` ``1.35`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.36`` ``GCCcore/10.2.0`` ======== ====================================================================================== @@ -17667,17 +17978,17 @@ Libint library is used to evaluate the traditional (electron repulsion) and cert *homepage*: https://github.com/evaleev/libint -========= ================ ================================================================================================================================================================== -version versionsuffix toolchain -========= ================ ================================================================================================================================================================== -``1.1.4`` ``intel/2016a`` -``1.1.6`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``2.0.3`` ``foss/2018b``, ``gompi/2019a``, ``intel/2018b`` -``2.1.0`` ``intel/2016b`` -``2.4.2`` ``intel/2018a`` -``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` -``2.6.0`` ``-lmax-6-cp2k`` ``gompi/2020a``, ``iimpi/2020a`` -========= ================ ================================================================================================================================================================== +========= ================ =================================================================================================================================================================================== +version versionsuffix toolchain +========= ================ =================================================================================================================================================================================== +``1.1.4`` ``intel/2016a`` +``1.1.6`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` +``2.0.3`` ``foss/2018b``, ``gompi/2019a``, ``intel/2018b`` +``2.1.0`` ``intel/2016b`` +``2.4.2`` ``intel/2018a`` +``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` +``2.6.0`` ``-lmax-6-cp2k`` ``gompi/2020a``, ``iimpi/2020a`` +========= ================ =================================================================================================================================================================================== .. _list_software_LiBis_467: @@ -17770,6 +18081,22 @@ version toolchain ========== ==================================== +.. _list_software_libmicrohttpd_1397: + +*libmicrohttpd* ++++++++++++++++ + +GNU libmicrohttpd is a small C library that is supposed to make it easy to run an HTTP server as part of another application. + +*homepage*: https://www.gnu.org/software/libmicrohttpd/ + +========== ================= +version toolchain +========== ================= +``0.9.71`` ``GCCcore/9.3.0`` +========== ================= + + .. _list_software_libmo_unpack_1268: *libmo_unpack* @@ -18093,11 +18420,11 @@ Libsndfile is a C library for reading and writing files containing sampled sound *homepage*: http://www.mega-nerd.com/libsndfile -========== ============================================================================================================== -version toolchain -========== ============================================================================================================== -``1.0.28`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a`` -========== ============================================================================================================== +========== ================================================================================================================================== +version toolchain +========== ================================================================================================================================== +``1.0.28`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a`` +========== ================================================================================================================================== .. _list_software_libsodium_968: @@ -18190,6 +18517,22 @@ version toolchain ========= ================= +.. _list_software_libStatGen_1005: + +*libStatGen* +++++++++++++ + +Useful set of classes for creating statistical genetic programs. + +*homepage*: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen + +============ ================= +version toolchain +============ ================= +``20190330`` ``GCCcore/6.4.0`` +============ ================= + + .. _list_software_LIBSVM_461: *LIBSVM* @@ -18460,18 +18803,18 @@ Libxc is a library of exchange-correlation functionals for density-functional th *homepage*: https://www.tddft.org/programs/libxc -========= ============================================================================================================================================== -version toolchain -========= ============================================================================================================================================== -``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` -``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` -``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` -``4.0.1`` ``foss/2017b``, ``intel/2017b`` -``4.0.3`` ``foss/2016b``, ``foss/2017a`` -``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` -``4.3.4`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217`` -========= ============================================================================================================================================== +========= ======================================================================================================================================================================================= +version toolchain +========= ======================================================================================================================================================================================= +``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` +``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` +``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` +``4.0.1`` ``foss/2017b``, ``intel/2017b`` +``4.0.3`` ``foss/2016b``, ``foss/2017a`` +``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` +``4.3.4`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` +========= ======================================================================================================================================================================================= .. _list_software_libxcb_628: @@ -18836,7 +19179,7 @@ version toolchain ``1.8.2`` ``intel/2017b`` ``1.8.3`` ``foss/2018a``, ``intel/2018a`` ``1.10`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``1.16.1`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` +``1.16.1`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` ========== =============================================================================== @@ -18888,9 +19231,26 @@ version toolchain ``0.1.7`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``system`` ``0.2.1`` ``GCCcore/7.3.0``, ``system`` ``0.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.2.5`` ``GCCcore/10.2.0`` ========= =================================================================== +.. _list_software_libzeep_747: + +*libzeep* ++++++++++ + +Libzeep was originally developed to make it easy to create SOAP servers. + +*homepage*: https://github.com/mhekkel/libzeep + +========= =============== +version toolchain +========= =============== +``5.0.1`` ``gompi/2019b`` +========= =============== + + .. _list_software_libzip_650: *libzip* @@ -19001,13 +19361,30 @@ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, *homepage*: http://www.littlecms.com/ -======= ============================================================================================================================================== -version toolchain -======= ============================================================================================================================================== -``2.7`` ``intel/2016a`` -``2.8`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``2.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` -======= ============================================================================================================================================== +======== ============================================================================================================================================== +version toolchain +======== ============================================================================================================================================== +``2.7`` ``intel/2016a`` +``2.8`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``2.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` +``2.11`` ``GCCcore/10.2.0`` +======== ============================================================================================================================================== + + +.. _list_software_LLDB_286: + +*LLDB* +++++++ + +The debugger component of the LLVM project + +*homepage*: https://lldb.llvm.org/ + +========== ================= ================= +version versionsuffix toolchain +========== ================= ================= +``11.0.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +========== ================= ================= .. _list_software_LLVM_315: @@ -19051,15 +19428,15 @@ LMDB is a fast, memory-efficient database. With memory-mapped files, it has the *homepage*: https://symas.com/lmdb -========== ==================================== -version toolchain -========== ==================================== -``0.9.18`` ``foss/2016a`` -``0.9.21`` ``GCCcore/6.4.0``, ``intel/2017a`` -``0.9.22`` ``GCCcore/7.3.0`` -``0.9.23`` ``GCCcore/8.2.0`` -``0.9.24`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ==================================== +========== ======================================================== +version toolchain +========== ======================================================== +``0.9.18`` ``foss/2016a`` +``0.9.21`` ``GCCcore/6.4.0``, ``intel/2017a`` +``0.9.22`` ``GCCcore/7.3.0`` +``0.9.23`` ``GCCcore/8.2.0`` +``0.9.24`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ======================================================== .. _list_software_LMfit_476: @@ -19479,7 +19856,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -19623,6 +20000,7 @@ version versionsuffix toolchain ``2.4.0`` ``fosscuda/2018b`` ``2.5.0`` ``fosscuda/2018b`` ``2.5.1`` ``fosscuda/2019a``, ``fosscuda/2019b`` +``2.5.4`` ``fosscuda/2019a``, ``fosscuda/2019b`` ========= ================ ======================================= @@ -19689,6 +20067,7 @@ version toolchain ``3.82`` ``GCC/4.8.2`` ``4.1`` ``GCC/4.9.2`` ``4.2.1`` ``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` +``4.3`` ``GCC/9.3.0`` ========= ===================================== @@ -20077,7 +20456,8 @@ version versionsuffix toolchain ``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` ``3.0.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` ``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``3.2.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``3.2.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` +``3.3.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ========= ================================= ======================================================================== @@ -20696,6 +21076,22 @@ version toolchain ========== ==================================================================== +.. _list_software_meshalyzer_1092: + +*meshalyzer* +++++++++++++ + +Graphical program for display time dependent data on 3D finite elment meshes + +*homepage*: https://git.opencarp.org/openCARP/meshalyzer + +======= ================= ============== +version versionsuffix toolchain +======= ================= ============== +``2.0`` ``-Python-3.8.2`` ``foss/2020a`` +======= ================= ============== + + .. _list_software_meshio_645: *meshio* @@ -20714,6 +21110,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_meshtool_875: + +*meshtool* +++++++++++ + +Meshtool is a comand-line tool written in C++. It is designed to apply various manipulations to volumetric meshes. + +*homepage*: https://bitbucket.org/aneic/meshtool + +======= ============= +version toolchain +======= ============= +``16`` ``GCC/9.3.0`` +======= ============= + + .. _list_software_Meson_514: *Meson* @@ -20836,6 +21248,22 @@ version versionsuffix toolchain ============ ============= ========== +.. _list_software_Metagenome-Atlas_1572: + +*Metagenome-Atlas* +++++++++++++++++++ + +Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation. + +*homepage*: https://github.com/metagenome-atlas/atlas + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``2.4.3`` ``-Python-3.8.2`` ``intel/2020a`` +========= ================= =============== + + .. _list_software_Metal_499: *Metal* @@ -20944,13 +21372,13 @@ METIS is a set of serial programs for partitioning graphs, partitioning finite e *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview -========= ============= ================================================================================================================================================================================================================================== -version versionsuffix toolchain -========= ============= ================================================================================================================================================================================================================================== -``5.0.2`` ``gimkl/2.11.5`` -``5.1.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``5.1.0`` ``-32bitIDX`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -========= ============= ================================================================================================================================================================================================================================== +========= ============= ====================================================================================================================================================================================================================================================== +version versionsuffix toolchain +========= ============= ====================================================================================================================================================================================================================================================== +``5.0.2`` ``gimkl/2.11.5`` +``5.1.0`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``5.1.0`` ``-32bitIDX`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +========= ============= ====================================================================================================================================================================================================================================================== .. _list_software_mhcflurry_988: @@ -21359,6 +21787,22 @@ version toolchain ======= ========== +.. _list_software_MLxtend_700: + +*MLxtend* ++++++++++ + +Mlxtend (machine learning extensions) is a Python library of useful tools for the day-to-day data science tasks. + +*homepage*: https://rasbt.github.io/mlxtend/ + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.17.3`` ``-Python-3.8.2`` ``foss/2020a`` +========== ================= ============== + + .. _list_software_Mmg_289: *Mmg* @@ -21767,6 +22211,7 @@ version toolchain ``3.1.6`` ``GCCcore/6.4.0`` ``4.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``4.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.1.0`` ``GCCcore/10.2.0`` ========= ================================================================ @@ -21912,6 +22357,38 @@ version toolchain ========= ============== +.. _list_software_MRChem_540: + +*MRChem* +++++++++ + +MRChem is a numerical real-space code for molecular electronic structure calculations within the self-consistent field (SCF) approximations of quantum chemistry: Hartree-Fock and Density Functional Theory. + +*homepage*: https://mrchem.readthedocs.io + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.0.0`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + +.. _list_software_MRCPP_386: + +*MRCPP* ++++++++ + +MultiResolution Computation Program Package + +*homepage*: https://mrcpp.readthedocs.io + +========= ============== +version toolchain +========= ============== +``1.3.6`` ``foss/2020a`` +========= ============== + + .. _list_software_MRIcron_666: *MRIcron* @@ -22245,6 +22722,38 @@ version toolchain ========= ================== +.. _list_software_mxml_446: + +*mxml* +++++++ + +Mini-XML is a tiny XML library that you can use to read and write XML and XML-like data files in your application without requiring large non-standard libraries. + +*homepage*: https://github.com/michaelrsweet/mxml + +======= ================= +version toolchain +======= ================= +``3.2`` ``GCCcore/8.3.0`` +======= ================= + + +.. _list_software_mxmlplus_898: + +*mxmlplus* +++++++++++ + +Mxml is a pure C library (yet having an object oriented layout) that is meant to help developers implementing XML file interpretation in their projects. + +*homepage*: http://mxml.sourceforge.net + +========= ============= +version toolchain +========= ============= +``0.9.2`` ``GCC/9.3.0`` +========= ============= + + .. _list_software_MXNet_460: *MXNet* @@ -22403,7 +22912,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_neon_432` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -22477,6 +22986,22 @@ version versionsuffix toolchain ========== ================= =============== +.. _list_software_nanocompore_1185: + +*nanocompore* ++++++++++++++ + +Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples + +*homepage*: https://nanocompore.rna.rocks/ + +============== ================= =============== +version versionsuffix toolchain +============== ================= =============== +``1.0.0rc3-2`` ``-Python-3.8.2`` ``intel/2020a`` +============== ================= =============== + + .. _list_software_NanoFilt_795: *NanoFilt* @@ -22718,6 +23243,8 @@ version versionsuffix toolchain ``2.3.7`` ``fosscuda/2018b`` ``2.4.2`` ``gcccuda/2019a`` ``2.4.8`` ``gcccuda/2019b`` +``2.8.3`` ``-CUDA-11.0.2`` ``system`` +``2.8.3`` ``-CUDA-11.1.1`` ``system`` ========== =================== ================== @@ -22951,6 +23478,22 @@ version toolchain ======== =============== +.. _list_software_neon_432: + +*neon* +++++++ + +neon is an HTTP/1.1 and WebDAV client library, with a C interface. + +*homepage*: https://github.com/notroj/neon + +========== ================= +version toolchain +========== ================= +``0.31.2`` ``GCCcore/8.3.0`` +========== ================= + + .. _list_software_Net-core_765: *Net-core* @@ -22993,7 +23536,7 @@ version versionsuffix toolchain ``4.6.1`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``4.6.2`` ``gompi/2019a``, ``iimpi/2019a`` ``4.7.1`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` -``4.7.4`` ``gompi/2020a``, ``iimpi/2020a`` +``4.7.4`` ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020a``, ``iimpi/2020b`` =========== ================ ========================================================================================================================== @@ -23028,7 +23571,7 @@ version versionsuffix toolchain ``4.3.0`` ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``4.3.0`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.3.0`` ``-HDF5-1.8.19`` ``intel/2017b`` -``4.3.1`` ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a`` +``4.3.1`` ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2019b``, ``iimpi/2020a`` ========= ================ ====================================================================================================================================================== @@ -23052,6 +23595,7 @@ version versionsuffix toolchain ``4.4.4`` ``-HDF5-1.8.19`` ``foss/2017b``, ``intel/2017b`` ``4.4.5`` ``gompi/2019a``, ``iimpi/2019a`` ``4.5.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` +``4.5.3`` ``gompi/2020b``, ``iimpi/2020b`` ========= ================ ==================================================================================================================================================================================================================================================================================================================================== @@ -23197,7 +23741,7 @@ version toolchain ``3.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018a`` ``3.4.1`` ``GCCcore/8.2.0`` ``3.5.1`` ``GCCcore/8.3.0`` -``3.6`` ``GCCcore/9.3.0`` +``3.6`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= =========================================================================================================================================== @@ -23225,7 +23769,7 @@ version versionsuffix toolchain ``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``2.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``2.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``2.4`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` ======== ================== =================================================== @@ -23279,6 +23823,7 @@ version toolchain ``19.12.0`` ``system`` ``20.01.0`` ``system`` ``20.04.1`` ``system`` +``20.10.0`` ``system`` =========== ========== @@ -23442,7 +23987,8 @@ version versionsuffix toolchain ``2.3.0`` ``-Python-3.6.6`` ``foss/2018b`` ``2.4.0`` ``foss/2019a``, ``intel/2019a`` ``2.5.1`` ``-Python-3.6.6`` ``foss/2018b`` -``3.1.0`` ``-Python-3.7.4`` ``intel/2019b`` +``3.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.2.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================================= =============================== @@ -23597,6 +24143,7 @@ version toolchain ========= =================================================================================================================================================================================================================================================== ``2.4.2`` ``GCC/5.4.0-2.26``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``iomkl/2018a`` ``2.6.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.6.2`` ``GCCcore/10.2.0`` ========= =================================================================================================================================================================================================================================================== @@ -23804,11 +24351,11 @@ nsync is a C library that exports various synchronization primitives, such as mu *homepage*: https://github.com/google/nsync -========== ==================================== -version toolchain -========== ==================================== -``1.24.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ==================================== +========== ======================================================== +version toolchain +========== ======================================================== +``1.24.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ======================================================== .. _list_software_ntCard_604: @@ -23972,6 +24519,22 @@ version versionsuffix toolchain ========== ================== =============================== +.. _list_software_NVHPC_383: + +*NVHPC* ++++++++ + +C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) + +*homepage*: https://developer.nvidia.com/hpc-sdk/ + +======== ========== +version toolchain +======== ========== +``20.7`` ``system`` +======== ========== + + .. _list_software_nvtop_567: *nvtop* @@ -24029,7 +24592,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_orca_421` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_orca_421` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -24185,6 +24748,22 @@ version toolchain ========= ======================================================= +.. _list_software_Open-Data-Cube-Core_1691: + +*Open-Data-Cube-Core* ++++++++++++++++++++++ + +The Open Data Cube Core provides an integrated gridded data analysis environment for decades of analysis ready earth observation satellite and related data from multiple satellite and other acquisition systems. + +*homepage*: https://github.com/opendatacube/datacube-core + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.8.3`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_OpenAI-Gym_886: *OpenAI-Gym* @@ -24254,6 +24833,7 @@ version versionsuffix toolchain ``0.3.7`` ``GCC/8.3.0`` ``0.3.8`` ``GCC/9.2.0`` ``0.3.9`` ``GCC/9.3.0`` +``0.3.12`` ``GCC/10.2.0`` ========== ================= ========================================================== @@ -24564,6 +25144,7 @@ OpenMolcas is a quantum chemistry software package version versionsuffix toolchain ========= ================= =============== ``18.09`` ``-Python-3.6.6`` ``intel/2018b`` +``20.10`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================= =============== @@ -24611,7 +25192,7 @@ version versionsuffix toolchain ``4.0.1`` ``GCC/8.3.0-2.32`` ``4.0.2`` ``GCC/9.2.0-2.32`` ``4.0.3`` ``GCC/9.3.0``, ``gcccuda/2020a``, ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` -``4.0.5`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``4.0.5`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``gcccuda/2020b`` ``system`` ``GCC/system-2.29`` ========== ============= ==================================================================================================================== @@ -24715,6 +25296,22 @@ version versionsuffix toolchain ========= =================== ========== +.. _list_software_OpenSees_802: + +*OpenSees* +++++++++++ + +Open System for Earthquake Engineering Simulation + +*homepage*: https://opensees.berkeley.edu/index.php + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``3.2.0`` ``-Python-3.8.2`` ``intel/2020a`` +========= ================= =============== + + .. _list_software_OpenSlide_899: *OpenSlide* @@ -24989,13 +25586,13 @@ OSU Micro-Benchmarks *homepage*: https://mvapich.cse.ohio-state.edu/benchmarks/ -========= ========================================================================================================================= -version toolchain -========= ========================================================================================================================= -``5.3.2`` ``foss/2016a``, ``foss/2017a`` -``5.6.2`` ``gompi/2019a`` -``5.6.3`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpic/2019b``, ``iimpic/2020a`` -========= ========================================================================================================================= +========= ============================================================================================================================================================================================= +version toolchain +========= ============================================================================================================================================================================================= +``5.3.2`` ``foss/2016a``, ``foss/2017a`` +``5.6.2`` ``gompi/2019a`` +``5.6.3`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2019b``, ``iimpic/2020a`` +========= ============================================================================================================================================================================================= .. _list_software_OTF2_283: @@ -25054,7 +25651,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -25138,6 +25735,7 @@ version toolchain ========== =============================== ``16.103`` ``intel/2016a`` ``18.013`` ``foss/2018a``, ``intel/2018a`` +``20.2.2`` ``GCC/10.2.0`` ========== =============================== @@ -25847,7 +26445,7 @@ version toolchain ========== ========================================================== ``0.9.8`` ``foss/2016b``, ``intel/2016b`` ``0.9.10`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` -``0.9.11`` ``GCCcore/7.3.0``, ``foss/2018a`` +``0.9.11`` ``GCCcore/7.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` ========== ========================================================== @@ -25948,6 +26546,22 @@ version versionsuffix toolchain ========= ================ =============== +.. _list_software_PEST++_402: + +*PEST++* +++++++++ + +PEST++ is a software suite aimed at supporting complex numerical models in the decision-support context. Much focus has been devoted to supporting environmental models (groundwater, surface water, etc) but these tools are readily applicable to any computer model. + +*homepage*: https://github.com/usgs/pestpp + +========= ============== +version toolchain +========= ============== +``5.0.5`` ``foss/2020a`` +========= ============== + + .. _list_software_PETSc_415: *PETSc* @@ -26432,6 +27046,7 @@ version versionsuffix toolchain ``6.0.0`` ``GCCcore/8.2.0`` ``6.2.1`` ``GCCcore/8.3.0`` ``7.0.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``8.0.1`` ``GCCcore/10.2.0`` ========= ================================= =================================================== @@ -26450,6 +27065,7 @@ version versionsuffix toolchain ``5.0.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``5.3.0.post0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``6.0.x.post0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``7.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` =============== ================= =================================================== @@ -26699,7 +27315,7 @@ version versionsuffix toolchain ``1.3.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``1.5.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``1.5.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``1.5.1`` ``-python`` ``GCCcore/8.2.0`` +``1.5.1`` ``-python`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0`` ========= ================== =================================================== @@ -27004,13 +27620,14 @@ Parallel netCDF: A Parallel I/O Library for NetCDF File Access *homepage*: https://trac.mcs.anl.gov/projects/parallel-netcdf -========== =============================== -version toolchain -========== =============================== -``1.8.1`` ``intel/2017a`` -``1.9.0`` ``intel/2018a`` -``1.10.0`` ``foss/2018b``, ``intel/2018b`` -========== =============================== +========== ================================ +version toolchain +========== ================================ +``1.8.1`` ``intel/2017a`` +``1.9.0`` ``intel/2018a`` +``1.10.0`` ``foss/2018b``, ``intel/2018b`` +``1.12.1`` ``gompi/2020a``, ``iimpi/2020a`` +========== ================================ .. _list_software_pocl_430: @@ -27670,6 +28287,7 @@ version toolchain ``3.7.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.10.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``3.13.0`` ``GCCcore/9.3.0`` +``3.14.0`` ``GCCcore/10.2.0`` =========== =================================================== @@ -27700,6 +28318,7 @@ version versionsuffix toolchain ``3.6.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``3.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``3.13.0`` ``-Python-3.8.2`` ``foss/2020a`` +``3.14.0`` ``GCCcore/10.2.0`` ========== ================== ================================== @@ -27946,6 +28565,7 @@ version versionsuffix toolchain ========= ================== =============================== ``2.7`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2.8.3`` ``-Python-3.7.2`` ``foss/2019a`` +``2.8.6`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ================== =============================== @@ -28122,12 +28742,12 @@ A python extension, written in C, for quick access to bigBed files and access t *homepage*: https://github.com/deeptools/pyBigWig -========== ================= ================= -version versionsuffix toolchain -========== ================= ================= -``0.3.13`` ``-Python-3.6.6`` ``foss/2018b`` -``0.3.17`` ``GCCcore/8.2.0`` -========== ================= ================= +========== ================= ==================================== +version versionsuffix toolchain +========== ================= ==================================== +``0.3.13`` ``-Python-3.6.6`` ``foss/2018b`` +``0.3.17`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +========== ================= ==================================== .. _list_software_pybind11_744: @@ -28139,14 +28759,15 @@ pybind11 is a lightweight header-only library that exposes C++ types in Python a *homepage*: https://pybind11.readthedocs.io -========= ================= ================= -version versionsuffix toolchain -========= ================= ================= -``2.2.4`` ``-Python-3.6.4`` ``foss/2018a`` -``2.2.4`` ``-Python-3.6.6`` ``intel/2018b`` -``2.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``2.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -========= ================= ================= +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``2.2.4`` ``-Python-3.6.4`` ``foss/2018a`` +``2.2.4`` ``-Python-3.6.6`` ``intel/2018b`` +``2.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``2.6.0`` ``GCCcore/10.2.0`` +========= ================= ================== .. _list_software_PyCairo_695: @@ -28210,15 +28831,16 @@ version toolchain *pycocotools* +++++++++++++ -Tools for working with the MSCOCO dataset +Official APIs for the MS-COCO dataset -*homepage*: https://github.com/cocodataset/cocoapi +*homepage*: https://pypi.org/project/pycocotools ========= ================= ================================== version versionsuffix toolchain ========= ================= ================================== ``2.0.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.0.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.0.2`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` ========= ================= ================================== @@ -28409,6 +29031,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_pyFAI_441: + +*pyFAI* ++++++++ + +Python implementation of fast azimuthal integration. + +*homepage*: https://github.com/silx-kit/pyFAI + +========== ================= ================================== +version versionsuffix toolchain +========== ================= ================================== +``0.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========== ================= ================================== + + .. _list_software_PyFFmpeg_766: *PyFFmpeg* @@ -28821,6 +29459,22 @@ version versionsuffix toolchain ======= ================= =============================== +.. _list_software_pymca_538: + +*pymca* ++++++++ + +The PyMca X-Ray Fluorescence Toolkit, including PyMca5 and fisx. + +*homepage*: https://github.com/vasole/pymca + +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``5.6.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========= ================= ================================== + + .. _list_software_pymemcache_1052: *pymemcache* @@ -29034,6 +29688,7 @@ version versionsuffix toolchain ``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``5.13.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``5.15.1`` ``GCCcore/10.2.0`` ``5.15.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========== ================== =============================== @@ -29151,7 +29806,7 @@ version versionsuffix toolchain ``0.15.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``0.15.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``0.15.3`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``0.16.0.1`` ``GCC/8.3.0``, ``GCC/9.3.0`` +``0.16.0.1`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217`` ============ ================== ============================================================== @@ -29180,11 +29835,11 @@ pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Singl *homepage*: https://github.com/aertslab/pySCENIC -========== ================= =============== -version versionsuffix toolchain -========== ================= =============== -``0.10.3`` ``-Python-3.8.2`` ``intel/2020a`` -========== ================= =============== +========== ================= =============================== +version versionsuffix toolchain +========== ================= =============================== +``0.10.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +========== ================= =============================== .. _list_software_PySCF_421: @@ -29638,6 +30293,7 @@ version versionsuffix toolchain ``5.1`` ``GCCcore/8.2.0`` ``5.1.2`` ``GCCcore/8.3.0`` ``5.3`` ``GCCcore/9.3.0`` +``5.3.1`` ``GCCcore/10.2.0`` ========= ================== ==================================================================================== @@ -29986,6 +30642,7 @@ version toolchain ``5.12.3`` ``GCCcore/8.2.0`` ``5.13.1`` ``GCCcore/8.3.0`` ``5.14.1`` ``GCCcore/9.3.0`` +``5.14.2`` ``GCCcore/10.2.0`` ========== ==================================================================================== @@ -30140,7 +30797,7 @@ version versionsuffix toolchain ``6.3`` ``foss/2018b``, ``intel/2018b`` ``6.4.1`` ``intel/2019a`` ``6.5`` ``intel/2019a``, ``intel/2019b`` -``6.6`` ``intel/2019b`` +``6.6`` ``foss/2019b``, ``intel/2019b`` ========= ============= ================================ @@ -30289,7 +30946,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray_300` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_rstudio_778` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -30478,11 +31135,11 @@ A fast JSON parser/generator for C++ with both SAX/DOM style API *homepage*: https://rapidjson.org -========= ==================================== -version toolchain -========= ==================================== -``1.1.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= ==================================== +========= ======================================================= +version toolchain +========= ======================================================= +``1.1.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================= .. _list_software_rapidtide_950: @@ -30596,28 +31253,45 @@ RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML *homepage*: https://github.com/amkozlov/raxml-ng +========= ============================== +version toolchain +========= ============================== +``0.9.0`` ``GCC/8.3.0``, ``gompi/2019b`` +``1.0.1`` ``gompi/2019b`` +========= ============================== + + +.. _list_software_Ray-assembler_1303: + +*Ray-assembler* ++++++++++++++++ + +Parallel genome assemblies for parallel DNA sequencing + +*homepage*: http://denovoassembler.sourceforge.net/ + ========= =============== version toolchain ========= =============== -``0.9.0`` ``gompi/2019b`` +``2.3.1`` ``iimpi/2019a`` ========= =============== -.. _list_software_Ray_300: +.. _list_software_Ray-project_1104: -*Ray* -+++++ +*Ray-project* ++++++++++++++ -Parallel genome assemblies for parallel DNA sequencing +Ray is a fast and simple framework for building and running distributed applications. -*homepage*: http://denovoassembler.sourceforge.net/ +*homepage*: https://docs.ray.io/en/latest/ -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``0.8.4`` ``-Python-3.7.4`` ``foss/2019b`` -``2.3.1`` ``iimpi/2019a`` -========= ================= =============== +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``0.8.4`` ``-Python-3.7.4`` ``foss/2019b`` +``1.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +========= ================= ================== .. _list_software_RBFOpt_525: @@ -30737,6 +31411,22 @@ version versionsuffix toolchain ======== ================== ========== +.. _list_software_RE2_201: + +*RE2* ++++++ + +RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++ library. + +*homepage*: https://github.com/google/re2 + +============== ================= +version toolchain +============== ================= +``2020-07-01`` ``GCCcore/8.3.0`` +============== ================= + + .. _list_software_re2c_364: *re2c* @@ -31068,6 +31758,7 @@ version versionsuffix toolchain ========== ================= =============== ``0.0.12`` ``-Python-3.7.2`` ``intel/2019a`` ``0.0.24`` ``-Python-3.7.4`` ``foss/2019b`` +``0.1.1`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================= =============== @@ -31467,6 +32158,7 @@ version versionsuffix toolchain ``2.6.4`` ``-Python-2.7.12-R-3.3.1`` ``foss/2016b`` ``2.6.4`` ``-Python-2.7.14`` ``intel/2018a`` ``3.0.0`` ``-Python-3.6.6`` ``foss/2018b`` +``4.0.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ========================== =============== @@ -31503,12 +32195,12 @@ version versionsuffix toolchain ========== ============= ============== -.. _list_software_rstudio_778: +.. _list_software_RStudio-Server_1390: -*rstudio* -+++++++++ +*RStudio-Server* +++++++++++++++++ -This RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) +This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) *homepage*: https://www.rstudio.com/ @@ -31518,6 +32210,7 @@ version versionsuffix toolchain ``1.2.5033`` ``-Java-11`` ``fosscuda/2019b`` ``1.2.5042`` ``-Java-11`` ``foss/2019b`` ``1.3.959`` ``-Java-11-R-4.0.0`` ``foss/2020a`` +``1.3.1093`` ``-Java-11-R-4.0.0`` ``foss/2020a`` ============ ==================== ================== @@ -31626,7 +32319,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_Sumo_420` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -31936,7 +32629,7 @@ version toolchain *ScaLAPACK* +++++++++++ -The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. +The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. *homepage*: https://www.netlib.org/scalapack/ @@ -31954,7 +32647,9 @@ version versionsuffix toolchain ``2.0.2`` ``-OpenBLAS-0.3.1`` ``gompi/2018b``, ``gompic/2018b`` ``2.0.2`` ``-OpenBLAS-0.3.3`` ``gompi/2018.08`` ``2.0.2`` ``-OpenBLAS-0.3.5`` ``gompi/2019a``, ``gompic/2019a`` -``2.1.0`` ``gompi/2020a``, ``gompic/2020a`` +``2.1.0`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b`` +``2.1.0`` ``-bf`` ``gompi/2020a`` +``2.2`` ``-amd`` ``gompi/2020a`` ========= ================================= ============================================================================================================================================ @@ -32040,6 +32735,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_scikit-bio_1006: + +*scikit-bio* +++++++++++++ + +scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics. + +*homepage*: http://scikit-bio.org + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.5.6`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_scikit-build_1220: *scikit-build* @@ -32122,7 +32833,8 @@ version versionsuffix toolchain ``0.20.3`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``0.20.4`` ``-Python-2.7.16`` ``intel/2019b`` ``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``0.23.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.23.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` +``0.23.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ========== ================================= ======================================================================== @@ -32227,7 +32939,8 @@ version versionsuffix toolchain ``2019.10`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``2019.10`` ``-Python-3.7.2`` ``intel/2019a`` ``2019.10`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` -``2020.03`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``2020.03`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` +``2020.11`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` =========== ================== ======================================================================== @@ -32349,6 +33062,7 @@ version versionsuffix toolchain ``6.0.4`` ``-64bitint`` ``foss/2017b`` ``6.0.6`` ``foss/2018a``, ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2018a`` ``6.0.9`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` +``6.1.0`` ``gompi/2020b``, ``iimpi/2020b`` =================== ============= ===================================================================================================================================================== @@ -32524,7 +33238,7 @@ version toolchain Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. -*homepage*: http://stanford.edu/~mwaskom/software/seaborn/ +*homepage*: https://stanford.edu/~mwaskom/software/seaborn/ ========== ================== ========================================================================================= version versionsuffix toolchain @@ -32538,8 +33252,9 @@ version versionsuffix toolchain ``0.9.0`` ``-Python-3.6.4`` ``intel/2018a`` ``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``0.9.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``0.9.1`` ``-Python-2.7.16`` ``foss/2019b`` ``0.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``0.10.1`` ``-Python-3.8.2`` ``foss/2020a`` +``0.10.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ================== ========================================================================================= @@ -32637,6 +33352,7 @@ Unsupervised text tokenizer for Neural Network-based text generation. version versionsuffix toolchain ========== ================= ============= ``0.1.85`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``0.1.94`` ``-Python-3.8.2`` ``GCC/9.3.0`` ========== ================= ============= @@ -33578,13 +34294,14 @@ The Snakemake workflow management system is a tool to create reproducible and sc *homepage*: https://snakemake.readthedocs.io -========= ================= =============================== -version versionsuffix toolchain -========= ================= =============================== -``5.2.2`` ``-Python-3.6.4`` ``intel/2018a`` -``5.2.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``5.7.1`` ``-Python-3.7.2`` ``foss/2019a`` -========= ================= =============================== +========== ================= =============================== +version versionsuffix toolchain +========== ================= =============================== +``5.2.2`` ``-Python-3.6.4`` ``intel/2018a`` +``5.2.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``5.7.1`` ``-Python-3.7.2`` ``foss/2019a`` +``5.26.1`` ``-Python-3.8.2`` ``intel/2020a`` +========== ================= =============================== .. _list_software_SNAP_306: @@ -33870,6 +34587,22 @@ version toolchain ========== ============= +.. _list_software_SpaceRanger_1099: + +*SpaceRanger* ++++++++++++++ + +Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image. + +*homepage*: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger + +========= ============= +version toolchain +========= ============= +``1.1.0`` ``GCC/9.3.0`` +========= ============= + + .. _list_software_Spack_498: *Spack* @@ -34126,6 +34859,22 @@ version versionsuffix toolchain ============ ============= =============== +.. _list_software_SplAdder_783: + +*SplAdder* +++++++++++ + +Splicing Adder is a toolbox for alternative splicing analysis based on RNA-Seq alignment data. Briefly, the software takes a given annotation and RNA-Seq read alignments in standardized formats, transforms the annotation into a splicing graph representation, augments the splicing graph with additional information extracted from the read data, extracts alternative splicing events from the graph and quantifies the events based on the alignment data. + +*homepage*: https://github.com/ratschlab/spladder + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``2.4.2`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_SPLASH_459: *SPLASH* @@ -34581,7 +35330,7 @@ version versionsuffix toolchain ``0.9.0`` ``-Python-3.6.6`` ``intel/2018b`` ``0.10.1`` ``foss/2019a`` ``0.11.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``0.11.1`` ``-Python-3.8.2`` ``foss/2020a`` +``0.11.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ================== =============================== @@ -34689,6 +35438,7 @@ version toolchain ``2.1.0`` ``foss/2018b`` ``2.1.1`` ``GCC/8.3.0`` ``2.1.3`` ``GCC/8.3.0``, ``GCC/9.3.0`` +``2.1.4`` ``GCC/8.3.0``, ``GCC/9.3.0`` ========== ================================== @@ -34831,26 +35581,11 @@ version toolchain *homepage*: https://sumo.dlr.de/ -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``1.7.0`` ``-Python-3.8.2`` ``foss/2020a`` -========= ================= ============== - - -.. _list_software_Sumo_420: - -*Sumo* -++++++ - -Sumo is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large road networks. - -*homepage*: https://sumo.sourceforge.net/ - ========= ================= ================= version versionsuffix toolchain ========= ================= ================= ``1.3.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``1.7.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ================= @@ -34895,13 +35630,14 @@ version versionsuffix toolchain SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. -*homepage*: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ +*homepage*: https://crd-legacy.lbl.gov/~xiaoye/SuperLU/ ========= =============================== version toolchain ========= =============================== ``5.1.1`` ``foss/2016a``, ``intel/2016a`` ``5.2.1`` ``foss/2017b``, ``intel/2017b`` +``5.2.2`` ``intel/2020a`` ========= =============================== @@ -35019,6 +35755,22 @@ version versionsuffix toolchain ======== ============= ================================ +.. _list_software_SWAT+_362: + +*SWAT+* ++++++++ + +The Soil & Water Assessment Tool (SWAT) is a small watershed to river basin-scale model used to simulate the quality and quantity of surface and ground water and predict the environmental impact of land use, land management practices, and climate change. In order to face present and future challenges in water resources modeling SWAT code has undergone major modifications over the past few years, resulting in SWAT+, a completely revised version of the model. SWAT+ provides a more flexible spatial representation of interactions and processes within a watershed. + +*homepage*: https://swatplus.gitbook.io + +========== ============= +version toolchain +========== ============= +``60.4.1`` ``GCC/9.3.0`` +========== ============= + + .. _list_software_SWIG_314: *SWIG* @@ -35047,6 +35799,7 @@ version versionsuffix toolchain ``3.0.12`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.0.12`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``4.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.0.2`` ``GCCcore/10.2.0`` ========== ============================ ================================================================ @@ -35816,12 +36569,12 @@ The `time' command runs another program, then displays information about the res *homepage*: https://www.gnu.org/software/time/ -======= ================= -version toolchain -======= ================= -``1.7`` ``system`` -``1.9`` ``GCCcore/8.3.0`` -======= ================= +======= ==================================== +version toolchain +======= ==================================== +``1.7`` ``system`` +``1.9`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ==================================== .. _list_software_TINKER_461: @@ -36046,6 +36799,7 @@ Data loaders and abstractions for text and NLP version versionsuffix toolchain ========= =============================== ================== ``0.5.0`` ``-PyTorch-1.4.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b`` ========= =============================== ================== @@ -36067,7 +36821,7 @@ version versionsuffix toolchain ``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` ``0.4.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``0.5.0`` ``-Python-3.7.4-PyTorch-1.4.0`` ``fosscuda/2019b`` -``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``fosscuda/2019b`` +``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` ========= =============================== ================================== @@ -36094,7 +36848,7 @@ version versionsuffix toolchain *tqdm* ++++++ -A fast, extensible progress bar for Python and CLI +Instantly make your loops show a smart progress meter. *homepage*: https://github.com/tqdm/tqdm @@ -36108,6 +36862,7 @@ version versionsuffix toolchain ``4.41.1`` ``GCCcore/8.3.0`` ``4.41.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``4.47.0`` ``GCCcore/9.3.0`` +``4.51.0`` ``-Python-3.8.2`` ``intel/2020a`` ========== ================== =============================== @@ -36626,6 +37381,7 @@ version versionsuffix toolchain ``1.8.0`` ``GCCcore/9.3.0`` ``1.8.0`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` ``1.9.0`` ``GCCcore/10.2.0`` +``1.9.0`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` ============ ================ ======================================================= @@ -36655,14 +37411,14 @@ UDUNITS supports conversion of unit specifications between formatted and binary *homepage*: https://www.unidata.ucar.edu/software/udunits/ -========== =========================================================================================================================================================================== -version toolchain -========== =========================================================================================================================================================================== -``2.2.20`` ``foss/2016a``, ``intel/2016b`` -``2.2.24`` ``intel/2017a`` -``2.2.25`` ``foss/2017b``, ``intel/2017b`` -``2.2.26`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -========== =========================================================================================================================================================================== +========== =============================================================================================================================================================================================== +version toolchain +========== =============================================================================================================================================================================================== +``2.2.20`` ``foss/2016a``, ``intel/2016b`` +``2.2.24`` ``intel/2017a`` +``2.2.25`` ``foss/2017b``, ``intel/2017b`` +``2.2.26`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +========== =============================================================================================================================================================================================== .. _list_software_UFL_231: @@ -36949,7 +37705,7 @@ version toolchain --- -:ref:`list_software_V8_142` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VMD_231` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` +:ref:`list_software_V8_142` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VMD_231` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` .. _list_software_V8_142: @@ -37189,6 +37945,22 @@ version toolchain ========== ========== +.. _list_software_velocyto_885: + +*velocyto* +++++++++++ + +Velocyto is a library for the analysis of RNA velocity. + +*homepage*: https://velocyto.org/velocyto.py/ + +=========== ================= =============== +version versionsuffix toolchain +=========== ================= =============== +``0.17.17`` ``-Python-3.8.2`` ``intel/2020a`` +=========== ================= =============== + + .. _list_software_Velvet_630: *Velvet* @@ -37447,6 +38219,10 @@ version versionsuffix toolchain ``4.1.9`` ``system`` ``5.1.0`` ``system`` ``5.2.0`` ``system`` +``5.2.2`` ``system`` +``5.2.3`` ``system`` +``5.2.4`` ``system`` +``5.2.5`` ``system`` =========== ================================== =============== @@ -37616,7 +38392,7 @@ version toolchain --- -:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_WHAM_301` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` +:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_WCT_238` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_WHAM_301` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` .. _list_software_wandb_524: @@ -37671,6 +38447,22 @@ version toolchain ========= =============== +.. _list_software_WCT_238: + +*WCT* ++++++ + +NOAA's Weather and Climate Toolkit (WCT) is free, platform independent software distributed from NOAA's National Centers for Environmental Information (NCEI). The WCT allows the visualization and data export of weather and climate data, including Radar, Satellite and Model data. The WCT also provides access to weather/climate web services provided from NCEI and other organizations. + +*homepage*: https://www.ncdc.noaa.gov/wct/index.php + +========= ============= ========== +version versionsuffix toolchain +========= ============= ========== +``4.6.0`` ``-Java-11`` ``system`` +========= ============= ========== + + .. _list_software_wcwidth_762: *wcwidth* @@ -37749,14 +38541,14 @@ GNU Wget is a free software package for retrieving files using HTTP, HTTPS and F *homepage*: https://www.gnu.org/software/wget -========== ==================================== -version toolchain -========== ==================================== -``1.17.1`` ``foss/2016a``, ``foss/2016b`` -``1.19.4`` ``GCCcore/6.4.0`` -``1.20.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` -``1.20.3`` ``GCCcore/9.3.0`` -========== ==================================== +========== ===================================== +version toolchain +========== ===================================== +``1.17.1`` ``foss/2016a``, ``foss/2016b`` +``1.19.4`` ``GCCcore/6.4.0`` +``1.20.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +``1.20.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========== ===================================== .. _list_software_WHAM_301: @@ -37951,15 +38743,16 @@ The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale *homepage*: http://www.wrf-model.org -========= ============= ================================ -version versionsuffix toolchain -========= ============= ================================ -``3.8.0`` ``-dmpar`` ``intel/2016a``, ``intel/2016b`` -``4.0.1`` ``-dmpar`` ``intel/2018b`` -``4.0.2`` ``-dmpar`` ``foss/2018b`` -``4.1.3`` ``-dm+sm`` ``intel/2019b`` -``4.1.3`` ``-dmpar`` ``foss/2019b``, ``intel/2019b`` -========= ============= ================================ +=========== ============= ================================ +version versionsuffix toolchain +=========== ============= ================================ +``3.8.0`` ``-dmpar`` ``intel/2016a``, ``intel/2016b`` +``3.9.1.1`` ``-dmpar`` ``foss/2020a``, ``intel/2020a`` +``4.0.1`` ``-dmpar`` ``intel/2018b`` +``4.0.2`` ``-dmpar`` ``foss/2018b`` +``4.1.3`` ``-dm+sm`` ``intel/2019b`` +``4.1.3`` ``-dmpar`` ``foss/2019b``, ``intel/2019b`` +=========== ============= ================================ .. _list_software_WRF-Fire_674: @@ -38074,7 +38867,7 @@ version toolchain --- -:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCfun_484` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_XZ_178` +:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_XZ_178` .. _list_software_X11_186: @@ -38127,6 +38920,7 @@ version toolchain ``20190413`` ``GCCcore/8.2.0`` ``20190925`` ``GCCcore/8.3.0`` ``20191217`` ``GCCcore/9.3.0`` +``20201026`` ``GCCcore/10.2.0`` ============ ================================= @@ -38139,18 +38933,18 @@ x265 is a free software library and application for encoding video streams into *homepage*: https://x265.org/ -======= ================================== -version toolchain -======= ================================== -``2.4`` ``foss/2016b`` -``2.5`` ``intel/2017a`` -``2.6`` ``GCCcore/6.4.0``, ``intel/2017b`` -``2.7`` ``GCCcore/6.4.0`` -``2.9`` ``GCCcore/7.3.0`` -``3.0`` ``GCCcore/8.2.0`` -``3.2`` ``GCCcore/8.3.0`` -``3.3`` ``GCCcore/9.3.0`` -======= ================================== +======= ===================================== +version toolchain +======= ===================================== +``2.4`` ``foss/2016b`` +``2.5`` ``intel/2017a`` +``2.6`` ``GCCcore/6.4.0``, ``intel/2017b`` +``2.7`` ``GCCcore/6.4.0`` +``2.9`` ``GCCcore/7.3.0`` +``3.0`` ``GCCcore/8.2.0`` +``3.2`` ``GCCcore/8.3.0`` +``3.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +======= ===================================== .. _list_software_XALT_313: @@ -38192,7 +38986,7 @@ version versionsuffix toolchain ``0.12.1`` ``-Python-3.6.6`` ``intel/2018b`` ``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` ``0.15.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``0.16.1`` ``-Python-3.8.2`` ``intel/2020a`` +``0.16.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ================== =============================== @@ -38326,21 +39120,22 @@ version versionsuffix toolchain ======== ============= ============== -.. _list_software_XCfun_484: +.. _list_software_XCFun_452: -*XCfun* +*XCFun* +++++++ XCFun is a library of DFT exchange-correlation (XC) functionals. It is based on automatic differentiation and can therefore generate arbitrary order derivatives of these functionals. *homepage*: http://dftlibs.org/xcfun/ -============ ================== =============== -version versionsuffix toolchain -============ ================== =============== -``20180122`` ``-Python-2.7.14`` ``intel/2017b`` -``20190127`` ``-Python-3.7.2`` ``foss/2019a`` -============ ================== =============== +============ ================== ================= +version versionsuffix toolchain +============ ================== ================= +``2.1.0`` ``GCCcore/9.3.0`` +``20180122`` ``-Python-2.7.14`` ``intel/2017b`` +``20190127`` ``-Python-3.7.2`` ``foss/2019a`` +============ ================== ================= .. _list_software_XCrySDen_752: @@ -38736,12 +39531,12 @@ Xvfb is an X server that can run on machines with no display hardware and no phy *homepage*: https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml -========== ==================================== -version toolchain -========== ==================================== -``1.20.8`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``1.20.9`` ``GCCcore/9.3.0`` -========== ==================================== +========== ===================================== +version toolchain +========== ===================================== +``1.20.8`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.20.9`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========== ===================================== .. _list_software_XZ_178: @@ -38862,11 +39657,11 @@ Yasm: Complete rewrite of the NASM assembler with BSD license *homepage*: http://www.tortall.net/projects/yasm/ -========= =================================================================================================================================================================================================================================== -version toolchain -========= =================================================================================================================================================================================================================================== -``1.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -========= =================================================================================================================================================================================================================================== +========= ======================================================================================================================================================================================================================================================= +version toolchain +========= ======================================================================================================================================================================================================================================================= +``1.3.0`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +========= ======================================================================================================================================================================================================================================================= .. _list_software_YAXT_326: @@ -39028,13 +39823,13 @@ Zsh is a shell designed for interactive use, although it is also a powerful scri *homepage*: https://www.zsh.org/ -========= ================== -version toolchain -========= ================== -``5.1.1`` ``GNU/4.9.3-2.25`` -``5.2`` ``foss/2016b`` -``5.8`` ``GCC/8.3.0`` -========= ================== +========= ========================= +version toolchain +========= ========================= +``5.1.1`` ``GNU/4.9.3-2.25`` +``5.2`` ``foss/2016b`` +``5.8`` ``GCC/8.3.0``, ``system`` +========= ========================= .. _list_software_zstd_453: diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index 45d262ec..b4c5cd6d 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -23,6 +23,7 @@ * EB_ant * EB_BiSearch * EB_Chimera + * EB_code_minus_server * EB_COMSOL * EB_FDTD_underscore_Solutions * EB_FLUENT @@ -212,6 +213,7 @@ * EB_Boost * EB_CFDEMcoupling * EB_CHARMM + * EB_code_minus_server * EB_CP2K * EB_FSL * EB_GAMESS_minus_US @@ -256,6 +258,7 @@ * EB_EasyBuildMeta * EB_EggLib * EB_libxml2 + * EB_Metagenome_Atlas * EB_netcdf4_minus_python * EB_nose * EB_numexpr @@ -331,6 +334,7 @@ * EB_ant * EB_BiSearch * EB_Chimera + * EB_code_minus_server * EB_COMSOL * EB_FDTD_underscore_Solutions * EB_FLUENT @@ -384,6 +388,7 @@ * EB_EasyBuildMeta * EB_EggLib * EB_libxml2 + * EB_Metagenome_Atlas * EB_netcdf4_minus_python * EB_nose * EB_numexpr diff --git a/docs/version-specific/easyconfig_templates.rst b/docs/version-specific/easyconfig_templates.rst index b838bfe3..f247ae89 100644 --- a/docs/version-specific/easyconfig_templates.rst +++ b/docs/version-specific/easyconfig_templates.rst @@ -9,6 +9,7 @@ Template names/values derived from easyconfig instance Template name Template value =========================== ======================================================== ``%(arch)s`` System architecture (e.g. x86_64, aarch64, ppc64le, ...) +``%(module_name)s`` Module name ``%(nameletter)s`` First letter of software name ``%(toolchain_name)s`` Toolchain name ``%(toolchain_version)s`` Toolchain version @@ -64,8 +65,8 @@ Template values set outside EasyBlock runstep ================== ====================== Template name Template value ================== ====================== -``%(installdir)s`` Installation directory ``%(builddir)s`` Build directory +``%(installdir)s`` Installation directory ================== ====================== Template constants that can be used in easyconfigs diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index 3d860914..79c5200e 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -1160,6 +1160,7 @@ easyconfig parameter description ``withisl`` Build GCC with ISL support ``False`` ``withlibiberty`` Enable installing of libiberty ``False`` ``withlto`` Enable LTO support ``True`` +``withnvptx`` Build GCC with NVPTX offload support ``False`` ``withppl`` Build GCC with PPL support ``False`` ============================== =================================================================================================================================================================================================== ==================== diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index f3d02352..9a22d1c2 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -126,10 +126,10 @@ Container options Option flag Option description =============================================== =========================================================================================================== ``--container-build-image`` Build container image (requires sudo privileges!) (default: False) -``--container-config=CONFIG`` Configuration for container image (type ) +``--container-config=CONFIG`` Configuration for container image (type ) ``--container-image-format=IMAGE-FORMAT`` Container image format (type choice) (choices: ext3, sandbox, sif, squashfs) ``--container-image-name=IMAGE-NAME`` Custom name for container image (defaults to name of easyconfig) -``--container-template-recipe=TEMPLATE-RECIPE`` Template recipe for container image (type ) +``--container-template-recipe=TEMPLATE-RECIPE`` Template recipe for container image (type ) ``--container-tmpdir=TMPDIR`` Temporary directory where container image is built ``--container-type=TYPE`` Type of container recipe/image to create (type choice; default: singularity) (choices: docker, singularity) =============================================== =========================================================================================================== @@ -143,7 +143,7 @@ Option flag Option description ``--create-index=CREATE-INDEX`` Create index for files in specified directory ``--fix-deprecated-easyconfigs`` Fix use of deprecated functionality in specified easyconfig files. (default: False) ``--ignore-index`` Ignore index when searching for files (default: False) -``--index-max-age=INDEX-MAX-AGE`` Maximum age for index before it is considered stale (in seconds) (type ; default: 604800) +``--index-max-age=INDEX-MAX-AGE`` Maximum age for index before it is considered stale (in seconds) (type ; default: 604800) ``--inject-checksums=INJECT-CHECKSUMS`` Inject checksums of specified type for sources/patches into easyconfig file(s) (type choice; default: sha256) (choices: adler32, crc32, md5, sha1, sha256, sha512, size) ``--local-var-naming-check=LOCAL-VAR-NAMING-CHECK`` Mode to use when checking whether local variables follow the recommended naming scheme ('log': only log warnings (no printed messages); 'warn': print warnings; 'error': fail with an error) (type choice; default: warn) (choices: error, log, warn) =================================================== ===================================================================================================================================================================================================================================================== @@ -151,44 +151,44 @@ Option flag Option description GitHub integration options -------------------------- -======================================================= ================================================================================================================================ -Option flag Option description -======================================================= ================================================================================================================================ -``--check-contrib`` Runs checks to see whether the given easyconfigs are ready to be contributed back (default: False) -``--check-github`` Check status of GitHub integration, and report back (default: False) -``--check-style`` Run a style check on the given easyconfigs (default: False) -``--cleanup-easyconfigs`` Clean up easyconfig files for pull request (default: True; disable with --disable-cleanup-easyconfigs) -``--close-pr=PR#`` Close pull request (type ) -``--close-pr-msg=CLOSE-PR-MSG`` Custom close message for pull request closed with --close-pr; (type ) -``--close-pr-reasons=CLOSE-PR-REASONS`` Close reason for pull request closed with --close-pr; supported values: archived, inactive, obsolete, retest (type ) -``--dump-test-report=DUMP-TEST-REPORT`` Dump test report to specified path (default: test_report.md) -``--from-pr=PR#`` Obtain easyconfigs from specified PR (type ) -``--git-working-dirs-path=GIT-WORKING-DIRS-PATH`` Path to Git working directories for EasyBuild repositories (type ) -``--github-org=GITHUB-ORG`` GitHub organization (type ) -``--github-user=GITHUB-USER`` GitHub username (type ) -``--include-easyblocks-from-pr=PR#`` Include easyblocks from specified PR (type comma-separated list; default: ) -``--install-github-token`` Install GitHub token (requires --github-user) (default: False) -``--list-prs=STATE,ORDER,DIRECTION`` List pull requests (type ; default: open,created,desc) -``--merge-pr=PR#`` Merge pull request (type ) -``--new-branch-github`` Create new branch in GitHub in preparation for a PR (default: False) -``--new-pr`` Open a new pull request (default: False) -``--new-pr-from-branch=NEW-PR-FROM-BRANCH`` Open a new pull request from branch in GitHub (type ) -``--pr-branch-name=PR-BRANCH-NAME`` Branch name to use for new PRs; '_new_pr_' if unspecified (type ) -``--pr-commit-msg=PR-COMMIT-MSG`` Commit message for new/updated pull request created with --new-pr (type ) -``--pr-descr=PR-DESCR`` Description for new pull request created with --new-pr (type ) -``--pr-target-account=PR-TARGET-ACCOUNT`` Target account for new PRs (type ; default: easybuilders) -``--pr-target-branch=PR-TARGET-BRANCH`` Target branch for new PRs (type ; default: develop) -``--pr-target-repo=PR-TARGET-REPO`` Target repository for new/updating PRs (default: auto-detect based on provided files) (type ) -``--pr-title=PR-TITLE`` Title for new pull request created with --new-pr (type ) -``--preview-pr`` Preview a new pull request (default: False) -``--review-pr=PR#`` Review specified pull request (type ) -``--sync-branch-with-develop=SYNC-BRANCH-WITH-DEVELOP`` Sync branch with current 'develop' branch (type ) -``--sync-pr-with-develop=PR#`` Sync pull request with current 'develop' branch (type ) -``--test-report-env-filter=TEST-REPORT-ENV-FILTER`` Regex used to filter out variables in environment dump of test report -``--update-branch-github=UPDATE-BRANCH-GITHUB`` Update specified branch in GitHub (type ) -``--update-pr=PR#`` Update an existing pull request (type ) -``-u, --upload-test-report`` Upload full test report as a gist on GitHub (default: False) -======================================================= ================================================================================================================================ +======================================================= ================================================================================================================================= +Option flag Option description +======================================================= ================================================================================================================================= +``--check-contrib`` Runs checks to see whether the given easyconfigs are ready to be contributed back (default: False) +``--check-github`` Check status of GitHub integration, and report back (default: False) +``--check-style`` Run a style check on the given easyconfigs (default: False) +``--cleanup-easyconfigs`` Clean up easyconfig files for pull request (default: True; disable with --disable-cleanup-easyconfigs) +``--close-pr=PR#`` Close pull request (type ) +``--close-pr-msg=CLOSE-PR-MSG`` Custom close message for pull request closed with --close-pr; (type ) +``--close-pr-reasons=CLOSE-PR-REASONS`` Close reason for pull request closed with --close-pr; supported values: archived, inactive, obsolete, retest (type ) +``--dump-test-report=DUMP-TEST-REPORT`` Dump test report to specified path (default: test_report.md) +``--from-pr=PR#`` Obtain easyconfigs from specified PR (type ) +``--git-working-dirs-path=GIT-WORKING-DIRS-PATH`` Path to Git working directories for EasyBuild repositories (type ) +``--github-org=GITHUB-ORG`` GitHub organization (type ) +``--github-user=GITHUB-USER`` GitHub username (type ) +``--include-easyblocks-from-pr=PR#`` Include easyblocks from specified PR (type comma-separated list; default: ) +``--install-github-token`` Install GitHub token (requires --github-user) (default: False) +``--list-prs=STATE,ORDER,DIRECTION`` List pull requests (type ; default: open,created,desc) +``--merge-pr=PR#`` Merge pull request (type ) +``--new-branch-github`` Create new branch in GitHub in preparation for a PR (default: False) +``--new-pr`` Open a new pull request (default: False) +``--new-pr-from-branch=NEW-PR-FROM-BRANCH`` Open a new pull request from branch in GitHub (type ) +``--pr-branch-name=PR-BRANCH-NAME`` Branch name to use for new PRs; '_new_pr_' if unspecified (type ) +``--pr-commit-msg=PR-COMMIT-MSG`` Commit message for new/updated pull request created with --new-pr (type ) +``--pr-descr=PR-DESCR`` Description for new pull request created with --new-pr (type ) +``--pr-target-account=PR-TARGET-ACCOUNT`` Target account for new PRs (type ; default: easybuilders) +``--pr-target-branch=PR-TARGET-BRANCH`` Target branch for new PRs (type ; default: develop) +``--pr-target-repo=PR-TARGET-REPO`` Target repository for new/updating PRs (default: auto-detect based on provided files) (type ) +``--pr-title=PR-TITLE`` Title for new pull request created with --new-pr (type ) +``--preview-pr`` Preview a new pull request (default: False) +``--review-pr=PR#`` Review specified pull request (type ) +``--sync-branch-with-develop=SYNC-BRANCH-WITH-DEVELOP`` Sync branch with current 'develop' branch (type ) +``--sync-pr-with-develop=PR#`` Sync pull request with current 'develop' branch (type ) +``--test-report-env-filter=TEST-REPORT-ENV-FILTER`` Regex used to filter out variables in environment dump of test report +``--update-branch-github=UPDATE-BRANCH-GITHUB`` Update specified branch in GitHub (type ) +``--update-pr=PR#`` Update an existing pull request (type ) +``-u, --upload-test-report`` Upload full test report as a gist on GitHub (default: False) +======================================================= ================================================================================================================================= Informative options @@ -206,6 +206,7 @@ Option flag Option description ``--check-conflicts`` Check for version conflicts in dependency graphs (default: False) ``--dep-graph=depgraph.`` Create dependency graph ``--dump-env-script`` Dump source script to set up build environment based on toolchain/dependencies (default: False) +``--easystack=EASYSTACK`` Path to easystack file in YAML format, specifying details of a software stack ``--last-log`` Print location to EasyBuild log file of last (failed) session (default: False) ``--list-easyblocks=LIST-EASYBLOCKS`` Show list of available easyblocks (type choice; default: simple) (choices: simple, detailed) ``--list-installed-software=LIST-INSTALLED-SOFTWARE`` Show list of installed software (type choice; default: simple) (choices: simple, detailed) @@ -235,91 +236,92 @@ Option flag Option description ``--job-max-jobs=MAX-JOBS`` Maximum number of concurrent jobs (queued and running, 0 = unlimited) (type int; default: 0) ``--job-max-walltime=MAX-WALLTIME`` Maximum walltime for jobs (in hours) (type int; default: 24) ``--job-output-dir=OUTPUT-DIR`` Output directory for jobs (default: current directory) (default: /Volumes/work/easybuild/docs) -``--job-polling-interval=POLLING-INTERVAL`` Interval between polls for status of jobs (in seconds) (type ; default: 30.0) +``--job-polling-interval=POLLING-INTERVAL`` Interval between polls for status of jobs (in seconds) (type ; default: 30.0) ``--job-target-resource=TARGET-RESOURCE`` Target resource for jobs =========================================== =========================================================================================================================== Override options ---------------- -========================================================================= ============================================================================================================================================================================================================================================ -Option flag Option description -========================================================================= ============================================================================================================================================================================================================================================ -``--add-dummy-to-minimal-toolchains`` Include dummy toolchain in minimal toolchain searches [DEPRECATED, use --add-system-to-minimal-toolchains instead!) (default: False) -``--add-system-to-minimal-toolchains`` Include system toolchain in minimal toolchain searches (default: False) -``--allow-loaded-modules=ALLOW-LOADED-MODULES`` List of software names for which to allow loaded modules in initial environment (type comma-separated list; default: EasyBuild) -``--allow-modules-tool-mismatch`` Allow mismatch of modules tool and definition of 'module' function (default: False) -``--allow-use-as-root-and-accept-consequences`` Allow using of EasyBuild as root (NOT RECOMMENDED!) (default: False) -``--backup-modules`` Back up an existing module file, if any. Only works when using --module-only -``--check-ebroot-env-vars=CHECK-EBROOT-ENV-VARS`` Action to take when defined $EBROOT* environment variables are found for which there is no matching loaded module; supported values: error, ignore, unset, warn (default: warn) -``--cleanup-builddir`` Cleanup build dir after successful installation. (default: True; disable with --disable-cleanup-builddir) -``--cleanup-tmpdir`` Cleanup tmp dir after successful run. (default: True; disable with --disable-cleanup-tmpdir) -``--color=WHEN`` Colorize output (type choice; default: auto) (choices: auto, always, never) -``--consider-archived-easyconfigs`` Also consider archived easyconfigs (default: False) -``-C, --containerize`` Generate container recipe/image (default: False) -``--copy-ec`` Copy specified easyconfig(s) to specified location (default: False) -``--cuda-compute-capabilities=CUDA-COMPUTE-CAPABILITIES`` List of CUDA compute capabilities to use when building GPU software (type comma-separated list) -``--debug-lmod`` Run Lmod modules tool commands in debug module (default: False) -``--default-opt-level=DEFAULT-OPT-LEVEL`` Specify default optimisation level (type choice; default: defaultopt) (choices: noopt, lowopt, defaultopt, opt) -``--deprecated=DEPRECATED`` Run pretending to be (future) version, to test removal of deprecated code. -``--detect-loaded-modules=DETECT-LOADED-MODULES`` Detect loaded EasyBuild-generated modules, act accordingly; supported values: error, ignore, purge, unload, warn (default: warn) -``--devel`` Enable including of development log messages (default: False) -``--download-timeout=DOWNLOAD-TIMEOUT`` Timeout for initiating downloads (in seconds) (type ) -``--dump-autopep8`` Reformat easyconfigs using autopep8 when dumping them (default: False) -``-e CLASS, --easyblock=CLASS`` easyblock to use for processing the spec file or dumping the options -``--enforce-checksums`` Enforce availability of checksums for all sources/patches, so they can be verified (default: False) -``--experimental`` Allow experimental code (with behaviour that can be changed/removed at any given time). (default: False) -``--extra-modules=EXTRA-MODULES`` List of extra modules to load after setting up the build environment (type comma-separated list) -``--fetch`` Allow downloading sources ignoring OS and modules tool dependencies, implies --stop=fetch, --ignore-osdeps and ignore modules tool (default: False) -``--filter-deps=FILTER-DEPS`` List of dependencies that you do *not* want to install with EasyBuild, because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses) (type comma-separated list) -``--filter-env-vars=FILTER-ENV-VARS`` List of names of environment variables that should *not* be defined/updated by module files generated by EasyBuild (type comma-separated list) -``--fixed-installdir-naming-scheme`` Use fixed naming scheme for installation directories (default: True; disable with --disable-fixed-installdir-naming-scheme) -``--force-download=FORCE-DOWNLOAD`` Force re-downloading of sources and/or patches, even if they are available already in source path (type choice; default: sources) (choices: all, patches, sources) -``--generate-devel-module`` Generate a develop module file, implies --force if disabled (default: True; disable with --disable-generate-devel-module) -``--group=GROUP`` Group to be used for software installations (only verified, not set) -``--group-writable-installdir`` Enable group write permissions on installation directory after installation (default: False) -``--hidden`` Install 'hidden' module file(s) by prefixing their version with '.' (default: False) -``--hide-deps=HIDE-DEPS`` Comma separated list of dependencies that you want automatically hidden, (e.g. --hide-deps=zlib,ncurses) (type comma-separated list) -``--hide-toolchains=HIDE-TOOLCHAINS`` Comma separated list of toolchains that you want automatically hidden, (e.g. --hide-toolchains=GCCcore) (type comma-separated list) -``--ignore-checksums`` Ignore failing checksum verification (default: False) -``--ignore-osdeps`` Ignore any listed OS dependencies (default: False) -``--install-latest-eb-release`` Install latest known version of easybuild (default: False) -``--lib64-fallback-sanity-check`` Fallback in sanity check to lib64/ equivalent for missing libraries (default: True; disable with --disable-lib64-fallback-sanity-check) -``--lib64-lib-symlink`` Automatically create symlinks for lib64/ pointing to lib/ if the former is missing (default: True; disable with --disable-lib64-lib-symlink) -``--max-fail-ratio-adjust-permissions=MAX-FAIL-RATIO-ADJUST-PERMISSIONS`` Maximum ratio for failures to allow when adjusting permissions (type float; default: 0.5) -``--minimal-build-env=MINIMAL-BUILD-ENV`` Minimal build environment to define when using system toolchain, specified as a comma-separated list that defines a mapping between name of environment variable and its value separated by a colon (':') (default: CC:gcc,CXX:g++) -``--minimal-toolchains`` Use minimal toolchain when resolving dependencies (default: False) -``--module-only`` Only generate module file(s); skip all steps except for module, prepare, ready, postiter, sanitycheck (default: False) -``--modules-tool-version-check`` Check version of modules tool being used (default: True; disable with --disable-modules-tool-version-check) -``--mpi-cmd-template=MPI-CMD-TEMPLATE`` Template for MPI commands (template keys: %(nr_ranks)s, %(cmd)s) -``--mpi-tests`` Run MPI tests (when relevant) (default: True; disable with --disable-mpi-tests) -``--optarch=OPTARCH`` Set architecture optimization, overriding native architecture optimizations -``--output-format=OUTPUT-FORMAT`` Set output format (type choice; default: txt) (choices: txt, rst) -``--parallel=PARALLEL`` Specify (maximum) level of parallellism used during build procedure (type int) -``--pre-create-installdir`` Create installation directory before submitting build jobs (default: True; disable with --disable-pre-create-installdir) -``-p, --pretend`` Does the build/installation in a test directory located in $HOME/easybuildinstall (default: False) -``--read-only-installdir`` Set read-only permissions on installation directory after installation (default: False) -``--remove-ghost-install-dirs`` Remove ghost installation directories when --force or --rebuild is used, rather than just warning about them (default: False) -``--rpath`` Enable use of RPATH for linking with libraries (default: False) -``--rpath-filter=RPATH-FILTER`` List of regex patterns to use for filtering out RPATH paths (type comma-separated list) -``--set-default-module`` Set the generated module as default (default: False) -``--set-gid-bit`` Set group ID bit on newly created directories (default: False) -``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` Silence specified deprecation warnings (type comma-separated list) -``-t, --skip-test-cases`` Skip running test cases (default: False) -``--sticky-bit`` Set sticky bit on newly created directories (default: False) -``--sysroot=SYSROOT`` Location root directory of system, prefix for standard paths like /usr/lib and /usr/include -``-T, --trace`` Provide more information in output to stdout on progress (default: False) -``--umask=UMASK`` umask to use (e.g. '022'); non-user write permissions on install directories are removed -``--update-modules-tool-cache`` Update modules tool cache file(s) after generating module file (default: False) -``--use-ccache=PATH`` Enable use of ccache to speed up compilation, with specified cache dir (type ; default: False) -``--use-existing-modules`` Use existing modules when resolving dependencies with minimal toolchains (default: False) -``--use-f90cache=PATH`` Enable use of f90cache to speed up compilation, with specified cache dir (type ; default: False) -``--verify-easyconfig-filenames`` Verify whether filename of specified easyconfigs matches with contents (default: False) -``--wait-on-lock=WAIT-ON-LOCK`` Wait for lock to be released; 0 implies no waiting (exit with an error if the lock already exists), non-zero value specified waiting interval [DEPRECATED: use --wait-on-lock-interval and --wait-on-lock-limit instead] (type ) -``--wait-on-lock-interval=WAIT-ON-LOCK-INTERVAL`` Wait interval (in seconds) to use when waiting for existing lock to be removed (type ; default: 60) -``--wait-on-lock-limit=WAIT-ON-LOCK-LIMIT`` Maximum amount of time (in seconds) to wait until lock is released (0 means no waiting at all, exit with error; -1 means no waiting limit, keep waiting) (type ; default: 0) -``--zip-logs=ZIP-LOGS`` Zip logs that are copied to install directory, using specified command (default: gzip) -========================================================================= ============================================================================================================================================================================================================================================ +========================================================================= ============================================================================================================================================================================================================================================= +Option flag Option description +========================================================================= ============================================================================================================================================================================================================================================= +``--add-dummy-to-minimal-toolchains`` Include dummy toolchain in minimal toolchain searches [DEPRECATED, use --add-system-to-minimal-toolchains instead!) (default: False) +``--add-system-to-minimal-toolchains`` Include system toolchain in minimal toolchain searches (default: False) +``--allow-loaded-modules=ALLOW-LOADED-MODULES`` List of software names for which to allow loaded modules in initial environment (type comma-separated list; default: EasyBuild) +``--allow-modules-tool-mismatch`` Allow mismatch of modules tool and definition of 'module' function (default: False) +``--allow-use-as-root-and-accept-consequences`` Allow using of EasyBuild as root (NOT RECOMMENDED!) (default: False) +``--backup-modules`` Back up an existing module file, if any. Only works when using --module-only +``--check-ebroot-env-vars=CHECK-EBROOT-ENV-VARS`` Action to take when defined $EBROOT* environment variables are found for which there is no matching loaded module; supported values: error, ignore, unset, warn (default: warn) +``--cleanup-builddir`` Cleanup build dir after successful installation. (default: True; disable with --disable-cleanup-builddir) +``--cleanup-tmpdir`` Cleanup tmp dir after successful run. (default: True; disable with --disable-cleanup-tmpdir) +``--color=WHEN`` Colorize output (type choice; default: auto) (choices: auto, always, never) +``--consider-archived-easyconfigs`` Also consider archived easyconfigs (default: False) +``-C, --containerize`` Generate container recipe/image (default: False) +``--copy-ec`` Copy specified easyconfig(s) to specified location (default: False) +``--cuda-compute-capabilities=CUDA-COMPUTE-CAPABILITIES`` List of CUDA compute capabilities to use when building GPU software; values should be specified as digits separated by a dot, for example: 3.5,5.0,7.2 (type comma-separated list) +``--debug-lmod`` Run Lmod modules tool commands in debug module (default: False) +``--default-opt-level=DEFAULT-OPT-LEVEL`` Specify default optimisation level (type choice; default: defaultopt) (choices: noopt, lowopt, defaultopt, opt) +``--deprecated=DEPRECATED`` Run pretending to be (future) version, to test removal of deprecated code. +``--detect-loaded-modules=DETECT-LOADED-MODULES`` Detect loaded EasyBuild-generated modules, act accordingly; supported values: error, ignore, purge, unload, warn (default: warn) +``--devel`` Enable including of development log messages (default: False) +``--download-timeout=DOWNLOAD-TIMEOUT`` Timeout for initiating downloads (in seconds) (type ) +``--dump-autopep8`` Reformat easyconfigs using autopep8 when dumping them (default: False) +``-e CLASS, --easyblock=CLASS`` easyblock to use for processing the spec file or dumping the options +``--enforce-checksums`` Enforce availability of checksums for all sources/patches, so they can be verified (default: False) +``--experimental`` Allow experimental code (with behaviour that can be changed/removed at any given time). (default: False) +``--extra-modules=EXTRA-MODULES`` List of extra modules to load after setting up the build environment (type comma-separated list) +``--fetch`` Allow downloading sources ignoring OS and modules tool dependencies, implies --stop=fetch, --ignore-osdeps and ignore modules tool (default: False) +``--filter-deps=FILTER-DEPS`` List of dependencies that you do *not* want to install with EasyBuild, because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses) (type comma-separated list) +``--filter-env-vars=FILTER-ENV-VARS`` List of names of environment variables that should *not* be defined/updated by module files generated by EasyBuild (type comma-separated list) +``--fixed-installdir-naming-scheme`` Use fixed naming scheme for installation directories (default: True; disable with --disable-fixed-installdir-naming-scheme) +``--force-download=FORCE-DOWNLOAD`` Force re-downloading of sources and/or patches, even if they are available already in source path (type choice; default: sources) (choices: all, patches, sources) +``--generate-devel-module`` Generate a develop module file, implies --force if disabled (default: True; disable with --disable-generate-devel-module) +``--group=GROUP`` Group to be used for software installations (only verified, not set) +``--group-writable-installdir`` Enable group write permissions on installation directory after installation (default: False) +``--hidden`` Install 'hidden' module file(s) by prefixing their version with '.' (default: False) +``--hide-deps=HIDE-DEPS`` Comma separated list of dependencies that you want automatically hidden, (e.g. --hide-deps=zlib,ncurses) (type comma-separated list) +``--hide-toolchains=HIDE-TOOLCHAINS`` Comma separated list of toolchains that you want automatically hidden, (e.g. --hide-toolchains=GCCcore) (type comma-separated list) +``--ignore-checksums`` Ignore failing checksum verification (default: False) +``--ignore-osdeps`` Ignore any listed OS dependencies (default: False) +``--install-latest-eb-release`` Install latest known version of easybuild (default: False) +``--lib64-fallback-sanity-check`` Fallback in sanity check to lib64/ equivalent for missing libraries (default: True; disable with --disable-lib64-fallback-sanity-check) +``--lib64-lib-symlink`` Automatically create symlinks for lib64/ pointing to lib/ if the former is missing (default: True; disable with --disable-lib64-lib-symlink) +``--max-fail-ratio-adjust-permissions=MAX-FAIL-RATIO-ADJUST-PERMISSIONS`` Maximum ratio for failures to allow when adjusting permissions (type float; default: 0.5) +``--minimal-build-env=MINIMAL-BUILD-ENV`` Minimal build environment to define when using system toolchain, specified as a comma-separated list that defines a mapping between name of environment variable and its value separated by a colon (':') (default: CC:gcc,CXX:g++) +``--minimal-toolchains`` Use minimal toolchain when resolving dependencies (default: False) +``--module-only`` Only generate module file(s); skip all steps except for module, prepare, ready, postiter, sanitycheck (default: False) +``--modules-tool-version-check`` Check version of modules tool being used (default: True; disable with --disable-modules-tool-version-check) +``--mpi-cmd-template=MPI-CMD-TEMPLATE`` Template for MPI commands (template keys: %(nr_ranks)s, %(cmd)s) +``--mpi-tests`` Run MPI tests (when relevant) (default: True; disable with --disable-mpi-tests) +``--optarch=OPTARCH`` Set architecture optimization, overriding native architecture optimizations +``--output-format=OUTPUT-FORMAT`` Set output format (type choice; default: txt) (choices: txt, rst) +``--parallel=PARALLEL`` Specify (maximum) level of parallellism used during build procedure (type int) +``--pre-create-installdir`` Create installation directory before submitting build jobs (default: True; disable with --disable-pre-create-installdir) +``-p, --pretend`` Does the build/installation in a test directory located in $HOME/easybuildinstall (default: False) +``--read-only-installdir`` Set read-only permissions on installation directory after installation (default: False) +``--remove-ghost-install-dirs`` Remove ghost installation directories when --force or --rebuild is used, rather than just warning about them (default: False) +``--rpath`` Enable use of RPATH for linking with libraries (default: False) +``--rpath-filter=RPATH-FILTER`` List of regex patterns to use for filtering out RPATH paths (type comma-separated list) +``--set-default-module`` Set the generated module as default (default: False) +``--set-gid-bit`` Set group ID bit on newly created directories (default: False) +``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` Silence specified deprecation warnings (type comma-separated list) +``-t, --skip-test-cases`` Skip running test cases (default: False) +``--skip-test-step`` Skip running the test step (e.g. unit tests) (default: False) +``--sticky-bit`` Set sticky bit on newly created directories (default: False) +``--sysroot=SYSROOT`` Location root directory of system, prefix for standard paths like /usr/lib and /usr/include +``-T, --trace`` Provide more information in output to stdout on progress (default: False) +``--umask=UMASK`` umask to use (e.g. '022'); non-user write permissions on install directories are removed +``--update-modules-tool-cache`` Update modules tool cache file(s) after generating module file (default: False) +``--use-ccache=PATH`` Enable use of ccache to speed up compilation, with specified cache dir (type ; default: False) +``--use-existing-modules`` Use existing modules when resolving dependencies with minimal toolchains (default: False) +``--use-f90cache=PATH`` Enable use of f90cache to speed up compilation, with specified cache dir (type ; default: False) +``--verify-easyconfig-filenames`` Verify whether filename of specified easyconfigs matches with contents (default: False) +``--wait-on-lock=WAIT-ON-LOCK`` Wait for lock to be released; 0 implies no waiting (exit with an error if the lock already exists), non-zero value specified waiting interval [DEPRECATED: use --wait-on-lock-interval and --wait-on-lock-limit instead] (type ) +``--wait-on-lock-interval=WAIT-ON-LOCK-INTERVAL`` Wait interval (in seconds) to use when waiting for existing lock to be removed (type ; default: 60) +``--wait-on-lock-limit=WAIT-ON-LOCK-LIMIT`` Maximum amount of time (in seconds) to wait until lock is released (0 means no waiting at all, exit with error; -1 means no waiting limit, keep waiting) (type ; default: 0) +``--zip-logs=ZIP-LOGS`` Zip logs that are copied to install directory, using specified command (default: gzip) +========================================================================= ============================================================================================================================================================================================================================================= Package options diff --git a/docs/version-specific/toolchain_opts.rst b/docs/version-specific/toolchain_opts.rst index e3b55763..5104988b 100644 --- a/docs/version-specific/toolchain_opts.rst +++ b/docs/version-specific/toolchain_opts.rst @@ -5,7 +5,7 @@ Available toolchain options (by toolchain) *(see also* ``eb --avail-toolchain-opts `` *)* -ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - goblf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ +ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ .. _ClangGCC: @@ -22,6 +22,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -61,6 +66,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``dynamic`` Generate dynamically linked executable ``True`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -101,6 +111,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``dynamic`` Generate dynamically linked executable ``True`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -141,6 +156,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``dynamic`` Generate dynamically linked executable ``True`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -181,6 +201,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``dynamic`` Generate dynamically linked executable ``True`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -220,6 +245,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -260,6 +290,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -300,6 +335,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -340,6 +380,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -377,6 +422,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -415,6 +465,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -455,6 +510,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -495,6 +555,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -535,6 +600,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -575,6 +645,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -615,6 +690,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -654,6 +734,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -695,6 +780,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -736,6 +826,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -776,6 +871,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -817,6 +917,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -858,6 +963,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -899,6 +1009,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -940,6 +1055,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -981,6 +1101,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1022,6 +1147,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1062,6 +1192,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1102,6 +1237,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1143,6 +1283,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1184,6 +1329,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1225,6 +1375,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1266,6 +1421,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1307,6 +1467,57 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``f2c`` Generate code compatible with f2c and f77 ``False`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``loop`` Automatic loop parallellisation ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``lto`` Enable Link Time Optimization ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + +.. _gobff: + +Available options for gobff toolchain +------------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1348,6 +1559,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1389,6 +1605,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1429,6 +1650,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1469,6 +1695,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1510,6 +1741,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1551,6 +1787,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1592,6 +1833,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1633,6 +1879,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1674,6 +1925,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1715,6 +1971,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1756,6 +2017,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1797,6 +2063,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1838,6 +2109,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1879,6 +2155,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1921,6 +2202,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -1961,6 +2247,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2001,6 +2292,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2042,6 +2338,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2082,6 +2383,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2122,6 +2428,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2163,6 +2474,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2204,6 +2520,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2245,6 +2566,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2286,6 +2612,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2327,6 +2658,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2368,6 +2704,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2409,6 +2750,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2450,6 +2796,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2491,6 +2842,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2532,6 +2888,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2573,6 +2934,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2614,6 +2980,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2655,6 +3026,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2696,6 +3072,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2736,6 +3117,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -2773,6 +3159,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -2811,6 +3202,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -2849,6 +3245,11 @@ option description ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -2887,6 +3288,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ibm-static`` Link IBM XL provided libraries statically ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -2926,6 +3332,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ibm-static`` Link IBM XL provided libraries statically ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -2966,6 +3377,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ibm-static`` Link IBM XL provided libraries statically ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -3006,6 +3422,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ibm-static`` Link IBM XL provided libraries statically ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -3046,6 +3467,11 @@ option description ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ibm-static`` Link IBM XL provided libraries statically ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` diff --git a/docs/version-specific/toolchains.rst b/docs/version-specific/toolchains.rst index f1e87f54..60d5b83e 100644 --- a/docs/version-specific/toolchains.rst +++ b/docs/version-specific/toolchains.rst @@ -3,86 +3,87 @@ List of known toolchains ------------------------ -================ ================ =========== ======================= ======== -Name Compiler(s) MPI Linear algebra FFT -================ ================ =========== ======================= ======== -**cgmpich** Clang, GCC MPICH *(none)* *(none)* -**cgmpolf** Clang, GCC MPICH OpenBLAS, ScaLAPACK FFTW -**cgmvapich2** Clang, GCC MVAPICH2 *(none)* *(none)* -**cgmvolf** Clang, GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW -**cgompi** Clang, GCC OpenMPI *(none)* *(none)* -**cgoolf** Clang, GCC OpenMPI OpenBLAS, ScaLAPACK FFTW -**ClangGCC** Clang, GCC *(none)* *(none)* *(none)* -**CrayCCE** PrgEnv-cray cray-mpich cray-libsci *(none)* -**CrayGNU** PrgEnv-gnu cray-mpich cray-libsci *(none)* -**CrayIntel** PrgEnv-intel cray-mpich cray-libsci *(none)* -**CrayPGI** PrgEnv-pgi cray-mpich cray-libsci *(none)* -**foss** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW -**fosscuda** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW -**GCC** GCC *(none)* *(none)* *(none)* -**GCCcore** GCCcore *(none)* *(none)* *(none)* -**gcccuda** GCC, CUDA *(none)* *(none)* *(none)* -**gimkl** GCC impi imkl imkl -**gimpi** GCC impi *(none)* *(none)* -**gimpic** GCC, CUDA impi *(none)* *(none)* -**giolf** GCC impi OpenBLAS, ScaLAPACK FFTW -**giolfc** GCC, CUDA impi OpenBLAS, ScaLAPACK FFTW -**gmacml** GCC MVAPICH2 ACML, ScaLAPACK FFTW -**gmkl** GCC *(none)* imkl imkl -**gmklc** GCC, CUDA *(none)* imkl imkl -**gmpich** GCC MPICH *(none)* *(none)* -**gmpich2** GCC MPICH2 *(none)* *(none)* -**gmpolf** GCC MPICH OpenBLAS, ScaLAPACK FFTW -**gmvapich2** GCC MVAPICH2 *(none)* *(none)* -**gmvolf** GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW -**GNU** GCC *(none)* *(none)* *(none)* -**goalf** GCC OpenMPI ATLAS, ScaLAPACK FFTW -**goblf** GCC OpenMPI BLIS, LAPACK, ScaLAPACK FFTW -**golf** GCC *(none)* OpenBLAS FFTW -**golfc** GCC, CUDA *(none)* OpenBLAS FFTW -**gomkl** GCC OpenMPI imkl imkl -**gomklc** GCC, CUDA OpenMPI imkl imkl -**gompi** GCC OpenMPI *(none)* *(none)* -**gompic** GCC, CUDA OpenMPI *(none)* *(none)* -**goolf** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW -**goolfc** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW -**gpsmpi** GCC psmpi *(none)* *(none)* -**gpsolf** GCC psmpi OpenBLAS, ScaLAPACK FFTW -**gqacml** GCC QLogicMPI ACML, ScaLAPACK FFTW -**gsmpi** GCC SpectrumMPI *(none)* *(none)* -**gsolf** GCC SpectrumMPI OpenBLAS, ScaLAPACK FFTW -**iccifort** icc, ifort *(none)* *(none)* *(none)* -**iccifortcuda** icc, ifort, CUDA *(none)* *(none)* *(none)* -**ictce** icc, ifort impi imkl imkl -**iimkl** icc, ifort *(none)* imkl imkl -**iimklc** icc, ifort, CUDA *(none)* imkl imkl -**iimpi** icc, ifort impi *(none)* *(none)* -**iimpic** icc, ifort, CUDA impi *(none)* *(none)* -**iiqmpi** icc, ifort QLogicMPI *(none)* *(none)* -**impich** icc, ifort MPICH *(none)* *(none)* -**impmkl** icc, ifort MPICH imkl imkl -**intel** icc, ifort impi imkl imkl -**intel-para** icc, ifort psmpi imkl imkl -**intelcuda** icc, ifort, CUDA impi imkl imkl -**iomkl** icc, ifort OpenMPI imkl imkl -**iomklc** icc, ifort, CUDA OpenMPI imkl imkl -**iompi** icc, ifort OpenMPI *(none)* *(none)* -**iompic** icc, ifort, CUDA OpenMPI *(none)* *(none)* -**ipsmpi** icc, ifort psmpi *(none)* *(none)* -**iqacml** icc, ifort QLogicMPI ACML, ScaLAPACK FFTW -**ismkl** icc, ifort MPICH2 imkl imkl -**NVHPC** NVHPC *(none)* *(none)* *(none)* -**PGI** PGI *(none)* *(none)* *(none)* -**pmkl** PGI *(none)* imkl imkl -**pomkl** PGI OpenMPI imkl imkl -**pompi** PGI OpenMPI *(none)* *(none)* -**system** *(none)* *(none)* *(none)* *(none)* -**xlcxlf** xlc, xlf *(none)* *(none)* *(none)* -**xlmpich** xlc, xlf MPICH *(none)* *(none)* -**xlmpich2** xlc, xlf MPICH2 *(none)* *(none)* -**xlmvapich2** xlc, xlf MVAPICH2 *(none)* *(none)* -**xlompi** xlc, xlf OpenMPI *(none)* *(none)* -================ ================ =========== ======================= ======== +================ ================ =========== ========================= ======== +Name Compiler(s) MPI Linear algebra FFT +================ ================ =========== ========================= ======== +**cgmpich** Clang, GCC MPICH *(none)* *(none)* +**cgmpolf** Clang, GCC MPICH OpenBLAS, ScaLAPACK FFTW +**cgmvapich2** Clang, GCC MVAPICH2 *(none)* *(none)* +**cgmvolf** Clang, GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW +**cgompi** Clang, GCC OpenMPI *(none)* *(none)* +**cgoolf** Clang, GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**ClangGCC** Clang, GCC *(none)* *(none)* *(none)* +**CrayCCE** PrgEnv-cray cray-mpich cray-libsci *(none)* +**CrayGNU** PrgEnv-gnu cray-mpich cray-libsci *(none)* +**CrayIntel** PrgEnv-intel cray-mpich cray-libsci *(none)* +**CrayPGI** PrgEnv-pgi cray-mpich cray-libsci *(none)* +**foss** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**fosscuda** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW +**GCC** GCC *(none)* *(none)* *(none)* +**GCCcore** GCCcore *(none)* *(none)* *(none)* +**gcccuda** GCC, CUDA *(none)* *(none)* *(none)* +**gimkl** GCC impi imkl imkl +**gimpi** GCC impi *(none)* *(none)* +**gimpic** GCC, CUDA impi *(none)* *(none)* +**giolf** GCC impi OpenBLAS, ScaLAPACK FFTW +**giolfc** GCC, CUDA impi OpenBLAS, ScaLAPACK FFTW +**gmacml** GCC MVAPICH2 ACML, ScaLAPACK FFTW +**gmkl** GCC *(none)* imkl imkl +**gmklc** GCC, CUDA *(none)* imkl imkl +**gmpich** GCC MPICH *(none)* *(none)* +**gmpich2** GCC MPICH2 *(none)* *(none)* +**gmpolf** GCC MPICH OpenBLAS, ScaLAPACK FFTW +**gmvapich2** GCC MVAPICH2 *(none)* *(none)* +**gmvolf** GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW +**GNU** GCC *(none)* *(none)* *(none)* +**goalf** GCC OpenMPI ATLAS, ScaLAPACK FFTW +**gobff** GCC OpenMPI BLIS, libFLAME, ScaLAPACK FFTW +**goblf** GCC OpenMPI BLIS, LAPACK, ScaLAPACK FFTW +**golf** GCC *(none)* OpenBLAS FFTW +**golfc** GCC, CUDA *(none)* OpenBLAS FFTW +**gomkl** GCC OpenMPI imkl imkl +**gomklc** GCC, CUDA OpenMPI imkl imkl +**gompi** GCC OpenMPI *(none)* *(none)* +**gompic** GCC, CUDA OpenMPI *(none)* *(none)* +**goolf** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**goolfc** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW +**gpsmpi** GCC psmpi *(none)* *(none)* +**gpsolf** GCC psmpi OpenBLAS, ScaLAPACK FFTW +**gqacml** GCC QLogicMPI ACML, ScaLAPACK FFTW +**gsmpi** GCC SpectrumMPI *(none)* *(none)* +**gsolf** GCC SpectrumMPI OpenBLAS, ScaLAPACK FFTW +**iccifort** icc, ifort *(none)* *(none)* *(none)* +**iccifortcuda** icc, ifort, CUDA *(none)* *(none)* *(none)* +**ictce** icc, ifort impi imkl imkl +**iimkl** icc, ifort *(none)* imkl imkl +**iimklc** icc, ifort, CUDA *(none)* imkl imkl +**iimpi** icc, ifort impi *(none)* *(none)* +**iimpic** icc, ifort, CUDA impi *(none)* *(none)* +**iiqmpi** icc, ifort QLogicMPI *(none)* *(none)* +**impich** icc, ifort MPICH *(none)* *(none)* +**impmkl** icc, ifort MPICH imkl imkl +**intel** icc, ifort impi imkl imkl +**intel-para** icc, ifort psmpi imkl imkl +**intelcuda** icc, ifort, CUDA impi imkl imkl +**iomkl** icc, ifort OpenMPI imkl imkl +**iomklc** icc, ifort, CUDA OpenMPI imkl imkl +**iompi** icc, ifort OpenMPI *(none)* *(none)* +**iompic** icc, ifort, CUDA OpenMPI *(none)* *(none)* +**ipsmpi** icc, ifort psmpi *(none)* *(none)* +**iqacml** icc, ifort QLogicMPI ACML, ScaLAPACK FFTW +**ismkl** icc, ifort MPICH2 imkl imkl +**NVHPC** NVHPC *(none)* *(none)* *(none)* +**PGI** PGI *(none)* *(none)* *(none)* +**pmkl** PGI *(none)* imkl imkl +**pomkl** PGI OpenMPI imkl imkl +**pompi** PGI OpenMPI *(none)* *(none)* +**system** *(none)* *(none)* *(none)* *(none)* +**xlcxlf** xlc, xlf *(none)* *(none)* *(none)* +**xlmpich** xlc, xlf MPICH *(none)* *(none)* +**xlmpich2** xlc, xlf MPICH2 *(none)* *(none)* +**xlmvapich2** xlc, xlf MVAPICH2 *(none)* *(none)* +**xlompi** xlc, xlf OpenMPI *(none)* *(none)* +================ ================ =========== ========================= ======== *(see also* ``eb --list-toolchains`` *)* From 16b84ee4a83d0c6a3197c0285779c45c41ef31fe Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 10 Dec 2020 12:55:16 +0800 Subject: [PATCH 097/286] update release notes and changelog for EasyBuild v4.3.2 + bump version to 4.3.2 --- docs/Changelog.rst | 2 + docs/Contributing.rst | 2 +- docs/Release_notes.rst | 168 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 4 files changed, 170 insertions(+), 6 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index f2c22ea4..53c0e74b 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,8 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20201210.01** (`Dec 10th 2020`): update release notes for EasyBuild v4.3.2 (see :ref:`release_notes_eb432`) +* **release 20201029.01** (`Oct 29th 2020`): update release notes for EasyBuild v4.3.1 (see :ref:`release_notes_eb431`) * **release 20200913.01** (`Sep 13th 2020`): update release notes for EasyBuild v4.3.0 (see :ref:`release_notes_eb430`) * **release 20200708.01** (`July 8th 2020`): update release notes for EasyBuild v4.2.2 (see :ref:`release_notes_eb422`) * **release 20200520.01** (`May 20th 2020`): update release notes for EasyBuild v4.2.1 (see :ref:`release_notes_eb421`) diff --git a/docs/Contributing.rst b/docs/Contributing.rst index ff1469b6..4bb59f33 100644 --- a/docs/Contributing.rst +++ b/docs/Contributing.rst @@ -497,7 +497,7 @@ Some aspects of this are automated, others require human intervention. Requirements for pull requests ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -**Only pull requests (PRs) that fullfil these requirements are eligible to be merged:** +**Only pull requests (PRs) that fulfill these requirements are eligible to be merged:** (i) *the PR must target the* ``develop`` *branch of the repository*; see :ref:`contributing_review_process_develop_branch` diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 1d87cc0b..045fb3f7 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,174 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,134** different software packages, -including 31 different (compiler) toolchains. It contains 225 software-specific easyblocks and 37 generic easyblocks, -alongside 10,794 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,175** different software packages, +including 32 different (compiler) toolchains. It contains 227 software-specific easyblocks and 37 generic easyblocks, +alongside 11,054 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb432: + +EasyBuild v4.3.2 (December 10th 2020) +------------------------------------- + +bugfix/update release + +**framework** + +* add (experimental) support for specifying easyconfig files via an "easystack" file (`#3479 `_, `#3511 `_, `#3515 `_, `#3517 `_, `#3520 `_, `#3521 `_) + + * see also https://easybuild.readthedocs.io/en/latest/Easystack-files.html + +* add definition for new ``gobff`` toolchain using BLIS and LibFLAME (`#3505 `_) + +* various enhancements, including: + + * add support for toolchain options like ``extra_cxxflags`` to specify extra compiler options (`#2193 `_) + * fix combination of ``--copy-ec`` and ``--from-pr`` (`#3482 `_) + * enhance ``copy_files`` function: support single file target, error on empty input list, support verbose mode (`#3483 `_) + * cache result of ``fetch_files_from_pr`` function (mainly to speed up framework test suite) (`#3484 `_) + * add ``locate_files`` function to filetools module (`#3485 `_) + * add support for ``%(module_name)s`` template value (`#3497 `_) + * clarify input format for ``--cuda-compute-capabilities`` in ``eb --help`` output (`#3509 `_) + * add support for skipping unit tests (test step) via ``--skip-test-step`` (`#3524 `_) + +* various bug fixes, including: + + * also ignore ``vsc.*`` imports coming from from ``pkg_resources/__init__.py`` (setuptools) in fake vsc namespace (`#3491 `_) + * don't pass username in ``github_api_get_request`` when no GitHub token is available (`#3494 `_) + * also inject ``-rpath`` options for all entries in ``$LIBRARY_PATH`` in ``RPATH`` wrappers (`#3495 `_) + * avoid ``TypeError`` being raised by ``list_toolchains`` (`#3499 `_) + * check if PR is already merged in ``--merge-pr`` (`#3502 `_) + * graciously handle wrong PR id in ``fetch_pr_data`` (`#3503 `_) + * fix regression in ``apply_regex_substitutions``: also accept list of paths to patch (`#3507 `_) + * update installation procedure for EasyBuild in generated Singularity container recipes (`#3510 `_) + * fix GitHub Actions workflow for test suite: run outside of repo checkout + also test bootstrap script with Python 3.9 (`#3518 `_) + * bump cryptography from 2.9.2 to 3.2 for Python 2 in ``requirements.txt`` (`#3519 `_) + * fix ``eb --help=rst`` when running with Python 3 (`#3525 `_) + +* other changes: + + * exclude test configurations with Lmod 7 and Python 3, except for Python 3.6 (`#3496 `_) + * significantly speed up parsing of easyconfig files by only extracting comments from an easyconfig file when they're actually needed (`#3498 `_) + * don't include ``file``/``ldd``/``readelf`` commands run during RPATH sanity check in ``--trace`` output (`#3508 `_) + +**easyblocks** + +* 2 new software-specific easyblocks: + + * code-server (`#2255 `_), Metagenome-Atlas (`#2219 `_) + +* minor enhancements, including: + + * add ``-fallow-argument-mismatch`` option when building CP2K 7.1 or older with GCC 10.x (`#2223 `_) + * update TensorFlow easyblock for upcoming TensorFlow 2.4 (`#2225 `_) + * add support for building Clang with OpenMP offload support (`#2229 `_) + * enhance OpenMPI easyblock to catch any ``--with-ucx*`` configure options (`#2230 `_) + * take into account ``preinstallopts`` and ``installopts`` in custom easyblock for NCL (`#2234 `_) + * add support for ``withnvptx`` easyconfig parameter, to enable GPU offloading, in GCC easyblock (`#2235 `_) + * take into account versions like ``4.x`` in OpenFOAM easyblock (`#2239 `_) + * also add ``bin`` subdir to ``$PATH`` when installing a Python package (`#2244 `_) + +* various bug fixes, including: + + * fix two bugs in GROMACS easyblock when using GCC & MKL for FFT and BLAS/LAPACK (`#2212 `_) + * fix version check in Qt5 easyblock w.r.t. disabling features on old Linux kernel versions (`#2220 `_) + * always define ``$FCCPP`` in QuantumESPRESSO easyblock (not just when using Intel compilers) (`#2221 `_) + * allow wxPython to be installed as an extension (`#2227 `_, `#2275 `_) + * only configure Python with ``--enable-optimizations`` when compiling Python with (recent) GCC compiler (`#2228 `_) + * fix sanity check for Boost MT libraries (`#2231 `_) + * fix hardcoded path in NVHPC easyblock to support multiple architectures (`#2233 `_) + * fix ``CPASSERT`` test faults on RHEL8 in CP2K easyblock (`#2236 `_) + * stop silently ignoring failing numpy tests, but include support for ignoring (failing) numpy tests (`#2238 `_, `#2271 `_) + * append to module guesses in easyblocks for Chapel, icc, imkl and impi (rather than overwriting guesses from parent easyblock) (`#2242 `_) + * weed out duplicates when determining paths to ``include-fixed`` subdirectory in GCC easyblock (`#2245 `_) + * prepend all hardcoded ``/usr/*`` paths with sysroot in Python's setup.py installation script (`#2246 `_) + * don't try to patch newer versions of Bazel where the patches won't apply (`#2249 `_) + * fix setting of ``$RUNPARALLEL`` in HDF5 easyblock (`#2250 `_) + * move ``--build`` and ``--host`` logic to ``run_configure_cmd`` in GCC easyblock (`#2252 `_) + * set ``$UCX_TLS`` in module for impi installation on top of UCX, and allow it to be overwritten in impi easyconfig file (`#2253 `_, `#2258 `_) + * enhance PyTorch easyblock to ensure it finds MKL (via ``$MKLROOT``) (`#2257 `_) + * use integer division to determine number MPI ranks to use in WRF test step (`#2266 `_) + * also specify ``locincpth`` and ``glibpth`` configure options for Perl based on ``--sysroot`` (`#2268 `_) + +* other changes, including: + + * add link to GCC mailing list thread confirming that binutils should not be configured with ``--with-sysroot=$EASYBUILD_SYSROOT`` when GCC is being configured like that (`#2215 `_) + * pass paths to patch one by one to ``apply_regex_substitutions`` in GCC easyblock when ``--sysroot`` is set (`#2217 `_) + + * workaround for regression in ``apply_regex_substitutions`` introduced in EasyBuild v4.3.1 (which was fixed for v4.3.2) + +**easyconfigs** + +* add easyconfigs for new gobff toolchain: gobff/2020.11 + gobff/2020.06-amd (`#11761 `_) + +* add easyconfigs for updates of common toolchains: foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b + + * see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html + +* added example easyconfig files for 41 new software packages: + + * alsa-lib (`#11658 `_), assimp (`#11759 `_), BioServices (`#11602 `_), carputils (`#11270 `_), cctools (`#11799 `_), + code-server (`#11778 `_), CRISPResso2 (`#11775 `_), elfutils (`#11783 `_), EMU (`#11641 `_), fgbio (`#11519 `_), Flink (`#11747 `_), + FreeSASA (`#11699 `_), Geant4-data (`#11610 `_), geocube (`#11714 `_), IPM (`#11768 `_, `#11772 `_), libmicrohttpd (`#11783 `_), + libStatGen (`#7982 `_), libzeep (`#11687 `_), LLDB (`#11822 `_), meshalyzer (`#11270 `_), meshtool (`#11270 `_), + Metagenome-Atlas (`#11620 `_), MLxtend (`#11601 `_), MRChem (`#11604 `_), MRCPP (`#11579 `_), mxml (`#11769 `_), mxmlplus (`#11771 `_), + nanocompore (`#11690 `_), neon (`#11797 `_), Open-Data-Cube-Core (`#11713 `_), OpenSees (`#11613 `_), PEST++ (`#11565 `_), + pyFAI (`#11849 `_), pymca (`#11848 `_), RE2 (`#11718 `_), scikit-bio (`#11660 `_), SpaceRanger (`#11776 `_), SplAdder (`#11607 `_), + SWAT+ (`#11615 `_), velocyto (`#11744 `_), WCT (`#11779 `_) + +* added additional easyconfigs for various supported software packages, including: + + * BBMap 38.87, Boost 1.74.0, CUDA 11.1.1, CellRanger 5.0.0.eb, CheckM 1.1.3, Clang 11.0.0, cuDNN 8.0.4.30, + DMTCP 2.6.0, FDS 6.7.5, FFmpeg 4.3.1, GROMACS 2020.4, Geant4 10.6.2, Ghostscript 9.53.3, GitPython 3.1.9, + GlobalArrays 5.8, HDF5 1.10.7, h5py 3.1.0, hypothesis 5.41.5, JasPer 2.0.16, LittleCMS 2.11, libedit 20191231, + libyaml 0.2.5, MPFR 4.1.0, magma 2.5.4, matplotlib 3.3.3, NCCL 2.8.3, NLopt 2.6.2, Nextflow 20.10.0, + netCDF-Fortran 4.5.3, OpenBLAS 0.3.12, OpenMolcas 20.10, Pillow 8.0.1, PnetCDF 1.12.1, PyYAML 5.3.1, + packmol 20.2.2, protobuf 3.14.0, psycopg2 2.8.6, pybind11 2.6.0, pycocotools 2.0.2, Qt5 5.14.2, RAxML-NG 1.0.1, + RSeQC 4.0.0, rioxarray 0.1.1, SCOTCH 6.1.0, SciPy-bundle 2020.11, SentencePiece 0.1.94, StringTie 2.1.4, + SuperLU 5.2.2, scikit-learn 0.23.2, snakemake 5.26.1, tqdm 4.51.0, vsc-mympirun 5.2.5, x264 20201026 + +* minor enhancements, including: + + * add extension to R-bundle-Bioconductor 3.11: snpStats (`#11586 `_), SCANVIS (`#11638 `_) + * add extensions to R 4.0.0: coloc, Exact, lmom, gld, DescTools (`#11587 `_); nlsem (`#11733 `_); mitools, survey, tableone, jstable (`#11841 `_) + * add gxmapi extension (Python bindings) to GROMACS 2020.4 (`#11640 `_) + * add missing extensions for QIIME2 to Perl 5.30.2 and 5.32.0 easyconfigs (`#11654 `_) + * enable NVPTX offload support in GCCcore 10.2.0 easyconfig (`#11720 `_) + +* various bug fixes, including: + + * prevent Minimac4 easyconfig from downloading libStatGen from GitHub (`#7982 `_) + * limit build parallelism for RAxML-NG to avoid build failure (`#10363 `_) + * fix ``source_urls`` in Geant4 easyconfigs (`#11596 `_) + * add alternate checksum for extensions in R easyconfigs: KernSmooth (`#11600 `_), codetools (`#11616 `_, `#11736 `_) + * fix BBMap version check in FusionCatcher v1.20 (`#11608 `_) + * add patch for TensorFlow 2.3.1 to fix installation on Arm64 (`#11614 `_) + * add patch for GCCcore 10.2 to fix ``__has_include`` regression (`#11627 `_) + * change default ``bitmaptype`` for IRkernel to cairo (`#11645 `_) + * set ``$JUPYTER_PATH`` to make Jupyter find the ipywidgets extension in recent IPython easyconfigs (`#11649 `_) + * add missing dependencies + fix moduleclass in CheckM easyconfigs (should be bio) (`#11662 `_) + * use Python 2 build dep for nodejs 12.19.0 (`#11679 `_) + * use correct OS deps in UCX (`#11702 `_) + * in-place update to magma 2.5.4 for PyTorch 1.2.0 (`#11723 `_) + * in-place update to magma 2.5.4 for PyTorch easyconfigs using fosscuda/2019b toolchain (`#11726 `_) + * add missing Java dep to Prokka (`#11732 `_) + * add patch to fix possible memory leak in OpenBLAS 0.3.3+ (`#11745 `_) + * do not treat warnings as errors in Java v1.8_191-b26-OpenJDK (POWER) (`#11755 `_) + * add missing PEAR dependency in easyconfig for GBprocesS v2.3 + enhance sanity check (`#11767 `_) + * add missing gnuplot dependency in OpenFOAM easyconfigs (`#11770 `_, `#11800 `_) + * consistently add Java as a dep for prokka 1.14.5 (`#11782 `_) + * stick to http download URL in fetchMG easyconfig (https doesn't work) (`#11788 `_) + +* other changes: + + * rename XCfun to XCFun (`#11603 `_) + * rename ambiguous Ray easyconfigs to Ray-assembler and Ray-project (`#11727 `_) + * change 'rstudio' name to 'RStudio-Server' to agree with official name and better reflect what it provides (`#11764 `_) + * rename Sumo to SUMO for consistency (`#11791 `_) + + .. _release_notes_eb431: EasyBuild v4.3.1 (October 29th 2020) diff --git a/docs/conf.py b/docs/conf.py index b325ea80..235b9ee4 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.3.0' # this is meant to reference the version of EasyBuild +version = '4.3.2' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20200913.0' # this is meant to reference the version of the documentation itself +release = '20201210.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From b4c29b55cbea847775215667915070be82170237 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Dec 2020 09:04:08 +0100 Subject: [PATCH 098/286] minor formatting changes in v4.3.2 release notes for toolchain names --- docs/Release_notes.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 045fb3f7..31c58590 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -103,9 +103,9 @@ bugfix/update release **easyconfigs** -* add easyconfigs for new gobff toolchain: gobff/2020.11 + gobff/2020.06-amd (`#11761 `_) +* add easyconfigs for new `gobff` toolchain: `gobff/2020.11` + `gobff/2020.06-amd` (`#11761 `_) -* add easyconfigs for updates of common toolchains: foss/2020b, fosscuda/2020b, intel/2020b, intelcuda/2020b +* add easyconfigs for updates of common toolchains: `foss/2020b`, `fosscuda/2020b`, `intel/2020b`, `intelcuda/2020b` * see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html From 766e3a7bb5fdc5f634d7d5ffaa2f2745f051b778 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 10 Dec 2020 17:12:45 +0800 Subject: [PATCH 099/286] bump version to 4.3.2 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 4666f46a..780c58bd 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.3.1' +VERSION = '4.3.2' # Utility function to read README file From c4e81c0d6103fa717357d51989dc1586ab88aa3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Dec 2020 10:52:32 +0100 Subject: [PATCH 100/286] small fixes in easystack docs --- docs/Easystack-files.rst | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/docs/Easystack-files.rst b/docs/Easystack-files.rst index ab34b132..9c46e611 100644 --- a/docs/Easystack-files.rst +++ b/docs/Easystack-files.rst @@ -3,9 +3,9 @@ Easystack files =============== -This documentation covers aspects of specifying a software stack to instlal with Easybuild with *easystack files*. +This documentation covers aspects of specifying a software stack to install with Easybuild with *easystack files*. -**Note: this is an* :ref:`experimental feature `. *Some of the mentioned functionality may be subject to change or be prone to errors.** +**Note: this is an** :ref:`experimental feature `. **Some of the mentioned functionality may be subject to change or be prone to errors.** .. contents:: :depth: 3 @@ -52,7 +52,7 @@ Can be in form of a list or consecutive line entries (see example). **General structure of YAML-formatted easystack:** -.. code:: +.. code:: yaml software: : @@ -63,7 +63,7 @@ Can be in form of a list or consecutive line entries (see example). **Example of YAML-formatted easystack:** -.. code:: +.. code:: yaml software: Bioconductor: @@ -116,6 +116,5 @@ Optionally, more advanced keywords can be specified: *easybuild_version*, *robot can be used (regardless of whether the pull request is merged or not). (see :ref:`Integration_with_GitHub` for more details). - *versionsuffix:* additional suffix for software version (placed after toolchain name) - (see :ref:`easyconfig_parameters` for more details). -- *include-labels:* -- *exclude-labels:* +- *include-labels:* only include this software when EasyBuild is configured with one of the specified labels +- *exclude-labels:* **do not** include this software when EasyBuild is configured with one of the specified labels From 64c3e8e467a3e3b5edac7fbaf4c0b9a15cf81c7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Dec 2020 11:09:16 +0100 Subject: [PATCH 101/286] fix silly typo in GitHub integration docs --- docs/Integration_with_GitHub.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Integration_with_GitHub.rst b/docs/Integration_with_GitHub.rst index 2eb48350..093f5f71 100644 --- a/docs/Integration_with_GitHub.rst +++ b/docs/Integration_with_GitHub.rst @@ -377,7 +377,7 @@ For example, to use the LAMMPS easyblock contributed via `easyblocks pull reques `_ together with the LAMMPS v7Aug2019 easyconfigs contributed via `easyconfigs pull request #9884 `_:: - $ eb --from-pr 9884 --include-easyblocks--from-pr 1964 --list-easyblocks=detailed + $ eb --from-pr 9884 --include-easyblocks-from-pr 1964 --list-easyblocks=detailed == temporary log file in case of crash /tmp/eb-Eq2zsJ/easybuild-1AaWf8.log EasyBlock (easybuild.framework.easyblock) ... From b9b5e4c6c4fa31c2397c2d32041e9d50e01ae30f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 Jan 2021 17:11:18 +0100 Subject: [PATCH 102/286] add Simon as EasyBuild maintainer --- docs/Maintainers.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/Maintainers.rst b/docs/Maintainers.rst index f593fd55..f040bb68 100644 --- a/docs/Maintainers.rst +++ b/docs/Maintainers.rst @@ -71,6 +71,10 @@ The EasyBuild maintainers all have admin access to the different EasyBuild GitHu * GitHub: `@damianam `_ - e-mail: ``d.alvarez (at) fz-juelich.de`` - IRC/Slack: ``dalvarez`` +* **Simon Branford** (`BEAR - University of Birmingham `_) + + * GitHub: `@branfosj `_ - e-mail: ``s.j.branford (at) bham.ac.uk`` - IRC/Slack: ``@Simon`` + * **Miguel Dias Costa** (National University of Singapore) * GitHub: `@migueldiascosta `_ - e-mail: ``migueldiascosta (at) nus.edu.sg`` - IRC/Slack: ``migueldiascosta`` From 3bb64dedebbfe88285798e2c3a3d239091307502 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Jan 2021 11:20:47 +0100 Subject: [PATCH 103/286] drop @ in Slack handle for @branfosj Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- docs/Maintainers.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Maintainers.rst b/docs/Maintainers.rst index f040bb68..19448cd4 100644 --- a/docs/Maintainers.rst +++ b/docs/Maintainers.rst @@ -73,7 +73,7 @@ The EasyBuild maintainers all have admin access to the different EasyBuild GitHu * **Simon Branford** (`BEAR - University of Birmingham `_) - * GitHub: `@branfosj `_ - e-mail: ``s.j.branford (at) bham.ac.uk`` - IRC/Slack: ``@Simon`` + * GitHub: `@branfosj `_ - e-mail: ``s.j.branford (at) bham.ac.uk`` - IRC/Slack: ``Simon`` * **Miguel Dias Costa** (National University of Singapore) From efb0c0ac32b27ecb7778d5bbc4ad10f34c9c96da Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 7 Feb 2021 15:57:42 +0000 Subject: [PATCH 104/286] Prevent wrong dash appearing in doc --- docs/Integration_with_GitHub.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Integration_with_GitHub.rst b/docs/Integration_with_GitHub.rst index 093f5f71..6f71472d 100644 --- a/docs/Integration_with_GitHub.rst +++ b/docs/Integration_with_GitHub.rst @@ -637,7 +637,7 @@ has been created. EasyBuild does *not* make changes to an existing working copy (cfr. :ref:`github_git_working_dirs_path`). .. note:: When modifying existing files via ``--new-pr``, - you *must* specify a (meaningful) commit message using `--pr-commit-msg`, see :ref:`github_controlling_pr_metadata`. + you *must* specify a (meaningful) commit message using ``--pr-commit-msg``, see :ref:`github_controlling_pr_metadata`. Example +++++++ From e9823083186fec22576dab8aa2e5fd8622096702 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 7 Feb 2021 16:05:24 +0000 Subject: [PATCH 105/286] strong incorrect rendering --- docs/Installation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Installation.rst b/docs/Installation.rst index d3ceb3cb..25e56ec8 100644 --- a/docs/Installation.rst +++ b/docs/Installation.rst @@ -522,7 +522,7 @@ Some dependencies are optional and are only required to support certain features Optional Python packages ^^^^^^^^^^^^^^^^^^^^^^^^ -* `GC3Pie `_, only needed when using `GC3Pie` as a backend for `--job`, +* `GC3Pie `_, only needed when using `GC3Pie` as a backend for ``--job``, see also :ref:`submitting_jobs`; * `GitPython `_, only needed if EasyBuild is hosted in a git repository or if you’re using a git From 0c7af60bb7e59b85fce31bd88846b381e244edd8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 7 Feb 2021 16:06:28 +0000 Subject: [PATCH 106/286] Update Using_the_EasyBuild_command_line.rst --- docs/Using_the_EasyBuild_command_line.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Using_the_EasyBuild_command_line.rst b/docs/Using_the_EasyBuild_command_line.rst index 33dcad82..a464d11e 100644 --- a/docs/Using_the_EasyBuild_command_line.rst +++ b/docs/Using_the_EasyBuild_command_line.rst @@ -591,7 +591,7 @@ Tweaking existing easyconfig files, using ``--try-*`` Making minor changes to existing easyconfig files can be done straight from the ``eb`` command line. This way, having to manually copying and editing easyconfig files can be avoided. -Tweaking existing easyconfig files can be done using the **--try-*** command line options. +Tweaking existing easyconfig files can be done using the **``--try-``*** command line options. For each of the software build options that can be used as an alternative to specifying easyconfig file names, a matching ``--try-X`` command line options is available: From a6a4fec9ff7d04ab8890dc522c570daf9e724afe Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 7 Feb 2021 16:09:05 +0000 Subject: [PATCH 107/286] correct formatting --- docs/Using_the_EasyBuild_command_line.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Using_the_EasyBuild_command_line.rst b/docs/Using_the_EasyBuild_command_line.rst index a464d11e..183bd892 100644 --- a/docs/Using_the_EasyBuild_command_line.rst +++ b/docs/Using_the_EasyBuild_command_line.rst @@ -591,7 +591,7 @@ Tweaking existing easyconfig files, using ``--try-*`` Making minor changes to existing easyconfig files can be done straight from the ``eb`` command line. This way, having to manually copying and editing easyconfig files can be avoided. -Tweaking existing easyconfig files can be done using the **``--try-``*** command line options. +Tweaking existing easyconfig files can be done using the ``--try-*`` command line options. For each of the software build options that can be used as an alternative to specifying easyconfig file names, a matching ``--try-X`` command line options is available: From 2dd567c534713ccddbb3d013af43499b9253abe3 Mon Sep 17 00:00:00 2001 From: Bennet Fauber Date: Mon, 8 Feb 2021 09:46:08 -0500 Subject: [PATCH 108/286] Adding conditional symlinking of lua posix lib --- .github/workflows/scripts.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/scripts.yml b/.github/workflows/scripts.yml index cb735b6f..3c107a62 100644 --- a/.github/workflows/scripts.yml +++ b/.github/workflows/scripts.yml @@ -21,7 +21,10 @@ jobs: run: | sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl-dev # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082 - sudo ln -s /usr/lib/x86_64-linux-gnu/lua/5.2/posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so + # needed for 18.04 not for 20.04. Conditional added to skip if posix.so exists + if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then + sudo ln -s /usr/lib/x86_64-linux-gnu/lua/5.2/posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so + fi # use script provided by easybuild-framework to install recent Lmod source install_eb_dep.sh Lmod-8.3.8 $HOME echo $MOD_INIT > $HOME/mod_init From 56e856973fdefc49fb9dbb052800af36d3f39b4a Mon Sep 17 00:00:00 2001 From: justbennet Date: Mon, 8 Feb 2021 12:48:32 -0500 Subject: [PATCH 109/286] Change comment phrasing to be more clear Add Ubuntu to the comment text and modify to be not quite so ungrammatically 'concise'. Co-authored-by: Kenneth Hoste --- .github/workflows/scripts.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/scripts.yml b/.github/workflows/scripts.yml index 3c107a62..3cb92dbf 100644 --- a/.github/workflows/scripts.yml +++ b/.github/workflows/scripts.yml @@ -21,7 +21,7 @@ jobs: run: | sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl-dev # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082 - # needed for 18.04 not for 20.04. Conditional added to skip if posix.so exists + # needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then sudo ln -s /usr/lib/x86_64-linux-gnu/lua/5.2/posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so fi From c85054cc7a116b6da49255e30bb181e717d0e3c1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2021 22:56:47 +0100 Subject: [PATCH 110/286] auto-update docs for EasyBuild v4.3.3 --- docs/api/framework.easyblock.rst | 7 + docs/api/framework.easyconfig.constants.rst | 7 + docs/api/framework.easyconfig.default.rst | 7 + docs/api/framework.easyconfig.easyconfig.rst | 7 + .../framework.easyconfig.format.convert.rst | 7 + .../framework.easyconfig.format.format.rst | 7 + docs/api/framework.easyconfig.format.one.rst | 7 + ...rk.easyconfig.format.pyheaderconfigobj.rst | 7 + docs/api/framework.easyconfig.format.rst | 24 + docs/api/framework.easyconfig.format.two.rst | 7 + .../framework.easyconfig.format.version.rst | 7 + docs/api/framework.easyconfig.format.yeb.rst | 7 + docs/api/framework.easyconfig.licenses.rst | 7 + docs/api/framework.easyconfig.parser.rst | 7 + docs/api/framework.easyconfig.rst | 35 + docs/api/framework.easyconfig.style.rst | 7 + docs/api/framework.easyconfig.templates.rst | 7 + docs/api/framework.easyconfig.tools.rst | 7 + docs/api/framework.easyconfig.tweak.rst | 7 + docs/api/framework.easyconfig.types.rst | 7 + docs/api/framework.easystack.rst | 7 + docs/api/framework.extension.rst | 7 + docs/api/framework.extensioneasyblock.rst | 7 + docs/api/framework.rst | 29 + docs/version-specific/Supported_software.rst | 2826 ++++++++++++----- docs/version-specific/easyblocks.rst | 3 + .../version-specific/easyconfig_constants.rst | 2 +- .../easyconfig_parameters.rst | 1 + .../version-specific/easyconfig_templates.rst | 68 +- docs/version-specific/generic_easyblocks.rst | 6 +- docs/version-specific/help.rst | 165 +- docs/version-specific/toolchain_opts.rst | 93 +- docs/version-specific/toolchains.rst | 164 +- 33 files changed, 2643 insertions(+), 920 deletions(-) create mode 100644 docs/api/framework.easyblock.rst create mode 100644 docs/api/framework.easyconfig.constants.rst create mode 100644 docs/api/framework.easyconfig.default.rst create mode 100644 docs/api/framework.easyconfig.easyconfig.rst create mode 100644 docs/api/framework.easyconfig.format.convert.rst create mode 100644 docs/api/framework.easyconfig.format.format.rst create mode 100644 docs/api/framework.easyconfig.format.one.rst create mode 100644 docs/api/framework.easyconfig.format.pyheaderconfigobj.rst create mode 100644 docs/api/framework.easyconfig.format.rst create mode 100644 docs/api/framework.easyconfig.format.two.rst create mode 100644 docs/api/framework.easyconfig.format.version.rst create mode 100644 docs/api/framework.easyconfig.format.yeb.rst create mode 100644 docs/api/framework.easyconfig.licenses.rst create mode 100644 docs/api/framework.easyconfig.parser.rst create mode 100644 docs/api/framework.easyconfig.rst create mode 100644 docs/api/framework.easyconfig.style.rst create mode 100644 docs/api/framework.easyconfig.templates.rst create mode 100644 docs/api/framework.easyconfig.tools.rst create mode 100644 docs/api/framework.easyconfig.tweak.rst create mode 100644 docs/api/framework.easyconfig.types.rst create mode 100644 docs/api/framework.easystack.rst create mode 100644 docs/api/framework.extension.rst create mode 100644 docs/api/framework.extensioneasyblock.rst create mode 100644 docs/api/framework.rst diff --git a/docs/api/framework.easyblock.rst b/docs/api/framework.easyblock.rst new file mode 100644 index 00000000..b5c3de0e --- /dev/null +++ b/docs/api/framework.easyblock.rst @@ -0,0 +1,7 @@ +framework.easyblock module +========================== + +.. automodule:: framework.easyblock + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.constants.rst b/docs/api/framework.easyconfig.constants.rst new file mode 100644 index 00000000..c0410a96 --- /dev/null +++ b/docs/api/framework.easyconfig.constants.rst @@ -0,0 +1,7 @@ +framework.easyconfig.constants module +===================================== + +.. automodule:: framework.easyconfig.constants + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.default.rst b/docs/api/framework.easyconfig.default.rst new file mode 100644 index 00000000..f374fe8f --- /dev/null +++ b/docs/api/framework.easyconfig.default.rst @@ -0,0 +1,7 @@ +framework.easyconfig.default module +=================================== + +.. automodule:: framework.easyconfig.default + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.easyconfig.rst b/docs/api/framework.easyconfig.easyconfig.rst new file mode 100644 index 00000000..1cb2421e --- /dev/null +++ b/docs/api/framework.easyconfig.easyconfig.rst @@ -0,0 +1,7 @@ +framework.easyconfig.easyconfig module +====================================== + +.. automodule:: framework.easyconfig.easyconfig + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.format.convert.rst b/docs/api/framework.easyconfig.format.convert.rst new file mode 100644 index 00000000..c86c298e --- /dev/null +++ b/docs/api/framework.easyconfig.format.convert.rst @@ -0,0 +1,7 @@ +framework.easyconfig.format.convert module +========================================== + +.. automodule:: framework.easyconfig.format.convert + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.format.format.rst b/docs/api/framework.easyconfig.format.format.rst new file mode 100644 index 00000000..9c701585 --- /dev/null +++ b/docs/api/framework.easyconfig.format.format.rst @@ -0,0 +1,7 @@ +framework.easyconfig.format.format module +========================================= + +.. automodule:: framework.easyconfig.format.format + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.format.one.rst b/docs/api/framework.easyconfig.format.one.rst new file mode 100644 index 00000000..83decc18 --- /dev/null +++ b/docs/api/framework.easyconfig.format.one.rst @@ -0,0 +1,7 @@ +framework.easyconfig.format.one module +====================================== + +.. automodule:: framework.easyconfig.format.one + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.format.pyheaderconfigobj.rst b/docs/api/framework.easyconfig.format.pyheaderconfigobj.rst new file mode 100644 index 00000000..776960dd --- /dev/null +++ b/docs/api/framework.easyconfig.format.pyheaderconfigobj.rst @@ -0,0 +1,7 @@ +framework.easyconfig.format.pyheaderconfigobj module +==================================================== + +.. automodule:: framework.easyconfig.format.pyheaderconfigobj + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.format.rst b/docs/api/framework.easyconfig.format.rst new file mode 100644 index 00000000..7c5d9601 --- /dev/null +++ b/docs/api/framework.easyconfig.format.rst @@ -0,0 +1,24 @@ +framework.easyconfig.format package +=================================== + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + framework.easyconfig.format.convert + framework.easyconfig.format.format + framework.easyconfig.format.one + framework.easyconfig.format.pyheaderconfigobj + framework.easyconfig.format.two + framework.easyconfig.format.version + framework.easyconfig.format.yeb + +Module contents +--------------- + +.. automodule:: framework.easyconfig.format + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.format.two.rst b/docs/api/framework.easyconfig.format.two.rst new file mode 100644 index 00000000..9d4e204e --- /dev/null +++ b/docs/api/framework.easyconfig.format.two.rst @@ -0,0 +1,7 @@ +framework.easyconfig.format.two module +====================================== + +.. automodule:: framework.easyconfig.format.two + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.format.version.rst b/docs/api/framework.easyconfig.format.version.rst new file mode 100644 index 00000000..9ccf8df3 --- /dev/null +++ b/docs/api/framework.easyconfig.format.version.rst @@ -0,0 +1,7 @@ +framework.easyconfig.format.version module +========================================== + +.. automodule:: framework.easyconfig.format.version + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.format.yeb.rst b/docs/api/framework.easyconfig.format.yeb.rst new file mode 100644 index 00000000..36574b5f --- /dev/null +++ b/docs/api/framework.easyconfig.format.yeb.rst @@ -0,0 +1,7 @@ +framework.easyconfig.format.yeb module +====================================== + +.. automodule:: framework.easyconfig.format.yeb + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.licenses.rst b/docs/api/framework.easyconfig.licenses.rst new file mode 100644 index 00000000..65618c13 --- /dev/null +++ b/docs/api/framework.easyconfig.licenses.rst @@ -0,0 +1,7 @@ +framework.easyconfig.licenses module +==================================== + +.. automodule:: framework.easyconfig.licenses + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.parser.rst b/docs/api/framework.easyconfig.parser.rst new file mode 100644 index 00000000..12a94972 --- /dev/null +++ b/docs/api/framework.easyconfig.parser.rst @@ -0,0 +1,7 @@ +framework.easyconfig.parser module +================================== + +.. automodule:: framework.easyconfig.parser + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.rst b/docs/api/framework.easyconfig.rst new file mode 100644 index 00000000..c517f94c --- /dev/null +++ b/docs/api/framework.easyconfig.rst @@ -0,0 +1,35 @@ +framework.easyconfig package +============================ + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + framework.easyconfig.format + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + framework.easyconfig.constants + framework.easyconfig.default + framework.easyconfig.easyconfig + framework.easyconfig.licenses + framework.easyconfig.parser + framework.easyconfig.style + framework.easyconfig.templates + framework.easyconfig.tools + framework.easyconfig.tweak + framework.easyconfig.types + +Module contents +--------------- + +.. automodule:: framework.easyconfig + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.style.rst b/docs/api/framework.easyconfig.style.rst new file mode 100644 index 00000000..906b4450 --- /dev/null +++ b/docs/api/framework.easyconfig.style.rst @@ -0,0 +1,7 @@ +framework.easyconfig.style module +================================= + +.. automodule:: framework.easyconfig.style + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.templates.rst b/docs/api/framework.easyconfig.templates.rst new file mode 100644 index 00000000..63fb08ff --- /dev/null +++ b/docs/api/framework.easyconfig.templates.rst @@ -0,0 +1,7 @@ +framework.easyconfig.templates module +===================================== + +.. automodule:: framework.easyconfig.templates + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.tools.rst b/docs/api/framework.easyconfig.tools.rst new file mode 100644 index 00000000..7f8c3230 --- /dev/null +++ b/docs/api/framework.easyconfig.tools.rst @@ -0,0 +1,7 @@ +framework.easyconfig.tools module +================================= + +.. automodule:: framework.easyconfig.tools + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.tweak.rst b/docs/api/framework.easyconfig.tweak.rst new file mode 100644 index 00000000..72e69799 --- /dev/null +++ b/docs/api/framework.easyconfig.tweak.rst @@ -0,0 +1,7 @@ +framework.easyconfig.tweak module +================================= + +.. automodule:: framework.easyconfig.tweak + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easyconfig.types.rst b/docs/api/framework.easyconfig.types.rst new file mode 100644 index 00000000..ede2d00c --- /dev/null +++ b/docs/api/framework.easyconfig.types.rst @@ -0,0 +1,7 @@ +framework.easyconfig.types module +================================= + +.. automodule:: framework.easyconfig.types + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.easystack.rst b/docs/api/framework.easystack.rst new file mode 100644 index 00000000..c0c7f8c9 --- /dev/null +++ b/docs/api/framework.easystack.rst @@ -0,0 +1,7 @@ +framework.easystack module +========================== + +.. automodule:: framework.easystack + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.extension.rst b/docs/api/framework.extension.rst new file mode 100644 index 00000000..890e96c9 --- /dev/null +++ b/docs/api/framework.extension.rst @@ -0,0 +1,7 @@ +framework.extension module +========================== + +.. automodule:: framework.extension + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.extensioneasyblock.rst b/docs/api/framework.extensioneasyblock.rst new file mode 100644 index 00000000..5f682bcb --- /dev/null +++ b/docs/api/framework.extensioneasyblock.rst @@ -0,0 +1,7 @@ +framework.extensioneasyblock module +=================================== + +.. automodule:: framework.extensioneasyblock + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/api/framework.rst b/docs/api/framework.rst new file mode 100644 index 00000000..4fb1d3dd --- /dev/null +++ b/docs/api/framework.rst @@ -0,0 +1,29 @@ +framework package +================= + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + framework.easyconfig + +Submodules +---------- + +.. toctree:: + :maxdepth: 4 + + framework.easyblock + framework.easystack + framework.extension + framework.extensioneasyblock + +Module contents +--------------- + +.. automodule:: framework + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 71800a44..b7b3d50d 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -1,9 +1,10 @@ .. _list_software: +== Temporary log file in case of crash /tmp/eb-rvg3pj0d/easybuild-jo5_l5pb.log List of supported software ========================== -EasyBuild |version| supports 2176 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2248 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +66,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -176,13 +177,14 @@ version toolchain ack is a tool like grep, optimized for programmers -*homepage*: http://beyondgrep.com/ +*homepage*: https://beyondgrep.com -======== ========== -version toolchain -======== ========== -``2.14`` ``system`` -======== ========== +========= ================== +version toolchain +========= ================== +``2.14`` ``system`` +``3.4.0`` ``GCCcore/10.2.0`` +========= ================== .. _list_software_ACT_216: @@ -316,6 +318,7 @@ A small library for automatically adjustment of text position in matplotlib plot ========= ================= =============== version versionsuffix toolchain ========= ================= =============== +``0.7.3`` ``-Python-3.6.6`` ``foss/2018b`` ``0.7.3`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================= =============== @@ -529,13 +532,14 @@ version toolchain *almosthere* ++++++++++++ -Progress indicator C library. ATHR is a simple yet powerful progress indicator library that works on Windows, Linux, and macOS. It is non-blocking as the progress update is done via a dedicated, lightweight thread, as to not impair the performance of the calling program. +Progress indicator C library. ATHR is a simple yet powerful progress indicator library that works on Windows, Linux, and macOS. It is non-blocking as the progress update is done via a dedicated, lightweight thread, as to not impair the performance of the calling program. *homepage*: https://github.com/horta/almosthere ========== ================= version toolchain ========== ================= +``1.0.1`` ``GCCcore/7.3.0`` ``1.0.10`` ``GCCcore/9.3.0`` ========== ================= @@ -670,13 +674,14 @@ version toolchain AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. -*homepage*: http://ambermd.org/ +*homepage*: https://ambermd.org/ ======= ================== ================================ version versionsuffix toolchain ======= ================== ================================ ``17`` ``intel/2017b``, ``intel/2018a`` ``17`` ``-Python-2.7.14`` ``foss/2018a`` +``20`` ``-Python-3.8.2`` ``intel/2020a`` ======= ================== ================================ @@ -685,15 +690,16 @@ version versionsuffix toolchain *AMD-LibM* ++++++++++ -AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor based machines. +AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor based machines. *homepage*: https://developer.amd.com/amd-cpu-libraries/amd-math-library-libm/ -========= ================== -version toolchain -========= ================== -``3.2.2`` ``GCC/7.3.0-2.30`` -========= ================== +=========== ================== +version toolchain +=========== ================== +``3.2.2`` ``GCC/7.3.0-2.30`` +``3.6.0-4`` ``GCC/9.3.0`` +=========== ================== .. _list_software_AMD-RNG_486: @@ -705,11 +711,12 @@ AMD Random Number Generator Library is a pseudorandom number generator library. *homepage*: https://developer.amd.com/amd-cpu-libraries/rng-library/ -======= ================== -version toolchain -======= ================== -``1.0`` ``GCC/7.3.0-2.30`` -======= ================== +========= ================== +version toolchain +========= ================== +``1.0`` ``GCC/7.3.0-2.30`` +``2.2-4`` ``GCC/9.3.0`` +========= ================== .. _list_software_AMD-SecureRNG_1101: @@ -717,15 +724,16 @@ version toolchain *AMD-SecureRNG* +++++++++++++++ -The AMD Secure Random Number Generator (RNG) is a library that provides APIs to access the cryptographically secure random numbers generated by AMD’s hardware-based random number generator implementation. +The AMD Secure Random Number Generator (RNG) is a library that provides APIs to access the cryptographically secure random numbers generated by AMD’s hardware-based random number generator implementation. *homepage*: https://developer.amd.com/amd-cpu-libraries/rng-library/ -======= ================== -version toolchain -======= ================== -``1.0`` ``GCC/7.3.0-2.30`` -======= ================== +========= ================== +version toolchain +========= ================== +``1.0`` ``GCC/7.3.0-2.30`` +``2.2-4`` ``GCC/9.3.0`` +========= ================== .. _list_software_AMOS_304: @@ -825,6 +833,7 @@ version toolchain ``2019.10`` ``system`` ``2020.02`` ``system`` ``2020.07`` ``system`` +``2020.11`` ``system`` =========== ========== @@ -884,15 +893,16 @@ version versionsuffix toolchain *annovar* +++++++++ -ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). +ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). *homepage*: http://annovar.openbioinformatics.org/en/latest/ -============= ================ ============== -version versionsuffix toolchain -============= ================ ============== -``2016Feb01`` ``-Perl-5.22.1`` ``foss/2016a`` -============= ================ ============== +============= ================ ================= +version versionsuffix toolchain +============= ================ ================= +``2016Feb01`` ``-Perl-5.22.1`` ``foss/2016a`` +``20191024`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +============= ================ ================= .. _list_software_ANSYS_398: @@ -995,7 +1005,7 @@ ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language to version versionsuffix toolchain ========= ================== ===================================================================================================== ``2.7.7`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b`` -``2.7.7`` ``-Java-11`` ``GCCcore/8.3.0`` +``2.7.7`` ``-Java-11`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.7.7`` ``-Python-2.7.11`` ``foss/2016a`` ``2.7.7`` ``-Python-2.7.13`` ``intel/2017a`` ``2.7.7`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` @@ -1055,6 +1065,22 @@ version versionsuffix toolchain ========= ================ ================= +.. _list_software_AOCC_278: + +*AOCC* +++++++ + +AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 11.0 + +*homepage*: https://developer.amd.com/amd-aocc/ + +========= ================= +version toolchain +========= ================= +``2.3.0`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_APBS_294: *APBS* @@ -1143,12 +1169,13 @@ version toolchain Arb is a C library for arbitrary-precision interval arithmetic. It has full support for both real and complex numbers. The library is thread-safe, portable, and extensively tested. -*homepage*: http://arblib.org +*homepage*: https://arblib.org/ ========== ================================================================================ version toolchain ========== ================================================================================ ``2.16.0`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` +``2.17.0`` ``GCC/8.3.0`` ========== ================================================================================ @@ -1358,6 +1385,7 @@ version versionsuffix toolchain ``0.12.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.12.0`` ``-Python-3.6.6`` ``intel/2018b`` ``0.16.0`` ``-Python-3.7.4`` ``intel/2019b`` +``0.17.1`` ``intel/2020b`` ``0.17.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ================== =============================== @@ -1461,6 +1489,7 @@ version versionsuffix toolchain ``3.10.8`` ``-Python-3.6.3`` ``foss/2017b`` ``3.10.10`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.11.10`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.12.2`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` =========== ================= ================================================ @@ -1495,8 +1524,10 @@ version versionsuffix toolchain ``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``3.19.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``3.20.1`` ``foss/2020b``, ``intel/2020b`` ``3.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.20.1`` ``-Python-3.8.2`` ``intel/2020a`` +``3.21.1`` ``foss/2020b``, ``intel/2020b`` ============== ================== =================================================== @@ -1823,7 +1854,7 @@ version versionsuffix toolchain AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences -*homepage*: http://bioinf.uni-greifswald.de/augustus/ +*homepage*: https://bioinf.uni-greifswald.de/augustus/ ========= ================== =============================== version versionsuffix toolchain @@ -1835,6 +1866,7 @@ version versionsuffix toolchain ``3.3.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``3.3.2`` ``-Python-2.7.15`` ``intel/2018b`` ``3.3.3`` ``foss/2019b``, ``intel/2019b`` +``3.4.0`` ``foss/2020b`` ========= ================== =============================== @@ -2020,7 +2052,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` +:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` .. _list_software_Bader_478: @@ -2130,14 +2162,14 @@ BamTools provides both a programmer's API and an end-user's toolkit for handling *homepage*: https://github.com/pezmaster31/bamtools -========= ======================================================================================================================================================================================================= -version toolchain -========= ======================================================================================================================================================================================================= -``2.4.0`` ``foss/2016b`` -``2.4.1`` ``intel/2017a`` -``2.5.0`` ``foss/2016b``, ``intel/2017b`` -``2.5.1`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017b``, ``intel/2018b`` -========= ======================================================================================================================================================================================================= +========= ======================================================================================================================================================================================================================= +version toolchain +========= ======================================================================================================================================================================================================================= +``2.4.0`` ``foss/2016b`` +``2.4.1`` ``intel/2017a`` +``2.5.0`` ``foss/2016b``, ``intel/2017b`` +``2.5.1`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017b``, ``intel/2018b`` +========= ======================================================================================================================================================================================================================= .. _list_software_BamUtil_686: @@ -2350,6 +2382,8 @@ version toolchain ``2.0.0`` ``GCCcore/8.3.0`` ``3.4.1`` ``GCCcore/8.3.0`` ``3.6.0`` ``GCCcore/9.3.0`` +``3.7.1`` ``GCCcore/8.3.0`` +``3.7.2`` ``GCCcore/10.2.0`` ========== ==================================== @@ -2474,6 +2508,7 @@ version toolchain ``1.8`` ``GCC/6.4.0-2.28`` ``1.9`` ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` +``1.11`` ``GCC/10.2.0`` ========== ========================================================================================= @@ -2490,6 +2525,7 @@ Automatized phylogenetic tree building from bacterial core genomes. version versionsuffix toolchain ========== ================ =============== ``1.0.10`` ``-Perl-5.26.1`` ``intel/2018a`` +``1.1.0`` ``-Perl-5.28.0`` ``intel/2018b`` ========== ================ =============== @@ -2721,6 +2757,39 @@ version toolchain ======= ============== +.. _list_software_bgen_412: + +*bgen* +++++++ + +A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3. + +*homepage*: https://github.com/limix/bgen + +========= ================= +version toolchain +========= ================= +``3.0.2`` ``GCCcore/7.3.0`` +``3.0.3`` ``GCCcore/9.3.0`` +========= ================= + + +.. _list_software_bgen-reader_1084: + +*bgen-reader* ++++++++++++++ + +A bgen file format reader. This python package is a wrapper around the bgen library, a low-memory footprint reader that efficiently reads bgen files. It fully supports the bgen format specifications: 1.2 and 1.3; as well as their optional compressed formats. + +*homepage*: https://github.com/limix/bgen-reader-py + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` +========= ================= ============== + + .. _list_software_bibtexparser_1291: *bibtexparser* @@ -2929,11 +2998,11 @@ Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, *homepage*: https://github.com/BioPP/bpp-core -========= ============= -version toolchain -========= ============= -``2.4.1`` ``GCC/9.3.0`` -========= ============= +========= =================================== +version toolchain +========= =================================== +``2.4.1`` ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0`` +========= =================================== .. _list_software_Biopython_956: @@ -2956,7 +3025,7 @@ version versionsuffix toolchain ``1.70`` ``-Python-3.6.1`` ``intel/2017a`` ``1.70`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.71`` ``-Python-2.7.14`` ``intel/2018a`` -``1.71`` ``-Python-3.6.4`` ``foss/2018a`` +``1.71`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.72`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``1.72`` ``-Python-3.6.6`` ``foss/2018b`` ``1.73`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` @@ -2964,7 +3033,8 @@ version versionsuffix toolchain ``1.74`` ``foss/2019a`` ``1.75`` ``-Python-2.7.16`` ``foss/2019b`` ``1.75`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``1.78`` ``-Python-3.8.2`` ``intel/2020a`` +``1.78`` ``foss/2020b``, ``intel/2020b`` +``1.78`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ======== ================== =================================================== @@ -3151,6 +3221,7 @@ version versionsuffix toolchain ``2.8.1`` ``foss/2018b`` ``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a``, ``iimpi/2019b`` ``2.10.1`` ``gompi/2020a``, ``iimpi/2020a`` +``2.11.0`` ``gompi/2019b``, ``gompi/2020b`` ========== ================== ================================================================== @@ -3199,15 +3270,15 @@ AMD's fork of BLIS. BLIS is a portable software framework for instantiating high *homepage*: https://developer.amd.com/amd-cpu-libraries/blas-library/ -========= ============= ================== -version versionsuffix toolchain -========= ============= ================== -``0.3.2`` ``GCC/7.3.0-2.30`` -``0.6.0`` ``GCC/8.3.0-2.32`` -``0.8.0`` ``GCC/9.3.0`` -``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` -``2.2`` ``-amd`` ``GCC/9.3.0`` -========= ============= ================== +========= ============= ===================================== +version versionsuffix toolchain +========= ============= ===================================== +``0.3.2`` ``GCC/7.3.0-2.30`` +``0.6.0`` ``GCC/8.3.0-2.32`` +``0.8.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` +``2.2`` ``-amd`` ``GCCcore/9.3.0`` +========= ============= ===================================== .. _list_software_Blitz++_603: @@ -3366,6 +3437,8 @@ version versionsuffix toolchain ``0.1.4`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``0.2.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``0.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``0.3.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``0.3.5`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ================= ================================== @@ -3451,7 +3524,7 @@ version versionsuffix toolchain ``1.68.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``1.68.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.69.0`` ``intel/2019.01`` -``1.70.0`` ``gompi/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` +``1.70.0`` ``gompi/2019a``, ``gompic/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` ``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` ``1.72.0`` ``gompi/2020a``, ``iimpi/2020a`` ``1.72.0`` ``-no_mpi`` ``GCCcore/9.3.0`` @@ -3477,7 +3550,7 @@ version versionsuffix toolchain ``1.66.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.67.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``1.67.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.70.0`` ``gompi/2019a``, ``iimpi/2019a`` +``1.70.0`` ``gompi/2019a``, ``gompic/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` ``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` ``1.72.0`` ``gompi/2020a``, ``iimpi/2020a`` ========== ================== ==================================================================== @@ -3516,6 +3589,7 @@ version toolchain ``1.2.1.1`` ``foss/2016b``, ``intel/2017b`` ``1.2.2`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ``1.2.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` +``1.3.0`` ``GCC/9.3.0`` =========== ===================================================================================================================================== @@ -3541,6 +3615,7 @@ version toolchain ``2.3.4.3`` ``foss/2017b`` ``2.3.5.1`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` ``2.4.1`` ``GCC/9.3.0`` +``2.4.2`` ``GCC/9.3.0`` =========== ====================================================================================================== @@ -3560,52 +3635,20 @@ version toolchain =========== =============== -.. _list_software_bpp-core_792: - -*bpp-core* -++++++++++ - -Bio++ Core Library - -*homepage*: https://github.com/BioPP/bpp-core - -========= ==================== -version toolchain -========= ==================== -``2.4.1`` ``GCC/8.2.0-2.31.1`` -========= ==================== - - -.. _list_software_bpp-phyl_812: +.. _list_software_bpytop_670: -*bpp-phyl* -++++++++++ - -Bio++ Phylogenetic Library - -*homepage*: https://github.com/BioPP/bpp-phyl - -========= ==================== -version toolchain -========= ==================== -``2.4.1`` ``GCC/8.2.0-2.31.1`` -========= ==================== - - -.. _list_software_bpp-seq_696: - -*bpp-seq* -+++++++++ +*bpytop* +++++++++ -Bio++ Sequence Library +Resource monitor that shows usage and stats for processor, memory, disks, network and processes. -*homepage*: https://github.com/BioPP/bpp-seq +*homepage*: https://github.com/aristocratos/bpytop/ -========= ==================== -version toolchain -========= ==================== -``2.4.1`` ``GCC/8.2.0-2.31.1`` -========= ==================== +========== ================== +version toolchain +========== ================== +``1.0.60`` ``GCCcore/10.2.0`` +========== ================== .. _list_software_Bracken_694: @@ -3964,6 +4007,22 @@ version toolchain ============ =============================== +.. _list_software_byobu_545: + +*byobu* ++++++++ + +Byobu is an elegant enhancement of the otherwise functional, plain, practical GNU Screen. Byobu includes an enhanced profile, configuration utilities, and system status notifications for the GNU screen window manager as well as the Tmux terminal multiplexer + +*homepage*: https://byobu.org + +========= ============= +version toolchain +========= ============= +``5.133`` ``GCC/8.3.0`` +========= ============= + + .. _list_software_bzip2_487: *bzip2* @@ -3987,7 +4046,7 @@ version toolchain --- -:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_C3D_186: @@ -4022,6 +4081,22 @@ version toolchain ========== =============== +.. _list_software_CaDiCaL_577: + +*CaDiCaL* ++++++++++ + +CaDiCaL is a simplified satisfiability solver. The original goal of the development of CaDiCaL was to obtain a CDCL solver, which is easy to understand and change, while at the same time not being much slower than other state-of-the-art CDCL solvers. + +*homepage*: https://github.com/arminbiere/cadical + +========= ============= +version toolchain +========= ============= +``1.3.0`` ``GCC/9.3.0`` +========= ============= + + .. _list_software_Caffe_469: *Caffe* @@ -4348,6 +4423,7 @@ Causal ML: A Python Package for Uplift Modeling and Causal Inference with ML version versionsuffix toolchain ================== ================= ============== ``0.3.0-20180610`` ``-Python-3.7.2`` ``foss/2019a`` +``0.8.0-20200909`` ``-Python-3.8.2`` ``foss/2020a`` ================== ================= ============== @@ -4510,14 +4586,14 @@ CD-HIT is a very widely used program for clustering and comparing protein or nu *homepage*: https://github.com/weizhongli/cdhit -========= ============== ====================================================== -version versionsuffix toolchain -========= ============== ====================================================== -``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` -``4.6.6`` ``foss/2016b`` -``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` -``4.8.1`` ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` -========= ============== ====================================================== +========= ============== ===================================================================== +version versionsuffix toolchain +========= ============== ===================================================================== +``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` +``4.6.6`` ``foss/2016b`` +``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` +``4.8.1`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` +========= ============== ===================================================================== .. _list_software_cdbfasta_824: @@ -4549,6 +4625,7 @@ An efficient implementation of the Double Description Method version toolchain ========= ================= ``0.94i`` ``GCCcore/8.2.0`` +``0.94j`` ``GCCcore/8.3.0`` ========= ================= @@ -4640,6 +4717,23 @@ version toolchain ``3.1.0`` ``system`` ``4.0.0`` ``system`` ``5.0.0`` ``system`` +``5.0.1`` ``system`` +========= ========== + + +.. _list_software_CellRanger-ARC_1250: + +*CellRanger-ARC* +++++++++++++++++ + +Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage. Furthermore, since the ATAC and gene expression measurements are on the very same cell, we are able to perform analyses that link chromatin accessibility and gene expression. + +*homepage*: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc + +========= ========== +version toolchain +========= ========== +``1.0.1`` ``system`` ========= ========== @@ -4699,7 +4793,7 @@ version toolchain CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. -*homepage*: http://www.cesm.ucar.edu/models/cesm2/ +*homepage*: https://www.cesm.ucar.edu/models/cesm2/ ======= ================================================ version toolchain @@ -4771,7 +4865,7 @@ version versionsuffix toolchain The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. -*homepage*: http://www.cgal.org/ +*homepage*: https://www.cgal.org/ ========== ================== ================================ version versionsuffix toolchain @@ -4791,6 +4885,7 @@ version versionsuffix toolchain ``4.14`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``4.14.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``4.14.3`` ``-Python-3.8.2`` ``gompi/2020a``, ``iimpi/2020a`` +``5.2`` ``gompi/2020b`` ========== ================== ================================ @@ -4872,7 +4967,7 @@ CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-los version toolchain ========= ==================================== ``2.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.1.0`` ``GCCcore/8.2.0`` +``2.1.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ==================================== @@ -5015,6 +5110,22 @@ version toolchain =========== ================================================================================= +.. _list_software_CHERAB_421: + +*CHERAB* +++++++++ + +CHERAB is a python library for forward modelling diagnostics based on spectroscopic plasma emission. + +*homepage*: https://cherab.github.io/documentation/index.html + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``1.2.0`` ``-Python-3.6.6`` ``intel/2018b`` +========= ================= =============== + + .. _list_software_chewBBACA_752: *chewBBACA* @@ -5031,6 +5142,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_chi2comb_775: + +*chi2comb* +++++++++++ + +Cumulative density function of linear combinations of independent chi-square random variables and a standard Normal distribution. As of now, this is basically a repackaging of the davies function implemented in the CompQuadForm library for R. + +*homepage*: https://github.com/limix/chi2comb + +========= ================= +version toolchain +========= ================= +``0.0.3`` ``GCCcore/7.3.0`` +========= ================= + + .. _list_software_Chimera_697: *Chimera* @@ -5448,6 +5575,7 @@ version toolchain ``3.11.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``3.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``system`` ``3.13.3`` ``GCCcore/8.2.0`` +``3.15.1`` ``system`` ``3.15.3`` ``GCCcore/8.3.0`` ``3.16.4`` ``GCCcore/9.3.0`` ``3.18.4`` ``GCCcore/10.2.0`` @@ -5483,6 +5611,7 @@ A command-line toolkit and Python library for detecting copy number variants an version versionsuffix toolchain ========= ========================= =============== ``0.9.2`` ``-Python-2.7.14`` ``intel/2017b`` +``0.9.3`` ``-Python-3.6.4`` ``intel/2018a`` ``0.9.6`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` ========= ========================= =============== @@ -5516,6 +5645,7 @@ CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebr version toolchain =========== ==================== ``0.99601`` ``GCC/8.2.0-2.31.1`` +``0.99700`` ``GCC/8.3.0`` =========== ==================== @@ -5676,16 +5806,17 @@ version versionsuffix toolchain *ConnectomeWorkbench* +++++++++++++++++++++ -Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. +Connectome Workbench is an open-source visualization and discovery tool used to explore data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualization platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data. *homepage*: https://www.humanconnectome.org/software/connectome-workbench -========= ================================================== -version toolchain -========= ================================================== -``1.2.2`` ``system`` -``1.3.2`` ``GCCcore/8.2.0``, ``foss/2017b``, ``intel/2017b`` -========= ================================================== +========= =============== ================================================== +version versionsuffix toolchain +========= =============== ================================================== +``1.2.2`` ``system`` +``1.3.2`` ``GCCcore/8.2.0``, ``foss/2017b``, ``intel/2017b`` +``1.4.2`` ``-rh_linux64`` ``system`` +========= =============== ================================================== .. _list_software_Control-FREEC_1139: @@ -5838,7 +5969,7 @@ version versionsuffix toolchain ``4.1`` ``-psmp`` ``foss/2016b`` ``5.1`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a``, ``intel/2020a`` ``6.1`` ``foss/2019a``, ``intel/2018a``, ``intel/2020a`` -``7.1`` ``intel/2020a`` +``7.1`` ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` ======= ============= ================================================================== @@ -6297,6 +6428,7 @@ version toolchain ========== ========== ``11.0.2`` ``system`` ``11.1.1`` ``system`` +``11.2.1`` ``system`` ========== ========== @@ -6305,7 +6437,7 @@ version toolchain *cuDNN* +++++++ -The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. +The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. *homepage*: https://developer.nvidia.com/cudnn @@ -6327,11 +6459,13 @@ version versionsuffix toolchain ``7.1.4.18`` ``fosscuda/2018b`` ``7.4.2.24`` ``gcccuda/2019a`` ``7.4.2.24`` ``-CUDA-10.0.130`` ``system`` +``7.5.0.56`` ``-CUDA-10.0.130`` ``system`` ``7.6.2.24`` ``-CUDA-10.1.243`` ``system`` ``7.6.4.38`` ``gcccuda/2019a``, ``gcccuda/2019b`` ``7.6.4.38`` ``-CUDA-10.0.130`` ``system`` ``8.0.4.30`` ``-CUDA-11.0.2`` ``system`` ``8.0.4.30`` ``-CUDA-11.1.1`` ``system`` +``8.0.5.39`` ``-CUDA-11.1.1`` ``system`` ============ ================== =========================================================== @@ -6368,6 +6502,22 @@ version toolchain ========= ================= +.. _list_software_CuPy_385: + +*CuPy* +++++++ + +CuPy is an open-source array library accelerated with NVIDIA CUDA. + +*homepage*: https://cupy.dev + +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``8.2.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +========= ================= ================== + + .. _list_software_cURL_342: *cURL* @@ -6448,6 +6598,22 @@ version versionsuffix toolchain ========= ================== ================================================ +.. _list_software_cuTENSOR_691: + +*cuTENSOR* +++++++++++ + +The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, reduction and elementwise operations. + +*homepage*: https://developer.nvidia.com/cutensor + +=========== ================= +version toolchain +=========== ================= +``1.2.2.5`` ``gcccuda/2019b`` +=========== ================= + + .. _list_software_CVS_236: *CVS* @@ -6551,6 +6717,7 @@ Cython implementation of the toolz package, which provides high performance util ========== ================= ================= version versionsuffix toolchain ========== ================= ================= +``0.10.1`` ``-Python-3.6.6`` ``foss/2018b`` ``0.10.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================= ================= @@ -6594,7 +6761,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` .. _list_software_dadi_402: @@ -6910,6 +7077,8 @@ version toolchain ================ ==================================== ``1.0.20180622`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.0.20190902`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.0.20200331`` ``GCCcore/8.3.0`` +``1.0.20201102`` ``GCCcore/8.3.0`` ================ ==================================== @@ -6930,6 +7099,22 @@ version toolchain ========= ==================================== +.. _list_software_dd_200: + +*dd* +++++ + +dd is a package for working with binary decision diagrams that includes both a pure Python implementation and Cython bindings to C libraries (CUDD, Sylvan, BuDDy). The Python and Cython modules implement the same API, so the same user code runs with both. All the standard operations on BDDs are available, including dynamic variable reordering using sifting, garbage collection, dump/load from files, plotting, and a parser of quantified Boolean expressions. This module includes bindings for: CUDD v3.0.0, Sylvan v1.0.0 + +*homepage*: https://github.com/tulip-control/dd + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.5.6`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_deal.II_598: *deal.II* @@ -6962,6 +7147,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_decona_618: + +*decona* +++++++++ + +fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads + +*homepage*: https://github.com/Saskia-Oosterbroek/decona + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.1.2`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_deconf_623: *deconf* @@ -7094,6 +7295,7 @@ version versionsuffix toolchain ========= ================== ======================================================================== ``4.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2019a`` ``4.4.0`` ``-Python-2.7.15`` ``intel/2018b`` +``4.5.2`` ``GCCcore/10.2.0`` ========= ================== ======================================================================== @@ -7129,6 +7331,22 @@ version toolchain ======== =============== +.. _list_software_DFA_203: + +*DFA* ++++++ + +Python library for modeling DFAs, Moore Machines, and Transition Systems. + +*homepage*: https://github.com/mvcisback/dfa + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``0.3.4`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +========= ================= ================= + + .. _list_software_DFT-D3_386: *DFT-D3* @@ -7211,9 +7429,28 @@ version toolchain ``0.9.22`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` ``0.9.24`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``0.9.30`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``0.9.36`` ``GCC/9.3.0`` +``2.0.4`` ``GCC/9.3.0`` +``2.0.6`` ``GCC/7.3.0-2.30`` ========== ================================================================ +.. _list_software_dicom2nifti_1112: + +*dicom2nifti* ++++++++++++++ + +Python library for converting dicom files to nifti + +*homepage*: https://github.com/icometrix/dicom2nifti + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``2.2.12`` ``-Python-3.8.2`` ``foss/2020a`` +========== ================= ============== + + .. _list_software_DicomBrowser_1232: *DicomBrowser* @@ -7610,7 +7847,7 @@ version versionsuffix toolchain --- -:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExifTool_810` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExifTool_810` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_E-ANTIC_481: @@ -7626,6 +7863,7 @@ E-ANTIC is a C/C++ library to deal with real embedded number fields built on top version toolchain ========= ==================== ``0.1.2`` ``GCC/8.2.0-2.31.1`` +``0.1.5`` ``GCC/8.3.0`` ========= ==================== @@ -7751,6 +7989,7 @@ version toolchain ``4.2.2`` ``system`` ``4.3.0`` ``system`` ``4.3.1`` ``system`` +``4.3.2`` ``system`` ========== ========== @@ -7787,12 +8026,31 @@ version versionsuffix toolchain ``2.8.2`` ``intel/2018a`` ``2.9.2`` ``intel/2018b``, ``iomkl/2018b`` ``2.12.5`` ``gompi/2019a`` -``2.15.0`` ``iimpi/2019b`` -``2.17.0`` ``-Python-3.6.6`` ``foss/2018b`` -``2.17.0`` ``-Python-3.7.4`` ``foss/2019b`` +``2.15.0`` ``gompi/2019b``, ``iimpi/2019b`` +``2.17.0`` ``foss/2018b``, ``gompi/2019b`` +``2.18.0`` ``gompi/2020a`` +``2.20.0`` ``gompi/2020b`` ========== ================== ================================ +.. _list_software_eccodes-python_1445: + +*eccodes-python* +++++++++++++++++ + +Python 3 interface to decode and encode GRIB and BUFR files via the ECMWF ecCodes library. + +*homepage*: https://github.com/ecmwf/eccodes-python + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.0.0`` ``-Python-3.7.4`` ``foss/2019b`` +``1.0.0`` ``-Python-3.8.2`` ``foss/2020a`` +``1.1.0`` ``foss/2020b`` +========= ================= ============== + + .. _list_software_ED2_187: *ED2* @@ -7824,6 +8082,7 @@ version versionsuffix toolchain =============== ================= ====================================== ``1.3.8.post1`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ``1.3.8.post1`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``1.3.8.post2`` ``-Python-3.8.2`` ``iccifort/2020.1.217`` =============== ================= ====================================== @@ -7976,6 +8235,7 @@ version toolchain ``2018.11.001`` ``intel/2019a`` ``2019.11.001`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` ``2020.05.001`` ``intel/2020a`` +``2020.11.001`` ``foss/2020b``, ``intel/2020b`` =================== ================================================================ @@ -8031,6 +8291,7 @@ version versionsuffix toolchain ``25.1`` ``foss/2016a`` ``25.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``26.3`` ``GCCcore/8.3.0`` +``27.1`` ``GCCcore/9.3.0`` ======== ============= ======================================================= @@ -8228,17 +8489,17 @@ The Earth System Modeling Framework (ESMF) is a suite of software tools for deve *homepage*: https://www.earthsystemcog.org/projects/esmf/ -============ ================ ================================================================= -version versionsuffix toolchain -============ ================ ================================================================= -``6.3.0rp1`` ``intel/2017a`` -``6.3.0rp1`` ``-HDF5-1.8.18`` ``intel/2017a`` -``7.0.0`` ``foss/2016a`` -``7.0.2`` ``intel/2017b`` -``7.1.0r`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``8.0.0`` ``intel/2019b`` -``8.0.1`` ``foss/2020a``, ``intel/2020a`` -============ ================ ================================================================= +============ ================ ================================================================================= +version versionsuffix toolchain +============ ================ ================================================================================= +``6.3.0rp1`` ``intel/2017a`` +``6.3.0rp1`` ``-HDF5-1.8.18`` ``intel/2017a`` +``7.0.0`` ``foss/2016a`` +``7.0.2`` ``intel/2017b`` +``7.1.0r`` ``foss/2018b``, ``foss/2019a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +``8.0.0`` ``foss/2019b``, ``intel/2019b`` +``8.0.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a`` +============ ================ ================================================================================= .. _list_software_ESMValTool_934: @@ -8498,7 +8759,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -9177,6 +9438,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_fftlib_631: + +*fftlib* +++++++++ + +A library that intercepts FFTW calls and adds features on top of it. In particular, it enables FFT plan reuse when there are multiple calls for the same geometry. + +*homepage*: https://github.com/flwende/fftlib + +============ =============== +version toolchain +============ =============== +``20170628`` ``gompi/2020b`` +============ =============== + + .. _list_software_FFTW_311: *FFTW* @@ -9186,19 +9463,19 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: http://www.fftw.org -========= ============= ====================================================================================================================================================================================================================================================================================================== -version versionsuffix toolchain -========= ============= ====================================================================================================================================================================================================================================================================================================== -``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` -``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` -``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` -``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` -``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` -``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` -``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``gompic/2020b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``iomkl/2018b`` -``3.3.8`` ``-amd`` ``gompi/2020a`` -``3.3.8`` ``-serial`` ``GCC/9.3.0`` -========= ============= ====================================================================================================================================================================================================================================================================================================== +========= ============= ======================================================================================================================================================================================================================================================================================================================= +version versionsuffix toolchain +========= ============= ======================================================================================================================================================================================================================================================================================================================= +``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` +``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` +``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` +``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` +``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` +``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` +``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``iomkl/2018b`` +``3.3.8`` ``-amd`` ``gompi/2020a`` +``3.3.8`` ``-serial`` ``GCC/9.3.0`` +========= ============= ======================================================================================================================================================================================================================================================================================================================= .. _list_software_fgbio_519: @@ -9266,6 +9543,22 @@ version versionsuffix toolchain ============ ================== =============================== +.. _list_software_FIGARO_440: + +*FIGARO* +++++++++ + +FIGARO: An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters. + +*homepage*: https://github.com/Zymo-Research/figaro + +========= =============== +version toolchain +========= =============== +``1.1.2`` ``intel/2020b`` +========= =============== + + .. _list_software_FigureGen_892: *FigureGen* @@ -9426,13 +9719,13 @@ Fiona is designed to be simple and dependable. It focuses on reading and writing *homepage*: https://github.com/Toblerity/Fiona -================ ================= ================================== -version versionsuffix toolchain -================ ================= ================================== -``1.8.13`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``1.8.13.post1`` ``-Python-3.7.2`` ``foss/2019a`` -``1.8.16`` ``-Python-3.8.2`` ``foss/2020a`` -================ ================= ================================== +================ ================= =================================================== +version versionsuffix toolchain +================ ================= =================================================== +``1.8.13`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``1.8.13.post1`` ``-Python-3.7.2`` ``foss/2019a`` +``1.8.16`` ``-Python-3.8.2`` ``foss/2020a`` +================ ================= =================================================== .. _list_software_Firefox_723: @@ -9451,6 +9744,22 @@ version toolchain ========== ========== +.. _list_software_FIRESTARTER_843: + +*FIRESTARTER* ++++++++++++++ + +FIRESTARTER: A Processor Stress Test Utility. FIRESTARTER maximizes the energy consumption of 64-Bit x86 processors by generating heavy load on the execution units as well as transferring data between the cores and multiple levels of the memory hierarchy. + +*homepage*: https://github.com/tud-zih-energy/FIRESTARTER/ + +======= ==================================== +version toolchain +======= ==================================== +``2.0`` ``gcccuda/2020a``, ``gcccuda/2020b`` +======= ==================================== + + .. _list_software_FireWorks_924: *FireWorks* @@ -9467,6 +9776,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_FIt-SNE_534: + +*FIt-SNE* ++++++++++ + +t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we implement a heatmap-style visualization for scRNA-seq based on one-dimensional t-SNE for simultaneously visualizing the expression patterns of thousands of genes. + +*homepage*: https://github.com/KlugerLab/FIt-SNE + +========= =============== +version toolchain +========= =============== +``1.1.0`` ``gompi/2018b`` +========= =============== + + .. _list_software_FIX_231: *FIX* @@ -9508,11 +9833,12 @@ FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, iso *homepage*: https://github.com/BrooksLabUCSC/flair -======= ================= ============== -version versionsuffix toolchain -======= ================= ============== -``1.5`` ``-Python-3.7.4`` ``foss/2019b`` -======= ================= ============== +================== ================= ============== +version versionsuffix toolchain +================== ================= ============== +``1.5`` ``-Python-3.7.4`` ``foss/2019b`` +``1.5.1-20200630`` ``-Python-3.7.4`` ``foss/2019b`` +================== ================= ============== .. _list_software_FLANN_367: @@ -9554,16 +9880,18 @@ version toolchain *Flask* +++++++ -" Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications. +Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications. This module includes the Flask extensions: Flask-Cors *homepage*: https://www.palletsprojects.com/p/flask/ -========= ================= ================= -version versionsuffix toolchain -========= ================= ================= -``1.0.2`` ``-Python-3.6.6`` ``foss/2018b`` -``1.1.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -========= ================= ================= +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``1.0.2`` ``-Python-3.6.6`` ``foss/2018b`` +``1.1.2`` ``GCCcore/10.2.0`` +``1.1.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``1.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +========= ================= ================== .. _list_software_flatbuffers_1172: @@ -9575,11 +9903,28 @@ FlatBuffers: Memory Efficient Serialization Library *homepage*: https://github.com/google/flatbuffers/ -========== ==================================== -version toolchain -========== ==================================== -``1.12.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ==================================== +========== ======================================================== +version toolchain +========== ======================================================== +``1.12.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ======================================================== + + +.. _list_software_flatbuffers-python_1891: + +*flatbuffers-python* +++++++++++++++++++++ + +Python Flatbuffers runtime library. + +*homepage*: https://github.com/google/flatbuffers/ + +======== ================= ================== +version versionsuffix toolchain +======== ================= ================== +``1.12`` ``GCCcore/10.2.0`` +``1.12`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +======== ================= ================== .. _list_software_FLEUR_382: @@ -9677,11 +10022,11 @@ FLINT (Fast Library for Number Theory) is a C library in support of computations *homepage*: http://www.flintlib.org -========= ================================================================================ -version toolchain -========= ================================================================================ -``2.5.2`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` -========= ================================================================================ +========= =============================================================================================== +version toolchain +========= =============================================================================================== +``2.5.2`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` +========= =============================================================================================== .. _list_software_FLTK_305: @@ -9938,6 +10283,22 @@ version versionsuffix toolchain ========= =============== ========== +.. _list_software_fpocket_748: + +*fpocket* ++++++++++ + +The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. + +*homepage*: https://github.com/Discngine/fpocket + +=========== =============== +version toolchain +=========== =============== +``3.1.4.2`` ``gompi/2020a`` +=========== =============== + + .. _list_software_fqtrim_659: *fqtrim* @@ -10325,6 +10686,7 @@ FusionCatcher searches for novel/known somatic fusion genes, translocations, and version versionsuffix toolchain ======== ================== ============== ``1.20`` ``-Python-2.7.16`` ``foss/2019b`` +``1.30`` ``-Python-2.7.16`` ``foss/2019b`` ======== ================== ============== @@ -10369,7 +10731,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -10955,6 +11317,7 @@ version versionsuffix toolchain ``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` ``8.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``9.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``10.1`` ``GCCcore/10.2.0`` ========== ================== =============================== @@ -11347,13 +11710,14 @@ version versionsuffix toolchain Gensim is a Python library for topic modelling, document indexing and similarity retrieval with large corpora. -*homepage*: https://pypi.python.org/pypi/gensim +*homepage*: https://radimrehurek.com/gensim -========== ================== ============== -version versionsuffix toolchain -========== ================== ============== -``0.13.2`` ``-Python-2.7.11`` ``foss/2016a`` -========== ================== ============== +========== ================== =============================== +version versionsuffix toolchain +========== ================== =============================== +``0.13.2`` ``-Python-2.7.11`` ``foss/2016a`` +``3.8.3`` ``foss/2020b``, ``intel/2020b`` +========== ================== =============================== .. _list_software_geocube_730: @@ -11386,6 +11750,7 @@ version versionsuffix toolchain ========= ================= ================================== ``0.7.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``0.8.0`` ``-Python-3.7.2`` ``foss/2019a`` +``0.8.1`` ``-Python-3.7.4`` ``intel/2019b`` ``0.8.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ================================== @@ -11468,6 +11833,22 @@ version toolchain ========= =============== +.. _list_software_GetOrganelle_1209: + +*GetOrganelle* +++++++++++++++ + +This toolkit assemblies organelle genome from genomic skimming data. + +*homepage*: https://github.com/Kinggerm/GetOrganelle + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.7.2`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_gettext_773: *gettext* @@ -11562,6 +11943,22 @@ version toolchain ========= =============== +.. _list_software_gh_207: + +*gh* +++++ + +gh is GitHub on the command line. + +*homepage*: https://github.com/cli/cli + +========= ========== +version toolchain +========= ========== +``1.3.1`` ``system`` +========= ========== + + .. _list_software_GHC_210: *GHC* @@ -11569,13 +11966,14 @@ version toolchain The Glorious/Glasgow Haskell Compiler -*homepage*: http://haskell.org/ghc/ +*homepage*: https://haskell.org/ghc/ -========== ========== -version toolchain -========== ========== -``6.12.3`` ``system`` -========== ========== +========== ============= ========== +version versionsuffix toolchain +========== ============= ========== +``6.12.3`` ``system`` +``8.6.5`` ``-x86_64`` ``system`` +========== ============= ========== .. _list_software_Ghostscript_1178: @@ -12048,14 +12446,14 @@ OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics s *homepage*: https://github.com/g-truc/glm -=========== ================= -version toolchain -=========== ================= -``0.9.7.6`` ``intel/2016a`` -``0.9.8.3`` ``GCCcore/5.4.0`` -``0.9.9.0`` ``GCCcore/6.4.0`` -``0.9.9.8`` ``GCCcore/8.3.0`` -=========== ================= +=========== ==================================== +version toolchain +=========== ==================================== +``0.9.7.6`` ``intel/2016a`` +``0.9.8.3`` ``GCCcore/5.4.0``, ``GCCcore/7.3.0`` +``0.9.9.0`` ``GCCcore/6.4.0`` +``0.9.9.8`` ``GCCcore/8.3.0`` +=========== ==================================== .. _list_software_GlobalArrays_1219: @@ -12163,6 +12561,22 @@ version toolchain ========== ================================================= +.. _list_software_Glucose_722: + +*Glucose* ++++++++++ + +Glucose is based on a new scoring scheme (well, not so new now, it was introduced in 2009) for the clause learning mechanism of so called Modern SAT solvers (it is based on our IJCAI'09 paper). It is designed to be parallel, since v4.0. + +*homepage*: https://www.labri.fr/perso/lsimon/glucose/ + +======= ============= +version toolchain +======= ============= +``4.1`` ``GCC/9.3.0`` +======= ============= + + .. _list_software_GMAP-GSNAP_715: *GMAP-GSNAP* @@ -12361,7 +12775,7 @@ version toolchain Portable interactive, function plotting utility -*homepage*: https://gnuplot.sourceforge.net/ +*homepage*: http://gnuplot.sourceforge.net/ ========= ================================================================ version toolchain @@ -12373,6 +12787,7 @@ version toolchain ``5.2.5`` ``foss/2018b`` ``5.2.6`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b`` ``5.2.8`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``5.4.1`` ``GCCcore/10.2.0`` ========= ================================================================ @@ -12449,6 +12864,7 @@ version versionsuffix toolchain =========== ============= ========== ``2020.06`` ``-amd`` ``system`` ``2020.11`` ``system`` +``2020b`` ``system`` =========== ============= ========== @@ -12482,6 +12898,22 @@ version versionsuffix toolchain ========== ================== ================================== +.. _list_software_goblf_522: + +*goblf* ++++++++ + +GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, BLIS (BLAS support), LAPACK, FFTW and ScaLAPACK. + +*homepage*: (none) + +========= ========== +version toolchain +========= ========== +``2018b`` ``system`` +========= ========== + + .. _list_software_golf_424: *golf* @@ -12514,6 +12946,7 @@ version toolchain ``2018b`` ``system`` ``2019a`` ``system`` ``2020a`` ``system`` +``2020b`` ``system`` ========= ========== @@ -12652,7 +13085,9 @@ version versionsuffix toolchain ``19.8.1`` ``-ASE-3.18.0-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``19.8.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``20.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``20.10.0`` ``foss/2020b``, ``intel/2020b`` ``20.10.0`` ``-ASE-3.20.1-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``21.1.0`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` =========== ============================ =============================== @@ -12728,6 +13163,22 @@ version versionsuffix toolchain ========= ================== ================== +.. _list_software_GPyTorch_784: + +*GPyTorch* +++++++++++ + +GPyTorch is a Gaussian process library implemented using PyTorch. + +*homepage*: https://gpytorch.ai + +========= ============== +version toolchain +========= ============== +``1.3.0`` ``foss/2020b`` +========= ============== + + .. _list_software_Grace_482: *Grace* @@ -12864,6 +13315,22 @@ version toolchain ========== ================= +.. _list_software_GraPhlAn_749: + +*GraPhlAn* +++++++++++ + +GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. + +*homepage*: https://segatalab.github.io/tools/graphlan + +========= ================== ============== +version versionsuffix toolchain +========= ================== ============== +``1.1.3`` ``-Python-2.7.16`` ``foss/2019b`` +========= ================== ============== + + .. _list_software_GraphMap2_834: *GraphMap2* @@ -12889,16 +13356,18 @@ Graphviz is open source graph visualization software. Graph visualization is a *homepage*: https://www.graphviz.org/ -========== ================== =============================== -version versionsuffix toolchain -========== ================== =============================== -``2.38.0`` ``foss/2016b``, ``intel/2016b`` -``2.40.1`` ``foss/2018b``, ``intel/2018a`` -``2.40.1`` ``-Python-2.7.15`` ``foss/2018b`` -``2.42.2`` ``foss/2019b`` -``2.42.2`` ``-Java-11`` ``GCCcore/8.3.0`` -``2.42.2`` ``-Python-3.7.4`` ``foss/2019b`` -========== ================== =============================== +========== ========================= =============================== +version versionsuffix toolchain +========== ========================= =============================== +``2.38.0`` ``foss/2016b``, ``intel/2016b`` +``2.40.1`` ``foss/2018b``, ``intel/2018a`` +``2.40.1`` ``-Python-2.7.15`` ``foss/2018b`` +``2.42.2`` ``foss/2019b`` +``2.42.2`` ``-Java-11`` ``GCCcore/8.3.0`` +``2.42.2`` ``-Python-3.7.4`` ``foss/2019b`` +``2.44.1`` ``-Java-11`` ``GCCcore/9.3.0`` +``2.44.1`` ``-Java-11-Python-3.8.2`` ``GCCcore/9.3.0`` +========== ========================= =============================== .. _list_software_graphviz_875: @@ -13124,6 +13593,7 @@ version versionsuffix toolchain ``2020.1`` ``-Python-3.8.2`` ``foss/2020a`` ``2020.3`` ``fosscuda/2019b`` ``2020.4`` ``-Python-3.8.2`` ``foss/2020a`` +``2020.5`` ``-Python-3.8.2`` ``fosscuda/2020a`` ========== ================= ============================================================================================================ @@ -13175,6 +13645,22 @@ version versionsuffix toolchain ========= ============= ========== +.. _list_software_GSEA_288: + +*GSEA* +++++++ + +Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). + +*homepage*: https://www.gsea-msigdb.org/gsea/index.jsp + +========= ========== +version toolchain +========= ========== +``4.0.3`` ``system`` +========= ========== + + .. _list_software_gsettings-desktop-schemas_2576: *gsettings-desktop-schemas* @@ -13372,12 +13858,12 @@ GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free *homepage*: http://gts.sourceforge.net/ -============ ==================================================================================================================================================== -version toolchain -============ ==================================================================================================================================================== -``0.7.6`` ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` -``20121130`` ``foss/2017b`` -============ ==================================================================================================================================================== +============ ======================================================================================================================================================================= +version toolchain +============ ======================================================================================================================================================================= +``0.7.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` +``20121130`` ``foss/2017b`` +============ ======================================================================================================================================================================= .. _list_software_gubbins_746: @@ -13469,6 +13955,7 @@ version versionsuffix toolchain ``9.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``9.0.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``9.0.1`` ``system`` +``9.1.0`` ``system`` ========= ================= =============================== @@ -13686,12 +14173,12 @@ Harminv is a free program (and accompanying library) to solve the problem of har *homepage*: https://github.com/stevengj/harminv -========= =============== -version toolchain -========= =============== -``1.4`` ``foss/2016a`` -``1.4.1`` ``intel/2020a`` -========= =============== +========= ================================================================ +version toolchain +========= ================================================================ +``1.4`` ``foss/2016a`` +``1.4.1`` ``foss/2017b``, ``foss/2018a``, ``intel/2018a``, ``intel/2020a`` +========= ================================================================ .. _list_software_harmony_766: @@ -13820,7 +14307,7 @@ version versionsuffix toolchain ``1.8.18`` ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a`` ``1.8.18`` ``-serial`` ``intel/2017a`` ``1.8.19`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``1.8.20`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``1.8.20`` ``foss/2018a``, ``gmpolf/2017.10``, ``intel/2017b``, ``intel/2018a`` ``1.10.0-patch1`` ``foss/2016b``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a`` ``1.10.1`` ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2017b``, ``iomkl/2018a`` ``1.10.2`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` @@ -13966,6 +14453,7 @@ version toolchain ============== =============== ``3.0-beta.3`` ``intel/2018a`` ``3.2.0`` ``foss/2019b`` +``3.3.0`` ``foss/2020a`` ============== =============== @@ -14101,6 +14589,7 @@ version toolchain ``3.1b2`` ``GCC/6.4.0-2.28``, ``foss/2016a``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a``, ``intel/2018a`` ``3.2.1`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iimpi/2019b``, ``intel/2018b`` ``3.3.1`` ``gompi/2020a``, ``iimpi/2020a`` +``3.3.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b`` ========= ============================================================================================================================================ @@ -14133,6 +14622,7 @@ hmmlearn is a set of algorithms for unsupervised learning and inference of Hidde version versionsuffix toolchain ========= ================== =============== ``0.2.0`` ``-Python-2.7.14`` ``intel/2017b`` +``0.2.0`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================== =============== @@ -14172,6 +14662,9 @@ version versionsuffix toolchain ``0.19.1`` ``-TensorFlow-2.1.0-Python-3.7.4`` ``fosscuda/2019b`` ``0.19.5`` ``-TensorFlow-2.2.0-Python-3.7.4`` ``fosscuda/2019b`` ``0.20.3`` ``-TensorFlow-2.3.1-Python-3.7.4`` ``fosscuda/2019b`` +``0.21.1`` ``-PyTorch-1.7.1-Python-3.7.4`` ``fosscuda/2019b`` +``0.21.1`` ``-TensorFlow-2.4.1`` ``fosscuda/2020b`` +``0.21.1`` ``-TensorFlow-2.4.1-Python-3.7.4`` ``fosscuda/2019b`` ========== =================================== ================== @@ -14249,13 +14742,13 @@ HPL is a software package that solves a (random) dense linear system in double p *homepage*: http://www.netlib.org/benchmark/hpl/ -======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= -version toolchain -======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= -``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` -``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gomkl/2019a``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020a``, ``intel/2020b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01`` -======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +version toolchain +======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` +``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020a``, ``intel/2020b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01`` +======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_htop_443: @@ -14324,6 +14817,7 @@ version versionsuffix toolchain ``1.8`` ``GCC/6.4.0-2.28``, ``foss/2018a``, ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` +``1.11`` ``GCC/10.2.0`` ``20160107`` ``-PacBio`` ``intel/2017a`` ============ ============= =========================================================================================================================================================== @@ -14526,7 +15020,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -14891,6 +15385,7 @@ version toolchain ``0.7.1`` ``foss/2018b``, ``intel/2016b``, ``intel/2017b`` ``0.8.0`` ``foss/2019b`` ``0.8.2`` ``foss/2020a`` +``0.8.5`` ``foss/2020b`` ========= ================================================ @@ -14948,6 +15443,38 @@ version versionsuffix toolchain ========== ================== ========== +.. _list_software_iibff_512: + +*iibff* ++++++++ + +GCC and GFortran based compiler toolchain with OpenMPI, BLIS, libFLAME, ScaLAPACK and FFTW. + +*homepage*: (none) + +========= ========== +version toolchain +========= ========== +``2020b`` ``system`` +========= ========== + + +.. _list_software_iimkl_534: + +*iimkl* ++++++++ + +Intel C/C++ and Fortran compilers, alongside Intel Math Kernel Library (MKL). + +*homepage*: https://software.intel.com/en-us/intel-cluster-toolkit-compiler/ + +========= ========== +version toolchain +========= ========== +``2018a`` ``system`` +========= ========== + + .. _list_software_iimpi_536: *iimpi* @@ -15185,6 +15712,7 @@ version versionsuffix toolchain ``0.2.1`` ``-Python-3.5.2`` ``intel/2016b`` ``0.3.3`` ``-Python-3.6.4`` ``foss/2018a`` ``0.4.3`` ``-Python-3.6.6`` ``foss/2018b`` +``0.7.0`` ``foss/2020b`` ========= ================== =============== @@ -15214,33 +15742,34 @@ Intel Math Kernel Library is a library of highly optimized, extensively threade *homepage*: https://software.intel.com/mkl -============== ====================================================================================================================================================================================================================================================================== -version toolchain -============== ====================================================================================================================================================================================================================================================================== -``11.2.3.187`` ``gimpi/2.11.5`` -``11.3.0.109`` ``iimpi/2016.00-GCC-4.9.3-2.25`` -``11.3.1.150`` ``iimpi/2016.01-GCC-4.9.3-2.25``, ``iimpi/8.1.5-GCC-4.9.3-2.25`` -``11.3.2.181`` ``iimpi/2016.02-GCC-4.9.3-2.25``, ``iimpi/2016.02-GCC-5.3.0-2.26``, ``pompi/2016.03`` -``11.3.3.210`` ``iimpi/2016.03-GCC-4.9.3-2.25``, ``iimpi/2016.03-GCC-5.3.0-2.26``, ``iimpi/2016.03-GCC-5.4.0-2.26``, ``iimpi/2016b``, ``iimpic/2016.10``, ``iompi/2016.07``, ``iompi/2016.09-GCC-4.9.3-2.25``, ``iompi/2016.09-GCC-5.4.0-2.26``, ``pompi/2016.04``, ``pompi/2016.09`` -``2017.0.098`` ``iimpi/2017.00-GCC-5.4.0-2.26`` -``2017.1.132`` ``gimpi/2017a``, ``iimpi/2017.01-GCC-5.4.0-2.26``, ``iimpi/2017a``, ``iompi/2017.01``, ``iompi/2017a`` -``2017.2.174`` ``iimpi/2017.02-GCC-6.3.0-2.27`` -``2017.3.196`` ``gompi/2017b``, ``iimpi/2017b``, ``iimpic/2017b``, ``iompi/2017b`` -``2017.4.239`` ``iimpi/2017.09`` -``2018.0.128`` ``iimpi/2018.00`` -``2018.1.163`` ``iimpi/2018.01``, ``iimpi/2018a``, ``iompi/2018a`` -``2018.2.199`` ``iimpi/2018.02``, ``iompi/2018.02`` -``2018.3.222`` ``gimpi/2018b``, ``gompi/2018b``, ``iimpi/2018b``, ``iompi/2018b`` -``2018.4.274`` ``iimpi/2018.04`` -``2019.0.117`` ``iimpi/2019.00`` -``2019.1.144`` ``gompi/2019a``, ``iimpi/2019.01``, ``iimpi/2019a``, ``iimpic/2019a``, ``iompi/2019.01`` -``2019.2.187`` ``iimpi/2019.02`` -``2019.3.199`` ``iimpi/2019.03`` -``2019.5.281`` ``gompi/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` -``2020.0.166`` ``iimpi/2020.00`` -``2020.1.217`` ``gompi/2020a``, ``iimpi/2020.06-impi-18.5``, ``iimpi/2020a``, ``iimpic/2020a``, ``iompi/2020a`` -``2020.4.304`` ``iimpi/2020b``, ``iimpic/2020b`` -============== ====================================================================================================================================================================================================================================================================== +============== ============= ====================================================================================================================================================================================================================================================================== +version versionsuffix toolchain +============== ============= ====================================================================================================================================================================================================================================================================== +``11.2.3.187`` ``gimpi/2.11.5`` +``11.3.0.109`` ``iimpi/2016.00-GCC-4.9.3-2.25`` +``11.3.1.150`` ``iimpi/2016.01-GCC-4.9.3-2.25``, ``iimpi/8.1.5-GCC-4.9.3-2.25`` +``11.3.2.181`` ``iimpi/2016.02-GCC-4.9.3-2.25``, ``iimpi/2016.02-GCC-5.3.0-2.26``, ``pompi/2016.03`` +``11.3.3.210`` ``iimpi/2016.03-GCC-4.9.3-2.25``, ``iimpi/2016.03-GCC-5.3.0-2.26``, ``iimpi/2016.03-GCC-5.4.0-2.26``, ``iimpi/2016b``, ``iimpic/2016.10``, ``iompi/2016.07``, ``iompi/2016.09-GCC-4.9.3-2.25``, ``iompi/2016.09-GCC-5.4.0-2.26``, ``pompi/2016.04``, ``pompi/2016.09`` +``2017.0.098`` ``iimpi/2017.00-GCC-5.4.0-2.26`` +``2017.1.132`` ``gimpi/2017a``, ``iimpi/2017.01-GCC-5.4.0-2.26``, ``iimpi/2017a``, ``iompi/2017.01``, ``iompi/2017a`` +``2017.2.174`` ``iimpi/2017.02-GCC-6.3.0-2.27`` +``2017.3.196`` ``gompi/2017b``, ``iimpi/2017b``, ``iimpic/2017b``, ``iompi/2017b`` +``2017.4.239`` ``iimpi/2017.09`` +``2018.0.128`` ``iimpi/2018.00`` +``2018.1.163`` ``iimpi/2018.01``, ``iimpi/2018a``, ``iompi/2018a`` +``2018.1.163`` ``-serial`` ``iccifort/2018.1.163-GCC-6.4.0-2.28`` +``2018.2.199`` ``iimpi/2018.02``, ``iompi/2018.02`` +``2018.3.222`` ``gimpi/2018b``, ``gompi/2018b``, ``iimpi/2018b``, ``iompi/2018b`` +``2018.4.274`` ``iimpi/2018.04`` +``2019.0.117`` ``iimpi/2019.00`` +``2019.1.144`` ``gompi/2019a``, ``iimpi/2019.01``, ``iimpi/2019a``, ``iimpic/2019a``, ``iompi/2019.01`` +``2019.2.187`` ``iimpi/2019.02`` +``2019.3.199`` ``iimpi/2019.03`` +``2019.5.281`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b``, ``iompi/2019b`` +``2020.0.166`` ``iimpi/2020.00`` +``2020.1.217`` ``gompi/2020a``, ``iimpi/2020.06-impi-18.5``, ``iimpi/2020a``, ``iimpic/2020a``, ``iompi/2020a`` +``2020.4.304`` ``gompi/2020b``, ``iimpi/2020b``, ``iimpic/2020b``, ``iompi/2020b`` +============== ============= ====================================================================================================================================================================================================================================================================== .. _list_software_Imlib2_543: @@ -15335,6 +15864,7 @@ version versionsuffix toolchain ``2019.6.166`` ``iccifort/2020.0.166-GCC-9.2.0`` ``2019.7.217`` ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` ``2019.9.304`` ``iccifort/2020.4.304``, ``iccifortcuda/2020b`` +``2021.1.1`` ``intel-compilers/2021.1.2`` ``system`` ``iccifort/system-GCC-system-2.29`` ============== ============= ================================================================================================================================================================================================================================ @@ -15388,6 +15918,7 @@ version versionsuffix toolchain ========= ========================= ============== ``1.0.4`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` ``1.2.1`` ``-Python-3.7.4`` ``foss/2019b`` +``1.3.3`` ``-Python-3.8.2`` ``foss/2020a`` ========= ========================= ============== @@ -15559,6 +16090,22 @@ version versionsuffix toolchain ===================== ============= ========== +.. _list_software_intel-compilers_1559: + +*intel-compilers* ++++++++++++++++++ + +Intel C, C++ & Fortran compilers (classic and oneAPI) + +*homepage*: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html + +============ ========== +version toolchain +============ ========== +``2021.1.2`` ``system`` +============ ========== + + .. _list_software_IntelClusterChecker_1939: *IntelClusterChecker* @@ -15724,7 +16271,9 @@ version toolchain ``2018a`` ``system`` ``2018b`` ``system`` ``2019.01`` ``system`` +``2019b`` ``system`` ``2020a`` ``system`` +``2020b`` ``system`` ========================== ========== @@ -15750,7 +16299,9 @@ version toolchain ``2018a`` ``system`` ``2018b`` ``system`` ``2019.01`` ``system`` +``2019b`` ``system`` ``2020a`` ``system`` +``2020b`` ``system`` ========================== ========== @@ -15938,6 +16489,7 @@ version versionsuffix toolchain ``1.5.5`` ``-omp-mpi`` ``foss/2016a`` ``1.6.6`` ``intel/2018a`` ``1.6.12`` ``foss/2018b``, ``foss/2020a``, ``intel/2019b`` +``2.1.2`` ``foss/2020a`` ========== ============= =============================================== @@ -15991,6 +16543,7 @@ version toolchain ``0.15`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a`` ``0.16`` ``GCC/4.9.3-2.25`` ``0.17`` ``foss/2016a`` +``0.23`` ``GCCcore/10.2.0`` ======== ====================================================== @@ -16044,20 +16597,22 @@ Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite *homepage*: https://itk.org -========== ================== ============== -version versionsuffix toolchain -========== ================== ============== -``4.12.2`` ``-Python-2.7.12`` ``foss/2016b`` -``4.13.0`` ``-Python-2.7.14`` ``foss/2018a`` -``4.13.0`` ``-Python-3.6.4`` ``foss/2018a`` -``4.13.1`` ``-Python-2.7.14`` ``foss/2018a`` -``4.13.1`` ``-Python-2.7.15`` ``foss/2018b`` -``4.13.1`` ``-Python-3.6.4`` ``foss/2018a`` -``4.13.1`` ``-Python-3.6.6`` ``foss/2018b`` -``5.0.1`` ``-Python-3.7.2`` ``foss/2019a`` -``5.0.1`` ``-Python-3.7.4`` ``foss/2019b`` -``5.0b01`` ``-Python-3.6.6`` ``foss/2018b`` -========== ================== ============== +========== ================== ================================== +version versionsuffix toolchain +========== ================== ================================== +``4.12.2`` ``-Python-2.7.12`` ``foss/2016b`` +``4.13.0`` ``-Python-2.7.14`` ``foss/2018a`` +``4.13.0`` ``-Python-3.6.4`` ``foss/2018a`` +``4.13.1`` ``-Python-2.7.14`` ``foss/2018a`` +``4.13.1`` ``-Python-2.7.15`` ``foss/2018b`` +``4.13.1`` ``-Python-3.6.4`` ``foss/2018a`` +``4.13.1`` ``-Python-3.6.6`` ``foss/2018b`` +``5.0.1`` ``-Python-3.7.2`` ``foss/2019a`` +``5.0.1`` ``-Python-3.7.4`` ``foss/2019b`` +``5.0b01`` ``-Python-3.6.6`` ``foss/2018b`` +``5.1.2`` ``foss/2020a``, ``fosscuda/2020a`` +``5.1.2`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +========== ================== ================================== .. _list_software_itpp_445: @@ -16094,6 +16649,22 @@ version versionsuffix toolchain ========= ================== ================= +.. _list_software_ITSx_360: + +*ITSx* +++++++ + +ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing. + +*homepage*: https://microbiology.se/software/itsx/ + +========= ================= +version toolchain +========= ================= +``1.1.2`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_iVar_402: *iVar* @@ -16169,6 +16740,7 @@ version toolchain ``2.0.12`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` ``2.0.14`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.0.16`` ``GCCcore/9.3.0`` +``2.0.24`` ``GCCcore/10.2.0`` =========== ========================================================================================================================================================== @@ -16223,6 +16795,8 @@ version versionsuffix toolchain ``1.8.0_221`` ``system`` ``1.8.0_231`` ``system`` ``1.8.0_241`` ``system`` +``1.8.0_271`` ``system`` +``1.8.0_281`` ``system`` ``1.8_191`` ``-b26-OpenJDK`` ``system`` ``1.8_265`` ``-b01-OpenJDK-aarch64`` ``system`` ``1.9.0.4`` ``system`` @@ -16296,18 +16870,18 @@ jemalloc is a general purpose malloc(3) implementation that emphasizes fragmenta *homepage*: http://jemalloc.net -========= ==================================== -version toolchain -========= ==================================== -``4.1.0`` ``intel/2016a`` -``4.2.0`` ``foss/2016a``, ``intel/2016a`` -``4.2.1`` ``intel/2016b`` -``4.5.0`` ``intel/2017a`` -``5.0.1`` ``GCCcore/6.4.0`` -``5.1.0`` ``GCCcore/7.3.0`` -``5.2.0`` ``GCCcore/8.2.0`` -``5.2.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ==================================== +========= ======================================================== +version toolchain +========= ======================================================== +``4.1.0`` ``intel/2016a`` +``4.2.0`` ``foss/2016a``, ``intel/2016a`` +``4.2.1`` ``intel/2016b`` +``4.5.0`` ``intel/2017a`` +``5.0.1`` ``GCCcore/6.4.0`` +``5.1.0`` ``GCCcore/7.3.0`` +``5.2.0`` ``GCCcore/8.2.0`` +``5.2.1`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================== .. _list_software_jhbuild_738: @@ -16372,6 +16946,7 @@ Joyplots in Python with matplotlib & pandas version versionsuffix toolchain ========= ================= =============== ``0.2.2`` ``-Python-3.7.4`` ``intel/2019b`` +``0.2.4`` ``intel/2020b`` ========= ================= =============== @@ -16425,6 +17000,7 @@ version toolchain ``2.0.4`` ``system`` ``2.0.5`` ``system`` ``2.4.0`` ``system`` +``2.4.1`` ``system`` ========= ========== @@ -16437,11 +17013,11 @@ A C library that implements a dynamic array. *homepage*: http://judy.sourceforge.net/ -========= ==================================== -version toolchain -========= ==================================== -``1.0.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= ==================================== +========= ======================================================== +version toolchain +========= ======================================================== +``1.0.5`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ======================================================== .. _list_software_Julia_501: @@ -16556,7 +17132,7 @@ version toolchain --- -:ref:`list_software_Kaiju_500` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_kedro_533` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_king_425` - :ref:`list_software_kma_313` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` +:ref:`list_software_Kaiju_500` - :ref:`list_software_Kaleido_697` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_kedro_533` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_king_425` - :ref:`list_software_kma_313` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` .. _list_software_Kaiju_500: @@ -16577,6 +17153,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_Kaleido_697: + +*Kaleido* ++++++++++ + +Fast static image export for web-based visualization libraries with zero dependencies + +*homepage*: https://github.com/plotly/Kaleido + +========= ================== +version toolchain +========= ================== +``0.1.0`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_kallisto_867: *kallisto* @@ -16700,6 +17292,7 @@ version versionsuffix toolchain ``2.2.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``2.2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``2.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.3.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ================================== @@ -16734,6 +17327,7 @@ version toolchain ========= ================================================================ ``2.1.2`` ``foss/2019a``, ``intel/2019a`` ``2.1.3`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` +``2.2.1`` ``GCCcore/10.2.0`` ========= ================================================================ @@ -16980,7 +17574,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_limix-bgen_1004` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -17051,6 +17645,22 @@ version toolchain ========= ======================= +.. _list_software_LAPACK_428: + +*LAPACK* +++++++++ + +LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. + +*homepage*: https://www.netlib.org/lapack/ + +========= ================== +version toolchain +========= ================== +``3.8.0`` ``GCC/7.3.0-2.30`` +========= ================== + + .. _list_software_LAST_308: *LAST* @@ -17248,6 +17858,7 @@ Asynchronous input/output library that uses the kernels native interface. version toolchain =========== ==================================== ``0.3.111`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.3.112`` ``GCCcore/10.2.0`` =========== ==================================== @@ -17334,6 +17945,7 @@ version toolchain ``1.7`` ``GCCcore/7.3.0`` ``1.11`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.14`` ``GCCcore/10.2.0`` ======== ========================================================================================================= @@ -17413,12 +18025,12 @@ Libcroco is a standalone css2 parsing and manipulation library. *homepage*: https://github.com/GNOME/libcroco -========== =============== -version toolchain -========== =============== -``0.6.11`` ``intel/2016a`` -``0.6.13`` ``foss/2019a`` -========== =============== +========== ============================== +version toolchain +========== ============================== +``0.6.11`` ``intel/2016a`` +``0.6.13`` ``GCC/10.2.0``, ``foss/2019a`` +========== ============================== .. _list_software_libctl_634: @@ -17428,13 +18040,14 @@ version toolchain libctl is a free Guile-based library implementing flexible control files for scientific simulations. -*homepage*: http://ab-initio.mit.edu/libctl +*homepage*: https://libctl.readthedocs.io/en/latest/ -========= ============== -version toolchain -========= ============== -``3.2.2`` ``foss/2016a`` -========= ============== +========= ================= +version toolchain +========= ================= +``3.2.2`` ``foss/2016a`` +``4.1.3`` ``GCCcore/6.4.0`` +========= ================= .. _list_software_libdap_620: @@ -17455,6 +18068,7 @@ version versionsuffix toolchain ``3.20.3`` ``GCCcore/7.3.0`` ``3.20.4`` ``GCCcore/8.2.0`` ``3.20.6`` ``GCCcore/8.3.0`` +``3.20.7`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========== ================== ================================================== @@ -17543,13 +18157,13 @@ version toolchain libelf is a free ELF object file access library -*homepage*: http://www.mr511.de/software/english.html +*homepage*: https://directory.fsf.org/wiki/Libelf -========== ===================================================================================== -version toolchain -========== ===================================================================================== -``0.8.13`` ``GCC/4.8.3``, ``GCC/4.9.2``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/8.2.0`` -========== ===================================================================================== +========== ======================================================================================================== +version toolchain +========== ======================================================================================================== +``0.8.13`` ``GCC/4.8.3``, ``GCC/4.9.2``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +========== ======================================================================================================== .. _list_software_libepoxy_876: @@ -17650,13 +18264,13 @@ libFLAME is a portable library for dense matrix computations, providing much of *homepage*: https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame -========= ============= ================== -version versionsuffix toolchain -========= ============= ================== -``1.0`` ``-amd`` ``GCC/7.3.0-2.30`` -``2.2`` ``-amd`` ``GCC/9.3.0`` -``5.2.0`` ``GCC/9.3.0`` -========= ============= ================== +========= ============= ===================================== +version versionsuffix toolchain +========= ============= ===================================== +``1.0`` ``-amd`` ``GCC/7.3.0-2.30`` +``2.2`` ``-amd`` ``GCCcore/9.3.0`` +``5.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========= ============= ===================================== .. _list_software_libfontenc_1060: @@ -17709,10 +18323,26 @@ version toolchain ``2.2.3`` ``foss/2016b``, ``intel/2016b`` ``2.2.4`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` ``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b``, ``intel/2018a`` -``2.3.0`` ``GCCcore/9.3.0`` +``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================ +.. _list_software_libGDSII_679: + +*libGDSII* +++++++++++ + +libGDSII is a C++ library for working with GDSII binary data files, intended primarily for use with the computational electromagnetism codes scuff-em and meep but sufficiently general-purpose to allow other uses as well. + +*homepage*: https://github.com/HomerReid/libGDSII + +======== ================= +version toolchain +======== ================= +``0.21`` ``GCCcore/6.4.0`` +======== ================= + + .. _list_software_libgeotiff_1051: *libgeotiff* @@ -17739,11 +18369,12 @@ libgit2 is a portable, pure C implementation of the Git core methods provided as *homepage*: https://libgit2.org/ -========= ================= -version toolchain -========= ================= -``1.0.0`` ``GCCcore/8.3.0`` -========= ================= +========= ===================================== +version toolchain +========= ===================================== +``1.0.0`` ``GCCcore/8.3.0`` +``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========= ===================================== .. _list_software_libglade_820: @@ -17987,7 +18618,7 @@ version versionsuffix toolchain ``2.1.0`` ``intel/2016b`` ``2.4.2`` ``intel/2018a`` ``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` -``2.6.0`` ``-lmax-6-cp2k`` ``gompi/2020a``, ``iimpi/2020a`` +``2.6.0`` ``-lmax-6-cp2k`` ``GCC/10.2.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a`` ========= ================ =================================================================================================================================================================================== @@ -18146,6 +18777,22 @@ version versionsuffix toolchain ========== ================= ============== +.. _list_software_libpci_627: + +*libpci* +++++++++ + +Library for portable access to PCI bus configuration registers from PCI Utils. + +*homepage*: https://github.com/pciutils/pciutils + +========= ===================================== +version toolchain +========= ===================================== +``3.7.0`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0`` +========= ===================================== + + .. _list_software_libpciaccess_1253: *libpciaccess* @@ -18620,6 +19267,7 @@ version toolchain ========= ==================================== ``1.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.2.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.3.1`` ``GCCcore/10.2.0`` ========= ==================================== @@ -18736,12 +19384,12 @@ libvdwxc is a general library for evaluating energy and potential for exchange-c *homepage*: https://libvdwxc.org -========= ============================== -version toolchain -========= ============================== -``0.3.2`` ``foss/2018b`` -``0.4.0`` ``foss/2019a``, ``foss/2019b`` -========= ============================== +========= ============================================== +version toolchain +========= ============================================== +``0.3.2`` ``foss/2018b`` +``0.4.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020b`` +========= ============================================== .. _list_software_libwebp_741: @@ -18753,13 +19401,13 @@ WebP is a modern image format that provides superior lossless and lossy compress *homepage*: https://developers.google.com/speed/webp/ -========= ==================================== -version toolchain -========= ==================================== -``1.0.0`` ``foss/2018b`` -``1.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.1.0`` ``GCCcore/8.3.0`` -========= ==================================== +========= ===================================== +version toolchain +========= ===================================== +``1.0.0`` ``foss/2018b`` +``1.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +========= ===================================== .. _list_software_libX11_497: @@ -19170,17 +19818,17 @@ LIBXSMM is a library for small dense and small sparse matrix-matrix multiplicati *homepage*: https://github.com/hfp/libxsmm -========== =============================================================================== -version toolchain -========== =============================================================================== -``1.4`` ``intel/2016a`` -``1.4.4`` ``foss/2016b``, ``intel/2016b`` -``1.6.4`` ``foss/2016b``, ``intel/2016b`` -``1.8.2`` ``intel/2017b`` -``1.8.3`` ``foss/2018a``, ``intel/2018a`` -``1.10`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``1.16.1`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` -========== =============================================================================== +========== =============================================================================================== +version toolchain +========== =============================================================================================== +``1.4`` ``intel/2016a`` +``1.4.4`` ``foss/2016b``, ``intel/2016b`` +``1.6.4`` ``foss/2016b``, ``intel/2016b`` +``1.8.2`` ``intel/2017b`` +``1.8.3`` ``foss/2018a``, ``intel/2018a`` +``1.10`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` +``1.16.1`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` +========== =============================================================================================== .. _list_software_libXt_515: @@ -19260,11 +19908,12 @@ libzip is a C library for reading, creating, and modifying zip archives. *homepage*: https://libzip.org/ -========= ================= -version toolchain -========= ================= -``1.5.2`` ``GCCcore/8.2.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``1.5.2`` ``GCCcore/8.2.0`` +``1.7.3`` ``GCCcore/10.2.0`` +========= ================== .. _list_software_lifelines_955: @@ -19300,6 +19949,22 @@ version toolchain ========= ============== +.. _list_software_liknorm_764: + +*liknorm* ++++++++++ + +Moments of the product of an exponential-family likelihood with a Normal distribution. + +*homepage*: https://github.com/limix/liknorm + +========= ================= +version toolchain +========= ================= +``1.5.2`` ``GCCcore/7.3.0`` +========= ================= + + .. _list_software_likwid_644: *likwid* @@ -19317,23 +19982,24 @@ version toolchain ``4.2.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2017a``, ``intel/2017a`` ``4.3.2`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``5.0.1`` ``GCCcore/8.3.0`` +``5.1.0`` ``GCCcore/9.3.0`` ========= ===================================================================== -.. _list_software_limix-bgen_1004: +.. _list_software_limix_547: -*limix-bgen* -++++++++++++ +*limix* ++++++++ -A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3. +Limix is a flexible and efficient linear mixed model library with interfaces to Python. Genomic analyses require flexible models that can be adapted to the needs of the user. Limix is smart about how particular models are fitted to save computational cost. -*homepage*: https://github.com/limix/bgen +*homepage*: https://github.com/limix/limix -========= ================= -version toolchain -========= ================= -``3.0.3`` ``GCCcore/9.3.0`` -========= ================= +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``2.0.4`` ``-Python-3.6.6`` ``foss/2018b`` +========= ================= ============== .. _list_software_LinBox_588: @@ -19352,6 +20018,22 @@ version toolchain ========= ============== +.. _list_software_Lingeling_921: + +*Lingeling* ++++++++++++ + +One of the design principles of the state-of-the-art SAT solver Lingeling is to use as compact data structures as possible. These reduce memory usage, increase cache efficiency and thus improve runtime, particularly, when using multiple solver instances on multi-core machines, as in our parallel portfolio solver Plingeling and our cube and conquer solver Treengeling. + +*homepage*: http://fmv.jku.at/lingeling/ + +======= ============= +version toolchain +======= ============= +``bcp`` ``GCC/9.3.0`` +======= ============= + + .. _list_software_LittleCMS_849: *LittleCMS* @@ -19454,6 +20136,7 @@ version versionsuffix toolchain ``0.9.9`` ``-Python-3.6.4`` ``intel/2018a`` ``0.9.14`` ``-Python-2.7.15`` ``intel/2018b`` ``1.0.0`` ``-Python-3.7.4`` ``intel/2019b`` +``1.0.1`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================== =============== @@ -19536,6 +20219,22 @@ version toolchain ======== ============== +.. _list_software_logaddexp_952: + +*logaddexp* ++++++++++++ + +C library that implements the logarithm of the sum of exponentiations. Inspired by NumPy's logaddexp function. + +*homepage*: https://github.com/horta/logaddexp + +========= ================= +version toolchain +========= ================= +``1.0.3`` ``GCCcore/7.3.0`` +========= ================= + + .. _list_software_LOHHLA_440: *LOHHLA* @@ -19594,11 +20293,12 @@ Mixed Integer Linear Programming (MILP) solver *homepage*: https://sourceforge.net/projects/lpsolve/ -=========== ============================================================================================================================================================================================== -version toolchain -=========== ============================================================================================================================================================================================== -``5.5.2.5`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a``, ``intel/2018b`` -=========== ============================================================================================================================================================================================== +============ ============================================================================================================================================================================================== +version toolchain +============ ============================================================================================================================================================================================== +``5.5.2.5`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a``, ``intel/2018b`` +``5.5.2.11`` ``GCC/10.2.0`` +============ ============================================================================================================================================================================================== .. _list_software_lrslib_648: @@ -19638,6 +20338,22 @@ version versionsuffix toolchain ========== ============= ========== +.. _list_software_LSD2_277: + +*LSD2* +++++++ + +Least-squares methods to estimate rates and dates from phylogenies + +*homepage*: https://github.com/tothuhien/lsd2 + +========= ================= +version toolchain +========= ================= +``1.9.7`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_LSMS_319: *LSMS* @@ -19677,7 +20393,7 @@ version versionsuffix toolchain Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. -*homepage*: http://www.lua.org/ +*homepage*: https://www.lua.org/ =========== =================================================================== version toolchain @@ -19688,6 +20404,7 @@ version toolchain ``5.2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``5.3.4`` ``GCCcore/7.2.0``, ``system`` ``5.3.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +``5.4.2`` ``GCCcore/10.2.0`` =========== =================================================================== @@ -19856,7 +20573,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -19992,16 +20709,16 @@ The MAGMA project aims to develop a dense linear algebra library similar to LAP *homepage*: https://icl.cs.utk.edu/magma/ -========= ================ ======================================= -version versionsuffix toolchain -========= ================ ======================================= -``2.3.0`` ``fosscuda/2017b``, ``intelcuda/2017b`` -``2.3.0`` ``-CUDA-9.1.85`` ``foss/2018a`` -``2.4.0`` ``fosscuda/2018b`` -``2.5.0`` ``fosscuda/2018b`` -``2.5.1`` ``fosscuda/2019a``, ``fosscuda/2019b`` -``2.5.4`` ``fosscuda/2019a``, ``fosscuda/2019b`` -========= ================ ======================================= +========= ================ ============================================================================== +version versionsuffix toolchain +========= ================ ============================================================================== +``2.3.0`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``2.3.0`` ``-CUDA-9.1.85`` ``foss/2018a`` +``2.4.0`` ``fosscuda/2018b`` +``2.5.0`` ``fosscuda/2018b`` +``2.5.1`` ``fosscuda/2019a``, ``fosscuda/2019b`` +``2.5.4`` ``fosscuda/2019a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b`` +========= ================ ============================================================================== .. _list_software_MagresPython_1249: @@ -20067,7 +20784,7 @@ version toolchain ``3.82`` ``GCC/4.8.2`` ``4.1`` ``GCC/4.9.2`` ``4.2.1`` ``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` -``4.3`` ``GCC/9.3.0`` +``4.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= ===================================== @@ -20113,11 +20830,11 @@ makeinfo is part of the Texinfo project, the official documentation format of th *homepage*: https://www.gnu.org/software/texinfo/ -======= ==================================== -version toolchain -======= ==================================== -``6.7`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ==================================== +======= ======================================================== +version toolchain +======= ======================================================== +``6.7`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ======================================================== .. _list_software_Mako_392: @@ -20236,6 +20953,7 @@ version toolchain ``10.3.10`` ``foss/2018b`` ``10.3.14`` ``foss/2019a`` ``10.4.13`` ``gompi/2019b`` +``10.5.8`` ``GCC/10.2.0`` =========== =============================== @@ -20248,14 +20966,15 @@ MariaDB Connector/C is used to connect applications developed in C/C++ to MariaD *homepage*: https://downloads.mariadb.org/connector-c/ -========= ==================================================== -version toolchain -========= ==================================================== -``2.3.4`` ``foss/2017b``, ``intel/2017b`` -``2.3.5`` ``intel/2018a``, ``iomkl/2018a`` -``2.3.7`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` -``3.1.7`` ``GCCcore/9.3.0`` -========= ==================================================== +========== ==================================================== +version toolchain +========== ==================================================== +``2.3.4`` ``foss/2017b``, ``intel/2017b`` +``2.3.5`` ``intel/2018a``, ``iomkl/2018a`` +``2.3.7`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` +``3.1.7`` ``GCCcore/9.3.0`` +``3.1.11`` ``GCCcore/10.2.0`` +========== ==================================================== .. _list_software_MARS_307: @@ -20367,6 +21086,7 @@ version toolchain ``1.5.11`` ``foss/2017b`` ``1.5.12`` ``GCCcore/6.4.0`` ``1.5.17`` ``GCCcore/8.3.0`` +``1.5.19`` ``GCCcore/9.3.0`` ========== ================= @@ -20452,6 +21172,7 @@ version versionsuffix toolchain ``2.2.4`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` ``2.2.4`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``2.2.5`` ``-Python-2.7.16`` ``foss/2019b`` +``2.2.5`` ``-Python-2.7.18`` ``foss/2020a``, ``intel/2020a`` ``3.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` ``3.0.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` @@ -20578,6 +21299,7 @@ The Mayavi scientific data 3-dimensional visualizer version versionsuffix toolchain ========= ================== =============== ``4.4.4`` ``-Python-2.7.11`` ``intel/2016a`` +``4.6.2`` ``-Python-3.6.6`` ``foss/2018b`` ``4.7.1`` ``-Python-2.7.15`` ``foss/2019a`` ``4.7.1`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================== =============== @@ -20811,6 +21533,7 @@ version versionsuffix toolchain ``0.12.0`` ``-Python-3.6.6`` ``foss/2018b`` ``1.1.1`` ``-Python-3.7.4`` ``foss/2019b`` ``1.1.3`` ``-Python-3.7.4`` ``foss/2019b`` +``1.2.0`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================= ============== @@ -20853,13 +21576,14 @@ version versionsuffix toolchain Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. -*homepage*: http://ab-initio.mit.edu/wiki/index.php/Meep +*homepage*: https://meep.readthedocs.io/en/latest/ -======= ============== -version toolchain -======= ============== -``1.3`` ``foss/2016a`` -======= ============== +========= ================== =============================================== +version versionsuffix toolchain +========= ================== =============================================== +``1.3`` ``foss/2016a`` +``1.6.0`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2018a`` +========= ================== =============================================== .. _list_software_MEGA_282: @@ -20903,17 +21627,17 @@ An ultra-fast single-node solution for large and complex metagenomics assembly *homepage*: https://github.com/voutcn/megahit -========= ================== ============================== -version versionsuffix toolchain -========= ================== ============================== -``1.1.2`` ``-Python-2.7.14`` ``foss/2018a`` -``1.1.3`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a`` -``1.1.3`` ``-Python-3.6.3`` ``foss/2017b`` -``1.1.4`` ``-Python-2.7.15`` ``foss/2018b`` -``1.1.4`` ``-Python-3.6.6`` ``foss/2018b`` -``1.2.8`` ``GCCcore/8.2.0`` -``1.2.9`` ``GCCcore/9.3.0`` -========= ================== ============================== +========= ================== ================================= +version versionsuffix toolchain +========= ================== ================================= +``1.1.2`` ``-Python-2.7.14`` ``foss/2018a`` +``1.1.3`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a`` +``1.1.3`` ``-Python-3.6.3`` ``foss/2017b`` +``1.1.4`` ``-Python-2.7.15`` ``foss/2018b`` +``1.1.4`` ``-Python-3.6.6`` ``foss/2018b`` +``1.2.8`` ``GCCcore/8.2.0`` +``1.2.9`` ``GCCcore/9.3.0``, ``foss/2018b`` +========= ================== ================================= .. _list_software_Meld_386: @@ -21507,9 +22231,26 @@ Dual barcode and primer demultiplexing for MinION sequenced reads version versionsuffix toolchain ============ ================= ======================= ``20200326`` ``-Python-3.7.4`` ``iccifort/2019.5.281`` +``20200326`` ``-Python-3.8.2`` ``iccifort/2020.1.217`` ============ ================= ======================= +.. _list_software_MiniCARD_679: + +*MiniCARD* +++++++++++ + +MiniCARD is a *cardinality solver* based on MiniSAT [www.minisat.se]. MiniCARD handles cardinality constraints natively, using the same efficient data structures and techniques MiniSAT uses for clauses, giving it much better performance on cardinality constraints than CNF encodings of those constraints passed to a typical SAT solver. It can read the standard DIMACS CNF format, the OPB pseudo-boolean format (with linear cardinality constraints only), and CNF+, a format that extends CNF to include cardinality constraints. + +*homepage*: https://github.com/liffiton/minicard + +======= ============= +version toolchain +======= ============= +``1.2`` ``GCC/9.3.0`` +======= ============= + + .. _list_software_Miniconda2_964: *Miniconda2* @@ -21544,6 +22285,8 @@ version toolchain ``4.5.12`` ``system`` ``4.6.14`` ``system`` ``4.7.10`` ``system`` +``4.8.3`` ``system`` +``4.9.2`` ``system`` ========== ========== @@ -21603,6 +22346,23 @@ version toolchain ========== ====================================================== +.. _list_software_MiniSat_693: + +*MiniSat* ++++++++++ + +MiniSat is a minimalistic, open-source SAT solver, developed to help researchers and developers alike to get started on SAT. + +*homepage*: http://minisat.se/ + +============ ============= +version toolchain +============ ============= +``2.2.0`` ``GCC/9.3.0`` +``20130925`` ``GCC/9.3.0`` +============ ============= + + .. _list_software_MinPath_689: *MinPath* @@ -21748,11 +22508,13 @@ Python hooks for Intel(R) Math Kernel Library runtime control settings. *homepage*: https://github.com/IntelPython/mkl-service -========= =============== -version toolchain -========= =============== -``2.0.2`` ``intel/2019a`` -========= =============== +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``2.0.2`` ``intel/2019a`` +``2.3.0`` ``intel/2020b`` +``2.3.0`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== .. _list_software_mkl_fft_739: @@ -22175,6 +22937,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_MPB_223: + +*MPB* ++++++ + +MPB is a free and open-source software package for computing the band structures, or dispersion relations, and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers. MPB is an acronym for MIT Photonic Bands. + +*homepage*: https://mpb.readthedocs.io/en/latest/ + +========= ================== =============================================== +version versionsuffix toolchain +========= ================== =============================================== +``1.6.2`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2018a`` +========= ================== =============================================== + + .. _list_software_MPC_224: *MPC* @@ -22190,6 +22968,7 @@ version versionsuffix toolchain ``1.0.3`` ``intel/2017a`` ``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` ``1.1.0`` ``GCC/8.3.0``, ``GCC/9.3.0`` +``1.2.1`` ``GCCcore/10.2.0`` ========= =============== =============================== @@ -22243,9 +23022,9 @@ version versionsuffix toolchain *MPICH* +++++++ -MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). +MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3). -*homepage*: http://www.mpich.org/ +*homepage*: https://www.mpich.org/ ========= ====================================== version toolchain @@ -22253,6 +23032,7 @@ version toolchain ``3.0.4`` ``GCC/4.8.1`` ``3.2`` ``GCC/4.9.3-2.25``, ``GCC/7.2.0-2.29`` ``3.2.1`` ``GCC/7.2.0-2.29`` +``3.3.2`` ``GCC/10.2.0``, ``GCC/9.3.0`` ========= ====================================== @@ -22350,11 +23130,11 @@ MrBayes is a program for the Bayesian estimation of phylogeny. *homepage*: http://mrbayes.csit.fsu.edu -========= ============== -version toolchain -========= ============== -``3.2.6`` ``foss/2016a`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``3.2.6`` ``foss/2016a``, ``foss/2017a`` +========= ============================== .. _list_software_MRChem_540: @@ -22594,12 +23374,13 @@ version versionsuffix toolchain muParser is an extensible high performance math expression parser library written in C++. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression. -*homepage*: http://beltoforion.de/article.php?a=muparser +*homepage*: https://beltoforion.de/article.php?a=muparser ========= ================= version toolchain ========= ================= ``2.2.5`` ``GCCcore/6.4.0`` +``2.3.2`` ``GCCcore/9.3.0`` ========= ================= @@ -22912,7 +23693,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_neon_432` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -22983,6 +23764,7 @@ Comparing runs of Oxford Nanopore sequencing data and alignments version versionsuffix toolchain ========== ================= =============== ``1.10.1`` ``-Python-3.7.4`` ``intel/2019b`` +``1.13.1`` ``intel/2020b`` ========== ================= =============== @@ -23027,11 +23809,13 @@ Filtering and trimming of long read sequencing data. *homepage*: https://github.com/wdecoster/nanofilt -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``2.5.0`` ``-Python-3.6.6`` ``foss/2018b`` -========= ================= ============== +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``2.5.0`` ``-Python-3.6.6`` ``foss/2018b`` +``2.6.0`` ``-Python-3.7.4`` ``foss/2019b`` +``2.6.0`` ``-Python-3.8.2`` ``intel/2020a`` +========= ================= =============== .. _list_software_nanoget_748: @@ -23047,6 +23831,7 @@ Functions to extract information from Oxford Nanopore sequencing data and alignm version versionsuffix toolchain ========== ================= =============== ``1.12.1`` ``-Python-3.7.4`` ``intel/2019b`` +``1.15.0`` ``intel/2020b`` ========== ================= =============== @@ -23063,6 +23848,7 @@ A few simple math function for other Oxford Nanopore processing scripts version versionsuffix toolchain ========== ================= =============== ``0.23.1`` ``-Python-3.7.4`` ``intel/2019b`` +``1.2.0`` ``intel/2020b`` ========== ================= =============== @@ -23111,6 +23897,7 @@ Plotting suite for long read sequencing data and alignments version versionsuffix toolchain ========== ================= =============== ``1.28.4`` ``-Python-3.7.4`` ``intel/2019b`` +``1.33.0`` ``intel/2020b`` ========== ================= =============== @@ -23129,9 +23916,26 @@ version versionsuffix toolchain ``0.9.2`` ``intel/2018a`` ``0.10.2`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.13.1`` ``-Python-3.6.6`` ``foss/2018b`` +``0.13.2`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================== =============================== +.. _list_software_NanopolishComp_1450: + +*NanopolishComp* +++++++++++++++++ + +NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files + +*homepage*: https://adrienleger.com/NanopolishComp/ + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.6.11`` ``-Python-3.8.2`` ``foss/2020a`` +========== ================= ============== + + .. _list_software_NASM_303: *NASM* @@ -23161,13 +23965,14 @@ version toolchain nauty and Traces are programs for computing automorphism groups of graphs and digraphs. They can also produce a canonical label. -*homepage*: http://pallini.di.uniroma1.it/ +*homepage*: https://pallini.di.uniroma1.it/ ========== ==================== version toolchain ========== ==================== ``2.6r12`` ``GCC/8.2.0-2.31.1`` ``2.7rc2`` ``GCC/8.2.0-2.31.1`` +``2.7rc5`` ``GCC/8.3.0`` ========== ==================== @@ -23267,6 +24072,7 @@ version versionsuffix toolchain ``1.16.1`` ``-R-3.6.0`` ``foss/2019a`` ``1.17`` ``foss/2019b`` ``1.17`` ``-R-4.0.0`` ``foss/2020a`` +``1.17`` ``-R-4.0.3`` ``foss/2020b`` ========== ============= =============================== @@ -23359,7 +24165,8 @@ version toolchain ``4.7.6`` ``intel/2018a`` ``4.7.9`` ``foss/2018b``, ``intel/2018b`` ``4.8.1`` ``foss/2019a`` -``4.9.3`` ``gompi/2019b`` +``4.9.3`` ``foss/2019b`` +``4.9.7`` ``foss/2020a``, ``foss/2020b`` ========= =============================== @@ -23494,6 +24301,22 @@ version toolchain ========== ================= +.. _list_software_neptune-client_1451: + +*neptune-client* +++++++++++++++++ + +Neptune is an experiment tracking hub that brings organization and collaboration to your data science team. + +*homepage*: https://docs.neptune.ai + +=========== ================= ============== +version versionsuffix toolchain +=========== ================= ============== +``0.4.129`` ``-Python-3.8.2`` ``foss/2020a`` +=========== ================= ============== + + .. _list_software_Net-core_765: *Net-core* @@ -23536,7 +24359,7 @@ version versionsuffix toolchain ``4.6.1`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``4.6.2`` ``gompi/2019a``, ``iimpi/2019a`` ``4.7.1`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` -``4.7.4`` ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020a``, ``iimpi/2020b`` +``4.7.4`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpi/2020b`` =========== ================ ========================================================================================================================== @@ -23571,7 +24394,7 @@ version versionsuffix toolchain ``4.3.0`` ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``4.3.0`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.3.0`` ``-HDF5-1.8.19`` ``intel/2017b`` -``4.3.1`` ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2019b``, ``iimpi/2020a`` +``4.3.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2019b``, ``iimpi/2020a`` ========= ================ ====================================================================================================================================================== @@ -23608,22 +24431,24 @@ Python/numpy interface to netCDF. *homepage*: https://unidata.github.io/netcdf4-python/ -========= ============================= =============================== -version versionsuffix toolchain -========= ============================= =============================== -``1.2.9`` ``-Python-2.7.13`` ``intel/2017a`` -``1.3.1`` ``-Python-3.6.3`` ``intel/2017b`` -``1.3.1`` ``-Python-3.6.3-HDF5-1.8.19`` ``intel/2017b`` -``1.4.0`` ``-Python-3.6.2-HDF5-1.8.19`` ``foss/2017b`` -``1.4.0`` ``-Python-3.6.4`` ``intel/2018a`` -``1.4.1`` ``-Python-2.7.15`` ``intel/2018b`` -``1.4.1`` ``-Python-3.6.6`` ``intel/2018b`` -``1.4.2`` ``-Python-3.6.4`` ``foss/2018a`` -``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` -``1.5.2`` ``intel/2019a`` -``1.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.5.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -========= ============================= =============================== +=========== ============================= =============================== +version versionsuffix toolchain +=========== ============================= =============================== +``1.2.9`` ``-Python-2.7.13`` ``intel/2017a`` +``1.3.1`` ``-Python-3.6.3`` ``intel/2017b`` +``1.3.1`` ``-Python-3.6.3-HDF5-1.8.19`` ``intel/2017b`` +``1.4.0`` ``-Python-3.6.2-HDF5-1.8.19`` ``foss/2017b`` +``1.4.0`` ``-Python-3.6.4`` ``intel/2018a`` +``1.4.1`` ``-Python-2.7.15`` ``intel/2018b`` +``1.4.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.4.2`` ``-Python-3.6.4`` ``foss/2018a`` +``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` +``1.5.2`` ``intel/2019a`` +``1.5.3`` ``-Python-2.7.16`` ``foss/2019b`` +``1.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.5.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.5.5.1`` ``intel/2020b`` +=========== ============================= =============================== .. _list_software_netloc_645: @@ -23770,6 +24595,7 @@ version versionsuffix toolchain ``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``2.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``2.4`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` +``2.5`` ``foss/2020b``, ``fosscuda/2020b`` ======== ================== =================================================== @@ -23950,6 +24776,22 @@ version toolchain ======= ================== +.. _list_software_NGSpeciesID_1006: + +*NGSpeciesID* ++++++++++++++ + +NGSpeciesID is a tool for clustering and consensus forming of targeted ONT reads. + +*homepage*: https://github.com/ksahlin/NGSpeciesID + +=========== ================= ============== +version versionsuffix toolchain +=========== ================= ============== +``0.1.1.1`` ``-Python-3.7.4`` ``foss/2019b`` +=========== ================= ============== + + .. _list_software_ngspice_745: *ngspice* @@ -24031,7 +24873,7 @@ version toolchain Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data. -*homepage*: http://nilearn.github.io/ +*homepage*: https://nilearn.github.io/ ========= ================== =============================== version versionsuffix toolchain @@ -24039,6 +24881,7 @@ version versionsuffix toolchain ``0.5.2`` ``foss/2019a``, ``intel/2019a`` ``0.5.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``0.5.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``0.7.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== =============================== @@ -24154,14 +24997,16 @@ version toolchain NLTK is a leading platform for building Python programs to work with human language data. -*homepage*: http://www.nltk.org/ +*homepage*: https://www.nltk.org/ -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``3.2.2`` ``-Python-2.7.13`` ``intel/2017a`` -``3.2.4`` ``-Python-2.7.13`` ``intel/2017a`` -========= ================== =============== +========= ================== ================================== +version versionsuffix toolchain +========= ================== ================================== +``3.2.2`` ``-Python-2.7.13`` ``intel/2017a`` +``3.2.4`` ``-Python-2.7.13`` ``intel/2017a`` +``3.5`` ``-Python-3.7.4`` ``foss/2019b`` +``3.5`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +========= ================== ================================== .. _list_software_Node-RED_654: @@ -24216,6 +25061,7 @@ version toolchain ========= =============== ``3.6.3`` ``intel/2018b`` ``3.7.4`` ``gompi/2019a`` +``3.8.4`` ``GCC/8.3.0`` ========= =============== @@ -24303,6 +25149,38 @@ version toolchain ============ ============== +.. _list_software_Nsight-Compute_1399: + +*Nsight-Compute* +++++++++++++++++ + +NVIDIA® Nsight™ Compute is an interactive kernel profiler for CUDA applications. It provides detailed performance metrics and API debugging via a user interface and command line tool. In addition, its baseline feature allows users to compare results within the tool. Nsight Compute provides a customizable and data-driven user interface and metric collection and can be extended with analysis scripts for post-processing results. + +*homepage*: https://developer.nvidia.com/nsight-compute + +============ ========== +version toolchain +============ ========== +``2020.3.0`` ``system`` +============ ========== + + +.. _list_software_Nsight-Systems_1426: + +*Nsight-Systems* +++++++++++++++++ + +NVIDIA® Nsight™ Systems is a system-wide performance analysis tool designed to visualize an application’s algorithm, help you select the largest opportunities to optimize, and tune to scale efficiently across any quantity of CPUs and GPUs in your computer; from laptops to DGX servers. + +*homepage*: https://developer.nvidia.com/nsight-compute + +============ ========== +version toolchain +============ ========== +``2020.5.1`` ``system`` +============ ========== + + .. _list_software_NSPR_323: *NSPR* @@ -24460,10 +25338,12 @@ version versionsuffix toolchain ``0.32.0`` ``-Python-2.7.13`` ``intel/2017a`` ``0.37.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` ``0.37.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.39.0`` ``-Python-3.6.6`` ``foss/2018b`` ``0.43.1`` ``intel/2019a`` ``0.46.0`` ``foss/2019a`` ``0.47.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``0.50.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.52.0`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================== ================================== @@ -24528,11 +25408,13 @@ C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) *homepage*: https://developer.nvidia.com/hpc-sdk/ -======== ========== -version toolchain -======== ========== -``20.7`` ``system`` -======== ========== +========= ========== +version toolchain +========= ========== +``20.7`` ``system`` +``20.9`` ``system`` +``20.11`` ``system`` +========= ========== .. _list_software_nvtop_567: @@ -24548,6 +25430,7 @@ htop-like GPU usage monitor version toolchain ========= ================== ``1.0.0`` ``fosscuda/2018b`` +``1.1.0`` ``fosscuda/2019b`` ========= ================== @@ -24592,7 +25475,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_orca_421` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -24868,6 +25751,7 @@ version toolchain ``1.9.0`` ``gompi/2017a`` ``2.2.0`` ``gompi/2018b`` ``2.8.0`` ``gompi/2019b`` +``2.9.2`` ``gompi/2020a`` ========= =============== @@ -24972,12 +25856,13 @@ version versionsuffix toolchain ``3.0.1`` ``intel/2016b``, ``intel/2018a`` ``4.0`` ``foss/2016b``, ``intel/2016b`` ``4.1`` ``foss/2016b``, ``intel/2017a`` +``4.x-20170904`` ``intel/2016b`` ``5.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``5.0-20180108`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``6`` ``foss/2018b``, ``foss/2019b``, ``intel/2018a`` ``7`` ``foss/2019b`` ``7`` ``-20200508`` ``foss/2019b`` -``8`` ``foss/2020a`` +``8`` ``foss/2020a``, ``foss/2020b`` ``v1606+`` ``foss/2018b`` ``v1612+`` ``foss/2018b`` ``v1712`` ``foss/2017b``, ``intel/2017b`` @@ -24986,6 +25871,7 @@ version versionsuffix toolchain ``v1906`` ``foss/2019b`` ``v1912`` ``foss/2019b``, ``intel/2019b`` ``v2006`` ``foss/2020a`` +``v2012`` ``foss/2020a`` ================ ============= ================================================= @@ -25055,13 +25941,14 @@ OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been d *homepage*: https://www.openjpeg.org/ -========= ==================================== -version toolchain -========= ==================================== -``2.1`` ``GCCcore/6.4.0`` -``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= ==================================== +========= ===================================== +version toolchain +========= ===================================== +``2.1`` ``GCCcore/6.4.0`` +``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.4.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========= ===================================== .. _list_software_OpenKIM-API_890: @@ -25090,11 +25977,11 @@ Open Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of *homepage*: https://openkim.org/ -============ ================================================================ -version toolchain -============ ================================================================ -``20190725`` ``foss/2019a``, ``foss/2019b``, ``intel/2019a``, ``intel/2019b`` -============ ================================================================ +============ ==================================================================================== +version toolchain +============ ==================================================================================== +``20190725`` ``GCCcore/10.2.0``, ``foss/2019a``, ``foss/2019b``, ``intel/2019a``, ``intel/2019b`` +============ ==================================================================================== .. _list_software_OpenMM_556: @@ -25186,13 +26073,14 @@ version versionsuffix toolchain ``3.1.1`` ``GCC/7.3.0-2.30``, ``gcccuda/2018b``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` ``3.1.2`` ``GCC/8.2.0-2.31.1`` ``3.1.3`` ``GCC/8.2.0-2.31.1``, ``gcccuda/2019a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``3.1.4`` ``GCC/8.3.0``, ``GCC/8.3.0-2.32``, ``gcccuda/2019b`` +``3.1.4`` ``GCC/8.3.0``, ``GCC/8.3.0-2.32``, ``gcccuda/2019b``, ``iccifort/2019.5.281`` ``4.0.0`` ``GCC/8.2.0-2.31.1`` ``4.0.0`` ``-hpcx`` ``GCC/8.2.0-2.31.1`` ``4.0.1`` ``GCC/8.3.0-2.32`` ``4.0.2`` ``GCC/9.2.0-2.32`` ``4.0.3`` ``GCC/9.3.0``, ``gcccuda/2020a``, ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` -``4.0.5`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``gcccuda/2020b`` +``4.0.5`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` +``4.1.0`` ``GCC/10.2.0`` ``system`` ``GCC/system-2.29`` ========== ============= ==================================================================================================================== @@ -25305,11 +26193,12 @@ Open System for Earthquake Engineering Simulation *homepage*: https://opensees.berkeley.edu/index.php -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``3.2.0`` ``-Python-3.8.2`` ``intel/2020a`` -========= ================= =============== +========= ========================== =============== +version versionsuffix toolchain +========= ========================== =============== +``3.2.0`` ``-Python-3.8.2`` ``intel/2020a`` +``3.2.0`` ``-Python-3.8.2-parallel`` ``intel/2020a`` +========= ========================== =============== .. _list_software_OpenSlide_899: @@ -25476,22 +26365,6 @@ version versionsuffix toolchain ====================== ================== =============== -.. _list_software_orca_421: - -*orca* -++++++ - -Orca is an Electron app that generates images and reports of Plotly things like plotly.js graphs, dash apps, dashboards from the command line. - -*homepage*: https://github.com/plotly/orca - -========= ================= -version toolchain -========= ================= -``1.3.0`` ``GCCcore/8.3.0`` -========= ================= - - .. _list_software_ORFfinder_863: *ORFfinder* @@ -25651,7 +26524,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -25677,7 +26550,7 @@ version toolchain p4est is a C library to manage a collection (a forest) of multiple connected adaptive quadtrees or octrees in parallel. -*homepage*: http://www.p4est.org +*homepage*: https://www.p4est.org ======= =============== version toolchain @@ -25730,13 +26603,14 @@ Packing Optimization for Molecular Dynamics Simulations *homepage*: http://m3g.iqm.unicamp.br/packmol -========== =============================== -version toolchain -========== =============================== -``16.103`` ``intel/2016a`` -``18.013`` ``foss/2018a``, ``intel/2018a`` -``20.2.2`` ``GCC/10.2.0`` -========== =============================== +=========== =============================== +version toolchain +=========== =============================== +``16.103`` ``intel/2016a`` +``18.013`` ``foss/2018a``, ``intel/2018a`` +``20.2.2`` ``GCC/10.2.0`` +``v20.2.2`` ``iccifort/2020.1.217`` +=========== =============================== .. _list_software_PAML_298: @@ -25952,13 +26826,14 @@ parasail is a SIMD C (C99) library containing implementations of the Smith-Wate *homepage*: https://github.com/jeffdaily/parasail -========= =============== -version toolchain -========= =============== -``2.2`` ``intel/2018a`` -``2.4`` ``foss/2018b`` -``2.4.1`` ``intel/2019b`` -========= =============== +========= ============================== +version toolchain +========= ============================== +``2.2`` ``intel/2018a`` +``2.4`` ``foss/2018b`` +``2.4.1`` ``GCC/8.3.0``, ``intel/2019b`` +``2.4.2`` ``iccifort/2020.1.217`` +========= ============================== .. _list_software_Paraver_721: @@ -25998,6 +26873,7 @@ version versionsuffix toolchain ``5.5.2`` ``-Python-2.7.15-mpi`` ``foss/2018b`` ``5.6.2`` ``-Python-3.7.4-mpi`` ``foss/2019b``, ``intel/2019b`` ``5.8.0`` ``-Python-3.8.2-mpi`` ``foss/2020a``, ``intel/2020a`` +``5.8.1`` ``-mpi`` ``foss/2020b`` ========= ====================== ================================================================================================= @@ -26183,6 +27059,7 @@ Tools for plotting Oxford Nanopore and other long-read data version versionsuffix toolchain ========== ================= =============== ``0.1923`` ``-Python-3.7.4`` ``intel/2019b`` +``0.1924`` ``intel/2020b`` ========== ================= =============== @@ -26687,6 +27564,22 @@ version versionsuffix toolchain ========= ======================= ========== +.. _list_software_PHANOTATE_676: + +*PHANOTATE* ++++++++++++ + +PHANOTATE: a tool to annotate phage genomes + +*homepage*: https://github.com/deprekate/PHANOTATE + +============ ============== +version toolchain +============ ============== +``20190724`` ``foss/2018b`` +============ ============== + + .. _list_software_PHASE_369: *PHASE* @@ -26834,12 +27727,12 @@ PHYLIP is a free package of programs for inferring phylogenies. *homepage*: http://evolution.genetics.washington.edu/phylip -========= ========================================================== -version toolchain -========= ========================================================== -``3.696`` ``foss/2016a``, ``intel/2016a`` -``3.697`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` -========= ========================================================== +========= ========================================================================= +version toolchain +========= ========================================================================= +``3.696`` ``foss/2016a``, ``intel/2016a`` +``3.697`` ``GCC/6.4.0-2.28``, ``GCC/9.3.0``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +========= ========================================================================= .. _list_software_PhyloBayes-MPI_1299: @@ -27065,6 +27958,7 @@ version versionsuffix toolchain ``5.0.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``5.3.0.post0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``6.0.x.post0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``7.1.2`` ``GCCcore/10.2.0`` ``7.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` =============== ================= =================================================== @@ -27171,6 +28065,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_PIPITS_473: + +*PIPITS* +++++++++ + +An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the Illumina sequencing platform. + +*homepage*: https://github.com/hsgweon/pipits + +======= ================= ============== +version versionsuffix toolchain +======= ================= ============== +``2.7`` ``-Python-3.8.2`` ``foss/2020a`` +======= ================= ============== + + .. _list_software_pIRS_350: *pIRS* @@ -27449,6 +28359,7 @@ version toolchain ``1.9b5`` ``golf/2020a`` ``1.9b_4.1-x86_64`` ``system`` ``1.9b_6.17-x86_64`` ``system`` +``1.9b_6.21-x86_64`` ``system`` ``2.00-alpha1-x86_64`` ``system`` ``2.00-alpha2-x86_64`` ``system`` ``2.00-alpha2-x86_64_avx2`` ``system`` @@ -27456,6 +28367,22 @@ version toolchain =========================== ============================== +.. _list_software_plinkQC_690: + +*plinkQC* ++++++++++ + +plinkQC is a R/CRAN package for genotype quality control in genetic association studies. It makes PLINK basic statistics (e.g.missing genotyping rates per individual, allele frequencies per genetic marker) and relationship functions easily accessible from within R and allows for automatic evaluation of the results. + +*homepage*: https://meyer-lab-cshl.github.io/plinkQC/ + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``0.3.3`` ``-R-4.0.0`` ``foss/2020a`` +========= ============= ============== + + .. _list_software_PLINKSEQ_615: *PLINKSEQ* @@ -27505,6 +28432,23 @@ version versionsuffix toolchain ========= ============= =============== +.. _list_software_plotly-orca_1142: + +*plotly-orca* ++++++++++++++ + +Orca is an Electron app that generates images and reports of Plotly things like plotly.js graphs, dash apps, dashboards from the command line. + +*homepage*: https://github.com/plotly/orca + +========= ===================================== +version toolchain +========= ===================================== +``1.3.0`` ``GCCcore/8.3.0`` +``1.3.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========= ===================================== + + .. _list_software_plotly.py_955: *plotly.py* @@ -27514,13 +28458,14 @@ An open-source, interactive graphing library for Python *homepage*: https://plot.ly/python -========= ================= -version toolchain -========= ================= -``4.1.0`` ``intel/2019a`` -``4.4.1`` ``intel/2019b`` -``4.8.1`` ``GCCcore/9.3.0`` -========= ================= +========== ================== +version toolchain +========== ================== +``4.1.0`` ``intel/2019a`` +``4.4.1`` ``intel/2019b`` +``4.8.1`` ``GCCcore/9.3.0`` +``4.14.3`` ``GCCcore/10.2.0`` +========== ================== .. _list_software_PLplot_603: @@ -27568,6 +28513,7 @@ version versionsuffix toolchain ``2.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``2.5b`` ``-Python-2.7.14`` ``intel/2018a`` ``2.6.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``2.6.2`` ``foss/2020b``, ``intel/2020b`` ========= ================== ================================================ @@ -27855,6 +28801,7 @@ version versionsuffix toolchain ``11.3`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``11.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``12.4`` ``GCCcore/9.3.0`` +``13.2`` ``GCCcore/10.2.0`` ========= ================== ================================================================ @@ -27988,6 +28935,22 @@ version toolchain ========= =============== +.. _list_software_preCICE_603: + +*preCICE* ++++++++++ + +preCICE (Precise Code Interaction Coupling Environment) is a coupling library for partitioned multi-physics simulations, including, but not restricted to fluid-structure interaction and conjugate heat transfer simulations. Partitioned means that preCICE couples existing programs (solvers) capable of simulating a subpart of the complete physics involved in a simulation. This allows for the high flexibility that is needed to keep a decent time-to-solution for complex multi-physics scenarios. + +*homepage*: https://www.precice.org/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``2.1.1`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_preseq_656: *preseq* @@ -28112,12 +29075,12 @@ Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbi *homepage*: https://github.com/hyattpd/Prodigal/ -========= ============================================================================================= -version toolchain -========= ============================================================================================= -``2.6.2`` ``GCC/4.9.3-binutils-2.25`` -``2.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ============================================================================================= +========= ================================================================================================================= +version toolchain +========= ================================================================================================================= +``2.6.2`` ``GCC/4.9.3-binutils-2.25`` +``2.6.3`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ================================================================================================================= .. _list_software_PROJ_315: @@ -28317,7 +29280,7 @@ version versionsuffix toolchain ``3.6.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``3.6.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``3.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``3.13.0`` ``-Python-3.8.2`` ``foss/2020a`` +``3.13.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` ``3.14.0`` ``GCCcore/10.2.0`` ========== ================== ================================== @@ -28650,6 +29613,38 @@ version versionsuffix toolchain ========== ================== ============== +.. _list_software_py-aiger_798: + +*py-aiger* +++++++++++ + +A python library for manipulating sequential and combinatorial circuits. This module provides the py-aiger extensions: aiger_bv, aiger_cnf, aiger_ptltl, aiger_coins, aiger_gridworld, aiger_dfa + +*homepage*: https://github.com/mvcisback/py-aiger + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``6.1.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +========= ================= ================= + + +.. _list_software_py-aiger-bdd_1141: + +*py-aiger-bdd* +++++++++++++++ + +Aiger to BDD bridge. + +*homepage*: https://github.com/mvcisback/py-aiger-bdd + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_py-cpuinfo_1034: *py-cpuinfo* @@ -28810,6 +29805,22 @@ version toolchain ============ ========== +.. _list_software_PyClone_698: + +*PyClone* ++++++++++ + +PyClone is a Python package that wraps rclone and provides a threaded interface for an installation at the host or container level. + +*homepage*: https://gitlab.com/ltgiv/pyclone + +============ ================== +version toolchain +============ ================== +``2020.9b2`` ``GCCcore/10.2.0`` +============ ================== + + .. _list_software_pycma_538: *pycma* @@ -28953,7 +29964,7 @@ version versionsuffix toolchain Pure python package for DICOM medical file reading and writing. -*homepage*: https://github.com/pydicom/pydicom +*homepage*: https://pydicom.github.io/ ========= ================== ================= version versionsuffix toolchain @@ -28961,6 +29972,7 @@ version versionsuffix toolchain ``0.9.9`` ``-Python-2.7.11`` ``intel/2016a`` ``1.2.2`` ``GCCcore/8.2.0`` ``1.4.2`` ``GCCcore/8.3.0`` +``2.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ================== ================= @@ -28990,11 +30002,11 @@ Python interface to Graphviz's Dot language. *homepage*: https://github.com/pydot/pydot -========= ============== -version toolchain -========= ============== -``1.4.1`` ``foss/2019b`` -========= ============== +========= ================================= +version toolchain +========= ================================= +``1.4.1`` ``GCCcore/9.3.0``, ``foss/2019b`` +========= ================================= .. _list_software_pyEGA3_489: @@ -29387,6 +30399,8 @@ Pylint is a tool that checks for errors in Python code, tries to enforce a codi version versionsuffix toolchain ========= ================== ================================================ ``1.9.3`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``1.9.5`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``1.9.5`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` ========= ================== ================================================ @@ -29440,6 +30454,7 @@ The pymbar package contains the pymbar suite of tools for the analysis of simula version versionsuffix toolchain ========= ================= =============== ``3.0.3`` ``-Python-3.6.3`` ``intel/2017b`` +``3.0.3`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================= =============== @@ -29452,11 +30467,12 @@ Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machin *homepage*: https://docs.pymc.io/ -======= ================= =============================== -version versionsuffix toolchain -======= ================= =============================== -``3.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -======= ================= =============================== +========== ================= =============================== +version versionsuffix toolchain +========== ================= =============================== +``3.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.11.1`` ``intel/2020b`` +========== ================= =============================== .. _list_software_pymca_538: @@ -29786,28 +30802,44 @@ Pysam is a python module for reading and manipulating Samfiles. It's a lightwe *homepage*: https://github.com/pysam-developers/pysam -============ ================== ============================================================== -version versionsuffix toolchain -============ ================== ============================================================== -``0.8.4`` ``-Python-2.7.12`` ``intel/2016b`` -``0.9.1.4`` ``-Python-2.7.12`` ``foss/2016b`` -``0.10.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``0.12.0.1`` ``-Python-2.7.13`` ``intel/2017a`` -``0.12.0.1`` ``-Python-2.7.14`` ``intel/2017b`` -``0.12.0.1`` ``-Python-3.6.3`` ``intel/2017b`` -``0.13`` ``-Python-2.7.14`` ``intel/2017b`` -``0.13.0`` ``-Python-3.6.3`` ``intel/2017b`` -``0.14`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``0.14`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``0.14`` ``-Python-3.6.4`` ``intel/2018a`` -``0.14.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``0.14.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``0.15.1`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``0.15.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.15.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``0.15.3`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``0.16.0.1`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217`` -============ ================== ============================================================== +============ ================== ============================================================================================== +version versionsuffix toolchain +============ ================== ============================================================================================== +``0.8.4`` ``-Python-2.7.12`` ``intel/2016b`` +``0.9.1.4`` ``-Python-2.7.12`` ``foss/2016b`` +``0.10.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``0.12.0.1`` ``-Python-2.7.13`` ``intel/2017a`` +``0.12.0.1`` ``-Python-2.7.14`` ``intel/2017b`` +``0.12.0.1`` ``-Python-3.6.3`` ``intel/2017b`` +``0.13`` ``-Python-2.7.14`` ``intel/2017b`` +``0.13.0`` ``-Python-3.6.3`` ``intel/2017b`` +``0.14`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``0.14`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``0.14`` ``-Python-3.6.4`` ``intel/2018a`` +``0.14.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``0.14.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.15.1`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.15.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.15.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``0.15.3`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``0.16.0.1`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` +============ ================== ============================================================================================== + + +.. _list_software_PySAT_433: + +*PySAT* ++++++++ + +PySAT is a Python toolkit, which aims at providing a simple and unified interface to a number of state-of-art Boolean satisfiability (SAT) solvers as well as to a variety of cardinality and pseudo-Boolean encodings. + +*homepage*: https://github.com/mvcisback/py-aiger + +=============== ================= ============= +version versionsuffix toolchain +=============== ================= ============= +``0.1.6.dev11`` ``-Python-3.8.2`` ``GCC/9.3.0`` +=============== ================= ============= .. _list_software_pyScaf_614: @@ -29954,6 +30986,7 @@ Python interface to Stan, a package for Bayesian inference using the No-U-Turn version versionsuffix toolchain ============ ================= =============== ``2.19.0.0`` ``-Python-3.6.4`` ``intel/2018a`` +``2.19.1.1`` ``intel/2020b`` ============ ================= =============== @@ -30030,6 +31063,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_pytest-xdist_1282: + +*pytest-xdist* +++++++++++++++ + +xdist: pytest distributed testing plugin The pytest-xdist plugin extends pytest with some unique test execution modes: * test run parallelization: if you have multiple CPUs or hosts you can use those for a combined test run. This allows to speed up development or to use special resources of remote machines. * --looponfail: run your tests repeatedly in a subprocess. After each run pytest waits until a file in your project changes and then re-runs the previously failing tests. This is repeated until all tests pass after which again a full run is performed. * Multi-Platform coverage: you can specify different Python interpreters or different platforms and run tests in parallel on all of them. Before running tests remotely, pytest efficiently “rsyncs” your program source code to the remote place. All test results are reported back and displayed to your local terminal. You may specify different Python versions and interpreters. + +*homepage*: https://github.com/pytest-dev/pytest-xdist + +========= ================== +version toolchain +========= ================== +``2.1.0`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_PYTHIA_463: *PYTHIA* @@ -30080,7 +31129,7 @@ version versionsuffix toolchain ``3.6.1`` ``foss/2017a``, ``intel/2017a`` ``3.6.2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.00`` ``3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018.01``, ``intelcuda/2017b`` -``3.6.4`` ``foss/2017a``, ``foss/2018a``, ``fosscuda/2018a``, ``golf/2018a``, ``intel/2018a``, ``iomkl/2018.02``, ``iomkl/2018a`` +``3.6.4`` ``foss/2017a``, ``foss/2018a``, ``fosscuda/2018a``, ``golf/2018a``, ``iimkl/2018a``, ``intel/2018a``, ``iomkl/2018.02``, ``iomkl/2018a`` ``3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.7.0`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.7.2`` ``GCCcore/8.2.0`` @@ -30150,13 +31199,14 @@ Python Bindings for the Parasail C Library *homepage*: https://github.com/jeffdaily/parasail-python -========== ================== =============== -version versionsuffix toolchain -========== ================== =============== -``1.1.12`` ``-Python-2.7.14`` ``intel/2018a`` -``1.1.16`` ``-Python-3.6.6`` ``foss/2018b`` -``1.2`` ``-Python-3.7.4`` ``intel/2019b`` -========== ================== =============== +========== ================== =================================================== +version versionsuffix toolchain +========== ================== =================================================== +``1.1.12`` ``-Python-2.7.14`` ``intel/2018a`` +``1.1.16`` ``-Python-3.6.6`` ``foss/2018b`` +``1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``1.2.2`` ``-Python-3.8.2`` ``intel/2020a`` +========== ================== =================================================== .. _list_software_python-weka-wrapper3_2008: @@ -30214,6 +31264,9 @@ version versionsuffix toolchain ``1.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``1.6.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.6.0`` ``-Python-3.7.4-imkl`` ``fosscuda/2019b`` +``1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` +``1.7.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ============================= ================================== @@ -30376,11 +31429,12 @@ qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from *homepage*: https://github.com/nanoporetech/qcat/releases -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``1.1.0`` ``-Python-3.7.4`` ``intel/2019b`` -========= ================= =============== +========= ================= =============================== +version versionsuffix toolchain +========= ================= =============================== +``1.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.1.0`` ``-Python-3.8.2`` ``intel/2020a`` +========= ================= =============================== .. _list_software_qcint_543: @@ -30498,6 +31552,8 @@ version toolchain ``2018.2`` ``system`` ``2019.4`` ``system`` ``2019.7`` ``system`` +``2020.8`` ``system`` +``2020.11`` ``system`` =========== ========== @@ -30784,21 +31840,22 @@ Quantum ESPRESSO is an integrated suite of computer codes for electronic-struc *homepage*: https://www.quantum-espresso.org -========= ============= ================================ -version versionsuffix toolchain -========= ============= ================================ -``5.3.0`` ``intel/2016.02-GCC-4.9`` -``5.4.0`` ``intel/2016.02-GCC-4.9`` -``5.4.0`` ``-hybrid`` ``foss/2016b`` -``6.0`` ``intel/2016b`` -``6.1`` ``intel/2017a`` -``6.2`` ``intel/2017b`` -``6.2.1`` ``iomkl/2017b`` -``6.3`` ``foss/2018b``, ``intel/2018b`` -``6.4.1`` ``intel/2019a`` -``6.5`` ``intel/2019a``, ``intel/2019b`` -``6.6`` ``foss/2019b``, ``intel/2019b`` -========= ============= ================================ +========= ============= =============================================== +version versionsuffix toolchain +========= ============= =============================================== +``5.3.0`` ``intel/2016.02-GCC-4.9`` +``5.4.0`` ``intel/2016.02-GCC-4.9`` +``5.4.0`` ``-hybrid`` ``foss/2016b`` +``6.0`` ``intel/2016b`` +``6.1`` ``intel/2017a`` +``6.2`` ``intel/2017b`` +``6.2.1`` ``iomkl/2017b`` +``6.3`` ``foss/2018b``, ``intel/2018b`` +``6.4.1`` ``intel/2019a`` +``6.5`` ``intel/2019a``, ``intel/2019b`` +``6.6`` ``foss/2019b``, ``foss/2020b``, ``intel/2019b`` +``6.7`` ``foss/2019b``, ``intel/2019b`` +========= ============= =============================================== .. _list_software_QUAST_398: @@ -30853,6 +31910,7 @@ version versionsuffix toolchain ``2.2.0`` ``-Python-2.7.14`` ``intel/2017b`` ``2.2.4`` ``-Python-3.7.2`` ``intel/2019a`` ``2.2.4`` ``-Python-3.8.2`` ``intel/2020a`` +``2.2.7`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================== =============== @@ -30946,7 +32004,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -30979,7 +32037,8 @@ version versionsuffix toolchain ``3.6.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``3.6.2`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``3.6.3`` ``foss/2020a`` -``4.0.0`` ``foss/2020a`` +``4.0.0`` ``foss/2020a``, ``fosscuda/2020a`` +``4.0.3`` ``foss/2020b`` ========= ============================= =================================================== @@ -31006,6 +32065,7 @@ version versionsuffix toolchain ``3.9`` ``-R-3.6.0`` ``foss/2019a`` ``3.10`` ``foss/2019b`` ``3.11`` ``-R-4.0.0`` ``foss/2020a`` +``3.12`` ``-R-4.0.3`` ``foss/2020b`` ======== ============= =============================== @@ -31231,17 +32291,17 @@ RAxML search algorithm for maximum likelihood based inference of phylogenetic tr *homepage*: https://github.com/stamatak/standard-RAxML -========== ================ ================================================ -version versionsuffix toolchain -========== ================ ================================================ -``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` -``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` -``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` -``8.2.12`` ``-hybrid-avx2`` ``iimpi/2019b``, ``intel/2019a`` -========== ================ ================================================ +========== ================ ================================================= +version versionsuffix toolchain +========== ================ ================================================= +``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` +``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` +``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` +``8.2.12`` ``-hybrid-avx2`` ``iimpi/2019b``, ``intel/2018b``, ``intel/2019a`` +========== ================ ================================================= .. _list_software_RAxML-NG_614: @@ -31294,6 +32354,22 @@ version versionsuffix toolchain ========= ================= ================== +.. _list_software_Raysect_731: + +*Raysect* ++++++++++ + +Raysect is an OOP ray-tracing framework for Python + +*homepage*: https://raysect.org + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.6.0`` ``-Python-3.6.6`` ``intel/2018b`` +========= ================= =============== + + .. _list_software_RBFOpt_525: *RBFOpt* @@ -31391,6 +32467,7 @@ version versionsuffix toolchain ``2018.09.3`` ``-Python-3.6.6`` ``intel/2018b`` ``2019.09.3`` ``-Python-3.7.4`` ``foss/2019b`` ``2020.03.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``2020.09.3`` ``-Python-3.7.4`` ``foss/2019b`` ============= ================= =============================== @@ -31408,6 +32485,7 @@ version versionsuffix toolchain ======== ================== ========== ``2.7`` ``-Java-1.7.0_60`` ``system`` ``2.12`` ``-Java-1.8`` ``system`` +``2.13`` ``-Java-11`` ``system`` ======== ================== ========== @@ -31519,16 +32597,18 @@ ReFrame is a framework for writing regression tests for HPC systems. *homepage*: https://github.com/eth-cscs/reframe -======== ========== -version toolchain -======== ========== -``2.18`` ``system`` -``2.19`` ``system`` -``2.20`` ``system`` -``2.21`` ``system`` -``3.0`` ``system`` -``3.2`` ``system`` -======== ========== +========= ========== +version toolchain +========= ========== +``2.18`` ``system`` +``2.19`` ``system`` +``2.20`` ``system`` +``2.21`` ``system`` +``3.0`` ``system`` +``3.2`` ``system`` +``3.3`` ``system`` +``3.4.1`` ``system`` +========= ========== .. _list_software_RELION_457: @@ -31813,6 +32893,7 @@ version versionsuffix toolchain ========== ================== =============== ``2.2.28`` ``-Python-2.7.11`` ``foss/2016a`` ``2.9.0`` ``gompi/2019b`` +``2.10.0`` ``gompi/2019b`` ========== ================== =============== @@ -31899,6 +32980,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_RNAmmer_658: + +*RNAmmer* ++++++++++ + +This is an example description. + +*homepage*: https://www.cbs.dtu.dk/services/RNAmmer + +======= ================ =============== +version versionsuffix toolchain +======= ================ =============== +``1.2`` ``-Perl-5.28.0`` ``intel/2018b`` +======= ================ =============== + + .. _list_software_rnaQUAST_719: *rnaQUAST* @@ -32130,7 +33227,7 @@ version versionsuffix toolchain RNA-Seq by Expectation-Maximization -*homepage*: http://deweylab.github.io/RSEM/ +*homepage*: https://deweylab.github.io/RSEM/ ========== ================================================ version toolchain @@ -32140,6 +33237,7 @@ version toolchain ``1.3.0`` ``foss/2016b``, ``intel/2017a`` ``1.3.1`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``1.3.2`` ``foss/2018b`` +``1.3.3`` ``foss/2019b`` ========== ================================================ @@ -32319,7 +33417,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -32426,6 +33524,7 @@ version versionsuffix toolchain ``1.1.0`` ``gompi/2019b`` ``1.2.0`` ``gompi/2019b`` ``1.3.0`` ``gompi/2020a`` +``1.4.0`` ``gompi/2020b`` ========== ================== ================================ @@ -32462,6 +33561,22 @@ version toolchain ========= ========== +.. _list_software_samblaster_1070: + +*samblaster* +++++++++++++ + +samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. + +*homepage*: https://github.com/GregoryFaust/samblaster + +========== ============== +version toolchain +========== ============== +``0.1.24`` ``foss/2018b`` +========== ============== + + .. _list_software_Samcef_591: *Samcef* @@ -32521,7 +33636,7 @@ version versionsuffix toolchain ``1.8`` ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.10`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` -``1.11`` ``GCC/9.3.0`` +``1.11`` ``GCC/10.2.0``, ``GCC/9.3.0`` ========== ================= ======================================================================================================================================= @@ -32637,6 +33752,7 @@ The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines version versionsuffix toolchain ========= ================================= ============================================================================================================================================ ``2.0.2`` ``gompi/2019b``, ``gompic/2019b`` +``2.0.2`` ``-BLIS-0.3.2`` ``gompi/2018b`` ``2.0.2`` ``-OpenBLAS-0.2.13-LAPACK-3.5.0`` ``gmvapich2/1.7.20`` ``2.0.2`` ``-OpenBLAS-0.2.15-LAPACK-3.6.0`` ``gmpich/2016a``, ``gmvapich2/2016a``, ``gompi/2016a`` ``2.0.2`` ``-OpenBLAS-0.2.18-LAPACK-3.6.0`` ``gompi/2016.04``, ``gompi/2016.06`` @@ -32648,7 +33764,7 @@ version versionsuffix toolchain ``2.0.2`` ``-OpenBLAS-0.3.3`` ``gompi/2018.08`` ``2.0.2`` ``-OpenBLAS-0.3.5`` ``gompi/2019a``, ``gompic/2019a`` ``2.1.0`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b`` -``2.1.0`` ``-bf`` ``gompi/2020a`` +``2.1.0`` ``-bf`` ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020b`` ``2.2`` ``-amd`` ``gompi/2020a`` ========= ================================= ============================================================================================================================================ @@ -32756,16 +33872,17 @@ version versionsuffix toolchain *scikit-build* ++++++++++++++ -Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions. +Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions. -*homepage*: https://scikit-build.github.io +*homepage*: https://scikit-build.readthedocs.io/en/latest -========== ================= =============================== -version versionsuffix toolchain -========== ================= =============================== -``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.10.0`` ``-Python-3.8.2`` ``foss/2020a`` -========== ================= =============================== +========== ================= ================================== +version versionsuffix toolchain +========== ================= ================================== +``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``0.11.1`` ``foss/2020b``, ``fosscuda/2020b`` +========== ================= ================================== .. _list_software_scikit-image_1207: @@ -32939,6 +34056,7 @@ version versionsuffix toolchain ``2019.10`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``2019.10`` ``-Python-3.7.2`` ``intel/2019a`` ``2019.10`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` +``2020.03`` ``-Python-2.7.18`` ``foss/2020a``, ``intel/2020a`` ``2020.03`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``2020.11`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` =========== ================== ======================================================================== @@ -32994,7 +34112,7 @@ version versionsuffix toolchain ``2.5.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2.5.1`` ``-Python-2.7.13`` ``intel/2017a`` ``3.0.1`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a``, ``iomkl/2018a`` -``3.0.1`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``3.0.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` ``3.0.1`` ``-Python-2.7.15-bare`` ``GCCcore/7.3.0`` ``3.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``3.0.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` @@ -33255,6 +34373,7 @@ version versionsuffix toolchain ``0.9.1`` ``-Python-2.7.16`` ``foss/2019b`` ``0.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``0.10.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.11.1`` ``intel/2020b`` ========== ================== ========================================================================================= @@ -33323,6 +34442,22 @@ version versionsuffix toolchain ========= ================= ================================== +.. _list_software_SeisSol_706: + +*SeisSol* ++++++++++ + +SeisSol is a software package for simulating wave propagation and dynamic rupture based on the arbitrary high-order accurate derivative discontinuous Galerkin method (ADER-DG). + +*homepage*: http://www.seissol.org + +========== ================== ============== +version versionsuffix toolchain +========== ================== ============== +``201703`` ``-Python-2.7.15`` ``foss/2018b`` +========== ================== ============== + + .. _list_software_SelEstim_806: *SelEstim* @@ -33385,6 +34520,7 @@ SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic plac version versionsuffix toolchain ========== ================= ============== ``4.3.10`` ``-Python-3.7.4`` ``foss/2019b`` +``4.4.0`` ``foss/2020b`` ========== ================= ============== @@ -33665,11 +34801,12 @@ SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing *homepage*: https://odelaneau.github.io/shapeit4/ -========= ============== -version toolchain -========= ============== -``4.1.3`` ``foss/2019b`` -========= ============== +========= ============================================== +version toolchain +========= ============================================== +``4.1.3`` ``foss/2019b`` +``4.2.0`` ``foss/2019b``, ``foss/2020a``, ``foss/2020b`` +========= ============================================== .. _list_software_Shapely_726: @@ -33804,6 +34941,22 @@ version toolchain ========= ============== +.. _list_software_SICER2_424: + +*SICER2* +++++++++ + +Redesigned and improved ChIP-seq broad peak calling tool SICER + +*homepage*: https://zanglab.github.io/SICER2/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.0.3`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_sickle_635: *sickle* @@ -33842,6 +34995,22 @@ version versionsuffix toolchain =============== ============= =============================== +.. _list_software_SignalP_686: + +*SignalP* ++++++++++ + +SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms + +*homepage*: https://services.healthtech.dtu.dk/software.php + +======== ============= ========== +version versionsuffix toolchain +======== ============= ========== +``5.0b`` ``-Linux`` ``system`` +======== ============= ========== + + .. _list_software_silx_448: *silx* @@ -34309,15 +35478,31 @@ version versionsuffix toolchain *SNAP* ++++++ +Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data + +*homepage*: http://snap.cs.berkeley.edu/ + +============== =============== +version toolchain +============== =============== +``1.0beta.23`` ``intel/2017b`` +============== =============== + + +.. _list_software_SNAP-HMM_577: + +*SNAP-HMM* +++++++++++ + SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser. -*homepage*: http://korflab.ucdavis.edu/software.html +*homepage*: https://korflab.github.io/ ============== ========================================================================= version toolchain ============== ========================================================================= -``1.0beta.23`` ``intel/2017b`` ``2013-11-29`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +``20190603`` ``GCC/10.2.0`` ============== ========================================================================= @@ -34523,6 +35708,22 @@ version toolchain =========== ================= +.. _list_software_SOCI_302: + +*SOCI* +++++++ + +SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++. + +*homepage*: http://soci.sourceforge.net/ + +========= ================= +version toolchain +========= ================= +``4.0.1`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_SolexaQA++_852: *SolexaQA++* @@ -34600,6 +35801,7 @@ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq version toolchain ========= ============= ``1.1.0`` ``GCC/9.3.0`` +``1.2.2`` ``GCC/9.3.0`` ========= ============= @@ -34787,17 +35989,18 @@ Spglib for Python. Spglib is a library for finding and handling crystal symmetri *homepage*: https://pypi.python.org/pypi/spglib -================ ================== =============== -version versionsuffix toolchain -================ ================== =============== -``1.9.4.2`` ``-Python-2.7.12`` ``intel/2016b`` -``1.9.5`` ``-Python-2.7.12`` ``intel/2016b`` -``1.9.9.38`` ``-Python-2.7.13`` ``intel/2017a`` -``1.10.0.2`` ``-Python-2.7.14`` ``intel/2017b`` -``1.10.0.2`` ``-Python-3.6.3`` ``intel/2017b`` -``1.14.1.post0`` ``-Python-3.7.2`` ``intel/2019a`` -``1.16.0`` ``-Python-3.8.2`` ``intel/2020a`` -================ ================== =============== +================ ================== =============================== +version versionsuffix toolchain +================ ================== =============================== +``1.9.4.2`` ``-Python-2.7.12`` ``intel/2016b`` +``1.9.5`` ``-Python-2.7.12`` ``intel/2016b`` +``1.9.9.38`` ``-Python-2.7.13`` ``intel/2017a`` +``1.10.0.2`` ``-Python-2.7.14`` ``intel/2017b`` +``1.10.0.2`` ``-Python-3.6.3`` ``intel/2017b`` +``1.14.1.post0`` ``-Python-3.7.2`` ``intel/2019a`` +``1.16.0`` ``foss/2020b``, ``intel/2020b`` +``1.16.0`` ``-Python-3.8.2`` ``intel/2020a`` +================ ================== =============================== .. _list_software_Sphinx_634: @@ -35131,6 +36334,22 @@ version versionsuffix toolchain ========= ================ =============== +.. _list_software_Stack_502: + +*Stack* ++++++++ + +Stack is a cross-platform program for developing Haskell projects. It is intended for Haskellers both new and experienced. + +*homepage*: https://docs.haskellstack.org + +========= ============= ========== +version versionsuffix toolchain +========= ============= ========== +``2.3.3`` ``-x86_64`` ``system`` +========= ============= ========== + + .. _list_software_Stacks_617: *Stacks* @@ -35161,6 +36380,7 @@ version toolchain ``2.5`` ``iccifort/2019.5.281`` ``2.41`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.53`` ``foss/2019b`` +``2.54`` ``foss/2020a`` ============== ============================================================================== @@ -35239,6 +36459,10 @@ version toolchain ``2.7.1a`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` ``2.7.2b`` ``GCC/8.3.0`` ``2.7.3a`` ``GCC/8.3.0``, ``GCC/9.3.0`` +``2.7.4a`` ``GCC/9.3.0`` +``2.7.5b`` ``GCC/9.3.0`` +``2.7.6a`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``2.7.7a`` ``GCC/10.2.0``, ``GCC/9.3.0`` ========== ============================================================== @@ -35327,10 +36551,11 @@ version versionsuffix toolchain ``0.8.0`` ``-Python-2.7.13`` ``intel/2017a`` ``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.9.0`` ``-Python-2.7.16`` ``intel/2019b`` -``0.9.0`` ``-Python-3.6.6`` ``intel/2018b`` +``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``0.10.1`` ``foss/2019a`` ``0.11.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``0.11.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.12.1`` ``intel/2020b`` ========== ================== =============================== @@ -35537,6 +36762,7 @@ version versionsuffix toolchain ``5.4.0`` ``-METIS-5.1.0`` ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` ``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b``, ``intel/2019b`` ``5.7.1`` ``-METIS-5.1.0`` ``foss/2020a``, ``intel/2020a`` +``5.8.1`` ``-METIS-5.1.0`` ``foss/2020b`` ========= =================== ================================================================================================= @@ -35641,6 +36867,23 @@ version toolchain ========= =============================== +.. _list_software_SuperLU_DIST_1091: + +*SuperLU_DIST* +++++++++++++++ + +SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. + +*homepage*: https://crd-legacy.lbl.gov/~xiaoye/SuperLU/ + +========= =================== =============================== +version versionsuffix toolchain +========= =================== =============================== +``5.4.0`` ``-trisolve-merge`` ``intel/2020a`` +``6.4.0`` ``foss/2020a``, ``intel/2020a`` +========= =================== =============================== + + .. _list_software_supermagic_1072: *supermagic* @@ -35764,11 +37007,12 @@ The Soil & Water Assessment Tool (SWAT) is a small watershed to river basin-scal *homepage*: https://swatplus.gitbook.io -========== ============= -version toolchain -========== ============= -``60.4.1`` ``GCC/9.3.0`` -========== ============= +========== ======================= +version toolchain +========== ======================= +``60.4.1`` ``GCC/9.3.0`` +``60.5.1`` ``iccifort/2020.4.304`` +========== ======================= .. _list_software_SWIG_314: @@ -35791,6 +37035,7 @@ version versionsuffix toolchain ``3.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.0.12`` ``-Python-2.7.13`` ``intel/2017a`` ``3.0.12`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``3.0.12`` ``-Python-2.7.14-bare`` ``GCCcore/6.4.0`` ``3.0.12`` ``-Python-2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``intel/2018b`` ``3.0.12`` ``-Python-3.6.1`` ``intel/2017a`` ``3.0.12`` ``-Python-3.6.2`` ``foss/2017b``, ``intel/2018.00`` @@ -35884,12 +37129,12 @@ Szip compression software, providing lossless compression of scientific data *homepage*: https://www.hdfgroup.org/doc_resource/SZIP/ -========= ========================================================================================================================================================================================================================================================================= -version toolchain -========= ========================================================================================================================================================================================================================================================================= -``2.1`` ``GCC/4.8.1``, ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ========================================================================================================================================================================================================================================================================= +========= ============================================================================================================================================================================================================================================================================================= +version toolchain +========= ============================================================================================================================================================================================================================================================================================= +``2.1`` ``GCC/4.8.1``, ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``gmpolf/2017.10``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` +``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ============================================================================================================================================================================================================================================================================================= .. _list_software_letter_t: @@ -35898,7 +37143,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` +:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_typing-extensions_1816` .. _list_software_tabix_536: @@ -36029,6 +37274,7 @@ version toolchain ``2019_U9`` ``GCCcore/8.3.0`` ``2020.1`` ``GCCcore/9.3.0`` ``2020.2`` ``GCCcore/8.3.0`` +``2020.3`` ``GCCcore/10.2.0`` ============== ================================================== @@ -36156,6 +37402,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_Teneto_623: + +*Teneto* +++++++++ + +Teneto is package for deriving, analysing and plotting temporal network representations. Additional tools for temporal network analysis with neuroimaging contexts. + +*homepage*: https://teneto.readthedocs.io + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.5.1`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_tensorboardX_1275: *tensorboardX* @@ -36217,6 +37479,8 @@ version versionsuffix toolchain ``1.14.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``1.15.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``1.15.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.15.5`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.15.5`` ``-Python-3.7.4-nompi`` ``fosscuda/2019b`` ``2.0.0`` ``-Python-3.7.2`` ``foss/2019a`` ``2.0.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``2.0.1`` ``-Python-3.7.2`` ``foss/2019a`` @@ -36224,7 +37488,9 @@ version versionsuffix toolchain ``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``2.3.1`` ``-Python-3.8.2`` ``foss/2020a`` +``2.3.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``2.4.1`` ``foss/2020b``, ``fosscuda/2020b`` +``2.4.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========== ============================= =================================================== @@ -36260,6 +37526,22 @@ version versionsuffix toolchain =========== ================== ================== +.. _list_software_terastructure_1437: + +*terastructure* ++++++++++++++++ + +TeraStructure is a new algorithm to fit Bayesian models of genetic variation in human populations on tera-sample-sized data sets (10^12 observed genotypes, i.e., 1M individuals at 1M SNPs). This package provides a scalable, multi-threaded C++ implementation that can be run on a single computer. + +*homepage*: https://github.com/StoreyLab/terastructure + +======= ============= +version toolchain +======= ============= +``1.0`` ``GCC/8.3.0`` +======= ============= + + .. _list_software_Tesla-Deployment-Kit_1948: *Tesla-Deployment-Kit* @@ -36443,6 +37725,7 @@ version versionsuffix toolchain ``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` ``1.0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``1.0.4`` ``-Python-3.8.2`` ``foss/2020a`` +``1.1.2`` ``-PyMC`` ``intel/2020b`` ========= ================== =================================================== @@ -36812,17 +38095,19 @@ Datasets, Transforms and Models specific to Computer Vision *homepage*: https://github.com/pytorch/vision -========= =============================== ================================== -version versionsuffix toolchain -========= =============================== ================================== -``0.2.0`` ``-Python-3.6.4`` ``intel/2018a`` -``0.2.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` -``0.2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` -``0.4.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``0.5.0`` ``-Python-3.7.4-PyTorch-1.4.0`` ``fosscuda/2019b`` -``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` -========= =============================== ================================== +========= ==================================== ================================== +version versionsuffix toolchain +========= ==================================== ================================== +``0.2.0`` ``-Python-3.6.4`` ``intel/2018a`` +``0.2.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` +``0.2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` +``0.4.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``0.5.0`` ``-Python-3.7.4-PyTorch-1.4.0`` ``fosscuda/2019b`` +``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` +``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0-imkl`` ``fosscuda/2019b`` +``0.8.2`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` +========= ==================================== ================================== .. _list_software_TotalView_927: @@ -36848,7 +38133,7 @@ version versionsuffix toolchain *tqdm* ++++++ -Instantly make your loops show a smart progress meter. +A fast, extensible progress bar for Python and CLI *homepage*: https://github.com/tqdm/tqdm @@ -36863,6 +38148,7 @@ version versionsuffix toolchain ``4.41.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``4.47.0`` ``GCCcore/9.3.0`` ``4.51.0`` ``-Python-3.8.2`` ``intel/2020a`` +``4.56.2`` ``GCCcore/10.2.0`` ========== ================== =============================== @@ -36898,6 +38184,22 @@ version versionsuffix toolchain ========= ================ =============== +.. _list_software_Transformers_1286: + +*Transformers* +++++++++++++++ + +State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0 + +*homepage*: https://github.com/huggingface/transformers + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``4.2.1`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_Transrate_948: *Transrate* @@ -37336,6 +38638,23 @@ version versionsuffix toolchain ============ ================== =============== +.. _list_software_typing-extensions_1816: + +*typing-extensions* ++++++++++++++++++++ + +Typing Extensions – Backported and Experimental Type Hints for Python + +*homepage*: https://github.com/python/typing/blob/master/typing_extensions/README.rst + +=========== ================= ================== +version versionsuffix toolchain +=========== ================= ================== +``3.7.4.3`` ``GCCcore/10.2.0`` +``3.7.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +=========== ================= ================== + + .. _list_software_letter_u: *U* @@ -37352,7 +38671,7 @@ version versionsuffix toolchain UCLUST: Extreme high-speed sequence clustering, alignment and database search. -*homepage*: http://www.drive5.com/usearch/index.html +*homepage*: https://www.drive5.com/usearch/index.html =========== =============== ========== version versionsuffix toolchain @@ -37723,6 +39042,7 @@ version versionsuffix toolchain ``2.2`` ``-R-3.5.1`` ``foss/2018b`` ``2.3`` ``-R-3.6.0`` ``foss/2019a``, ``intel/2019a`` ``3.2.0`` ``-R-3.6.2`` ``foss/2019b`` +``3.4.0`` ``-R-4.0.0`` ``foss/2020a`` ========= ============= =============================== @@ -38273,6 +39593,7 @@ version toolchain ========== ======================================== ``2.9.1`` ``foss/2018b`` ``2.13.4`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.15.0`` ``GCC/9.3.0`` ========== ======================================== @@ -38301,25 +39622,25 @@ The Visualization Toolkit (VTK) is an open-source, freely available software sys *homepage*: https://www.vtk.org -========= ================== ================================== -version versionsuffix toolchain -========= ================== ================================== -``6.3.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``6.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``7.0.0`` ``-Python-2.7.12`` ``intel/2016b`` -``7.1.0`` ``-Python-2.7.12`` ``intel/2016b`` -``7.1.1`` ``-Python-2.7.13`` ``intel/2017a`` -``8.0.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``8.1.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``8.1.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` -``8.1.1`` ``-Python-2.7.15`` ``foss/2018b`` -``8.1.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``8.2.0`` ``-Python-2.7.15`` ``foss/2019a`` -``8.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``8.2.0`` ``-Python-3.7.4`` ``foss/2019b`` -``8.2.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -========= ================== ================================== +========= ================== =================================================== +version versionsuffix toolchain +========= ================== =================================================== +``6.3.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``6.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``7.0.0`` ``-Python-2.7.12`` ``intel/2016b`` +``7.1.0`` ``-Python-2.7.12`` ``intel/2016b`` +``7.1.1`` ``-Python-2.7.13`` ``intel/2017a`` +``8.0.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``8.1.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``8.1.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` +``8.1.1`` ``-Python-2.7.15`` ``foss/2018b`` +``8.1.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``8.2.0`` ``-Python-2.7.15`` ``foss/2019a`` +``8.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``8.2.0`` ``-Python-3.7.4`` ``foss/2019b`` +``8.2.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` +========= ================== =================================================== .. _list_software_VTune_498: @@ -38392,7 +39713,7 @@ version toolchain --- -:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_WCT_238` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_WHAM_301` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` +:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_WCT_238` - :ref:`list_software_wcwidth_762` - :ref:`list_software_webin-cli_890` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_WHAM_301` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` .. _list_software_wandb_524: @@ -38428,6 +39749,7 @@ version versionsuffix toolchain ``2.0.1.1`` ``-abinit`` ``intel/2018b`` ``2.1.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``3.0.0`` ``intel/2018b`` +``3.1.0`` ``foss/2020b``, ``intel/2020b`` =========== ============= ================================================ @@ -38482,6 +39804,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_webin-cli_890: + +*webin-cli* ++++++++++++ + +The Webin command line submission interface can be used to validate, upload and submit files to the European Nucleotide Archive (ENA) + +*homepage*: https://github.com/enasequence/webin-cli + +========= ========== +version toolchain +========= ========== +``1.8.9`` ``system`` +========= ========== + + .. _list_software_WebKitGTK+_855: *WebKitGTK+* @@ -38560,12 +39898,14 @@ An implementation of WHAM: the Weighted Histogram Analysis Method *homepage*: http://membrane.urmc.rochester.edu/?page_id=126 -=========== ============= =============== -version versionsuffix toolchain -=========== ============= =============== -``2.0.9.1`` ``intel/2019a`` -``2.0.9.1`` ``-kj_mol`` ``intel/2019a`` -=========== ============= =============== +============ ============= =============== +version versionsuffix toolchain +============ ============= =============== +``2.0.9.1`` ``intel/2019a`` +``2.0.9.1`` ``-kj_mol`` ``intel/2019a`` +``2.0.10.2`` ``intel/2020a`` +``2.0.10.2`` ``-kj_mol`` ``intel/2020a`` +============ ============= =============== .. _list_software_wheel_533: @@ -38797,11 +40137,12 @@ Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio *homepage*: https://github.com/ruanjue/wtdbg2 -======= ================= -version toolchain -======= ================= -``2.5`` ``GCCcore/9.3.0`` -======= ================= +======= ================== +version toolchain +======= ================== +``2.3`` ``GCC/7.3.0-2.30`` +``2.5`` ``GCCcore/9.3.0`` +======= ================== .. _list_software_wxPropertyGrid_1498: @@ -38983,10 +40324,11 @@ version versionsuffix toolchain ``0.10.3`` ``-Python-3.6.4`` ``intel/2018a`` ``0.10.4`` ``-Python-3.6.4`` ``intel/2018a`` ``0.10.8`` ``-Python-3.6.4`` ``intel/2018a`` -``0.12.1`` ``-Python-3.6.6`` ``intel/2018b`` +``0.12.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` ``0.15.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``0.16.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.16.2`` ``intel/2020b`` ========== ================== =============================== @@ -39567,7 +40909,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Yade_387` - :ref:`list_software_yaff_422` - :ref:`list_software_Yambo_504` - :ref:`list_software_YAPS_317` - :ref:`list_software_Yasm_410` - :ref:`list_software_YAXT_326` +:ref:`list_software_Yade_387` - :ref:`list_software_yaff_422` - :ref:`list_software_Yambo_504` - :ref:`list_software_YANK_307` - :ref:`list_software_YAPS_317` - :ref:`list_software_Yasm_410` - :ref:`list_software_YAXT_326` .. _list_software_Yade_387: @@ -39631,6 +40973,22 @@ version toolchain ========= ========================= +.. _list_software_YANK_307: + +*YANK* +++++++ + +A GPU-accelerated Python framework for exploring algorithms for alchemical free energy calculations + +*homepage*: http://getyank.org/ + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``0.25.2`` ``-Python-3.8.2`` ``intel/2020a`` +========== ================= =============== + + .. _list_software_YAPS_317: *YAPS* @@ -39688,7 +41046,23 @@ version toolchain --- -:ref:`list_software_zarr_447` - :ref:`list_software_ZeroMQ_574` - :ref:`list_software_zingeR_623` - :ref:`list_software_Zip_307` - :ref:`list_software_zlib_433` - :ref:`list_software_zlibbioc_846` - :ref:`list_software_ZPAQ_316` - :ref:`list_software_zsh_341` - :ref:`list_software_zstd_453` +:ref:`list_software_Z3_141` - :ref:`list_software_zarr_447` - :ref:`list_software_ZeroMQ_574` - :ref:`list_software_zingeR_623` - :ref:`list_software_Zip_307` - :ref:`list_software_zlib_433` - :ref:`list_software_zlibbioc_846` - :ref:`list_software_ZPAQ_316` - :ref:`list_software_zsh_341` - :ref:`list_software_zstd_453` + + +.. _list_software_Z3_141: + +*Z3* +++++ + +Z3 is a theorem prover from Microsoft Research. + +*homepage*: https://github.com/Z3Prover/z3 + +========= ==================================== +version toolchain +========= ==================================== +``4.8.9`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ==================================== .. _list_software_zarr_447: @@ -39841,12 +41215,12 @@ Zstandard is a real-time compression algorithm, providing high compression ratio *homepage*: https://facebook.github.io/zstd -========= ==================================== -version toolchain -========= ==================================== -``1.3.4`` ``foss/2016b`` -``1.4.0`` ``GCCcore/8.2.0``, ``foss/2018b`` -``1.4.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.4.5`` ``GCCcore/10.2.0`` -========= ==================================== +========= ==================================================== +version toolchain +========= ==================================================== +``1.3.4`` ``foss/2016b`` +``1.4.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2018b`` +``1.4.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.4.5`` ``GCCcore/10.2.0`` +========= ==================================================== diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index b4c5cd6d..1e04d258 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -21,6 +21,7 @@ * EB_ANSYS * EB_ant + * EB_AOCC * EB_BiSearch * EB_Chimera * EB_code_minus_server @@ -316,6 +317,7 @@ * SystemMPI * EB_Inspector + * EB_intel_minus_compilers * EB_ipp * EB_itac * EB_tbb @@ -332,6 +334,7 @@ * EB_ANSYS * EB_ant + * EB_AOCC * EB_BiSearch * EB_Chimera * EB_code_minus_server diff --git a/docs/version-specific/easyconfig_constants.rst b/docs/version-specific/easyconfig_constants.rst index 223bdc23..96f44a1f 100644 --- a/docs/version-specific/easyconfig_constants.rst +++ b/docs/version-specific/easyconfig_constants.rst @@ -19,6 +19,6 @@ Constant name Constant value ``OS_TYPE`` ``Darwin`` System type (e.g. 'Linux' or 'Darwin') ``OS_VERSION`` ``UNKNOWN`` System version ``SYSTEM`` ``{'name': 'system', 'version': 'system'}`` System toolchain -``SYS_PYTHON_VERSION`` ``3.8.5`` System Python version (platform.python_version()) +``SYS_PYTHON_VERSION`` ``3.9.0`` System Python version (platform.python_version()) ====================== ============================================================= ================================================================================ diff --git a/docs/version-specific/easyconfig_parameters.rst b/docs/version-specific/easyconfig_parameters.rst index c7bf2d89..566fd2ca 100644 --- a/docs/version-specific/easyconfig_parameters.rst +++ b/docs/version-specific/easyconfig_parameters.rst @@ -118,6 +118,7 @@ license parameters ======================= =================================================================================================================================================== ================= **Parameter name** **Description** **Default value** ======================= =================================================================================================================================================== ================= +``accept_eula`` Accepted End User License Agreement (EULA) for this software False ``group`` Name of the user group for which the software should be available; format: string or 2-tuple with group name + custom error for users outside group None ``key`` Key for installing software None ``license_file`` License file for software None diff --git a/docs/version-specific/easyconfig_templates.rst b/docs/version-specific/easyconfig_templates.rst index f247ae89..f248f8c0 100644 --- a/docs/version-specific/easyconfig_templates.rst +++ b/docs/version-specific/easyconfig_templates.rst @@ -5,37 +5,38 @@ Template names/values derived from easyconfig instance ------------------------------------------------------ -=========================== ======================================================== -Template name Template value -=========================== ======================================================== -``%(arch)s`` System architecture (e.g. x86_64, aarch64, ppc64le, ...) -``%(module_name)s`` Module name -``%(nameletter)s`` First letter of software name -``%(toolchain_name)s`` Toolchain name -``%(toolchain_version)s`` Toolchain version -``%(version_major_minor)s`` Major.Minor version -``%(version_major)s`` Major version -``%(version_minor)s`` Minor version -=========================== ======================================================== +=========================== ============================= +Template name Template value +=========================== ============================= +``%(module_name)s`` Module name +``%(nameletter)s`` First letter of software name +``%(toolchain_name)s`` Toolchain name +``%(toolchain_version)s`` Toolchain version +``%(version_major_minor)s`` Major.Minor version +``%(version_major)s`` Major version +``%(version_minor)s`` Minor version +=========================== ============================= Template names/values for (short) software versions --------------------------------------------------- -==================== ========================================== -Template name Template value -==================== ========================================== -``%(cudashortver)s`` short version for CUDA (.) -``%(cudaver)s`` full version for CUDA -``%(javashortver)s`` short version for Java (.) -``%(javaver)s`` full version for Java -``%(perlshortver)s`` short version for Perl (.) -``%(perlver)s`` full version for Perl -``%(pyshortver)s`` short version for Python (.) -``%(pyver)s`` full version for Python -``%(rshortver)s`` short version for R (.) -``%(rver)s`` full version for R -==================== ========================================== +==================== ============================================ +Template name Template value +==================== ============================================ +``%(cudashortver)s`` short version for CUDA (.) +``%(cudaver)s`` full version for CUDA +``%(cudashortver)s`` short version for CUDAcore (.) +``%(cudaver)s`` full version for CUDAcore +``%(javashortver)s`` short version for Java (.) +``%(javaver)s`` full version for Java +``%(perlshortver)s`` short version for Perl (.) +``%(perlver)s`` full version for Perl +``%(pyshortver)s`` short version for Python (.) +``%(pyver)s`` full version for Python +``%(rshortver)s`` short version for R (.) +``%(rver)s`` full version for R +==================== ============================================ Template names/values as set in easyconfig @@ -69,6 +70,21 @@ Template name Template value ``%(installdir)s`` Installation directory ================== ====================== +Template values which are defined dynamically +--------------------------------------------- + +================================= ========================================================================================================================================================================== +Template name Template value +================================= ========================================================================================================================================================================== +``%(arch)s`` System architecture (e.g. x86_64, aarch64, ppc64le, ...) +``%(mpi_cmd_prefix)s`` Prefix command for running MPI programs (with default number of ranks) +``%(cuda_compute_capabilities)s`` Comma-separated list of CUDA compute capabilities, as specified via --cuda-compute-capabilities configuration option or via cuda_compute_capabilities easyconfig parameter +``%(cuda_cc_space_sep)s`` Space-separated list of CUDA compute capabilities +``%(cuda_cc_semicolon_sep)s`` Semicolon-separated list of CUDA compute capabilities +``%(cuda_sm_comma_sep)s`` Comma-separated list of sm_* values that correspond with CUDA compute capabilities +``%(cuda_sm_space_sep)s`` Space-separated list of sm_* values that correspond with CUDA compute capabilities +================================= ========================================================================================================================================================================== + Template constants that can be used in easyconfigs -------------------------------------------------- diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index 79c5200e..1cdeaaae 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -724,11 +724,7 @@ Customised steps in ``IntelBase`` easyblock ------------------------------------------- * ``build_step`` - Binary installation files, so no building. * ``configure_step`` - Configure: handle license file and clean home dir. -* ``install_step`` - Actual installation - - - create silent cfg file - - set environment parameters - - execute command +* ``install_step`` - Install Intel software .. _JAR: diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index 9a22d1c2..56939da5 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -84,6 +84,7 @@ Option flag Option desc ``--avail-repositories`` Show all repository types (incl. non-usable) (default: False) ``--buildpath=BUILDPATH`` Temporary build path (default: /home/example/.local/easybuild/build) ``--containerpath=CONTAINERPATH`` Location where container recipe & image will be stored (default: /home/example/.local/easybuild/containers) +``--envvars-user-modules=ENVVARS-USER-MODULES`` List of environment variables that hold the base paths for which user-specific modules will be installed relative to (type comma-separated list; default: HOME) ``--external-modules-metadata=EXTERNAL-MODULES-METADATA`` List of (glob patterns for) paths to files specifying metadata for external modules (INI format) (type comma-separated list) ``--hooks=HOOKS`` Location of Python module with hook implementations (type str) ``--ignore-dirs=IGNORE-DIRS`` Directory names to ignore when searching for files/dirs (type comma-separated list; default: .git,.svn) @@ -112,7 +113,7 @@ Option flag Option desc ``--sourcepath=SOURCEPATH`` Path(s) to where sources should be downloaded (string, colon-separated) (default: /home/example/.local/easybuild/sources) ``--subdir-modules=SUBDIR-MODULES`` Installpath subdir for modules (default: modules) ``--subdir-software=SUBDIR-SOFTWARE`` Installpath subdir for software (default: software) -``--subdir-user-modules=SUBDIR-USER-MODULES`` Base path of user-specific modules relative to their $HOME +``--subdir-user-modules=SUBDIR-USER-MODULES`` Base path of user-specific modules relative to --envvar-user-modules ``--suffix-modules-path=SUFFIX-MODULES-PATH`` Suffix for module files install path (default: all) ``--testoutput=TESTOUTPUT`` Path to where a job should place the output (to be set within jobscript) ``--tmp-logdir=TMP-LOGDIR`` Log directory where temporary log files are stored @@ -154,6 +155,7 @@ GitHub integration options ======================================================= ================================================================================================================================= Option flag Option description ======================================================= ================================================================================================================================= +``--add-pr-labels=PR#`` Try to add labels to PR based on files changed (type ) ``--check-contrib`` Runs checks to see whether the given easyconfigs are ready to be contributed back (default: False) ``--check-github`` Check status of GitHub integration, and report back (default: False) ``--check-style`` Run a style check on the given easyconfigs (default: False) @@ -243,85 +245,88 @@ Option flag Option description Override options ---------------- -========================================================================= ============================================================================================================================================================================================================================================= -Option flag Option description -========================================================================= ============================================================================================================================================================================================================================================= -``--add-dummy-to-minimal-toolchains`` Include dummy toolchain in minimal toolchain searches [DEPRECATED, use --add-system-to-minimal-toolchains instead!) (default: False) -``--add-system-to-minimal-toolchains`` Include system toolchain in minimal toolchain searches (default: False) -``--allow-loaded-modules=ALLOW-LOADED-MODULES`` List of software names for which to allow loaded modules in initial environment (type comma-separated list; default: EasyBuild) -``--allow-modules-tool-mismatch`` Allow mismatch of modules tool and definition of 'module' function (default: False) -``--allow-use-as-root-and-accept-consequences`` Allow using of EasyBuild as root (NOT RECOMMENDED!) (default: False) -``--backup-modules`` Back up an existing module file, if any. Only works when using --module-only -``--check-ebroot-env-vars=CHECK-EBROOT-ENV-VARS`` Action to take when defined $EBROOT* environment variables are found for which there is no matching loaded module; supported values: error, ignore, unset, warn (default: warn) -``--cleanup-builddir`` Cleanup build dir after successful installation. (default: True; disable with --disable-cleanup-builddir) -``--cleanup-tmpdir`` Cleanup tmp dir after successful run. (default: True; disable with --disable-cleanup-tmpdir) -``--color=WHEN`` Colorize output (type choice; default: auto) (choices: auto, always, never) -``--consider-archived-easyconfigs`` Also consider archived easyconfigs (default: False) -``-C, --containerize`` Generate container recipe/image (default: False) -``--copy-ec`` Copy specified easyconfig(s) to specified location (default: False) -``--cuda-compute-capabilities=CUDA-COMPUTE-CAPABILITIES`` List of CUDA compute capabilities to use when building GPU software; values should be specified as digits separated by a dot, for example: 3.5,5.0,7.2 (type comma-separated list) -``--debug-lmod`` Run Lmod modules tool commands in debug module (default: False) -``--default-opt-level=DEFAULT-OPT-LEVEL`` Specify default optimisation level (type choice; default: defaultopt) (choices: noopt, lowopt, defaultopt, opt) -``--deprecated=DEPRECATED`` Run pretending to be (future) version, to test removal of deprecated code. -``--detect-loaded-modules=DETECT-LOADED-MODULES`` Detect loaded EasyBuild-generated modules, act accordingly; supported values: error, ignore, purge, unload, warn (default: warn) -``--devel`` Enable including of development log messages (default: False) -``--download-timeout=DOWNLOAD-TIMEOUT`` Timeout for initiating downloads (in seconds) (type ) -``--dump-autopep8`` Reformat easyconfigs using autopep8 when dumping them (default: False) -``-e CLASS, --easyblock=CLASS`` easyblock to use for processing the spec file or dumping the options -``--enforce-checksums`` Enforce availability of checksums for all sources/patches, so they can be verified (default: False) -``--experimental`` Allow experimental code (with behaviour that can be changed/removed at any given time). (default: False) -``--extra-modules=EXTRA-MODULES`` List of extra modules to load after setting up the build environment (type comma-separated list) -``--fetch`` Allow downloading sources ignoring OS and modules tool dependencies, implies --stop=fetch, --ignore-osdeps and ignore modules tool (default: False) -``--filter-deps=FILTER-DEPS`` List of dependencies that you do *not* want to install with EasyBuild, because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses) (type comma-separated list) -``--filter-env-vars=FILTER-ENV-VARS`` List of names of environment variables that should *not* be defined/updated by module files generated by EasyBuild (type comma-separated list) -``--fixed-installdir-naming-scheme`` Use fixed naming scheme for installation directories (default: True; disable with --disable-fixed-installdir-naming-scheme) -``--force-download=FORCE-DOWNLOAD`` Force re-downloading of sources and/or patches, even if they are available already in source path (type choice; default: sources) (choices: all, patches, sources) -``--generate-devel-module`` Generate a develop module file, implies --force if disabled (default: True; disable with --disable-generate-devel-module) -``--group=GROUP`` Group to be used for software installations (only verified, not set) -``--group-writable-installdir`` Enable group write permissions on installation directory after installation (default: False) -``--hidden`` Install 'hidden' module file(s) by prefixing their version with '.' (default: False) -``--hide-deps=HIDE-DEPS`` Comma separated list of dependencies that you want automatically hidden, (e.g. --hide-deps=zlib,ncurses) (type comma-separated list) -``--hide-toolchains=HIDE-TOOLCHAINS`` Comma separated list of toolchains that you want automatically hidden, (e.g. --hide-toolchains=GCCcore) (type comma-separated list) -``--ignore-checksums`` Ignore failing checksum verification (default: False) -``--ignore-osdeps`` Ignore any listed OS dependencies (default: False) -``--install-latest-eb-release`` Install latest known version of easybuild (default: False) -``--lib64-fallback-sanity-check`` Fallback in sanity check to lib64/ equivalent for missing libraries (default: True; disable with --disable-lib64-fallback-sanity-check) -``--lib64-lib-symlink`` Automatically create symlinks for lib64/ pointing to lib/ if the former is missing (default: True; disable with --disable-lib64-lib-symlink) -``--max-fail-ratio-adjust-permissions=MAX-FAIL-RATIO-ADJUST-PERMISSIONS`` Maximum ratio for failures to allow when adjusting permissions (type float; default: 0.5) -``--minimal-build-env=MINIMAL-BUILD-ENV`` Minimal build environment to define when using system toolchain, specified as a comma-separated list that defines a mapping between name of environment variable and its value separated by a colon (':') (default: CC:gcc,CXX:g++) -``--minimal-toolchains`` Use minimal toolchain when resolving dependencies (default: False) -``--module-only`` Only generate module file(s); skip all steps except for module, prepare, ready, postiter, sanitycheck (default: False) -``--modules-tool-version-check`` Check version of modules tool being used (default: True; disable with --disable-modules-tool-version-check) -``--mpi-cmd-template=MPI-CMD-TEMPLATE`` Template for MPI commands (template keys: %(nr_ranks)s, %(cmd)s) -``--mpi-tests`` Run MPI tests (when relevant) (default: True; disable with --disable-mpi-tests) -``--optarch=OPTARCH`` Set architecture optimization, overriding native architecture optimizations -``--output-format=OUTPUT-FORMAT`` Set output format (type choice; default: txt) (choices: txt, rst) -``--parallel=PARALLEL`` Specify (maximum) level of parallellism used during build procedure (type int) -``--pre-create-installdir`` Create installation directory before submitting build jobs (default: True; disable with --disable-pre-create-installdir) -``-p, --pretend`` Does the build/installation in a test directory located in $HOME/easybuildinstall (default: False) -``--read-only-installdir`` Set read-only permissions on installation directory after installation (default: False) -``--remove-ghost-install-dirs`` Remove ghost installation directories when --force or --rebuild is used, rather than just warning about them (default: False) -``--rpath`` Enable use of RPATH for linking with libraries (default: False) -``--rpath-filter=RPATH-FILTER`` List of regex patterns to use for filtering out RPATH paths (type comma-separated list) -``--set-default-module`` Set the generated module as default (default: False) -``--set-gid-bit`` Set group ID bit on newly created directories (default: False) -``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` Silence specified deprecation warnings (type comma-separated list) -``-t, --skip-test-cases`` Skip running test cases (default: False) -``--skip-test-step`` Skip running the test step (e.g. unit tests) (default: False) -``--sticky-bit`` Set sticky bit on newly created directories (default: False) -``--sysroot=SYSROOT`` Location root directory of system, prefix for standard paths like /usr/lib and /usr/include -``-T, --trace`` Provide more information in output to stdout on progress (default: False) -``--umask=UMASK`` umask to use (e.g. '022'); non-user write permissions on install directories are removed -``--update-modules-tool-cache`` Update modules tool cache file(s) after generating module file (default: False) -``--use-ccache=PATH`` Enable use of ccache to speed up compilation, with specified cache dir (type ; default: False) -``--use-existing-modules`` Use existing modules when resolving dependencies with minimal toolchains (default: False) -``--use-f90cache=PATH`` Enable use of f90cache to speed up compilation, with specified cache dir (type ; default: False) -``--verify-easyconfig-filenames`` Verify whether filename of specified easyconfigs matches with contents (default: False) -``--wait-on-lock=WAIT-ON-LOCK`` Wait for lock to be released; 0 implies no waiting (exit with an error if the lock already exists), non-zero value specified waiting interval [DEPRECATED: use --wait-on-lock-interval and --wait-on-lock-limit instead] (type ) -``--wait-on-lock-interval=WAIT-ON-LOCK-INTERVAL`` Wait interval (in seconds) to use when waiting for existing lock to be removed (type ; default: 60) -``--wait-on-lock-limit=WAIT-ON-LOCK-LIMIT`` Maximum amount of time (in seconds) to wait until lock is released (0 means no waiting at all, exit with error; -1 means no waiting limit, keep waiting) (type ; default: 0) -``--zip-logs=ZIP-LOGS`` Zip logs that are copied to install directory, using specified command (default: gzip) -========================================================================= ============================================================================================================================================================================================================================================= +========================================================================= ================================================================================================================================================================================================================================================================================ +Option flag Option description +========================================================================= ================================================================================================================================================================================================================================================================================ +``--accept-eula=ACCEPT-EULA`` Accept EULA for specified software (type comma-separated list; default: ) +``--add-dummy-to-minimal-toolchains`` Include dummy toolchain in minimal toolchain searches [DEPRECATED, use --add-system-to-minimal-toolchains instead!) (default: False) +``--add-system-to-minimal-toolchains`` Include system toolchain in minimal toolchain searches (default: False) +``--allow-loaded-modules=ALLOW-LOADED-MODULES`` List of software names for which to allow loaded modules in initial environment (type comma-separated list; default: EasyBuild) +``--allow-modules-tool-mismatch`` Allow mismatch of modules tool and definition of 'module' function (default: False) +``--allow-use-as-root-and-accept-consequences`` Allow using of EasyBuild as root (NOT RECOMMENDED!) (default: False) +``--backup-modules`` Back up an existing module file, if any. Only works when using --module-only +``--check-ebroot-env-vars=CHECK-EBROOT-ENV-VARS`` Action to take when defined $EBROOT* environment variables are found for which there is no matching loaded module; supported values: error, ignore, unset, warn (default: warn) +``--cleanup-builddir`` Cleanup build dir after successful installation. (default: True; disable with --disable-cleanup-builddir) +``--cleanup-tmpdir`` Cleanup tmp dir after successful run. (default: True; disable with --disable-cleanup-tmpdir) +``--color=WHEN`` Colorize output (type choice; default: auto) (choices: auto, always, never) +``--consider-archived-easyconfigs`` Also consider archived easyconfigs (default: False) +``-C, --containerize`` Generate container recipe/image (default: False) +``--copy-ec`` Copy specified easyconfig(s) to specified location (default: False) +``--cuda-compute-capabilities=CUDA-COMPUTE-CAPABILITIES`` List of CUDA compute capabilities to use when building GPU software; values should be specified as digits separated by a dot, for example: 3.5,5.0,7.2 (type comma-separated list) +``--debug-lmod`` Run Lmod modules tool commands in debug module (default: False) +``--default-opt-level=DEFAULT-OPT-LEVEL`` Specify default optimisation level (type choice; default: defaultopt) (choices: noopt, lowopt, defaultopt, opt) +``--deprecated=DEPRECATED`` Run pretending to be (future) version, to test removal of deprecated code. +``--detect-loaded-modules=DETECT-LOADED-MODULES`` Detect loaded EasyBuild-generated modules, act accordingly; supported values: error, ignore, purge, unload, warn (default: warn) +``--devel`` Enable including of development log messages (default: False) +``--download-timeout=DOWNLOAD-TIMEOUT`` Timeout for initiating downloads (in seconds) (type ) +``--dump-autopep8`` Reformat easyconfigs using autopep8 when dumping them (default: False) +``-e CLASS, --easyblock=CLASS`` easyblock to use for processing the spec file or dumping the options +``--enforce-checksums`` Enforce availability of checksums for all sources/patches, so they can be verified (default: False) +``--experimental`` Allow experimental code (with behaviour that can be changed/removed at any given time). (default: False) +``--extra-modules=EXTRA-MODULES`` List of extra modules to load after setting up the build environment (type comma-separated list) +``--fetch`` Allow downloading sources ignoring OS and modules tool dependencies, implies --stop=fetch, --ignore-osdeps and ignore modules tool (default: False) +``--filter-deps=FILTER-DEPS`` List of dependencies that you do *not* want to install with EasyBuild, because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses) (type comma-separated list) +``--filter-env-vars=FILTER-ENV-VARS`` List of names of environment variables that should *not* be defined/updated by module files generated by EasyBuild (type comma-separated list) +``--fixed-installdir-naming-scheme`` Use fixed naming scheme for installation directories (default: True; disable with --disable-fixed-installdir-naming-scheme) +``--force-download=FORCE-DOWNLOAD`` Force re-downloading of sources and/or patches, even if they are available already in source path (type choice; default: sources) (choices: all, patches, sources) +``--generate-devel-module`` Generate a develop module file, implies --force if disabled (default: True; disable with --disable-generate-devel-module) +``--group=GROUP`` Group to be used for software installations (only verified, not set) +``--group-writable-installdir`` Enable group write permissions on installation directory after installation (default: False) +``--hidden`` Install 'hidden' module file(s) by prefixing their version with '.' (default: False) +``--hide-deps=HIDE-DEPS`` Comma separated list of dependencies that you want automatically hidden, (e.g. --hide-deps=zlib,ncurses) (type comma-separated list) +``--hide-toolchains=HIDE-TOOLCHAINS`` Comma separated list of toolchains that you want automatically hidden, (e.g. --hide-toolchains=GCCcore) (type comma-separated list) +``--http-header-fields-urlpat=[URLPAT::][HEADER:]FILE|FIELD`` Set extra HTTP header FIELDs when downloading files from URL PATterns. To not log sensitive values, specify a file containing newline separated FIELDs. e.g. "^https://www.example.com::/path/to/headers.txt" or "client[A-z0-9]*.example.com': ['Authorization: Basic token']". +``--ignore-checksums`` Ignore failing checksum verification (default: False) +``--ignore-osdeps`` Ignore any listed OS dependencies (default: False) +``--install-latest-eb-release`` Install latest known version of easybuild (default: False) +``--lib-lib64-symlink`` Automatically create symlinks for lib/ pointing to lib64/ if the former is missing (default: True; disable with --disable-lib-lib64-symlink) +``--lib64-fallback-sanity-check`` Fallback in sanity check to lib64/ equivalent for missing libraries (default: True; disable with --disable-lib64-fallback-sanity-check) +``--lib64-lib-symlink`` Automatically create symlinks for lib64/ pointing to lib/ if the former is missing (default: True; disable with --disable-lib64-lib-symlink) +``--max-fail-ratio-adjust-permissions=MAX-FAIL-RATIO-ADJUST-PERMISSIONS`` Maximum ratio for failures to allow when adjusting permissions (type float; default: 0.5) +``--minimal-build-env=MINIMAL-BUILD-ENV`` Minimal build environment to define when using system toolchain, specified as a comma-separated list that defines a mapping between name of environment variable and its value separated by a colon (':') (default: CC:gcc,CXX:g++) +``--minimal-toolchains`` Use minimal toolchain when resolving dependencies (default: False) +``--module-only`` Only generate module file(s); skip all steps except for module, prepare, ready, postiter, sanitycheck (default: False) +``--modules-tool-version-check`` Check version of modules tool being used (default: True; disable with --disable-modules-tool-version-check) +``--mpi-cmd-template=MPI-CMD-TEMPLATE`` Template for MPI commands (template keys: %(nr_ranks)s, %(cmd)s) +``--mpi-tests`` Run MPI tests (when relevant) (default: True; disable with --disable-mpi-tests) +``--optarch=OPTARCH`` Set architecture optimization, overriding native architecture optimizations +``--output-format=OUTPUT-FORMAT`` Set output format (type choice; default: txt) (choices: txt, rst) +``--parallel=PARALLEL`` Specify (maximum) level of parallellism used during build procedure (type int) +``--pre-create-installdir`` Create installation directory before submitting build jobs (default: True; disable with --disable-pre-create-installdir) +``-p, --pretend`` Does the build/installation in a test directory located in $HOME/easybuildinstall (default: False) +``--read-only-installdir`` Set read-only permissions on installation directory after installation (default: False) +``--remove-ghost-install-dirs`` Remove ghost installation directories when --force or --rebuild is used, rather than just warning about them (default: False) +``--rpath`` Enable use of RPATH for linking with libraries (default: False) +``--rpath-filter=RPATH-FILTER`` List of regex patterns to use for filtering out RPATH paths (type comma-separated list) +``--set-default-module`` Set the generated module as default (default: False) +``--set-gid-bit`` Set group ID bit on newly created directories (default: False) +``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` Silence specified deprecation warnings (type comma-separated list) +``-t, --skip-test-cases`` Skip running test cases (default: False) +``--skip-test-step`` Skip running the test step (e.g. unit tests) (default: False) +``--sticky-bit`` Set sticky bit on newly created directories (default: False) +``--sysroot=SYSROOT`` Location root directory of system, prefix for standard paths like /usr/lib and /usr/include +``-T, --trace`` Provide more information in output to stdout on progress (default: False) +``--umask=UMASK`` umask to use (e.g. '022'); non-user write permissions on install directories are removed +``--update-modules-tool-cache`` Update modules tool cache file(s) after generating module file (default: False) +``--use-ccache=PATH`` Enable use of ccache to speed up compilation, with specified cache dir (type ; default: False) +``--use-existing-modules`` Use existing modules when resolving dependencies with minimal toolchains (default: False) +``--use-f90cache=PATH`` Enable use of f90cache to speed up compilation, with specified cache dir (type ; default: False) +``--verify-easyconfig-filenames`` Verify whether filename of specified easyconfigs matches with contents (default: False) +``--wait-on-lock=WAIT-ON-LOCK`` Wait for lock to be released; 0 implies no waiting (exit with an error if the lock already exists), non-zero value specified waiting interval [DEPRECATED: use --wait-on-lock-interval and --wait-on-lock-limit instead] (type ) +``--wait-on-lock-interval=WAIT-ON-LOCK-INTERVAL`` Wait interval (in seconds) to use when waiting for existing lock to be removed (type ; default: 60) +``--wait-on-lock-limit=WAIT-ON-LOCK-LIMIT`` Maximum amount of time (in seconds) to wait until lock is released (0 means no waiting at all, exit with error; -1 means no waiting limit, keep waiting) (type ; default: 0) +``--zip-logs=ZIP-LOGS`` Zip logs that are copied to install directory, using specified command (default: gzip) +========================================================================= ================================================================================================================================================================================================================================================================================ Package options diff --git a/docs/version-specific/toolchain_opts.rst b/docs/version-specific/toolchain_opts.rst index 5104988b..861c3fa7 100644 --- a/docs/version-specific/toolchain_opts.rst +++ b/docs/version-specific/toolchain_opts.rst @@ -5,7 +5,7 @@ Available toolchain options (by toolchain) *(see also* ``eb --avail-toolchain-opts `` *)* -ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ +ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ .. _ClangGCC: @@ -2323,6 +2323,52 @@ option description ========================= ======================================================================= ========= +.. _iibff: + +Available options for iibff toolchain +------------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``intel-static`` Link Intel provided libraries statically ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``no-icc`` Don't set Intel specific macros ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + .. _iimkl: Available options for iimkl toolchain @@ -2643,6 +2689,51 @@ option description ========================= ======================================================================= ========= +.. _intel-compilers: + +Available options for intel-compilers toolchain +----------------------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``intel-static`` Link Intel provided libraries statically ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``no-icc`` Don't set Intel specific macros ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + .. _intel-para: Available options for intel-para toolchain diff --git a/docs/version-specific/toolchains.rst b/docs/version-specific/toolchains.rst index 60d5b83e..baeed5cb 100644 --- a/docs/version-specific/toolchains.rst +++ b/docs/version-specific/toolchains.rst @@ -3,87 +3,89 @@ List of known toolchains ------------------------ -================ ================ =========== ========================= ======== -Name Compiler(s) MPI Linear algebra FFT -================ ================ =========== ========================= ======== -**cgmpich** Clang, GCC MPICH *(none)* *(none)* -**cgmpolf** Clang, GCC MPICH OpenBLAS, ScaLAPACK FFTW -**cgmvapich2** Clang, GCC MVAPICH2 *(none)* *(none)* -**cgmvolf** Clang, GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW -**cgompi** Clang, GCC OpenMPI *(none)* *(none)* -**cgoolf** Clang, GCC OpenMPI OpenBLAS, ScaLAPACK FFTW -**ClangGCC** Clang, GCC *(none)* *(none)* *(none)* -**CrayCCE** PrgEnv-cray cray-mpich cray-libsci *(none)* -**CrayGNU** PrgEnv-gnu cray-mpich cray-libsci *(none)* -**CrayIntel** PrgEnv-intel cray-mpich cray-libsci *(none)* -**CrayPGI** PrgEnv-pgi cray-mpich cray-libsci *(none)* -**foss** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW -**fosscuda** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW -**GCC** GCC *(none)* *(none)* *(none)* -**GCCcore** GCCcore *(none)* *(none)* *(none)* -**gcccuda** GCC, CUDA *(none)* *(none)* *(none)* -**gimkl** GCC impi imkl imkl -**gimpi** GCC impi *(none)* *(none)* -**gimpic** GCC, CUDA impi *(none)* *(none)* -**giolf** GCC impi OpenBLAS, ScaLAPACK FFTW -**giolfc** GCC, CUDA impi OpenBLAS, ScaLAPACK FFTW -**gmacml** GCC MVAPICH2 ACML, ScaLAPACK FFTW -**gmkl** GCC *(none)* imkl imkl -**gmklc** GCC, CUDA *(none)* imkl imkl -**gmpich** GCC MPICH *(none)* *(none)* -**gmpich2** GCC MPICH2 *(none)* *(none)* -**gmpolf** GCC MPICH OpenBLAS, ScaLAPACK FFTW -**gmvapich2** GCC MVAPICH2 *(none)* *(none)* -**gmvolf** GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW -**GNU** GCC *(none)* *(none)* *(none)* -**goalf** GCC OpenMPI ATLAS, ScaLAPACK FFTW -**gobff** GCC OpenMPI BLIS, libFLAME, ScaLAPACK FFTW -**goblf** GCC OpenMPI BLIS, LAPACK, ScaLAPACK FFTW -**golf** GCC *(none)* OpenBLAS FFTW -**golfc** GCC, CUDA *(none)* OpenBLAS FFTW -**gomkl** GCC OpenMPI imkl imkl -**gomklc** GCC, CUDA OpenMPI imkl imkl -**gompi** GCC OpenMPI *(none)* *(none)* -**gompic** GCC, CUDA OpenMPI *(none)* *(none)* -**goolf** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW -**goolfc** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW -**gpsmpi** GCC psmpi *(none)* *(none)* -**gpsolf** GCC psmpi OpenBLAS, ScaLAPACK FFTW -**gqacml** GCC QLogicMPI ACML, ScaLAPACK FFTW -**gsmpi** GCC SpectrumMPI *(none)* *(none)* -**gsolf** GCC SpectrumMPI OpenBLAS, ScaLAPACK FFTW -**iccifort** icc, ifort *(none)* *(none)* *(none)* -**iccifortcuda** icc, ifort, CUDA *(none)* *(none)* *(none)* -**ictce** icc, ifort impi imkl imkl -**iimkl** icc, ifort *(none)* imkl imkl -**iimklc** icc, ifort, CUDA *(none)* imkl imkl -**iimpi** icc, ifort impi *(none)* *(none)* -**iimpic** icc, ifort, CUDA impi *(none)* *(none)* -**iiqmpi** icc, ifort QLogicMPI *(none)* *(none)* -**impich** icc, ifort MPICH *(none)* *(none)* -**impmkl** icc, ifort MPICH imkl imkl -**intel** icc, ifort impi imkl imkl -**intel-para** icc, ifort psmpi imkl imkl -**intelcuda** icc, ifort, CUDA impi imkl imkl -**iomkl** icc, ifort OpenMPI imkl imkl -**iomklc** icc, ifort, CUDA OpenMPI imkl imkl -**iompi** icc, ifort OpenMPI *(none)* *(none)* -**iompic** icc, ifort, CUDA OpenMPI *(none)* *(none)* -**ipsmpi** icc, ifort psmpi *(none)* *(none)* -**iqacml** icc, ifort QLogicMPI ACML, ScaLAPACK FFTW -**ismkl** icc, ifort MPICH2 imkl imkl -**NVHPC** NVHPC *(none)* *(none)* *(none)* -**PGI** PGI *(none)* *(none)* *(none)* -**pmkl** PGI *(none)* imkl imkl -**pomkl** PGI OpenMPI imkl imkl -**pompi** PGI OpenMPI *(none)* *(none)* -**system** *(none)* *(none)* *(none)* *(none)* -**xlcxlf** xlc, xlf *(none)* *(none)* *(none)* -**xlmpich** xlc, xlf MPICH *(none)* *(none)* -**xlmpich2** xlc, xlf MPICH2 *(none)* *(none)* -**xlmvapich2** xlc, xlf MVAPICH2 *(none)* *(none)* -**xlompi** xlc, xlf OpenMPI *(none)* *(none)* -================ ================ =========== ========================= ======== +=================== ================ =========== ========================= ======== +Name Compiler(s) MPI Linear algebra FFT +=================== ================ =========== ========================= ======== +**cgmpich** Clang, GCC MPICH *(none)* *(none)* +**cgmpolf** Clang, GCC MPICH OpenBLAS, ScaLAPACK FFTW +**cgmvapich2** Clang, GCC MVAPICH2 *(none)* *(none)* +**cgmvolf** Clang, GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW +**cgompi** Clang, GCC OpenMPI *(none)* *(none)* +**cgoolf** Clang, GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**ClangGCC** Clang, GCC *(none)* *(none)* *(none)* +**CrayCCE** PrgEnv-cray cray-mpich cray-libsci *(none)* +**CrayGNU** PrgEnv-gnu cray-mpich cray-libsci *(none)* +**CrayIntel** PrgEnv-intel cray-mpich cray-libsci *(none)* +**CrayPGI** PrgEnv-pgi cray-mpich cray-libsci *(none)* +**foss** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**fosscuda** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW +**GCC** GCC *(none)* *(none)* *(none)* +**GCCcore** GCCcore *(none)* *(none)* *(none)* +**gcccuda** GCC, CUDA *(none)* *(none)* *(none)* +**gimkl** GCC impi imkl imkl +**gimpi** GCC impi *(none)* *(none)* +**gimpic** GCC, CUDA impi *(none)* *(none)* +**giolf** GCC impi OpenBLAS, ScaLAPACK FFTW +**giolfc** GCC, CUDA impi OpenBLAS, ScaLAPACK FFTW +**gmacml** GCC MVAPICH2 ACML, ScaLAPACK FFTW +**gmkl** GCC *(none)* imkl imkl +**gmklc** GCC, CUDA *(none)* imkl imkl +**gmpich** GCC MPICH *(none)* *(none)* +**gmpich2** GCC MPICH2 *(none)* *(none)* +**gmpolf** GCC MPICH OpenBLAS, ScaLAPACK FFTW +**gmvapich2** GCC MVAPICH2 *(none)* *(none)* +**gmvolf** GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW +**GNU** GCC *(none)* *(none)* *(none)* +**goalf** GCC OpenMPI ATLAS, ScaLAPACK FFTW +**gobff** GCC OpenMPI BLIS, libFLAME, ScaLAPACK FFTW +**goblf** GCC OpenMPI BLIS, LAPACK, ScaLAPACK FFTW +**golf** GCC *(none)* OpenBLAS FFTW +**golfc** GCC, CUDA *(none)* OpenBLAS FFTW +**gomkl** GCC OpenMPI imkl imkl +**gomklc** GCC, CUDA OpenMPI imkl imkl +**gompi** GCC OpenMPI *(none)* *(none)* +**gompic** GCC, CUDA OpenMPI *(none)* *(none)* +**goolf** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**goolfc** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW +**gpsmpi** GCC psmpi *(none)* *(none)* +**gpsolf** GCC psmpi OpenBLAS, ScaLAPACK FFTW +**gqacml** GCC QLogicMPI ACML, ScaLAPACK FFTW +**gsmpi** GCC SpectrumMPI *(none)* *(none)* +**gsolf** GCC SpectrumMPI OpenBLAS, ScaLAPACK FFTW +**iccifort** icc, ifort *(none)* *(none)* *(none)* +**iccifortcuda** icc, ifort, CUDA *(none)* *(none)* *(none)* +**ictce** icc, ifort impi imkl imkl +**iibff** icc, ifort impi BLIS, libFLAME, ScaLAPACK FFTW +**iimkl** icc, ifort *(none)* imkl imkl +**iimklc** icc, ifort, CUDA *(none)* imkl imkl +**iimpi** icc, ifort impi *(none)* *(none)* +**iimpic** icc, ifort, CUDA impi *(none)* *(none)* +**iiqmpi** icc, ifort QLogicMPI *(none)* *(none)* +**impich** icc, ifort MPICH *(none)* *(none)* +**impmkl** icc, ifort MPICH imkl imkl +**intel** icc, ifort impi imkl imkl +**intel-compilers** intel-compilers *(none)* *(none)* *(none)* +**intel-para** icc, ifort psmpi imkl imkl +**intelcuda** icc, ifort, CUDA impi imkl imkl +**iomkl** icc, ifort OpenMPI imkl imkl +**iomklc** icc, ifort, CUDA OpenMPI imkl imkl +**iompi** icc, ifort OpenMPI *(none)* *(none)* +**iompic** icc, ifort, CUDA OpenMPI *(none)* *(none)* +**ipsmpi** icc, ifort psmpi *(none)* *(none)* +**iqacml** icc, ifort QLogicMPI ACML, ScaLAPACK FFTW +**ismkl** icc, ifort MPICH2 imkl imkl +**NVHPC** NVHPC *(none)* *(none)* *(none)* +**PGI** PGI *(none)* *(none)* *(none)* +**pmkl** PGI *(none)* imkl imkl +**pomkl** PGI OpenMPI imkl imkl +**pompi** PGI OpenMPI *(none)* *(none)* +**system** *(none)* *(none)* *(none)* *(none)* +**xlcxlf** xlc, xlf *(none)* *(none)* *(none)* +**xlmpich** xlc, xlf MPICH *(none)* *(none)* +**xlmpich2** xlc, xlf MPICH2 *(none)* *(none)* +**xlmvapich2** xlc, xlf MVAPICH2 *(none)* *(none)* +**xlompi** xlc, xlf OpenMPI *(none)* *(none)* +=================== ================ =========== ========================= ======== *(see also* ``eb --list-toolchains`` *)* From 6086f7dfe7be6e2933d5408a5f0be68a463c3070 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 23 Feb 2021 14:10:20 +0800 Subject: [PATCH 111/286] update release notes and changelog for EasyBuild v4.3.3 + bump version to 4.3.3 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 219 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 219 insertions(+), 5 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 53c0e74b..89557958 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20210223.01** (`Feb 23rd 2021`): update release notes for EasyBuild v4.3.3 (see :ref:`release_notes_eb433`) * **release 20201210.01** (`Dec 10th 2020`): update release notes for EasyBuild v4.3.2 (see :ref:`release_notes_eb432`) * **release 20201029.01** (`Oct 29th 2020`): update release notes for EasyBuild v4.3.1 (see :ref:`release_notes_eb431`) * **release 20200913.01** (`Sep 13th 2020`): update release notes for EasyBuild v4.3.0 (see :ref:`release_notes_eb430`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 31c58590..84d8f3df 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,225 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,175** different software packages, -including 32 different (compiler) toolchains. It contains 227 software-specific easyblocks and 37 generic easyblocks, -alongside 11,054 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,248** different software packages, +including 33 different (compiler) toolchains. It contains 229 software-specific easyblocks and 37 generic easyblocks, +alongside 11,475 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb433: + +EasyBuild v4.3.3 (Feb 23rd 2021) +-------------------------------- + +bugfix/update release + +**framework** + +* various enhancements, including: + + * advise PR labels in ``--review-pr`` and add support for ``--add-pr-labels`` (`#3177 `_) + * add support for using customized HTTP headers in ``download_file`` (`#3472 `_, `#3583 `_) + * also take toolchain dependencies into account when defining template values (`#3541 `_, `#3560 `_) + * add support for ``--accept-eula`` configuration option + ``accept_eula`` easyconfig parameter (`#3535 `_, `#3536 `_, `#3546 `_) + * detect ``SYSTEM`` toolchain as special case in easystack files (`#3543 `_) + * enhance ``extract_cmd`` function to use ``cp -a`` for shell scripts (.sh) (`#3545 `_) + * allow use of alternate envvar(s) to ``$HOME`` for user modules (`#3558 `_) + * use ``https://sources/easybuild.io`` as fallback source URL (`#3572 `_, `#3576 `_) + * add toolchain definition for ``iibff`` toolchain (`#3574 `_) + * add ``%(cuda_cc_space_sep)s`` and ``%(cuda_cc_semicolon_sep)s`` templates (`#3578 `_) + * add support for intel-compiler toolchain (>= 2021.x versions, oneAPI) (`#3581 `_, `#3582 `_) + +* various bug fixes, including: + + * add ``--init`` and ``--recursive`` options to ``git submodule update`` command that is used when creating source tarball for specific commit (`#3537 `_) + * filter out duplicate paths in RPATH wrapper script (`#3538 `_) + * don't clean up imported modules after verifying imports of included Python modules (`#3544 `_) + * avoid no-op changes to ``$LD_*`` environment variables in ModulesTool (`#3553 `_) + * fix UTF-8 encoding errors when running EasyBuild with Python 3.0.x-3.6.x (`#3565 `_) + * create ``lib64`` symlink as a relative symlink (`#3566 `_) + * don't reuse variable name in the loop to fix adding extra compiler flags via toolchainopts (`#3571 `_) + * symlink ``lib`` to ``lib64`` if it doesn't exist (`#3580 `_) + * include ``%(mpi_cmd_prefix)s`` and ``%(cuda_*)s`` templates in output of ``--avail-easyconfig-templates`` (`#3586 `_) + +* other changes: + + * rename ``EasyBlock._skip_step`` to ``EasyBlock.skip_step``, to make it part of the public API (`#3561 `_) + * make symlinking of ``posix_c.so`` to ``posix.so`` in test suite configuration conditional (`#3570 `_) + +**easyblocks** + +* 2 new software-specific easyblocks: + + * AOCC (`#2295 `_), Intel compilers (v2021.x, oneAPI) (`#2305 `_) + +* minor enhancements, including: + + * run motorBike tutorial case as sanity check for recent (community) OpenFOAM versions (`#2201 `_) + * add foamMonitor to sanity checks of OpenFOAM (`#2256 `_) + * create versioned symlinks for CMake commands + create symlink for ``cmake3`` in PyTorch easyblock if ``cmake3`` command is not found (`#2259 `_) + * add support for skipping steps in Python packages installed as extension + print progress on individual steps for installing Python packages as extensions (`#2290 `_) + * update BerkeleyGW easyblock to support GCC 10 and fftlib (`#2297 `_) + * update QuantumESPRESSO easyblock to support GCC 10 (`#2298 `_) + * update Clang easyblock to add support for building extra tools + leveraging hwloc and Z3 as optional dependencies (`#2310 `_) + * add support for running TensorFlow CPU and GPU tests (`#2263 `_, `#2292 `_, `#2312 `_) + * update impi easyblock for impi 2021.x (oneAPI) (`#2313 `_) + * update QuantumESPRESSO easyblock to handle v6.7 (`#2319 `_) + * update OpenFOAM easyblock for changes in v2012 (`#2321 `_) + * add sanity check commands to GCC (including LTO support) (`#2322 `_) + * update FLUENT sanity check for v2021R1 (`#2334 `_) + +* various bug fixes, including: + + * filter out user packages in LAMMPS easyblock if corresponding dependency isn't included + only set ``-DUSER-INTEL`` on x86_64 systems (`#2254 `_) + * unify handling of ``pylibdirs`` and don't add duplicated ``$PYTHONPATH`` in PythonBundle (`#2281 `_) + * enhance Amber easyblock to fix running of ``update_amber`` script when ``python`` command is not available in OS (`#2282 `_) + * improve Bazel easyblock: add support for running tests, enable static linking, use build dir rather than ``tmpdir``, verbose output (`#2285 `_) + * guard ``module unload`` statements in modules for Cray* toolchains (`#2286 `_) + * set ``$PYTHONNOUSERSITE`` in ``PythonBundle.extensions_step`` to avoid picking up on Python packages installed in $HOME (`#2289 `_) + * create less temporary directories for TensorFlow by (only) using ``--output_user_root`` (`#2293 `_) + * fix logic w.r.t. enabling Python support in PETSc (`#2299 `_) + * make ``builddeps`` a list of names in SLEPc easyblock (`#2300 `_) + * make ``builddeps`` a list of names in Trilinos easyblock (`#2301 `_) + * make sure the installation of ``libiberty.a`` in the binutils easyblock goes into a populated directory (`#2308 `_) + * fix for building GCC with ``--sysroot`` on ppc64le (`#2315 `_) + * fix OpenFOAM sanity check on POWER (`#2320 `_) + * use library search paths of compiler for RPATH when building binutils with system compiler + enhance sanity check by running ``--version`` for binutils commands (`#2323 `_, `#2327 `_) + * pass ``$CXXFLAGS`` to PDT's configure script via ``-useropt`` (`#2324 `_) + * pass down compilation flags from build environment for ESMF (`#2325 `_) + * update URLs for test data for WRF to ``https`` (`#2335 `_) + * read MATLAB configuration file in binary mode to avoid UTF-8 encoding errors when using Python 3.6 (`#2340 `_) + * fix Boost sanity check on POWER (`#2291 `_) and aarch64 (`#2341 `_) + +* other changes, including: + + * rework module-only tests to use unique software name (rather than 'foo') (`#2287 `_) + * prefer default value for extra options in easyblock tests (`#2280 `_, `#2302 `_) + * add check for accepted EULA in custom easyblock for NVHPC (`#2311 `_) + * update optional feature support of TensorFlow (`#2314 `_) + * make symlinking of ``posix_c.so`` to ``posix.so`` in test suite configuration conditional (`#2330 `_) + +**easyconfigs** + +* add easyconfig for new iibff toolchain: iibff/2020b (`#12185 `_) + +* added easyconfigs for 6 new toolchains: + + * gobff/2020b (`#12098 `_), goblf/2018b (`#6615 `_), gomkl/2020b (`#12198 `_), iimkl/2018a (`#6092 `_), iomkl/2019b (`#11981 `_), iomkl/2020b (`#12009 `_) + +* added example easyconfig files for 72 new software packages: + + * AOCC (`#11868 `_), CHERAB (`#7141 `_), CaDiCaL (`#11966 `_), CellRanger-ARC (`#12114 `_), CuPy (`#11749 `_), DFA (`#11979 `_), + FIGARO (`#11924 `_), FIRESTARTER (`#12160 `_), FIt-SNE (`#8630 `_), GPyTorch (`#12010 `_), GSEA (`#10395 `_), GetOrganelle (`#11948 `_), + Glucose (`#11965 `_), GraPhlAn (`#10707 `_), ITSx (`#10558 `_), Kaleido (`#11998 `_), LAPACK (`#6615 `_), LSD2 (`#11903 `_), + Lingeling (`#11964 `_), MPB (`#7026 `_), MiniCARD (`#11963 `_), MiniSat (`#11962 `_), NGSpeciesID (`#11918 `_), NanopolishComp (`#11823 `_), + Nsight-Compute (`#12043 `_), Nsight-Systems (`#12042 `_), PHANOTATE (`#8667 `_), PIPITS (`#10558 `_), PyClone (`#11940 `_), + PySAT (`#12000 `_), RNAmmer (`#7262 `_), Raysect (`#7141 `_), SICER2 (`#12200 `_), SOCI (`#12045 `_), SeisSol (`#7194 `_), SignalP (`#11862 `_), + Stack (`#11310 `_), SuperLU_DIST (`#11693 `_), Teneto (`#12056 `_), Transformers (`#12032 `_), YANK (`#11742 `_), Z3 (`#12013 `_), + bgen (`#7456 `_, `#11867 `_), bgen-reader (`#7456 `_, `#11867 `_), bpytop (`#12040 `_), byobu (`#11932 `_), chi2comb (`#11867 `_), + cuTENSOR (`#11914 `_), dd (`#11978 `_), decona (`#11891 `_), dicom2nifti (`#11955 `_), eccodes-python (`#12083 `_), fftlib (`#11944 `_), + flatbuffers-python (`#12148 `_), fpocket (`#11980 `_), gh (`#11851 `_), intel-compilers (oneAPI) (`#11982 `_), libGDSII (`#7026 `_), + libpci (`#11871 `_), liknorm (`#7456 `_, `#11867 `_), limix (`#7456 `_, `#11867 `_), logaddexp (`#11867 `_), neptune-client (`#11985 `_), + plinkQC (`#12068 `_), preCICE (`#11886 `_), py-aiger (`#11999 `_), py-aiger-bdd (`#11999 `_), pytest-xdist (#11883, `#11893 `_), + samblaster (`#7378 `_), terastructure (`#12197 `_), typing-extensions (`#11636 `_), webin-cli (`#8674 `_) + +* added additional easyconfigs for various supported software packages, including: + + * ack 3.4.0, AmberTools 20, AMD-LibM 3.6.0-4, AMD-RNG 2.2, AMD-SecureRNG 2.2, annovar 20191024, ASE 3.21.1, + AUGUSTUS 3.4.0, Bazel 3.7.2, bcgTree 1.1.0, BLAST+ 2.11.0, Bonito 0.3.5, Bowtie2 2.4.2, causalml 0.8.0-20200909, + CGAL 5.2, ConnectomeWorkbench 1.4.2, CUDAcore 11.2.1, cuDNN 8.0.5.39, dcm2niix 1.0.20201102, DendroPy 4.5.2, + DIAMOND 0.9.36 + 2.0.6, ecCodes 2.20.0, ELPA 2020.11.001, Emacs 27.1, FusionCatcher 1.30, gensim 3.8.3, GHC 8.6.5, + gnuplot 5.4.1, GPAW 21.1.0, Graphviz 2.44.1, GROMACS 2020.5, Gurobi 9.1.0, HH-suite 3.3.0, HMMER 3.3.2, HTSlib 1.11, + Horovod 0.21.1, imbalanced-learn 0.7.0, impi 2021.1.1, inferCNV 1.3.3, ITK 5.1.2, IQ-TREE 2.1.2, JasPer 2.0.24, + JUBE 2.4.1, libgit2 1.1.0, libzip 1.7.3, likwid 5.1.0, MariaDB 10.5.8, medaka 1.2.0, Meep 1.6.0, mkl-service 2.3.0, + MPICH 3.3.2, muParser 2.3.2, NanoComp 1.13.1, NanoPlot 1.33.0, networkx 2.5, NLTK 3.5, numba 0.52.0, NVHPC 20.11, + nvtop 1.1.0, OpenCoarrays 2.9.2, OpenFOAM v2012, OpenJPEG 2.4.0, OpenMPI 4.1.0, parasail 2.4.2, PLUMED 2.6.2, + PostgreSQL 13.2, pydicom 2.1.2, PyMC3 3.11.0, python-parasail 1.2.2, PyTorch 1.7.1, QIIME2 2020.11, + QuantumESPRESSO 6.7, QuickFF 2.2.7, R 4.0.3, R-bundle-Bioconductor 3.12, ReFrame 3.4.1, RMBlast 2.10.0, RSEM 1.3.3, + Salmon 1.4.0, scikit-build 0.11.1, SciPy-bundle 2020.03 w/ Python 2.7.18, Seaborn 0.11.1, SEPP 4.4.0, + SHAPEIT4 4.2.0, SpaceRanger 1.2.2, Stacks 2.54, STAR 2.7.7.a, statsmodels 0.12.1, SuiteSparse 5.8.1, tbb 2020.3, + TensorFlow 1.15.5 + 2.4.1, Theano 1.1.2, torchvision 0.8.2, V8 3.4.0, Wannier90 3.1.0 + +* minor enhancements, including: + + * enable building of QtWebEngine in Qt5 easyconfig using foss/2017b or intel/2017b (`#7302 `_) + * enable NVPTX offload in GCCcore 9.3.0 easyconfig (`#11839 `_) + * also build shared library in recent HDF easyconfigs (`#11847 `_) + * add support for HDF4 to GDAL v3.0.2 and v3.0.4 (`#11855 `_) + * add patch for magma 2.5.4 with fosscuda/2019b to allow any ``sm_*`` value to be passed via ``GPU_TARGET`` (`#11861 `_) + * add missing M4 build dependency to recent SuiteSparse versions (`#11869 `_) + * enable tests for most recent Bazel versions (3.x) (`#11894 `_) + * enable gipaw in QuantumESPRESSO 6.6 easyconfig (`#11905 `_) + * add RCAL + sensemakr extensions to R 4.0.0 (`#11921 `_) + * add additional extensions to R v4.0.3 easyconfig (`#11922 `_, `#12057 `_) + * improve sanity_check_paths for AMD-LibM (`#11933 `_) + * symlink ``include``/``lib`` subdirs + enhance ``sanity_check_paths`` for AMD-RNG v2.2-4 (`#11934 `_) + * improve ``sanity_check_paths`` for AMD-SecureRNG (`#11935 `_) + * update Clang 10+ dependencies & build extra tools (`#12013 `_) + * add Inline extension to recent Perl easyconfigs (5.30+) (`#12029 `_) + * add EnsDb.Hsapiens.v86 to Bioconductor 3.11 (`#12078 `_) + * add sanity check command for bam-readcount v0.8.0 to check ``--version`` output (`#12092 `_) + * add EnsDb.Hsapiens.v75 + Signac extensions to R-bundle-Bioconductor 3.12 (`#12174 `_) + * add tensorboard profile plugin to recent TensorFlow 2.x easyconfigs (#12136, `#12137 `_) + +* various bug fixes, including: + + * added missing space in ``configopts`` in ParaView 5.8.0 easyconfigs using 2020a toolchain (`#10989 `_) + * use bfd linker for glibc 2.30 (`#11331 `_) + * add missing moduleclass in UCLUST easyconfig (`#11477 `_) + * don't disable optarch for Clang 11.0.0 (`#11814 `_) + * add patch to fix miscompilation bug on POWER for GCC 8.x and 9.x (`#11837 `_) + * fix compilation of TensorFlow 2.3.1 with CUDA and glibc 2.26 on POWER (`#11859 `_) + * disable building of manpages for GDCM to fix installation problem with docbook (`#11866 `_) + * add patch for LLVM 6.0.0 to fix missing exported symbol ``LLVMInitializeInstCombine`` (`#11873 `_) + * fix name of source file for GDRCopy v2.1 (`#11887 `_) + * fix Tombo to work with rpy2 v3 when creating DataFrames (`#11892 `_) + * fix GCCcore 8.1.0 w.r.t. removed ``sys/ustat.h`` in glibc 2.28 (`#11896 `_) + * add git as a dependency to GitPython version 3.x (`#11902 `_) + * fix undefined ``__ieee128`` on ppc64le with glibc 2.26 for magma (`#11930 `_) and PyTorch (`#11936 `_) + * update Hypre git location for PETSc 3.11.0 using downloaded dependencies (`#11947 `_) + * fix source URL in expat easyconfigs (and consistently add custom ``sanity_check_paths``) (`#11960 `_) + * use libpng provided by EasyBuild in VTK to fix build issue on ppc64le (`#11990 `_) + * add missing pkg-config build dependency for GObject-Introspection v1.66.1 (`#11949 `_) + * add missing plotly-orca dependency for NanoPlot (`#11967 `_, `#12015 `_) + * add patch for Boost 1.74.0 to fix missing include file (`#12007 `_) + * fix for ``error: 'runtime_error' is not a member of 'std'`` in qtlocation for Qt5 v5.14.2 (`#12012 `_) + * fix homepage for gnuplot 5.2.8, use ``http://`` since homepage is not reachable via ``https://`` (`#12047 `_) + * fix OS dependencies for libfabric (`#12058 `_) + * fix vector ``mul`` and ``div`` with broadcasts in ``-masm=intel`` mode in GCCcore v9.3.0 (`#12065 `_) + * add missing ESMF dependency in NCO easyconfigs (`#12071 `_, `#12072 `_) + * add patch to fix version for bam-readcount 0.8.0 (`#12075 `_) + * add missing Perl build dep for (recent) libcerf versions, required for ``pod2html`` command (`#12085 `_) + * add missing bzip2 dependency to recent ncbi-vdb easyconfigs (`#12120 `_) + * add missing Perl build dependency for BLIS 0.8.0 (`#12146 `_) + * use ``https://sources.easybuild.io`` as fallback source URL for UDUNITS (`#12049 `_, `#12156 `_, `#12182 `_) + * correct the GCC version check to allow IBM VSX builds of GROMACS 2020.4 and 2020.5 (`#12159 `_) + * add missing mkl-service dependency for Theano built with intel/2019b + enhance sanity check (`#12172 `_) + * add patches to fix test problems with p4est 2.2 (`#12028 `_) + * fix build of Bison using older system GCC (v4.x) (`#12203 `_) + * fix lack of optimisation for SHAPEIT4 v4.1.3 (`#12206 `_) + * add missing gnuplot dependency for OpenFOAM from v2.4.0 to v6 (`#11801 `_, `#12208 `_) + * fix source URL for libspatialite (`#12213 `_) + * add ``archive`` fallback source URL to MAGMA easyconfigs (`#12214 `_) + * fix checksum for patch in make 4.2.1 easyconfig using GCC/7.3.0-2.30 (`#12223 `_) + +* other changes: + + * replace easyconfigs for bpp-core/bpp-phyl/bpp-seq v2.4.1 with a single easyconfig for BioPP v2.4.1 (using Bundle easyblock) (`#11609 `_) + * add CESM-deps to whitelist in check for custom ``sanity_check_paths`` (`#11916 `_) + * include '-4' in version for AMD-SecureRNG v2.2-4 (`#11934 `_, `#11935 `_) + * switch to using python-parasail and tqdm dependencies in Bonito easyconfigs (`#11937 `_) + * rename orca to plotly-orca (`#12015 `_) + * remove duplicate extensions in R 3.5.x easyconfigs, and add test to detect such issues (`#12059 `_) + * remove Python dependency from ecCodes v2.17.0 since it doesn't provide Python bindings (`#12084 `_) + * update Java/1.8 wrapper to Java 1.8.0_281 (`#11928 `_, `#12088 `_) + * update Bison (build) dependency for flex built with system compiler to v3.5.3 (`#12111 `_) + * make symlinking of ``posix.so`` in test suite configuration conditional (`#12123 `_) + * move make 4.3 easyconfigs to GCCcore toolchain (`#12166 `_) + * move most recent BLIS and libFLAME easyconfigs from GCC to GCCcore (`#12168 `_) + * rename SNAP to SNAP-HMM and update easyconfig (`#12218 `_) + + .. _release_notes_eb432: EasyBuild v4.3.2 (December 10th 2020) diff --git a/docs/conf.py b/docs/conf.py index 235b9ee4..3f7e0859 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.3.2' # this is meant to reference the version of EasyBuild +version = '4.3.3' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20201210.0' # this is meant to reference the version of the documentation itself +release = '20210223.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 2d225fac89cb7f4d23635f02a22db448dfc1ef86 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2021 08:52:10 +0100 Subject: [PATCH 112/286] add preCICE to ignore list for codespell --- .github/workflows/check_with_codespell.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check_with_codespell.sh b/.github/workflows/check_with_codespell.sh index c1fa4b05..58d513c9 100644 --- a/.github/workflows/check_with_codespell.sh +++ b/.github/workflows/check_with_codespell.sh @@ -1 +1 @@ -codespell --skip='.git,version-specific,scripts' --ignore-words-list=atleast,ninjs,simpy,proovread,namd --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!'; else $(exit $retVal); fi; +codespell --skip='.git,version-specific,scripts' --ignore-words-list=atleast,ninjs,simpy,proovread,namd,preCICE --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!'; else $(exit $retVal); fi; From 4400b6f73d01cbcdbb2fcdf69e082a4e6ae8e81d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2021 08:52:10 +0100 Subject: [PATCH 113/286] add preCICE to ignore list for codespell --- .github/workflows/check_with_codespell.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check_with_codespell.sh b/.github/workflows/check_with_codespell.sh index c1fa4b05..58d513c9 100644 --- a/.github/workflows/check_with_codespell.sh +++ b/.github/workflows/check_with_codespell.sh @@ -1 +1 @@ -codespell --skip='.git,version-specific,scripts' --ignore-words-list=atleast,ninjs,simpy,proovread,namd --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!'; else $(exit $retVal); fi; +codespell --skip='.git,version-specific,scripts' --ignore-words-list=atleast,ninjs,simpy,proovread,namd,preCICE --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!'; else $(exit $retVal); fi; From eaed9e8ace8ed34722965c9917e2833df87831c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2021 11:25:34 +0100 Subject: [PATCH 114/286] add precice to ignore list for codespell --- .github/workflows/check_with_codespell.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check_with_codespell.sh b/.github/workflows/check_with_codespell.sh index 58d513c9..ef1f9122 100644 --- a/.github/workflows/check_with_codespell.sh +++ b/.github/workflows/check_with_codespell.sh @@ -1 +1 @@ -codespell --skip='.git,version-specific,scripts' --ignore-words-list=atleast,ninjs,simpy,proovread,namd,preCICE --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!'; else $(exit $retVal); fi; +codespell --skip='.git,version-specific,scripts' --ignore-words-list=atleast,ninjs,simpy,proovread,namd,precice --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!'; else $(exit $retVal); fi; From 08af14c4634500ae73c2ec24a03fcba6cf217a74 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2021 13:11:52 +0100 Subject: [PATCH 115/286] use 'main' rather than 'master' branch in test suite configuration --- .github/workflows/scripts.yml | 8 ++++---- docs/Archived-easyconfigs.rst | 2 +- docs/Contributing.rst | 8 ++++---- docs/Implementing-easyblocks.rst | 4 ++-- docs/Installation.rst | 2 +- docs/Installation_Alternative.rst | 4 ++-- docs/Unit-tests.rst | 6 +++--- docs/Useful-scripts.rst | 8 ++++---- docs/Using_external_modules.rst | 2 +- docs/Writing_easyconfig_files.rst | 8 ++++---- scripts/create_source_tarball.sh | 6 +++--- 11 files changed, 29 insertions(+), 29 deletions(-) diff --git a/.github/workflows/scripts.yml b/.github/workflows/scripts.yml index cb735b6f..88e7f625 100644 --- a/.github/workflows/scripts.yml +++ b/.github/workflows/scripts.yml @@ -36,7 +36,7 @@ jobs: export PATH=$(cat $HOME/path) cd $HOME/${{matrix.repo}} - git checkout master + git checkout main # file to figure out the version from depends on repo if [[ ${{matrix.repo}} == "easybuild-framework" ]]; then @@ -65,12 +65,12 @@ jobs: cd ${{matrix.repo}} - # script should make sure we're on master branch + # script should make sure we're on main branch git checkout develop &> /dev/null ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true - grep "ERROR: Not on master branch" $out + grep "ERROR: Not on main branch" $out echo "Expected error found in output: OK!" - git checkout master &> /dev/null + git checkout main &> /dev/null echo "================================================================================================" diff --git a/docs/Archived-easyconfigs.rst b/docs/Archived-easyconfigs.rst index 9c6cf8c4..0e7c59db 100644 --- a/docs/Archived-easyconfigs.rst +++ b/docs/Archived-easyconfigs.rst @@ -18,7 +18,7 @@ Once in a blue moon, we review the list of toolchains (& versions) that are incl Easyconfig files that use toolchains that become *deprecated* are then moved to the *easyconfigs archive*, i.e. the ``__archive__`` subdirectory in the ``easybuild-easyconfigs`` repository -(see https://github.com/easybuilders/easybuild-easyconfigs/tree/master/easybuild/easyconfigs/__archive__). +(see https://github.com/easybuilders/easybuild-easyconfigs/tree/main/easybuild/easyconfigs/__archive__). .. _archived_easyconfigs_deprecated_toolchains_what: diff --git a/docs/Contributing.rst b/docs/Contributing.rst index 4bb59f33..3a57ac39 100644 --- a/docs/Contributing.rst +++ b/docs/Contributing.rst @@ -428,10 +428,10 @@ you should use the GitHub interface, and follow the steps outlined below. i. visit https://github.com/EXAMPLE/easybuild-framework; ii. switch to the branch that includes the changes you want to contribute - using the '``Branch: master``' button on the left, + using the '``Branch: main``' button on the left, for example by selecting ``Branch: mybranch`` from the dropdown list iii. click the '``New pull request``' button; -iv. change the target branch to ``develop`` using the '``base: master``' button; +iv. change the target branch to ``develop`` using the '``base: main``' button; v. review your changes using the 'diff' view presented by GitHub; vi. provide an appropriate title and description for your contribution; vii. open the pull request by clicking the green '``Create pull request``' button @@ -525,8 +525,8 @@ Requirements for pull requests **Pull requests are only merged in the** '``develop``' **branch** of the EasyBuild repositories, which contains the changes that will be included in the next EasyBuild release. -The '``master``' branch provides the latest stable release of EasyBuild at all times. -Only the EasyBuild release manager should issue a pull request to the EasyBuild '``master``' branch, +The '``main``' branch provides the latest stable release of EasyBuild at all times. +Only the EasyBuild release manager should issue a pull request to the EasyBuild '``main``' branch, when preparing a new EasyBuild release. Occasionally, an additional version branch (e.g. '``3.3.x``') may be introduced temporarily, diff --git a/docs/Implementing-easyblocks.rst b/docs/Implementing-easyblocks.rst index f131bd8b..598de99c 100644 --- a/docs/Implementing-easyblocks.rst +++ b/docs/Implementing-easyblocks.rst @@ -35,7 +35,7 @@ Easyblocks can either be *generic* or *software-specific*. Generic easyblocks implement a 'standard' software build and installation procedure that is used by multiple different software packages. A commonly used example is the -`ConfigureMake `_ +`ConfigureMake `_ generic easyblock, which implements the standard ``configure`` - ``make`` - ``make install`` installation procedure used by most GNU software packages. @@ -176,7 +176,7 @@ Generic easyblocks are located in the ``easybuid.easyblocks.generic`` namespace, live in the ``easybuild.easyblocks`` namespace directly. To keep things organised, the actual Python module file for software-specific easyblocks are kept in 'letter' subdirectories, rather than in one large '``easyblocks``' directory -(see https://github.com/easybuilders/easybuild-easyblocks/blob/master/easybuild/easyblocks/). +(see https://github.com/easybuilders/easybuild-easyblocks/blob/main/easybuild/easyblocks/). Note that you shouldn't concern yourself too much with getting the location of an easyblock right, as long as you use ``--include-easyblocks`` to make EasyBuild use additional or customised easyblocks diff --git a/docs/Installation.rst b/docs/Installation.rst index 25e56ec8..688eb38f 100644 --- a/docs/Installation.rst +++ b/docs/Installation.rst @@ -367,7 +367,7 @@ To upgrade to a newer EasyBuild version (say, |version|) than the one currently * using the easyconfig file available on the develop branch at Github `__ * install EasyBuild version |version| from PyPI, using one of the standard Python installation tools (``easy_install``, ``pip``, ...), see also :ref:`alt_inst_easy_install_pip` - * update the ``master`` branch of your Git working copies of the different EasyBuild repositories + * update the ``main`` branch of your Git working copies of the different EasyBuild repositories .. _dependencies: diff --git a/docs/Installation_Alternative.rst b/docs/Installation_Alternative.rst index 4e4111d2..6686a5d3 100644 --- a/docs/Installation_Alternative.rst +++ b/docs/Installation_Alternative.rst @@ -152,7 +152,7 @@ Installation of latest release from GitHub To install the latest (stable) release of an EasyBuild package directly from GitHub, use the following command:: - pip install --install-option "--prefix=$HOME/EasyBuild" https://github.com/easybuilders/easybuild-framework/archive/master.tar.gz + pip install --install-option "--prefix=$HOME/EasyBuild" https://github.com/easybuilders/easybuild-framework/archive/main.tar.gz Again, the order in which the EasyBuild packages are installed is important to have full control over the installation process, see @@ -202,7 +202,7 @@ It can be used as follows:: # pick an installation prefix (adjust as you like) INSTALL_PREFIX=$(mktemp -d $HOME/EasyBuild-XXXXXX) # download script - curl -O https://raw.githubusercontent.com/easybuilders/easybuild-framework/master/easybuild/scripts/install-EasyBuild-develop.sh + curl -O https://raw.githubusercontent.com/easybuilders/easybuild-framework/main/easybuild/scripts/install-EasyBuild-develop.sh # run downloaded script, specifying *your* GitHub username and the installation prefix bash install-EasyBuild-develop.sh GITHUB_USERNAME $INSTALL_PREFIX # update $MODULEPATH via 'module use', and load the module diff --git a/docs/Unit-tests.rst b/docs/Unit-tests.rst index 84cb6687..04f7d904 100644 --- a/docs/Unit-tests.rst +++ b/docs/Unit-tests.rst @@ -106,10 +106,10 @@ The unit test suites are automatically triggered by `Jenkins `_. +`FFTW easyconfig files `_. Sanity check ~~~~~~~~~~~~ diff --git a/scripts/create_source_tarball.sh b/scripts/create_source_tarball.sh index 79e03797..0c9cbcbe 100755 --- a/scripts/create_source_tarball.sh +++ b/scripts/create_source_tarball.sh @@ -87,13 +87,13 @@ else ok fi -# make sure we're on the master branch +# make sure we're on the main branch curr_branch=$(git status -b --porcelain | grep '^##' | cut -f2 -d' ' | cut -f1 -d'.') echo -n ">> checking current Git branch ... ${curr_branch} " -if [ "$curr_branch" == "master" ]; then +if [ "$curr_branch" == "main" ]; then ok else - error "Not on master branch!" + error "Not on main branch!" fi # check that the working directory is clean From 008a32974d55d06f4cad9580d19215369418f8b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2021 11:25:34 +0100 Subject: [PATCH 116/286] add precice to ignore list for codespell --- .github/workflows/check_with_codespell.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check_with_codespell.sh b/.github/workflows/check_with_codespell.sh index 58d513c9..ef1f9122 100644 --- a/.github/workflows/check_with_codespell.sh +++ b/.github/workflows/check_with_codespell.sh @@ -1 +1 @@ -codespell --skip='.git,version-specific,scripts' --ignore-words-list=atleast,ninjs,simpy,proovread,namd,preCICE --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!'; else $(exit $retVal); fi; +codespell --skip='.git,version-specific,scripts' --ignore-words-list=atleast,ninjs,simpy,proovread,namd,precice --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!'; else $(exit $retVal); fi; From bb36d16b14e5bfeffcabef2832722e860147171c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2021 18:51:09 +0100 Subject: [PATCH 117/286] bump version to 4.3.3 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 780c58bd..7ddfc0f1 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.3.2' +VERSION = '4.3.3' # Utility function to read README file From 191950ecf06feccdd9d0e3026f5dbf0e81832886 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2021 19:02:54 +0100 Subject: [PATCH 118/286] also mention Slack channel in README --- README.rst | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/README.rst b/README.rst index b0a95e7f..c9d1d8b0 100644 --- a/README.rst +++ b/README.rst @@ -77,16 +77,15 @@ have any questions or suggestions, you can post them there. Only members can post to this mailinglist. To request membership, see https://lists.ugent.be/wws/info/easybuild. -IRC -^^^ +Slack/IRC +^^^^^^^^^ -An IRC channel #easybuild has been set up on the FreeNode network. +Contact the EasyBuild community via Slack: https://easybuild.slack.com, +self-request an invite via https://easybuild-slack.herokuapp.com. -Just connect your IRC client to the irc.freenode.net server, and join -the #easybuild channel. +An IRC channel #easybuild has been set up on the FreeNode network. -There is an IRC bot present (easybuilder). Just type !help to get -pointers to the available commands. +Just connect your IRC client to the chat.freenode.net server, and join the #easybuild channel. Twitter ^^^^^^^ From d862f1a37dfa3fd14645319d977987c728b1b7d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2021 19:50:08 +0100 Subject: [PATCH 119/286] fix typo in release notes --- docs/Release_notes.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 84d8f3df..3ae86a09 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -27,7 +27,7 @@ bugfix/update release * detect ``SYSTEM`` toolchain as special case in easystack files (`#3543 `_) * enhance ``extract_cmd`` function to use ``cp -a`` for shell scripts (.sh) (`#3545 `_) * allow use of alternate envvar(s) to ``$HOME`` for user modules (`#3558 `_) - * use ``https://sources/easybuild.io`` as fallback source URL (`#3572 `_, `#3576 `_) + * use https://sources.easybuild.io as fallback source URL (`#3572 `_, `#3576 `_) * add toolchain definition for ``iibff`` toolchain (`#3574 `_) * add ``%(cuda_cc_space_sep)s`` and ``%(cuda_cc_semicolon_sep)s`` templates (`#3578 `_) * add support for intel-compiler toolchain (>= 2021.x versions, oneAPI) (`#3581 `_, `#3582 `_) From 534021d4174176c8b1cad0da5bc582900f731f62 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Feb 2021 19:58:14 +0100 Subject: [PATCH 120/286] move entry on enhancement to Bazel easyblock in EasyBuild v4.3.3 release notes --- docs/Release_notes.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 3ae86a09..19120e6f 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -60,6 +60,7 @@ bugfix/update release * run motorBike tutorial case as sanity check for recent (community) OpenFOAM versions (`#2201 `_) * add foamMonitor to sanity checks of OpenFOAM (`#2256 `_) * create versioned symlinks for CMake commands + create symlink for ``cmake3`` in PyTorch easyblock if ``cmake3`` command is not found (`#2259 `_) + * improve Bazel easyblock: add support for running tests, enable static linking, use build dir rather than ``tmpdir``, verbose output (`#2285 `_) * add support for skipping steps in Python packages installed as extension + print progress on individual steps for installing Python packages as extensions (`#2290 `_) * update BerkeleyGW easyblock to support GCC 10 and fftlib (`#2297 `_) * update QuantumESPRESSO easyblock to support GCC 10 (`#2298 `_) @@ -76,7 +77,6 @@ bugfix/update release * filter out user packages in LAMMPS easyblock if corresponding dependency isn't included + only set ``-DUSER-INTEL`` on x86_64 systems (`#2254 `_) * unify handling of ``pylibdirs`` and don't add duplicated ``$PYTHONPATH`` in PythonBundle (`#2281 `_) * enhance Amber easyblock to fix running of ``update_amber`` script when ``python`` command is not available in OS (`#2282 `_) - * improve Bazel easyblock: add support for running tests, enable static linking, use build dir rather than ``tmpdir``, verbose output (`#2285 `_) * guard ``module unload`` statements in modules for Cray* toolchains (`#2286 `_) * set ``$PYTHONNOUSERSITE`` in ``PythonBundle.extensions_step`` to avoid picking up on Python packages installed in $HOME (`#2289 `_) * create less temporary directories for TensorFlow by (only) using ``--output_user_root`` (`#2293 `_) From 2d42e55cedab42428442048726cf9fe75d4301db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 Mar 2021 17:15:08 +0100 Subject: [PATCH 121/286] strip 'Temporary log file' line from docs page with list of supported software --- docs/scripts/update-all-docs.sh | 2 +- docs/version-specific/Supported_software.rst | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/scripts/update-all-docs.sh b/docs/scripts/update-all-docs.sh index 72b4ba61..4c0a6f4b 100755 --- a/docs/scripts/update-all-docs.sh +++ b/docs/scripts/update-all-docs.sh @@ -193,7 +193,7 @@ rm $temp_tc echo ".. _list_software:" > $VERSION_SPECIFIC_DIR/Supported_software.rst echo >> $VERSION_SPECIFIC_DIR/Supported_software.rst -skip_lines='temporary log file|Processed.*easyconfigs|Found.*different software packages' +skip_lines='Temporary log file|Processed.*easyconfigs|Found.*different software packages' eb --list-software=detailed --output-format=rst | egrep -v $skip_lines >> $VERSION_SPECIFIC_DIR/Supported_software.rst echo "* :ref:\`List of supported software \`" >> $overview diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index b7b3d50d..2e992354 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -1,6 +1,5 @@ .. _list_software: -== Temporary log file in case of crash /tmp/eb-rvg3pj0d/easybuild-jo5_l5pb.log List of supported software ========================== From 7d003b1833c19a03c01dbb210b41872785955bb2 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 6 Apr 2021 16:20:59 +0100 Subject: [PATCH 122/286] Minimal scope for GitHub token --- docs/Integration_with_GitHub.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Integration_with_GitHub.rst b/docs/Integration_with_GitHub.rst index 6f71472d..e347128a 100644 --- a/docs/Integration_with_GitHub.rst +++ b/docs/Integration_with_GitHub.rst @@ -103,7 +103,7 @@ To obtain a GitHub token: * visit https://github.com/settings/tokens/new and log in with your GitHub account * enter a token description, for example: "``EasyBuild``" -* make sure (only) the ``gist`` and ``repo`` scopes are fully enabled +* make sure (only) the ``gist`` and ``public_repo`` (in the ``repo`` section) scopes are fully enabled * click ``Generate token`` * *copy-paste* the generated token From 97322f81b2f3d566e149d743b703414d47063084 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Apr 2021 22:06:43 +0200 Subject: [PATCH 123/286] auto-update documentation for EasyBuild v4.3.4 --- docs/version-specific/Supported_software.rst | 2007 ++++++++++++----- .../version-specific/easyconfig_constants.rst | 2 +- .../easyconfig_parameters.rst | 1 + .../version-specific/easyconfig_templates.rst | 6 + docs/version-specific/generic_easyblocks.rst | 390 ++-- docs/version-specific/help.rst | 6 +- docs/version-specific/toolchain_opts.rst | 94 +- docs/version-specific/toolchains.rst | 2 + 8 files changed, 1703 insertions(+), 805 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 2e992354..86facbf3 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2248 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2287 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -166,6 +166,7 @@ version toolchain ``2.0.2`` ``foss/2016b``, ``foss/2018a``, ``gompi/2019a``, ``intel/2016b`` ``2.0.3`` ``foss/2017b``, ``intel/2017b`` ``2.1.5`` ``foss/2019b`` +``2.2.5`` ``foss/2020b`` ========= ================================================================ @@ -212,11 +213,11 @@ ACTC converts independent triangles into triangle strips or fans. *homepage*: https://sourceforge.net/projects/actc -======= =========================================================================================== -version toolchain -======= =========================================================================================== -``1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2016b`` -======= =========================================================================================== +======= =============================================================================================================== +version toolchain +======= =============================================================================================================== +``1.1`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2016b`` +======= =============================================================================================================== .. _list_software_ada_294: @@ -767,6 +768,22 @@ version toolchain ========= ================= +.. _list_software_amplimap_849: + +*amplimap* +++++++++++ + +amplimap is a command-line tool to automate the processing and analysis of data from targeted next-generation sequencing (NGS) experiments with PCR-based amplicons or capture-based enrichment systems. + +*homepage*: https://amplimap.readthedocs.io/en/latest/ + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.4.16`` ``-Python-3.6.6`` ``foss/2018b`` +========== ================= ============== + + .. _list_software_AmrPlusPlus_1128: *AmrPlusPlus* @@ -972,6 +989,7 @@ version versionsuffix toolchain ``1.10.6`` ``-Java-1.8`` ``system`` ``1.10.7`` ``-Java-11`` ``system`` ``1.10.8`` ``-Java-11`` ``system`` +``1.10.9`` ``-Java-11`` ``system`` ========== =================== ========== @@ -1073,11 +1091,12 @@ AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 11.0 *homepage*: https://developer.amd.com/amd-aocc/ -========= ================= -version toolchain -========= ================= -``2.3.0`` ``GCCcore/9.3.0`` -========= ================= +========= ===================================== +version toolchain +========= ===================================== +``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.0.0`` ``GCCcore/10.2.0`` +========= ===================================== .. _list_software_APBS_294: @@ -1332,6 +1351,7 @@ version toolchain ``3.5.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b`` ``3.6.2`` ``intel/2018a`` ``3.7.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` +``3.8.0`` ``foss/2020b`` ========= ================================================================================ @@ -1365,6 +1385,7 @@ Arriba is a command-line tool for the detection of gene fusions from RNA-Seq dat version toolchain ========= ============== ``1.1.0`` ``foss/2018b`` +``2.1.0`` ``GCC/10.2.0`` ========= ============== @@ -1377,16 +1398,16 @@ Apache Arrow is a cross-language development platform for in-memory data. *homepage*: https://arrow.apache.org -========== ================== =============================== -version versionsuffix toolchain -========== ================== =============================== -``0.7.1`` ``-Python-3.6.3`` ``intel/2017b`` -``0.12.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``0.12.0`` ``-Python-3.6.6`` ``intel/2018b`` -``0.16.0`` ``-Python-3.7.4`` ``intel/2019b`` -``0.17.1`` ``intel/2020b`` -``0.17.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -========== ================== =============================== +========== ================== =================================== +version versionsuffix toolchain +========== ================== =================================== +``0.7.1`` ``-Python-3.6.3`` ``intel/2017b`` +``0.12.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.12.0`` ``-Python-3.6.6`` ``intel/2018b`` +``0.16.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.17.1`` ``fosscuda/2020b``, ``intel/2020b`` +``0.17.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +========== ================== =================================== .. _list_software_arrow_555: @@ -1446,11 +1467,12 @@ Exploratory analysis of Bayesian models with Python *homepage*: https://github.com/arviz-devs/arviz -========= ================= =============================== -version versionsuffix toolchain -========= ================= =============================== -``0.7.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -========= ================= =============================== +========== ================= =============================== +version versionsuffix toolchain +========== ================= =============================== +``0.7.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.11.1`` ``intel/2020b`` +========== ================= =============================== .. _list_software_ARWEN_381: @@ -1523,10 +1545,10 @@ version versionsuffix toolchain ``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``3.19.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``3.20.1`` ``foss/2020b``, ``intel/2020b`` +``3.20.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``3.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.20.1`` ``-Python-3.8.2`` ``intel/2020a`` -``3.21.1`` ``foss/2020b``, ``intel/2020b`` +``3.21.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ============== ================== =================================================== @@ -1865,7 +1887,7 @@ version versionsuffix toolchain ``3.3.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``3.3.2`` ``-Python-2.7.15`` ``intel/2018b`` ``3.3.3`` ``foss/2019b``, ``intel/2019b`` -``3.4.0`` ``foss/2020b`` +``3.4.0`` ``foss/2020a``, ``foss/2020b`` ========= ================== =============================== @@ -1876,13 +1898,14 @@ version versionsuffix toolchain Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. -*homepage*: http://www.gnu.org/software/autoconf/ +*homepage*: https://www.gnu.org/software/autoconf/ ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= version toolchain ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= ``2.68`` ``foss/2016b`` ``2.69`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +``2.71`` ``system`` ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= @@ -2051,7 +2074,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` +:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` .. _list_software_Bader_478: @@ -2161,14 +2184,14 @@ BamTools provides both a programmer's API and an end-user's toolkit for handling *homepage*: https://github.com/pezmaster31/bamtools -========= ======================================================================================================================================================================================================================= -version toolchain -========= ======================================================================================================================================================================================================================= -``2.4.0`` ``foss/2016b`` -``2.4.1`` ``intel/2017a`` -``2.5.0`` ``foss/2016b``, ``intel/2017b`` -``2.5.1`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017b``, ``intel/2018b`` -========= ======================================================================================================================================================================================================================= +========= ================================================================================================================================================================================================================================================ +version toolchain +========= ================================================================================================================================================================================================================================================ +``2.4.0`` ``foss/2016b`` +``2.4.1`` ``intel/2017a`` +``2.5.0`` ``foss/2016b``, ``intel/2017b`` +``2.5.1`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018b`` +========= ================================================================================================================================================================================================================================================ .. _list_software_BamUtil_686: @@ -2228,7 +2251,7 @@ version toolchain The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python -*homepage*: http://matplotlib.org/basemap/ +*homepage*: https://matplotlib.org/basemap/ ========= ================== =============== version versionsuffix toolchain @@ -2237,6 +2260,7 @@ version versionsuffix toolchain ``1.0.7`` ``-Python-3.6.3`` ``intel/2017b`` ``1.0.7`` ``-Python-3.6.4`` ``intel/2018a`` ``1.2.0`` ``-Python-3.6.6`` ``intel/2018b`` +``1.2.2`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== =============== @@ -2508,6 +2532,7 @@ version toolchain ``1.9`` ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ``1.11`` ``GCC/10.2.0`` +``1.12`` ``GCC/10.2.0``, ``GCC/9.3.0`` ========== ========================================================================================= @@ -2684,9 +2709,26 @@ version toolchain ``2.27.1`` ``GCCcore/6.4.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` ``2.28.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.29.2`` ``GCC/8.3.0``, ``GCC/9.3.0`` +``2.30.0`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` ========== ==================================================================================== +.. _list_software_BEEF_274: + +*BEEF* +++++++ + +BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149. + +*homepage*: https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software + +========= ======================= +version toolchain +========= ======================= +``0.1.1`` ``iccifort/2020.4.304`` +========= ======================= + + .. _list_software_behave_619: *behave* @@ -2878,6 +2920,7 @@ version versionsuffix toolchain ``2.11`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``2.11`` ``-Perl-5.26.1`` ``intel/2018a`` ``2.11`` ``-Perl-5.28.0`` ``foss/2018b`` +``3.01`` ``GCC/10.2.0`` ``3.01`` ``-Perl-5.28.1`` ``GCC/8.2.0-2.31.1`` ======== ================ =============================== @@ -2985,6 +3028,7 @@ version versionsuffix toolchain ``1.7.2`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` ``1.7.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` ``1.7.7`` ``GCCcore/9.3.0`` +``1.7.8`` ``GCCcore/10.2.0`` =========== ================ =============================== @@ -3126,6 +3170,7 @@ version versionsuffix toolchain ========= ================== =============== ``0.8.3`` ``-Python-2.7.15`` ``intel/2018b`` ``0.8.3`` ``-Python-3.6.6`` ``intel/2018b`` +``1.2.1`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== =============== @@ -3331,6 +3376,7 @@ version toolchain ``1.14.4`` ``GCCcore/7.3.0`` ``1.17.0`` ``GCCcore/8.2.0`` ``1.17.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.21.0`` ``GCCcore/10.2.0`` ========== ================================================================== @@ -3401,6 +3447,7 @@ version versionsuffix toolchain ``1.3.4`` ``-Python-3.7.2`` ``foss/2019a`` ``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``2.0.2`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``2.2.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` =========== ================== =================================================== @@ -3552,6 +3599,7 @@ version versionsuffix toolchain ``1.70.0`` ``gompi/2019a``, ``gompic/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` ``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` ``1.72.0`` ``gompi/2020a``, ``iimpi/2020a`` +``1.74.0`` ``GCC/10.2.0`` ========== ================== ==================================================================== @@ -3614,7 +3662,7 @@ version toolchain ``2.3.4.3`` ``foss/2017b`` ``2.3.5.1`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` ``2.4.1`` ``GCC/9.3.0`` -``2.4.2`` ``GCC/9.3.0`` +``2.4.2`` ``GCC/10.2.0``, ``GCC/9.3.0`` =========== ====================================================================================================== @@ -3634,6 +3682,22 @@ version toolchain =========== =============== +.. _list_software_bpp_322: + +*bpp* ++++++ + +The aim of this project is to implement a versatile high-performance version of the BPP software. + +*homepage*: https://github.com/bpp/bpp + +========= ============= +version toolchain +========= ============= +``4.3.8`` ``GCC/8.3.0`` +========= ============= + + .. _list_software_bpytop_670: *bpytop* @@ -3716,6 +3780,22 @@ version versionsuffix toolchain ========== ============= =============== +.. _list_software_Brotli_620: + +*Brotli* +++++++++ + +Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932. + +*homepage*: https://github.com/google/brotli + +========= ================= +version toolchain +========= ================= +``1.0.9`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_bsddb3_562: *bsddb3* @@ -3807,11 +3887,11 @@ This module sets a group of environment variables for compilers, linkers, maths *homepage*: None -=========== ================================================================================================= -version toolchain -=========== ================================================================================================= -``default`` ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b`` -=========== ================================================================================================= +=========== ============================================================================================================================================================================================================================================================================================== +version toolchain +=========== ============================================================================================================================================================================================================================================================================================== +``default`` ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b`` +=========== ============================================================================================================================================================================================================================================================================================== .. _list_software_Bullet_616: @@ -3846,6 +3926,7 @@ version versionsuffix toolchain ``2.0.1`` ``-Python-2.7.13`` ``intel/2017a`` ``3.0.2`` ``-Python-2.7.15`` ``intel/2018b`` ``4.0.5`` ``-Python-3.7.4`` ``foss/2019b`` +``5.0.0`` ``foss/2020b`` ========= ================== =============== @@ -3874,15 +3955,15 @@ Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively sh *homepage*: http://bio-bwa.sourceforge.net/ -=========== ======================================================================================================================================================================================================================== -version toolchain -=========== ======================================================================================================================================================================================================================== -``0.7.12`` ``foss/2016b`` -``0.7.13`` ``foss/2016a``, ``intel/2016a`` -``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``0.7.16a`` ``foss/2016b``, ``intel/2017a`` -``0.7.17`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -=========== ======================================================================================================================================================================================================================== +=========== ================================================================================================================================================================================================================================================================= +version toolchain +=========== ================================================================================================================================================================================================================================================================= +``0.7.12`` ``foss/2016b`` +``0.7.13`` ``foss/2016a``, ``intel/2016a`` +``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``0.7.16a`` ``foss/2016b``, ``intel/2017a`` +``0.7.17`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +=========== ================================================================================================================================================================================================================================================================= .. _list_software_bwa-meth_789: @@ -4045,7 +4126,7 @@ version toolchain --- -:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_C3D_186: @@ -4374,6 +4455,7 @@ version toolchain ========== ========== ``2.9.1`` ``system`` ``2.11.0`` ``system`` +``2.13.4`` ``system`` ========== ========== @@ -4585,14 +4667,30 @@ CD-HIT is a very widely used program for clustering and comparing protein or nu *homepage*: https://github.com/weizhongli/cdhit -========= ============== ===================================================================== -version versionsuffix toolchain -========= ============== ===================================================================== -``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` -``4.6.6`` ``foss/2016b`` -``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` -``4.8.1`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` -========= ============== ===================================================================== +========= ============== ===================================================================================== +version versionsuffix toolchain +========= ============== ===================================================================================== +``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` +``4.6.6`` ``foss/2016b`` +``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` +``4.8.1`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` +========= ============== ===================================================================================== + + +.. _list_software_CDAT_284: + +*CDAT* +++++++ + +CDAT is a powerful and complete front-end to a rich set of visual-data exploration and analysis capabilities well suited for data analysis problems. + +*homepage*: https://github.com/CDAT/cdat + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``8.2.1`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== .. _list_software_cdbfasta_824: @@ -4717,6 +4815,7 @@ version toolchain ``4.0.0`` ``system`` ``5.0.0`` ``system`` ``5.0.1`` ``system`` +``6.0.0`` ``system`` ========= ========== @@ -5206,6 +5305,38 @@ version toolchain ========= ================= +.. _list_software_cicero_629: + +*cicero* +++++++++ + +Cicero is an R package that provides tools for analyzing single-cell chromatin accessibility experiments. + +*homepage*: https://cole-trapnell-lab.github.io/cicero-release + +============ ===================== ============== +version versionsuffix toolchain +============ ===================== ============== +``1.3.4.11`` ``-R-4.0.3-Monocle3`` ``foss/2020b`` +============ ===================== ============== + + +.. _list_software_CIF2Cell_644: + +*CIF2Cell* +++++++++++ + +CIF2Cell is a tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file. The program currently supports output for a number of popular electronic structure programs, including ABINIT, ASE, CASTEP, CP2K, CPMD, CRYSTAL09, Elk, EMTO, Exciting, Fleur, FHI-aims, Hutsepot, MOPAC, Quantum Espresso, RSPt, Siesta, SPR-KKR, VASP. Also exports some related formats like .coo, .cfg and .xyz-files. + +*homepage*: https://sourceforge.net/projects/cif2cell + +========== ================== ================= +version versionsuffix toolchain +========== ================== ================= +``1.2.10`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +========== ================== ================= + + .. _list_software_CIRCexplorer_1170: *CIRCexplorer* @@ -5343,6 +5474,7 @@ version versionsuffix toolchain ``10.0.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``10.0.1`` ``GCCcore/9.3.0`` ``11.0.0`` ``GCCcore/9.3.0`` +``11.0.1`` ``GCCcore/10.2.0``, ``gcccuda/2020b`` ========== ================== ====================================== @@ -5712,6 +5844,22 @@ version versionsuffix toolchain ============ ================== ============== +.. _list_software_CompareM_788: + +*CompareM* +++++++++++ + +A toolbox for comparative genomics. + +*homepage*: https://github.com/dparks1134/CompareM + +========== ================== ============== +version versionsuffix toolchain +========== ================== ============== +``0.0.23`` ``-Python-2.7.15`` ``foss/2018b`` +========== ================== ============== + + .. _list_software_COMSOL_461: *COMSOL* @@ -5969,6 +6117,8 @@ version versionsuffix toolchain ``5.1`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a``, ``intel/2020a`` ``6.1`` ``foss/2019a``, ``intel/2018a``, ``intel/2020a`` ``7.1`` ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` +``7.1`` ``-psmp`` ``foss/2020b`` +``8.1`` ``foss/2020b`` ======= ============= ================================================================== @@ -6428,6 +6578,7 @@ version toolchain ``11.0.2`` ``system`` ``11.1.1`` ``system`` ``11.2.1`` ``system`` +``11.2.2`` ``system`` ========== ========== @@ -6606,11 +6757,12 @@ The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providin *homepage*: https://developer.nvidia.com/cutensor -=========== ================= -version toolchain -=========== ================= -``1.2.2.5`` ``gcccuda/2019b`` -=========== ================= +=========== ================ ================= +version versionsuffix toolchain +=========== ================ ================= +``1.2.2.5`` ``gcccuda/2019b`` +``1.2.2.5`` ``-CUDA-11.1.1`` ``system`` +=========== ================ ================= .. _list_software_CVS_236: @@ -6760,7 +6912,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` .. _list_software_dadi_402: @@ -6884,28 +7036,29 @@ Dask natively scales Python. Dask provides advanced parallelism for analytics, e *homepage*: https://dask.org/ -========== ================== =================================================== -version versionsuffix toolchain -========== ================== =================================================== -``0.8.2`` ``-Python-2.7.11`` ``intel/2016a`` -``0.8.2`` ``-Python-3.5.1`` ``intel/2016a`` -``0.11.0`` ``-Python-2.7.11`` ``foss/2016a`` -``0.11.0`` ``-Python-2.7.12`` ``intel/2016b`` -``0.11.0`` ``-Python-3.5.2`` ``intel/2016b`` -``0.12.0`` ``-Python-2.7.12`` ``intel/2016b`` -``0.12.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``0.16.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``0.16.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``0.17.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` -``0.17.0`` ``-Python-3.6.1`` ``intel/2017a`` -``0.17.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``0.19.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``1.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.1.4`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``2.3.0`` ``-Python-3.7.2`` ``foss/2019a`` -``2.8.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``2.18.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -========== ================== =================================================== +============ ================== =================================================== +version versionsuffix toolchain +============ ================== =================================================== +``0.8.2`` ``-Python-2.7.11`` ``intel/2016a`` +``0.8.2`` ``-Python-3.5.1`` ``intel/2016a`` +``0.11.0`` ``-Python-2.7.11`` ``foss/2016a`` +``0.11.0`` ``-Python-2.7.12`` ``intel/2016b`` +``0.11.0`` ``-Python-3.5.2`` ``intel/2016b`` +``0.12.0`` ``-Python-2.7.12`` ``intel/2016b`` +``0.12.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``0.16.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``0.16.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``0.17.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``0.17.0`` ``-Python-3.6.1`` ``intel/2017a`` +``0.17.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.19.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``1.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.1.4`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``2.3.0`` ``-Python-3.7.2`` ``foss/2019a`` +``2.8.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2.18.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``2021.2.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +============ ================== =================================================== .. _list_software_datamash_835: @@ -6970,15 +7123,16 @@ version toolchain Perl5 access to Berkeley DB version 1.x. -*homepage*: http://perldoc.perl.org/DB_File.html +*homepage*: https://perldoc.perl.org/DB_File.html -========= ================ ================= -version versionsuffix toolchain -========= ================ ================= -``1.835`` ``GCCcore/9.3.0`` -``1.835`` ``-Perl-5.20.3`` ``intel/2016a`` -``1.835`` ``-Perl-5.22.1`` ``foss/2016a`` -========= ================ ================= +========= ================ ================== +version versionsuffix toolchain +========= ================ ================== +``1.835`` ``GCCcore/9.3.0`` +``1.835`` ``-Perl-5.20.3`` ``intel/2016a`` +``1.835`` ``-Perl-5.22.1`` ``foss/2016a`` +``1.855`` ``GCCcore/10.2.0`` +========= ================ ================== .. _list_software_DBD-mysql_813: @@ -6999,6 +7153,7 @@ version versionsuffix toolchain ``4.046`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``4.046`` ``-Perl-5.26.1`` ``intel/2018a`` ``4.048`` ``-Perl-5.28.0`` ``foss/2018b`` +``4.050`` ``GCC/10.2.0`` ``4.050`` ``-Perl-5.28.1`` ``foss/2019a`` ========= ================ =============================== @@ -7253,15 +7408,16 @@ version versionsuffix toolchain *Delly* +++++++ -Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. +Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. -*homepage*: https://github.com/dellytools/delly +*homepage*: https://github.com/dellytools/delly/ -========= ================= ========== -version versionsuffix toolchain -========= ================= ========== -``0.7.8`` ``-linux_x86_64`` ``system`` -========= ================= ========== +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.7.8`` ``-linux_x86_64`` ``system`` +``0.8.7`` ``gompi/2020b`` +========= ================= =============== .. _list_software_DeMixT_555: @@ -7418,7 +7574,7 @@ version toolchain *DIAMOND* +++++++++ -DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. +Accelerated BLAST compatible local sequence aligner *homepage*: https://github.com/bbuchfink/diamond @@ -7431,6 +7587,7 @@ version toolchain ``0.9.36`` ``GCC/9.3.0`` ``2.0.4`` ``GCC/9.3.0`` ``2.0.6`` ``GCC/7.3.0-2.30`` +``2.0.7`` ``GCC/10.2.0`` ========== ================================================================ @@ -7533,6 +7690,22 @@ version versionsuffix toolchain ========== ================== =============== +.. _list_software_DL_POLY_4_710: + +*DL_POLY_4* ++++++++++++ + +DL_POLY is a general purpose classical molecular dynamics (MD) simulation software + +*homepage*: https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx + +========= =============================== +version toolchain +========= =============================== +``5.0.0`` ``foss/2020b``, ``intel/2020b`` +========= =============================== + + .. _list_software_DL_POLY_Classic_1364: *DL_POLY_Classic* @@ -7560,11 +7733,28 @@ dm-tree provides tree, a library for working with nested data structures. In a w *homepage*: https://github.com/deepmind/tree -========= ================= -version toolchain -========= ================= -``0.1.1`` ``GCCcore/8.3.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``0.1.1`` ``GCCcore/8.3.0`` +``0.1.5`` ``GCCcore/10.2.0`` +========= ================== + + +.. _list_software_DMCfun_541: + +*DMCfun* +++++++++ + +Diffusion Model of Conflict (DMC) in Reaction Time Tasks + +*homepage*: https://cran.r-project.org/web/packages/DMCfun + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``1.3.0`` ``-R-3.6.2`` ``foss/2019b`` +========= ============= ============== .. _list_software_DMTCP_376: @@ -7846,7 +8036,7 @@ version versionsuffix toolchain --- -:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExifTool_810` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExifTool_810` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_E-ANTIC_481: @@ -7989,6 +8179,7 @@ version toolchain ``4.3.0`` ``system`` ``4.3.1`` ``system`` ``4.3.2`` ``system`` +``4.3.3`` ``system`` ========== ========== @@ -8211,6 +8402,7 @@ version toolchain ``4.0.15`` ``intel/2016b`` ``4.3.6`` ``intel/2017a`` ``6.3.2`` ``intel/2019b`` +``7.0.12`` ``foss/2020b`` ========== =============== @@ -8223,19 +8415,19 @@ Eigenvalue SoLvers for Petaflop-Applications . *homepage*: https://elpa.rzg.mpg.de -=================== ================================================================ -version toolchain -=================== ================================================================ -``2015.02.002`` ``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` -``2016.05.004`` ``intel/2016b``, ``intel/2017a`` -``2016.11.001.pre`` ``foss/2018b``, ``intel/2018b`` -``2017.11.001`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -``2018.05.001`` ``foss/2018b``, ``intel/2018b`` -``2018.11.001`` ``intel/2019a`` -``2019.11.001`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` -``2020.05.001`` ``intel/2020a`` -``2020.11.001`` ``foss/2020b``, ``intel/2020b`` -=================== ================================================================ +=================== ================================================================================= +version toolchain +=================== ================================================================================= +``2015.02.002`` ``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` +``2016.05.004`` ``intel/2016b``, ``intel/2017a`` +``2016.11.001.pre`` ``foss/2018b``, ``intel/2018b`` +``2017.11.001`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +``2018.05.001`` ``foss/2018b``, ``intel/2018b`` +``2018.11.001`` ``intel/2019a`` +``2019.11.001`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a``, ``iomkl/2019b`` +``2020.05.001`` ``intel/2020a`` +``2020.11.001`` ``foss/2020b``, ``intel/2020b`` +=================== ================================================================================= .. _list_software_ELPH_297: @@ -8290,7 +8482,7 @@ version versionsuffix toolchain ``25.1`` ``foss/2016a`` ``25.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``26.3`` ``GCCcore/8.3.0`` -``27.1`` ``GCCcore/9.3.0`` +``27.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ======== ============= ======================================================= @@ -8353,7 +8545,7 @@ version versionsuffix toolchain *EMU* +++++ -EMU infers population structure in the presence of missingness and works for both haploid, psuedo-haploid and diploid genotype datasets +EMU infers population structure in the presence of missingness and works for both haploid, psuedo-haploid and diploid genotype datasets *homepage*: http://www.popgen.dk/software/index.php/EMU @@ -8501,6 +8693,22 @@ version versionsuffix toolchain ============ ================ ================================================================================= +.. _list_software_ESMPy_430: + +*ESMPy* ++++++++ + +Earth System Modeling Framework (ESMF) Python Interface + +*homepage*: https://earthsystemmodeling.org/esmpy + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``8.0.0`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + .. _list_software_ESMValTool_934: *ESMValTool* @@ -8623,7 +8831,7 @@ version versionsuffix toolchain evmix: Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation -*homepage*: http://cran.r-project.org/web/packages/evmix +*homepage*: https://cran.r-project.org/web/packages/evmix ======= ============= =============== version versionsuffix toolchain @@ -8742,13 +8950,14 @@ version toolchain Extrae is the core instrumentation package developed by the Performance Tools group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered by Extrae typically includes timestamped events of runtime calls, performance counters and source code references. Besides, Extrae provides its own API to allow the user to manually instrument his or her application. -*homepage*: http://www.bsc.es/computer-sciences/performance-tools +*homepage*: https://www.bsc.es/computer-sciences/performance-tools ========= =============== version toolchain ========= =============== ``3.4.1`` ``foss/2017a`` ``3.7.1`` ``intel/2019a`` +``3.8.0`` ``gompi/2020b`` ========= =============== @@ -8758,7 +8967,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -8806,6 +9015,7 @@ FabIO is an I/O library for images produced by 2D X-ray detectors and written in version versionsuffix toolchain ========== ================= ================================== ``0.10.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``0.11.0`` ``foss/2020b`` ========== ================= ================================== @@ -9251,6 +9461,7 @@ version versionsuffix toolchain ``6.5.3`` ``intel/2017a`` ``6.6.0`` ``intel/2017b``, ``intel/2018a`` ``6.7.0`` ``intel/2018a`` +``6.7.4`` ``intel/2020a`` ``6.7.5`` ``intel/2020a`` ========= ============= ================================ @@ -9579,7 +9790,7 @@ version toolchain *Fiji* ++++++ -Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. This release is based on ImageJ 2.0.0-rc-69/1.52p. +Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. This release is based on ImageJ-2.1.0 and Fiji-2.1.1 *homepage*: https://fiji.sc/ @@ -9588,6 +9799,7 @@ version toolchain ================= ========== ``20170530`` ``system`` ``20191119-2057`` ``system`` +``20201104-1356`` ``system`` ================= ========== @@ -9610,6 +9822,7 @@ version toolchain ``5.33`` ``GCCcore/6.4.0`` ``5.35`` ``GCCcore/7.3.0`` ``5.38`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``5.39`` ``GCCcore/10.2.0`` ======== ==================================== @@ -9823,6 +10036,22 @@ version toolchain ======= ================================================= +.. _list_software_FLAC_278: + +*FLAC* +++++++ + +FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality. + +*homepage*: https://xiph.org/flac/ + +========= ================== +version toolchain +========= ================== +``1.3.3`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_FLAIR_366: *FLAIR* @@ -10042,7 +10271,7 @@ version toolchain ========= =================================================================================================================================================================================================== ``1.3.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.3.4`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b`` -``1.3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/9.3.0`` +``1.3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= =================================================================================================================================================================================================== @@ -10053,7 +10282,7 @@ version toolchain ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. -*homepage*: https://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent +*homepage*: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent ========== ========== version toolchain @@ -10065,6 +10294,7 @@ version toolchain ``18.0`` ``system`` ``18.1`` ``system`` ``18.2`` ``system`` +``2021R1`` ``system`` ========== ========== @@ -10084,6 +10314,7 @@ version versionsuffix toolchain ``2.6`` ``-Python-3.7.2`` ``foss/2019a`` ``2.6`` ``-Python-3.7.4`` ``intel/2019b`` ``2.8.1`` ``-Python-3.8.2`` ``intel/2020a`` +``2.8.2`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== =============== @@ -10447,6 +10678,9 @@ version versionsuffix toolchain ``5.3.0`` ``-centos6_x86_64`` ``system`` ``6.0.0`` ``-centos6_x86_64`` ``system`` ``6.0.1`` ``-centos6_x86_64`` ``system`` +``7.1.1`` ``-centos6_x86_64`` ``system`` +``7.1.1`` ``-centos7_x86_64`` ``system`` +``7.1.1`` ``-centos8_x86_64`` ``system`` ========= =================== ========== @@ -10457,7 +10691,7 @@ version versionsuffix toolchain FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. -*homepage*: http://freetype.org +*homepage*: https://freetype.org ========== ================== ====================================================================== version versionsuffix toolchain @@ -10730,7 +10964,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -10740,7 +10974,7 @@ version toolchain Library contains GRIB2 encoder/decoder ('C' version). -*homepage*: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ +*homepage*: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ ========= ======================================================================================================================== version toolchain @@ -11290,6 +11524,7 @@ version versionsuffix toolchain ``3.0.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``3.0.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``3.0.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``3.2.1`` ``foss/2020b``, ``fosscuda/2020b`` ========= ============================== ================================================================ @@ -11336,6 +11571,22 @@ version versionsuffix toolchain ============ ================= ================= +.. _list_software_gdbm_410: + +*gdbm* +++++++ + +GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database. + +*homepage*: https://www.gnu.org.ua/software/gdbm/ + +========== ============== +version toolchain +========== ============== +``1.18.1`` ``foss/2020a`` +========== ============== + + .. _list_software_gdc-client_986: *gdc-client* @@ -11797,6 +12048,7 @@ version versionsuffix toolchain ``3.7.2`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``3.8.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ``3.8.1`` ``-Python-3.8.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` +``3.9.1`` ``GCC/10.2.0`` ========= ================== ================================================================ @@ -11841,11 +12093,12 @@ This toolkit assemblies organelle genome from genomic skimming data. *homepage*: https://github.com/Kinggerm/GetOrganelle -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``1.7.2`` ``-Python-3.8.2`` ``foss/2020a`` -========= ================= ============== +============== ================= ============== +version versionsuffix toolchain +============== ================= ============== +``1.7.2`` ``-Python-3.8.2`` ``foss/2020a`` +``1.7.4-pre2`` ``foss/2020b`` +============== ================= ============== .. _list_software_gettext_773: @@ -12329,16 +12582,17 @@ version toolchain *GLFW* ++++++ -GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop +GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop *homepage*: https://www.glfw.org -========= ================= -version toolchain -========= ================= -``3.2.1`` ``intel/2018a`` -``3.3.2`` ``GCCcore/9.3.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``3.2.1`` ``intel/2018a`` +``3.3.2`` ``GCCcore/9.3.0`` +``3.3.3`` ``GCCcore/10.2.0`` +========= ================== .. _list_software_GLib_350: @@ -12594,6 +12848,7 @@ version toolchain ``2018-07-04`` ``intel/2018a`` ``2019-03-15`` ``foss/2018b`` ``2019-09-12`` ``GCC/8.3.0`` +``2020-12-17`` ``GCC/9.3.0`` ============== =============== @@ -12672,7 +12927,7 @@ version versionsuffix toolchain ``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``2.1.0b4`` ``GCC/8.3.0`` -``2.1.0b5`` ``GCC/9.3.0`` +``2.1.0b5`` ``GCC/10.2.0``, ``GCC/9.3.0`` =========== ================== =============================== @@ -12683,17 +12938,18 @@ version versionsuffix toolchain Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. -*homepage*: https://gmsh.info +*homepage*: https://gmsh.info/ -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``3.0.6`` ``-Python-2.7.14`` ``foss/2017b`` -``3.0.6`` ``-Python-3.6.6`` ``foss/2018b`` -``4.2.2`` ``-Python-3.6.6`` ``foss/2018b`` -``4.5.6`` ``-Python-2.7.16`` ``intel/2019b`` -``4.5.6`` ``-Python-3.7.4`` ``foss/2019b`` -========= ================== =============== +========= ================== =============================== +version versionsuffix toolchain +========= ================== =============================== +``3.0.6`` ``-Python-2.7.14`` ``foss/2017b`` +``3.0.6`` ``-Python-3.6.6`` ``foss/2018b`` +``4.2.2`` ``-Python-3.6.6`` ``foss/2018b`` +``4.5.6`` ``-Python-2.7.16`` ``intel/2019b`` +``4.5.6`` ``-Python-3.7.4`` ``foss/2019b`` +``4.7.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +========= ================== =============================== .. _list_software_GMT_232: @@ -12910,6 +13166,7 @@ GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for M version toolchain ========= ========== ``2018b`` ``system`` +``2020b`` ``system`` ========= ========== @@ -13530,11 +13787,11 @@ Groff (GNU troff) is a typesetting system that reads plain text mixed with forma *homepage*: https://www.gnu.org/software/groff -========== ================= -version toolchain -========== ================= -``1.22.4`` ``GCCcore/9.3.0`` -========== ================= +========== ======================================================== +version toolchain +========== ======================================================== +``1.22.4`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ======================================================== .. _list_software_GroIMP_526: @@ -13593,6 +13850,7 @@ version versionsuffix toolchain ``2020.3`` ``fosscuda/2019b`` ``2020.4`` ``-Python-3.8.2`` ``foss/2020a`` ``2020.5`` ``-Python-3.8.2`` ``fosscuda/2020a`` +``2021`` ``foss/2020b``, ``fosscuda/2020b`` ========== ================= ============================================================================================================ @@ -13857,12 +14115,12 @@ GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free *homepage*: http://gts.sourceforge.net/ -============ ======================================================================================================================================================================= -version toolchain -============ ======================================================================================================================================================================= -``0.7.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` -``20121130`` ``foss/2017b`` -============ ======================================================================================================================================================================= +============ =========================================================================================================================================================================================== +version toolchain +============ =========================================================================================================================================================================================== +``0.7.6`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` +``20121130`` ``foss/2017b`` +============ =========================================================================================================================================================================================== .. _list_software_gubbins_746: @@ -13937,7 +14195,7 @@ version toolchain *Gurobi* ++++++++ -The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. +The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. *homepage*: https://www.gurobi.com @@ -13955,6 +14213,7 @@ version versionsuffix toolchain ``9.0.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``9.0.1`` ``system`` ``9.1.0`` ``system`` +``9.1.1`` ``GCCcore/10.2.0`` ========= ================= =============================== @@ -14073,18 +14332,18 @@ Hadoop MapReduce by Cloudera *homepage*: https://archive.cloudera.com/cdh5/cdh/5/ -=================== ========================== ================= -version versionsuffix toolchain -=================== ========================== ================= -``2.4.0`` ``-seagate-722af1-native`` ``system`` -``2.5.0-cdh5.3.1`` ``-native`` ``system`` -``2.6.0-cdh5.4.5`` ``-native`` ``system`` -``2.6.0-cdh5.7.0`` ``-native`` ``system`` -``2.6.0-cdh5.8.0`` ``-native`` ``system`` -``2.6.0-cdh5.12.0`` ``-native`` ``system`` -``2.9.2`` ``-native`` ``GCCcore/7.3.0`` -``2.10.0`` ``-native`` ``GCCcore/8.3.0`` -=================== ========================== ================= +=================== ========================== ===================================== +version versionsuffix toolchain +=================== ========================== ===================================== +``2.4.0`` ``-seagate-722af1-native`` ``system`` +``2.5.0-cdh5.3.1`` ``-native`` ``system`` +``2.6.0-cdh5.4.5`` ``-native`` ``system`` +``2.6.0-cdh5.7.0`` ``-native`` ``system`` +``2.6.0-cdh5.8.0`` ``-native`` ``system`` +``2.6.0-cdh5.12.0`` ``-native`` ``system`` +``2.9.2`` ``-native`` ``GCCcore/7.3.0`` +``2.10.0`` ``-native`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +=================== ========================== ===================================== .. _list_software_hanythingondemand_1808: @@ -14247,7 +14506,7 @@ version versionsuffix toolchain ``4.2.13`` ``GCCcore/6.4.0`` ``4.2.13`` ``-no-netcdf`` ``intel/2017a`` ``4.2.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``4.2.15`` ``GCCcore/9.3.0`` +``4.2.15`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========== ============== ========================================================================== @@ -14310,7 +14569,7 @@ version versionsuffix toolchain ``1.10.0-patch1`` ``foss/2016b``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a`` ``1.10.1`` ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2017b``, ``iomkl/2018a`` ``1.10.2`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``1.10.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompic/2019a``, ``gompic/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpic/2019a``, ``iimpic/2019b`` +``1.10.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompic/2019a``, ``gompic/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpic/2019a``, ``iimpic/2019b``, ``iompi/2019b`` ``1.10.6`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpic/2020a`` ``1.10.7`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpic/2020b`` ``1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` @@ -14527,7 +14786,7 @@ version toolchain HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). -*homepage*: https://ccb.jhu.edu/software/hisat2/index.shtml +*homepage*: https://daehwankimlab.github.io/hisat2 ============== ================================================================================= version toolchain @@ -14537,7 +14796,7 @@ version toolchain ``2.0.5`` ``intel/2017a`` ``2.1.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``2.2.0`` ``foss/2018b`` -``2.2.1`` ``foss/2019b`` +``2.2.1`` ``foss/2019b``, ``gompi/2020b`` ============== ================================================================================= @@ -14746,7 +15005,7 @@ version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020a``, ``intel/2020b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020a``, ``intel/2020b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -14790,6 +15049,7 @@ version versionsuffix toolchain ``0.11.2`` ``-Python-3.6.6`` ``foss/2018b`` ``0.11.2`` ``-Python-3.7.2`` ``foss/2019a`` ``0.11.2`` ``-Python-3.7.4`` ``foss/2019b`` +``0.11.3`` ``foss/2020b`` =========== ================== ================================================ @@ -14816,7 +15076,8 @@ version versionsuffix toolchain ``1.8`` ``GCC/6.4.0-2.28``, ``foss/2018a``, ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` -``1.11`` ``GCC/10.2.0`` +``1.11`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``1.12`` ``GCC/10.2.0``, ``GCC/9.3.0`` ``20160107`` ``-PacBio`` ``intel/2017a`` ============ ============= =========================================================================================================================================================== @@ -14916,11 +15177,12 @@ Distributed Asynchronous Hyperparameter Optimization in Python *homepage*: https://github.com/hyperopt/hyperopt -========= ========================== =============== -version versionsuffix toolchain -========= ========================== =============== -``0.2.4`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` -========= ========================== =============== +========= ========================== ================== +version versionsuffix toolchain +========= ========================== ================== +``0.2.4`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` +``0.2.5`` ``fosscuda/2020b`` +========= ========================== ================== .. _list_software_hyperspy_900: @@ -15010,6 +15272,7 @@ version toolchain ``2.14.0`` ``foss/2018a``, ``intel/2018a`` ``2.15.1`` ``foss/2019a``, ``intel/2019a`` ``2.18.2`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` +``2.20.0`` ``foss/2020b`` ========== ================================================================ @@ -15385,6 +15648,7 @@ version toolchain ``0.8.0`` ``foss/2019b`` ``0.8.2`` ``foss/2020a`` ``0.8.5`` ``foss/2020b`` +``0.9.1`` ``fosscuda/2020b`` ========= ================================================ @@ -15666,15 +15930,16 @@ version versionsuffix toolchain *imake* +++++++ -imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems. +imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems. -*homepage*: http://www.x.org/ +*homepage*: https://www.x.org/ -========= =============== -version toolchain -========= =============== -``1.0.7`` ``intel/2016a`` -========= =============== +========= ================== +version toolchain +========= ================== +``1.0.7`` ``intel/2016a`` +``1.0.8`` ``GCCcore/10.2.0`` +========= ================== .. _list_software_IMB_216: @@ -16673,11 +16938,12 @@ iVar is a computational package that contains functions broadly useful for viral *homepage*: https://github.com/andersen-lab/ivar -========= ============== -version toolchain -========= ============== -``1.0.1`` ``foss/2018b`` -========= ============== +========= ============================= +version toolchain +========= ============================= +``1.0.1`` ``foss/2018b`` +``1.3.1`` ``GCC/10.2.0``, ``GCC/9.3.0`` +========= ============================= .. _list_software_letter_j: @@ -16686,7 +16952,7 @@ version toolchain --- -:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` +:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` .. _list_software_JAGS_293: @@ -16715,11 +16981,12 @@ Jansson is a C library for encoding, decoding and manipulating JSON data. Its m *homepage*: http://www.digip.org/jansson/ -======= ============= -version toolchain -======= ============= -``2.6`` ``GCC/4.8.3`` -======= ============= +========== ============== +version toolchain +========== ============== +``2.6`` ``GCC/4.8.3`` +``2.13.1`` ``GCC/10.2.0`` +========== ============== .. _list_software_JasPer_581: @@ -16737,7 +17004,7 @@ version toolchain ``1.900.1`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``2.0.10`` ``intel/2016b`` ``2.0.12`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` -``2.0.14`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.0.16`` ``GCCcore/9.3.0`` ``2.0.24`` ``GCCcore/10.2.0`` =========== ========================================================================================================================================================== @@ -16833,11 +17100,11 @@ JBIG-KIT is a software implementation of the JBIG1 data compression standard (I *homepage*: https://www.cl.cam.ac.uk/~mgk25/jbigkit/ -======= ========================================================================== -version toolchain -======= ========================================================================== -``2.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ========================================================================== +======= ============================================================================================== +version toolchain +======= ============================================================================================== +``2.1`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ============================================================================================== .. _list_software_Jellyfish_938: @@ -16965,6 +17232,22 @@ version toolchain ======= ================= +.. _list_software_json-c_586: + +*json-c* +++++++++ + +JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects. + +*homepage*: https://github.com/json-c/json-c + +======== ================== +version toolchain +======== ================== +``0.15`` ``GCCcore/10.2.0`` +======== ================== + + .. _list_software_JsonCpp_701: *JsonCpp* @@ -17038,6 +17321,7 @@ version versionsuffix toolchain ``1.4.1`` ``-linux-x86_64`` ``system`` ``1.4.2`` ``-linux-x86_64`` ``system`` ``1.5.1`` ``-linux-x86_64`` ``system`` +``1.5.3`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -17188,6 +17472,7 @@ version toolchain ``0.45.1`` ``foss/2019a`` ``0.46.0`` ``intel/2019a`` ``0.46.1`` ``foss/2019b`` +``0.46.2`` ``foss/2020b`` ========== ================================================ @@ -17253,6 +17538,7 @@ Kent utilities: collection of tools used by the UCSC genome browser. version versionsuffix toolchain ============ ================= =============== ``401`` ``gompi/2019b`` +``411`` ``GCC/10.2.0`` ``20130806`` ``-linux.x86_64`` ``system`` ``20171107`` ``-linux.x86_64`` ``system`` ``20180716`` ``-linux.x86_64`` ``system`` @@ -17573,7 +17859,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -17657,6 +17943,7 @@ LAPACK is written in Fortran90 and provides routines for solving systems of sim version toolchain ========= ================== ``3.8.0`` ``GCC/7.3.0-2.30`` +``3.9.1`` ``GCC/10.2.0`` ========= ================== @@ -17675,6 +17962,7 @@ version toolchain ``869`` ``intel/2017a`` ``914`` ``intel/2017b`` ``1045`` ``intel/2019b`` +``1179`` ``GCC/10.2.0`` ======== =============== @@ -17753,11 +18041,12 @@ Implementation of the Leiden algorithm for various quality functions to be used *homepage*: https://github.com/vtraag/leidenalg -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``0.8.2`` ``-Python-3.8.2`` ``foss/2020a`` -========= ================= ============== +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``0.8.2`` ``-Python-3.8.2`` ``foss/2020a`` +``0.8.3`` ``fosscuda/2020b`` +========= ================= ================== .. _list_software_LEMON_379: @@ -17823,7 +18112,7 @@ version toolchain ======== ================================================ ``1.18`` ``foss/2016a``, ``intel/2017a``, ``intel/2017b`` ``1.20`` ``GCCcore/7.3.0`` -``1.22`` ``GCCcore/8.2.0`` +``1.22`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` ======== ================================================ @@ -17927,6 +18216,22 @@ version toolchain ======= ========== +.. _list_software_libcdms_734: + +*libcdms* ++++++++++ + +Climate Data Management System Library. + +*homepage*: https://github.com/CDAT/libcdms/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``3.1.2`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_libcerf_727: *libcerf* @@ -17934,7 +18239,7 @@ version toolchain libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. -*homepage*: http://apps.jcns.fz-juelich.de/doku/sc/libcerf +*homepage*: https://jugit.fz-juelich.de/mlz/libcerf ======== ========================================================================================================= version toolchain @@ -18113,6 +18418,22 @@ version toolchain =========== ================================================== +.. _list_software_libdrs_640: + +*libdrs* +++++++++ + +PCMDI's old DRS format implementation + +*homepage*: https://github.com/CDAT/libdrs/ + +========= ============== +version toolchain +========= ============== +``3.1.2`` ``foss/2020a`` +========= ============== + + .. _list_software_libdwarf_843: *libdwarf* @@ -18120,7 +18441,7 @@ version toolchain The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers (and anyone interested in reading or writing DWARF information)) -*homepage*: http://www.prevanders.net/dwarf.html +*homepage*: https://www.prevanders.net/dwarf.html ============ =================================================== version toolchain @@ -18128,6 +18449,7 @@ version toolchain ``20140805`` ``GCC/4.9.2`` ``20150310`` ``GCC/4.9.2``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0`` ``20190529`` ``GCCcore/8.2.0`` +``20201201`` ``GCCcore/10.2.0`` ============ =================================================== @@ -18158,11 +18480,11 @@ libelf is a free ELF object file access library *homepage*: https://directory.fsf.org/wiki/Libelf -========== ======================================================================================================== -version toolchain -========== ======================================================================================================== -``0.8.13`` ``GCC/4.8.3``, ``GCC/4.9.2``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` -========== ======================================================================================================== +========== ============================================================================================================================ +version toolchain +========== ============================================================================================================================ +``0.8.13`` ``GCC/4.8.3``, ``GCC/4.9.2``, ``GCCcore/10.2.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +========== ============================================================================================================================ .. _list_software_libepoxy_876: @@ -18303,6 +18625,7 @@ version toolchain ``1.6.5`` ``intel/2016a`` ``1.8.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.8.5`` ``GCCcore/8.3.0`` +``1.9.2`` ``GCCcore/10.2.0`` ========= ==================================== @@ -18356,6 +18679,7 @@ version toolchain ========= ======================================================= ``1.4.2`` ``foss/2018a``, ``foss/2018b``, ``intel/2018b`` ``1.5.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.6.0`` ``GCCcore/10.2.0`` ========= ======================================================= @@ -18436,14 +18760,15 @@ Libgpg-error is a small library that defines common error values for all GnuPG c *homepage*: https://gnupg.org/related_software/libgpg-error/index.html -======== ================= -version toolchain -======== ================= -``1.21`` ``intel/2016a`` -``1.35`` ``GCCcore/7.3.0`` -``1.36`` ``GCCcore/8.2.0`` -``1.38`` ``GCCcore/8.3.0`` -======== ================= +======== ================== +version toolchain +======== ================== +``1.21`` ``intel/2016a`` +``1.35`` ``GCCcore/7.3.0`` +``1.36`` ``GCCcore/8.2.0`` +``1.38`` ``GCCcore/8.3.0`` +``1.41`` ``GCCcore/10.2.0`` +======== ================== .. _list_software_libgpuarray_1186: @@ -18460,7 +18785,7 @@ version versionsuffix toolchain ========= ================== ======================================================== ``0.7.5`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` ``0.7.5`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``0.7.6`` ``fosscuda/2019a`` +``0.7.6`` ``fosscuda/2019a``, ``fosscuda/2020b`` ``0.7.6`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``0.7.6`` ``-Python-3.6.6`` ``fosscuda/2018b`` ``0.7.6`` ``-Python-3.7.4`` ``fosscuda/2019b`` @@ -18759,6 +19084,22 @@ version toolchain ============ =============== +.. _list_software_libogg_628: + +*libogg* +++++++++ + +Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs. + +*homepage*: https://xiph.org/ogg/ + +========= ================== +version toolchain +========= ================== +``1.3.4`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_libosmium_977: *libosmium* @@ -18852,6 +19193,7 @@ version toolchain ========== ==================================== ``0.20.2`` ``GCCcore/7.3.0`` ``0.21.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.21.1`` ``GCCcore/10.2.0`` ========== ==================================== @@ -19105,12 +19447,13 @@ libsoup is an HTTP client/server library for GNOME. It uses GObjects and the gli *homepage*: https://wiki.gnome.org/Projects/libsoup -========== ================= -version toolchain -========== ================= -``2.66.1`` ``GCCcore/8.2.0`` -``2.70.0`` ``GCCcore/8.3.0`` -========== ================= +========== ================== +version toolchain +========== ================== +``2.66.1`` ``GCCcore/8.2.0`` +``2.70.0`` ``GCCcore/8.3.0`` +``2.72.0`` ``GCCcore/10.2.0`` +========== ================== .. _list_software_libspatialindex_1597: @@ -19227,7 +19570,7 @@ version toolchain ``4.7`` ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` ``4.12`` ``GCCcore/5.4.0`` ``4.13`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``4.16.0`` ``GCCcore/8.3.0`` +``4.16.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` ========== =================================================== @@ -19391,6 +19734,22 @@ version toolchain ========= ============================================== +.. _list_software_libvorbis_972: + +*libvorbis* ++++++++++++ + +Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format + +*homepage*: https://xiph.org/vorbis/ + +========= ================== +version toolchain +========= ================== +``1.3.7`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_libwebp_741: *libwebp* @@ -19400,13 +19759,13 @@ WebP is a modern image format that provides superior lossless and lossy compress *homepage*: https://developers.google.com/speed/webp/ -========= ===================================== -version toolchain -========= ===================================== -``1.0.0`` ``foss/2018b`` -``1.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` -========= ===================================== +========= ======================================================== +version toolchain +========= ======================================================== +``1.0.0`` ``foss/2018b`` +``1.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================== .. _list_software_libX11_497: @@ -19461,6 +19820,7 @@ version toolchain ``4.0.3`` ``foss/2016b``, ``foss/2017a`` ``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` ``4.3.4`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` +``5.1.2`` ``GCC/10.2.0`` ========= ======================================================================================================================================================================================= @@ -19804,7 +20164,7 @@ version versionsuffix toolchain ``1.1.30`` ``GCCcore/6.3.0`` ``1.1.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.1.33`` ``GCCcore/8.2.0`` -``1.1.34`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.1.34`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ================== ================================================================= @@ -20096,6 +20456,7 @@ version toolchain ``9.0.0`` ``GCCcore/8.3.0`` ``9.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``10.0.0`` ``GCCcore/8.3.0`` +``10.0.1`` ``GCCcore/10.2.0`` ``11.0.0`` ``GCCcore/10.2.0`` ========== ======================================================================== @@ -20168,6 +20529,22 @@ version toolchain ========= ============================ +.. _list_software_LncLOOM_596: + +*LncLOOM* ++++++++++ + +LncLOOM is a graph-based framework that uses integer programming to identify combinations of short motifs that are deeply conserved in rapidly evolving sequences. + +*homepage*: https://github.com/lncLOOM/lncLOOMv2/ + +======= ============== +version toolchain +======= ============== +``2.0`` ``foss/2020b`` +======= ============== + + .. _list_software_LocARNA_576: *LocARNA* @@ -20283,6 +20660,22 @@ version toolchain ========= ===================================== +.. _list_software_LPJmL_415: + +*LPJmL* ++++++++ + +Dynamic global vegetation model with managed land and river routing + +*homepage*: https://github.com/PIK-LPJmL/LPJmL + +=========== =============== +version toolchain +=========== =============== +``4.0.003`` ``iimpi/2020b`` +=========== =============== + + .. _list_software_lpsolve_773: *lpsolve* @@ -20296,7 +20689,7 @@ Mixed Integer Linear Programming (MILP) solver version toolchain ============ ============================================================================================================================================================================================== ``5.5.2.5`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a``, ``intel/2018b`` -``5.5.2.11`` ``GCC/10.2.0`` +``5.5.2.11`` ``GCC/10.2.0``, ``GCC/9.3.0`` ============ ============================================================================================================================================================================================== @@ -20511,6 +20904,7 @@ version versionsuffix toolchain ``4.3.3`` ``GCCcore/8.2.0`` ``4.4.2`` ``GCCcore/8.3.0`` ``4.5.2`` ``GCCcore/9.3.0`` +``4.6.2`` ``GCCcore/10.2.0`` ========= ================== =============================== @@ -20572,7 +20966,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -20663,6 +21057,7 @@ version versionsuffix toolchain ``7.453`` ``-with-extensions`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``gompi/2020a``, ``iccifort/2019.5.281``, ``iimpi/2020a`` ``7.470`` ``-with-extensions`` ``GCC/9.3.0``, ``gompi/2020a`` ``7.471`` ``-with-extensions`` ``iimpi/2020a`` +``7.475`` ``-with-extensions`` ``gompi/2020b`` ========= ==================== ======================================================================================= @@ -20870,14 +21265,14 @@ Manta calls structural variants (SVs) and indels from mapped paired-end sequenci *homepage*: https://github.com/Illumina/manta -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``1.1.1`` ``system`` -``1.6.0`` ``system`` -``1.6.0`` ``-Python-2.7.16`` ``gompi/2019b`` -``1.6.0`` ``-Python-2.7.18`` ``gompi/2020a`` -========= ================== =============== +========= ================== =============================== +version versionsuffix toolchain +========= ================== =============================== +``1.1.1`` ``system`` +``1.6.0`` ``system`` +``1.6.0`` ``-Python-2.7.16`` ``gompi/2019b`` +``1.6.0`` ``-Python-2.7.18`` ``GCC/10.2.0``, ``gompi/2020a`` +========= ================== =============================== .. _list_software_Maple_495: @@ -21014,7 +21409,7 @@ version toolchain *MaSuRCA* +++++++++ -MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). +MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). *homepage*: http://www.genome.umd.edu/masurca.html @@ -21026,6 +21421,7 @@ version versionsuffix toolchain ``3.2.4`` ``foss/2018a`` ``3.2.5`` ``-Perl-5.26.0`` ``foss/2017b`` ``3.3.1`` ``-Perl-5.28.0`` ``foss/2018b`` +``4.0.1`` ``-Perl-5.30.2`` ``foss/2020a`` ========= ================ ============== @@ -21304,6 +21700,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_maze_429: + +*maze* +++++++ + +In a similar manner to dot plots, maze highlights local sequence similarity between two DNA sequences. In particular, maximal exact substring matches are computed with MUMmer3 and visualised. + +*homepage*: https://github.com/dellytools/maze + +============ ============== +version toolchain +============ ============== +``20170124`` ``foss/2020b`` +============ ============== + + .. _list_software_MBROLA_445: *MBROLA* @@ -21378,23 +21790,27 @@ version versionsuffix toolchain The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. -*homepage*: http://www.mathworks.com/products/compiler/mcr/ +*homepage*: https://www.mathworks.com/products/compiler/mcr/ -========== ========== -version toolchain -========== ========== -``R2013a`` ``system`` -``R2013b`` ``system`` -``R2014a`` ``system`` -``R2014b`` ``system`` -``R2015a`` ``system`` -``R2015b`` ``system`` -``R2016a`` ``system`` -``R2016b`` ``system`` -``R2018a`` ``system`` -``R2018b`` ``system`` -``R2019a`` ``system`` -========== ========== +========== ============= ========== +version versionsuffix toolchain +========== ============= ========== +``R2013a`` ``system`` +``R2013b`` ``system`` +``R2014a`` ``system`` +``R2014b`` ``system`` +``R2015a`` ``system`` +``R2015b`` ``system`` +``R2016a`` ``system`` +``R2016b`` ``system`` +``R2018a`` ``system`` +``R2018b`` ``system`` +``R2019a`` ``system`` +``R2019b`` ``.8`` ``system`` +``R2020a`` ``.6`` ``system`` +``R2020b`` ``.5`` ``system`` +``R2021a`` ``.0`` ``system`` +========== ============= ========== .. _list_software_MDAnalysis_981: @@ -21503,7 +21919,7 @@ version toolchain Read, write and analyze MD trajectories with only a few lines of Python code. -*homepage*: http://mdtraj.org +*homepage*: https://mdtraj.org ========= ================= =============================== version versionsuffix toolchain @@ -21512,6 +21928,7 @@ version versionsuffix toolchain ``1.9.2`` ``-Python-3.6.6`` ``intel/2018b`` ``1.9.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``1.9.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.9.5`` ``foss/2020b``, ``intel/2020b`` ========= ================= =============================== @@ -21762,13 +22179,14 @@ version versionsuffix toolchain Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. -*homepage*: http://mercurial.selenic.com/ +*homepage*: https://www.mercurial-scm.org -========= ================== ============== -version versionsuffix toolchain -========= ================== ============== -``3.8.3`` ``-Python-2.7.11`` ``foss/2016a`` -========= ================== ============== +========= ================== ================== +version versionsuffix toolchain +========= ================== ================== +``3.8.3`` ``-Python-2.7.11`` ``foss/2016a`` +``5.7.1`` ``GCCcore/10.2.0`` +========= ================== ================== .. _list_software_Mesa_390: @@ -21955,6 +22373,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_MetaEuk_684: + +*MetaEuk* ++++++++++ + +MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. + +*homepage*: https://metaeuk.soedinglab.org + +======= ============== +version toolchain +======= ============== +``4`` ``GCC/10.2.0`` +======= ============== + + .. _list_software_MetaGeneAnnotator_1724: *MetaGeneAnnotator* @@ -22149,6 +22583,7 @@ MIGEC is a software pipeline that facilitates processing and analysis of immun version versionsuffix toolchain ========= =================== ========== ``1.2.8`` ``-Java-1.8.0_162`` ``system`` +``1.2.9`` ``-Java-1.8`` ``system`` ========= =================== ========== @@ -22471,12 +22906,13 @@ MiXCR processes big immunome data from raw sequences to quantitated clonotypes *homepage*: https://milaboratory.com/software/mixcr/ -========= =================== ========== -version versionsuffix toolchain -========= =================== ========== -``2.1.9`` ``-Java-1.8.0_162`` ``system`` -``3.0.3`` ``-Java-1.8`` ``system`` -========= =================== ========== +========== =================== ========== +version versionsuffix toolchain +========== =================== ========== +``2.1.9`` ``-Java-1.8.0_162`` ``system`` +``3.0.3`` ``-Java-1.8`` ``system`` +``3.0.13`` ``-Java-1.8`` ``system`` +========== =================== ========== .. _list_software_mkl-dnn_689: @@ -22781,6 +23217,7 @@ An analysis toolkit for single-cell RNA-seq. version versionsuffix toolchain ========= ========================= ============== ``0.2.0`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` +``0.2.3`` ``-R-4.0.3`` ``foss/2020b`` ========= ========================= ============== @@ -23108,7 +23545,7 @@ version versionsuffix toolchain mpmath can be used as an arbitrary-precision substitute for Python's float/complex types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation can be performed just as well at 10-digit or 1000-digit precision, with either real or complex numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely high precision work. -*homepage*: http://mpmath.org/ +*homepage*: https://mpmath.org/ ========= ================== =============================== version versionsuffix toolchain @@ -23136,6 +23573,22 @@ version toolchain ========= ============================== +.. _list_software_mrcfile_738: + +*mrcfile* ++++++++++ + +mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. It allows MRC files to be created and opened easily using a very simple API, which exposes the file’s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. This library aims to allow users and developers to read and write standard- compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions. + +*homepage*: https://github.com/ccpem/mrcfile + +========= ================================== +version toolchain +========= ================================== +``1.3.0`` ``foss/2020b``, ``fosscuda/2020b`` +========= ================================== + + .. _list_software_MRChem_540: *MRChem* @@ -23340,12 +23793,12 @@ MUMmer is a system for rapidly aligning entire genomes, whether in complete or *homepage*: http://mummer.sourceforge.net/ -============== ================================= -version toolchain -============== ================================= -``3.23`` ``GCCcore/9.3.0``, ``foss/2016b`` -``4.0.0beta2`` ``GCCcore/9.3.0``, ``foss/2018b`` -============== ================================= +============== ===================================================== +version toolchain +============== ===================================================== +``3.23`` ``GCCcore/9.3.0``, ``foss/2016b`` +``4.0.0beta2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0``, ``foss/2018b`` +============== ===================================================== .. _list_software_MUMPS_402: @@ -23363,6 +23816,7 @@ version versionsuffix toolchain ``5.1.2`` ``-metis`` ``foss/2017b`` ``5.2.1`` ``-metis`` ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a`` ``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` +``5.3.5`` ``-metis`` ``foss/2020b`` ========= ============== ================================================================================================================= @@ -23620,6 +24074,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_Myokit_637: + +*Myokit* +++++++++ + +Myokit is an open-source Python-based toolkit that facilitates modeling and simulation of cardiac cellular electrophysiology. + +*homepage*: http://myokit.org + +========== ============== +version toolchain +========== ============== +``1.32.0`` ``foss/2020b`` +========== ============== + + .. _list_software_mypy_463: *mypy* @@ -23692,7 +24162,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -24027,6 +24497,7 @@ version toolchain ``2.9.3`` ``foss/2018b`` ``2.10.4`` ``gompi/2019b`` ``2.10.7`` ``gompi/2020a`` +``2.10.9`` ``gompi/2020b`` =========== ================================================ @@ -24052,6 +24523,22 @@ version versionsuffix toolchain ========== =================== ================== +.. _list_software_NCCL-tests_896: + +*NCCL-tests* +++++++++++++ + +Tests check both the performance and the correctness of NCCL operations. + +*homepage*: https://github.com/NVIDIA/nccl-tests + +========= ================ +version toolchain +========= ================ +``2.0.0`` ``gompic/2019b`` +========= ================ + + .. _list_software_ncdf4_463: *ncdf4* @@ -24358,7 +24845,7 @@ version versionsuffix toolchain ``4.6.1`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``4.6.2`` ``gompi/2019a``, ``iimpi/2019a`` ``4.7.1`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` -``4.7.4`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpi/2020b`` +``4.7.4`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020a``, ``iimpi/2020b`` =========== ================ ========================================================================================================================== @@ -24430,24 +24917,24 @@ Python/numpy interface to netCDF. *homepage*: https://unidata.github.io/netcdf4-python/ -=========== ============================= =============================== -version versionsuffix toolchain -=========== ============================= =============================== -``1.2.9`` ``-Python-2.7.13`` ``intel/2017a`` -``1.3.1`` ``-Python-3.6.3`` ``intel/2017b`` -``1.3.1`` ``-Python-3.6.3-HDF5-1.8.19`` ``intel/2017b`` -``1.4.0`` ``-Python-3.6.2-HDF5-1.8.19`` ``foss/2017b`` -``1.4.0`` ``-Python-3.6.4`` ``intel/2018a`` -``1.4.1`` ``-Python-2.7.15`` ``intel/2018b`` -``1.4.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.4.2`` ``-Python-3.6.4`` ``foss/2018a`` -``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` -``1.5.2`` ``intel/2019a`` -``1.5.3`` ``-Python-2.7.16`` ``foss/2019b`` -``1.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.5.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.5.5.1`` ``intel/2020b`` -=========== ============================= =============================== +=========== ============================= =================================== +version versionsuffix toolchain +=========== ============================= =================================== +``1.2.9`` ``-Python-2.7.13`` ``intel/2017a`` +``1.3.1`` ``-Python-3.6.3`` ``intel/2017b`` +``1.3.1`` ``-Python-3.6.3-HDF5-1.8.19`` ``intel/2017b`` +``1.4.0`` ``-Python-3.6.2-HDF5-1.8.19`` ``foss/2017b`` +``1.4.0`` ``-Python-3.6.4`` ``intel/2018a`` +``1.4.1`` ``-Python-2.7.15`` ``intel/2018b`` +``1.4.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.4.2`` ``-Python-3.6.4`` ``foss/2018a`` +``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` +``1.5.2`` ``intel/2019a`` +``1.5.3`` ``-Python-2.7.16`` ``foss/2019b`` +``1.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.5.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.5.5.1`` ``fosscuda/2020b``, ``intel/2020b`` +=========== ============================= =================================== .. _list_software_netloc_645: @@ -24473,13 +24960,14 @@ version toolchain NetLogo is a multi-agent programmable modeling environment. It is used by tens of thousands of students, teachers and researchers worldwide. It also powers HubNet participatory simulations. It is authored by Uri Wilensky and developed at the CCL. -*homepage*: http://ccl.northwestern.edu/netlogo/ +*homepage*: https://ccl.northwestern.edu/netlogo/ ========= ============= ========== version versionsuffix toolchain ========= ============= ========== ``5.3.1`` ``-64`` ``system`` ``6.0.4`` ``-64`` ``system`` +``6.2.0`` ``-64`` ``system`` ========= ============= ========== @@ -24594,7 +25082,7 @@ version versionsuffix toolchain ``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``2.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``2.4`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` -``2.5`` ``foss/2020b``, ``fosscuda/2020b`` +``2.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ======== ================== =================================================== @@ -24649,6 +25137,7 @@ version toolchain ``20.01.0`` ``system`` ``20.04.1`` ``system`` ``20.10.0`` ``system`` +``21.03.0`` ``system`` =========== ========== @@ -24677,12 +25166,13 @@ The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transf *homepage*: https://www-user.tu-chemnitz.de/~potts/nfft/ -========= ============================== -version toolchain -========= ============================== -``3.5.1`` ``foss/2018b``, ``foss/2019a`` -``3.5.2`` ``foss/2020a`` -========= ============================== +========= ================================== +version toolchain +========= ================================== +``3.1.3`` ``foss/2020b``, ``fosscuda/2020b`` +``3.5.1`` ``foss/2018b``, ``foss/2019a`` +``3.5.2`` ``foss/2020a`` +========= ================================== .. _list_software_NGLess_556: @@ -24739,6 +25229,7 @@ version versionsuffix toolchain ``2.10.0`` ``-Java-11`` ``GCCcore/8.2.0`` ``2.10.4`` ``-Java-11`` ``GCCcore/8.3.0`` ``2.10.5`` ``GCCcore/9.3.0`` +``2.10.9`` ``GCCcore/10.2.0`` ========== =================== ================================== @@ -25328,22 +25819,23 @@ Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by *homepage*: https://numba.pydata.org/ -========== ================== ================================== -version versionsuffix toolchain -========== ================== ================================== -``0.24.0`` ``-Python-2.7.11`` ``intel/2016a`` -``0.24.0`` ``-Python-3.5.1`` ``intel/2016a`` -``0.26.0`` ``-Python-2.7.11`` ``intel/2016a`` -``0.32.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.37.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` -``0.37.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``0.39.0`` ``-Python-3.6.6`` ``foss/2018b`` -``0.43.1`` ``intel/2019a`` -``0.46.0`` ``foss/2019a`` -``0.47.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``0.50.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``0.52.0`` ``-Python-3.8.2`` ``foss/2020a`` -========== ================== ================================== +========== ================== =================================================== +version versionsuffix toolchain +========== ================== =================================================== +``0.24.0`` ``-Python-2.7.11`` ``intel/2016a`` +``0.24.0`` ``-Python-3.5.1`` ``intel/2016a`` +``0.26.0`` ``-Python-2.7.11`` ``intel/2016a`` +``0.32.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.37.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` +``0.37.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.39.0`` ``-Python-3.6.6`` ``foss/2018b`` +``0.43.1`` ``intel/2019a`` +``0.46.0`` ``foss/2019a`` +``0.47.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``0.50.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.52.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``0.52.0`` ``-Python-3.8.2`` ``foss/2020a`` +========== ================== =================================================== .. _list_software_numexpr_783: @@ -25413,6 +25905,7 @@ version toolchain ``20.7`` ``system`` ``20.9`` ``system`` ``20.11`` ``system`` +``21.2`` ``system`` ========= ========== @@ -25474,7 +25967,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -25775,45 +26268,32 @@ version toolchain *OpenCV* ++++++++ -OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. +OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Includes extra modules for OpenCV from the contrib repository. *homepage*: https://opencv.org/ -========== ================== ================================================================ -version versionsuffix toolchain -========== ================== ================================================================ -``2.4.12`` ``intel/2016a`` -``3.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``3.3.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``3.3.0`` ``-Python-3.6.1`` ``intel/2017a`` -``3.3.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``3.4.1`` ``-Python-2.7.14`` ``foss/2018a`` -``3.4.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``3.4.5`` ``-Python-2.7.15`` ``foss/2018b`` -``3.4.7`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a`` -``3.4.7`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` -``4.0.1`` ``-Python-2.7.15`` ``foss/2018b`` -``4.0.1`` ``-Python-3.6.6`` ``foss/2018b`` -``4.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``4.2.0`` ``-Python-3.8.2`` ``foss/2020a`` -========== ================== ================================================================ - - -.. _list_software_opencv_contrib_1499: - -*opencv_contrib* -++++++++++++++++ - -OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. - -*homepage*: https://opencv.org/ - -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``3.4.1`` ``-Python-3.6.4`` ``foss/2018a`` -========= ================= ============== +========== ========================= ================================================================ +version versionsuffix toolchain +========== ========================= ================================================================ +``2.4.12`` ``intel/2016a`` +``3.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``3.3.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``3.3.0`` ``-Python-3.6.1`` ``intel/2017a`` +``3.3.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``3.4.1`` ``-Python-2.7.14`` ``foss/2018a`` +``3.4.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``3.4.1`` ``-Python-3.6.4-contrib`` ``foss/2018a`` +``3.4.5`` ``-Python-2.7.15`` ``foss/2018b`` +``3.4.7`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a`` +``3.4.7`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` +``4.0.1`` ``-Python-2.7.15`` ``foss/2018b`` +``4.0.1`` ``-Python-3.6.6`` ``foss/2018b`` +``4.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``4.2.0`` ``-Python-3.8.2`` ``foss/2020a`` +``4.2.0`` ``-Python-3.8.2-contrib`` ``foss/2020a`` +``4.5.1`` ``-contrib`` ``foss/2020b``, ``fosscuda/2020b`` +========== ========================= ================================================================ .. _list_software_OpenEXR_641: @@ -25832,6 +26312,7 @@ version toolchain ``2.3.0`` ``foss/2018b``, ``intel/2018b`` ``2.4.0`` ``GCCcore/8.3.0`` ``2.4.1`` ``GCCcore/9.3.0`` +``2.5.5`` ``GCCcore/10.2.0`` ========= ================================ @@ -26324,6 +26805,7 @@ version toolchain ``3.8.0`` ``GNU/4.9.3-2.25`` ``3.9.0`` ``GNU/4.9.3-2.25`` ``6.5.0`` ``system`` +``7.2.0`` ``system`` ========= ================== @@ -26464,6 +26946,7 @@ version toolchain ``5.3.2`` ``foss/2016a``, ``foss/2017a`` ``5.6.2`` ``gompi/2019a`` ``5.6.3`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2019b``, ``iimpic/2020a`` +``5.7`` ``gompi/2020b``, ``gompic/2020b`` ========= ============================================================================================================================================================================================= @@ -26523,7 +27006,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -26590,6 +27073,7 @@ version toolchain ========== =========================================================================== ``9.38.1`` ``GCC/4.9.2``, ``system`` ``16.02`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2018a`` +``17.03`` ``GCCcore/10.2.0`` ========== =========================================================================== @@ -26743,15 +27227,15 @@ PAPI provides the tool designer and application engineer with a consistent inte *homepage*: https://icl.cs.utk.edu/projects/papi/ -========= ==================================== -version toolchain -========= ==================================== -``5.4.3`` ``foss/2016a`` -``5.5.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``5.6.0`` ``GCCcore/6.4.0`` -``5.7.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``6.0.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ==================================== +========= ======================================================== +version toolchain +========= ======================================================== +``5.4.3`` ``foss/2016a`` +``5.5.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``5.6.0`` ``GCCcore/6.4.0`` +``5.7.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``6.0.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================== .. _list_software_parallel_845: @@ -26935,11 +27419,11 @@ ParMGridGen is an MPI-based parallel library that is based on the serial package *homepage*: http://www-users.cs.umn.edu/~moulitsa/software.html -======= ==================================================================================== -version toolchain -======= ==================================================================================== -``1.0`` ``gimkl/2.11.5``, ``gompi/2019b``, ``iimpi/2019b``, ``intel/2016a``, ``intel/2017a`` -======= ==================================================================================== +======= ====================================================================================================================== +version toolchain +======= ====================================================================================================================== +``1.0`` ``gimkl/2.11.5``, ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``intel/2016a``, ``intel/2017a`` +======= ====================================================================================================================== .. _list_software_PartitionFinder_1554: @@ -27461,6 +27945,7 @@ version versionsuffix toolchain ``3.12.4`` ``-Python-2.7.16`` ``intel/2019b`` ``3.12.4`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.12.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``3.14.4`` ``foss/2020b`` ========== ==================== =============================== @@ -27503,12 +27988,13 @@ version toolchain pFUnit is a unit testing framework enabling JUnit-like testing of serial and MPI-parallel software written in Fortran. -*homepage*: http://pfunit.sourceforge.net +*homepage*: https://github.com/Goddard-Fortran-Ecosystem/pFUnit ========= =============== version toolchain ========= =============== ``3.2.9`` ``gompi/2018b`` +``4.2.0`` ``gompi/2020b`` ========= =============== @@ -27850,6 +28336,8 @@ version versionsuffix toolchain ``2.21.1`` ``-Java-11`` ``system`` ``2.21.6`` ``-Java-11`` ``system`` ``2.22.1`` ``-Java-11`` ``system`` +``2.25.0`` ``-Java-11`` ``system`` +``2.25.1`` ``-Java-11`` ``system`` =========== =================== ========== @@ -28513,6 +29001,7 @@ version versionsuffix toolchain ``2.5b`` ``-Python-2.7.14`` ``intel/2018a`` ``2.6.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``2.6.2`` ``foss/2020b``, ``intel/2020b`` +``2.7.0`` ``foss/2020b`` ========= ================== ================================================ @@ -28591,6 +29080,7 @@ version toolchain ``1.3`` ``GCC/8.2.0-2.31.1``, ``gcccuda/2019a`` ``1.4`` ``GCC/8.3.0``, ``gcccuda/2019b`` ``1.5`` ``GCC/9.3.0`` +``1.6`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` ======= ======================================= @@ -28827,13 +29317,14 @@ version versionsuffix toolchain The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. -*homepage*: http://www.povray.org/ +*homepage*: https://www.povray.org/ =========== ================================================================================= version toolchain =========== ================================================================================= ``3.7.0.0`` ``intel/2016b`` ``3.7.0.7`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``3.7.0.8`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` =========== ================================================================================= @@ -28943,11 +29434,12 @@ preCICE (Precise Code Interaction Coupling Environment) is a coupling library fo *homepage*: https://www.precice.org/ -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``2.1.1`` ``-Python-3.8.2`` ``foss/2020a`` -========= ================= ============== +========= ================= =============================== +version versionsuffix toolchain +========= ================= =============================== +``2.1.1`` ``-Python-3.8.2`` ``foss/2020a`` +``2.2.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +========= ================= =============================== .. _list_software_preseq_656: @@ -29100,6 +29592,7 @@ version toolchain ``6.0.0`` ``GCCcore/8.2.0`` ``6.2.1`` ``GCCcore/8.3.0`` ``7.0.0`` ``GCCcore/9.3.0`` +``7.2.1`` ``GCCcore/10.2.0`` ========= ================================================================================= @@ -29233,24 +29726,24 @@ Google Protocol Buffers *homepage*: https://github.com/google/protobuf/ -=========== =================================================== -version toolchain -=========== =================================================== -``2.5.0`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``system`` -``2.6.1`` ``system`` -``3.0.2`` ``foss/2016a`` -``3.2.0`` ``foss/2016b``, ``intel/2016b`` -``3.3.0`` ``foss/2016b``, ``intel/2017a`` -``3.4.0`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` -``3.5.1`` ``intel/2017b`` -``3.6.0`` ``GCCcore/7.3.0`` -``3.6.1`` ``GCCcore/7.3.0`` -``3.6.1.2`` ``GCCcore/8.2.0`` -``3.7.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.10.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``3.13.0`` ``GCCcore/9.3.0`` -``3.14.0`` ``GCCcore/10.2.0`` -=========== =================================================== +=========== ==================================================================== +version toolchain +=========== ==================================================================== +``2.5.0`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``system`` +``2.6.1`` ``system`` +``3.0.2`` ``foss/2016a`` +``3.2.0`` ``foss/2016b``, ``intel/2016b`` +``3.3.0`` ``foss/2016b``, ``intel/2017a`` +``3.4.0`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` +``3.5.1`` ``intel/2017b`` +``3.6.0`` ``GCCcore/7.3.0`` +``3.6.1`` ``GCCcore/7.3.0`` +``3.6.1.2`` ``GCCcore/8.2.0`` +``3.7.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.10.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``3.13.0`` ``GCCcore/9.3.0`` +``3.14.0`` ``GCCcore/10.2.0`` +=========== ==================================================================== .. _list_software_protobuf-python_1600: @@ -29660,6 +30153,22 @@ version toolchain ========= ========== +.. _list_software_pyABC_431: + +*pyABC* ++++++++ + +Massively parallel, distributed and scalable ABC-SMC (Approximate Bayesian Computation - Sequential Monte Carlo) for parameter estimation of complex stochastic models. Implemented in Python with support of the R language. + +*homepage*: https://github.com/icb-dcm/pyabc + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.10.4`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_PyAMG_414: *PyAMG* @@ -29667,13 +30176,14 @@ version toolchain PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface. -*homepage*: http://pyamg.org +*homepage*: https://pyamg.github.io -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``3.0.1`` ``-Python-2.7.11`` ``intel/2016a`` -========= ================== =============== +========= ================== =============================== +version versionsuffix toolchain +========= ================== =============================== +``3.0.1`` ``-Python-2.7.11`` ``intel/2016a`` +``4.0.0`` ``foss/2020b``, ``intel/2020b`` +========= ================== =============================== .. _list_software_PyAPS3_480: @@ -29701,14 +30211,15 @@ pybedtools wraps and extends BEDTools and offers feature-level manipulations fro *homepage*: https://daler.github.io/pybedtools -========== ================== ================================ -version versionsuffix toolchain -========== ================== ================================ -``0.7.10`` ``-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` -``0.7.10`` ``-Python-3.6.6`` ``foss/2018b`` -``0.8.0`` ``foss/2019a``, ``intel/2019a`` -``0.8.1`` ``foss/2019b`` -========== ================== ================================ +========== ================== ======================================= +version versionsuffix toolchain +========== ================== ======================================= +``0.7.10`` ``-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` +``0.7.10`` ``-Python-3.6.6`` ``foss/2018b`` +``0.8.0`` ``foss/2019a``, ``intel/2019a`` +``0.8.1`` ``foss/2019b`` +``0.8.2`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +========== ================== ======================================= .. _list_software_PyBerny_713: @@ -29741,6 +30252,7 @@ version versionsuffix toolchain ========== ================= ==================================== ``0.3.13`` ``-Python-3.6.6`` ``foss/2018b`` ``0.3.17`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +``0.3.18`` ``GCCcore/10.2.0`` ========== ================= ==================================== @@ -29784,6 +30296,7 @@ version versionsuffix toolchain ``1.18.0`` ``-Python-3.6.6`` ``foss/2018b`` ``1.18.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``1.18.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.20.0`` ``GCCcore/10.2.0`` ========== ================== ==================================== @@ -29804,6 +30317,22 @@ version toolchain ============ ========== +.. _list_software_PyCifRW_644: + +*PyCifRW* ++++++++++ + +PyCIFRW provides support for reading and writing CIF (Crystallographic Information Format) files using Python. + +*homepage*: https://bitbucket.org/jamesrhester/pycifrw/src/development + +========= ================= +version toolchain +========= ================= +``4.4.2`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_PyClone_698: *PyClone* @@ -29905,6 +30434,7 @@ version versionsuffix toolchain ``2017.1.1`` ``-Python-2.7.14`` ``intel/2018a`` ``2018.1`` ``-Python-3.6.4-CUDA-9.1.85`` ``intel/2018a`` ``2019.1.2`` ``-Python-3.7.4`` ``fosscuda/2019b``, ``intelcuda/2019b`` +``2020.1`` ``fosscuda/2020b`` ============ =============================== ======================================= @@ -30421,6 +30951,7 @@ version versionsuffix toolchain ``4.7.3`` ``-Python-2.7.13`` ``intel/2017a`` ``2017.10.16`` ``-Python-2.7.14`` ``intel/2017b`` ``2017.10.16`` ``-Python-3.6.3`` ``intel/2017b`` +``2022.0.4`` ``foss/2020b`` ============== ================== ========================= @@ -30466,12 +30997,12 @@ Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machin *homepage*: https://docs.pymc.io/ -========== ================= =============================== -version versionsuffix toolchain -========== ================= =============================== -``3.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``3.11.1`` ``intel/2020b`` -========== ================= =============================== +========== ================= =================================== +version versionsuffix toolchain +========== ================= =================================== +``3.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.11.1`` ``fosscuda/2020b``, ``intel/2020b`` +========== ================= =================================== .. _list_software_pymca_538: @@ -30486,6 +31017,7 @@ The PyMca X-Ray Fluorescence Toolkit, including PyMca5 and fisx. ========= ================= ================================== version versionsuffix toolchain ========= ================= ================================== +``5.6.3`` ``foss/2020b`` ``5.6.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========= ================= ================================== @@ -30539,6 +31071,22 @@ version versionsuffix toolchain =============== ================= =============== +.. _list_software_PyOD_348: + +*PyOD* +++++++ + +PyOD is a comprehensive and scalable Python toolkit for detecting outlying objects in multivariate data. + +*homepage*: https://pyod.readthedocs.io + +========= =============================== +version toolchain +========= =============================== +``0.8.7`` ``foss/2020b``, ``intel/2020b`` +========= =============================== + + .. _list_software_Pyomo_532: *Pyomo* @@ -30565,11 +31113,12 @@ PyOpenCL lets you access GPUs and other massively parallel compute devices from *homepage*: https://mathema.tician.de/software/pyopencl/ -============ ================= ================== -version versionsuffix toolchain -============ ================= ================== -``2020.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` -============ ================= ================== +============ ================= =============================== +version versionsuffix toolchain +============ ================= =============================== +``2020.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2021.1.2`` ``foss/2020b``, ``intel/2020b`` +============ ================= =============================== .. _list_software_PyOpenGL_750: @@ -30581,17 +31130,17 @@ PyOpenGL is the most common cross platform Python binding to OpenGL and related *homepage*: http://pyopengl.sourceforge.net -=========== ================== =============================== -version versionsuffix toolchain -=========== ================== =============================== -``3.1.1a1`` ``GCCcore/8.2.0`` -``3.1.1a1`` ``-Python-2.7.11`` ``intel/2016a`` -``3.1.1a1`` ``-Python-2.7.12`` ``foss/2016b`` -``3.1.1a1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` -``3.1.3b2`` ``-Python-2.7.14`` ``intel/2018a`` -``3.1.3b2`` ``-Python-2.7.15`` ``foss/2018b`` -``3.1.5`` ``GCCcore/8.3.0`` -=========== ================== =============================== +=========== ================== ===================================== +version versionsuffix toolchain +=========== ================== ===================================== +``3.1.1a1`` ``GCCcore/8.2.0`` +``3.1.1a1`` ``-Python-2.7.11`` ``intel/2016a`` +``3.1.1a1`` ``-Python-2.7.12`` ``foss/2016b`` +``3.1.1a1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` +``3.1.3b2`` ``-Python-2.7.14`` ``intel/2018a`` +``3.1.3b2`` ``-Python-2.7.15`` ``foss/2018b`` +``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +=========== ================== ===================================== .. _list_software_pyparsing_989: @@ -30717,14 +31266,15 @@ PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and n *homepage*: http://www.pyqtgraph.org/ -========== ================= =============================== -version versionsuffix toolchain -========== ================= =============================== -``0.10.0`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.10.0`` ``-Python-3.7.2`` ``intel/2019a`` -``0.11.0`` ``-Python-3.7.4`` ``foss/2019b`` -========== ================= =============================== +========== ================= ================================== +version versionsuffix toolchain +========== ================= ================================== +``0.10.0`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.10.0`` ``-Python-3.7.2`` ``intel/2019a`` +``0.11.0`` ``-Python-3.7.4`` ``foss/2019b`` +``0.11.1`` ``foss/2020b``, ``fosscuda/2020b`` +========== ================= ================================== .. _list_software_PyRe_384: @@ -30776,6 +31326,38 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_pyro-api_817: + +*pyro-api* +++++++++++ + +Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch. + +*homepage*: https://github.com/pyro-ppl/pyro-api + +========= ================== +version toolchain +========= ================== +``0.1.2`` ``fosscuda/2020b`` +========= ================== + + +.. _list_software_pyro-ppl_835: + +*pyro-ppl* +++++++++++ + +Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch. + +*homepage*: https://github.com/pyro-ppl/pyro + +========= ================== +version toolchain +========= ================== +``1.5.2`` ``fosscuda/2020b`` +========= ================== + + .. _list_software_Pyro4_478: *Pyro4* @@ -31031,6 +31613,7 @@ version versionsuffix toolchain ``3.5.2`` ``intel/2019a`` ``3.5.2`` ``-Python-2.7.14`` ``intel/2018a`` ``3.5.2`` ``-Python-2.7.16`` ``intel/2019b`` +``3.6.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``3.6.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``3.6.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` =========== ================== =================================================== @@ -31169,6 +31752,7 @@ version versionsuffix toolchain ``0.7.1.post6`` ``-Python-2.7.14`` ``intel/2017b`` ``0.7.1.post6`` ``-Python-3.6.6`` ``foss/2018b`` ``0.8.0`` ``foss/2019b``, ``foss/2020a`` +``0.9.0`` ``fosscuda/2020b`` =============== ================== ============================== @@ -31278,12 +31862,13 @@ PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTor *homepage*: https://github.com/rusty1s/pytorch_geometric -========= =============================== ============== -version versionsuffix toolchain -========= =============================== ============== -``1.3.2`` ``-Python-3.7.4`` ``foss/2019b`` -``1.4.2`` ``-Python-3.7.4-PyTorch-1.4.0`` ``foss/2019b`` -========= =============================== ============== +========= =============================== ================================== +version versionsuffix toolchain +========= =============================== ================================== +``1.3.2`` ``-Python-3.7.4`` ``foss/2019b`` +``1.4.2`` ``-Python-3.7.4-PyTorch-1.4.0`` ``foss/2019b`` +``1.6.3`` ``foss/2020b``, ``fosscuda/2020b`` +========= =============================== ================================== .. _list_software_PyVCF_424: @@ -31681,7 +32266,7 @@ version versionsuffix toolchain Qt is a comprehensive cross-platform C++ application framework. -*homepage*: http://qt.io/ +*homepage*: https://qt.io/ ========== ==================================================================================== version toolchain @@ -31730,6 +32315,7 @@ A rich Qt-based console for working with Jupyter kernels, supporting rich media version versionsuffix toolchain ========= ================= ================================== ``4.7.7`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``5.0.2`` ``GCCcore/10.2.0`` ========= ================= ================================== @@ -31790,11 +32376,12 @@ QtPy is a small abstraction layer that lets you write applications using a singl *homepage*: https://github.com/spyder-ide/qtpy -========= ================= ================= -version versionsuffix toolchain -========= ================= ================= -``1.9.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -========= ================= ================= +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``1.9.0`` ``GCCcore/10.2.0`` +``1.9.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================== .. _list_software_Qualimap_826: @@ -31839,22 +32426,22 @@ Quantum ESPRESSO is an integrated suite of computer codes for electronic-struc *homepage*: https://www.quantum-espresso.org -========= ============= =============================================== -version versionsuffix toolchain -========= ============= =============================================== -``5.3.0`` ``intel/2016.02-GCC-4.9`` -``5.4.0`` ``intel/2016.02-GCC-4.9`` -``5.4.0`` ``-hybrid`` ``foss/2016b`` -``6.0`` ``intel/2016b`` -``6.1`` ``intel/2017a`` -``6.2`` ``intel/2017b`` -``6.2.1`` ``iomkl/2017b`` -``6.3`` ``foss/2018b``, ``intel/2018b`` -``6.4.1`` ``intel/2019a`` -``6.5`` ``intel/2019a``, ``intel/2019b`` -``6.6`` ``foss/2019b``, ``foss/2020b``, ``intel/2019b`` -``6.7`` ``foss/2019b``, ``intel/2019b`` -========= ============= =============================================== +========= ============= ================================================ +version versionsuffix toolchain +========= ============= ================================================ +``5.3.0`` ``intel/2016.02-GCC-4.9`` +``5.4.0`` ``intel/2016.02-GCC-4.9`` +``5.4.0`` ``-hybrid`` ``foss/2016b`` +``6.0`` ``intel/2016b`` +``6.1`` ``intel/2017a`` +``6.2`` ``intel/2017b`` +``6.2.1`` ``iomkl/2017b`` +``6.3`` ``foss/2018b``, ``intel/2018b`` +``6.4.1`` ``intel/2019a`` +``6.5`` ``intel/2019a``, ``intel/2019b`` +``6.6`` ``foss/2019b``, ``foss/2020b``, ``intel/2019b`` +``6.7`` ``foss/2019b``, ``intel/2019b``, ``iomkl/2019b`` +========= ============= ================================================ .. _list_software_QUAST_398: @@ -32003,7 +32590,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -32037,7 +32624,8 @@ version versionsuffix toolchain ``3.6.2`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``3.6.3`` ``foss/2020a`` ``4.0.0`` ``foss/2020a``, ``fosscuda/2020a`` -``4.0.3`` ``foss/2020b`` +``4.0.3`` ``foss/2020b``, ``fosscuda/2020b`` +``4.0.4`` ``foss/2020b``, ``fosscuda/2020b`` ========= ============================= =================================================== @@ -32086,6 +32674,22 @@ version versionsuffix toolchain =========== ========================= ================================== +.. _list_software_R-opencv_778: + +*R-opencv* +++++++++++ + +Experimenting with computer vision and machine learning in R. This package exposes some of the available OpenCV algorithms, such as edge, body or face detection. These can either be applied to analyze static images, or to filter live video footage from a camera device. + +*homepage*: https://cran.r-project.org/web/packages/opencv/ + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``0.2.0`` ``-R-4.0.0`` ``foss/2020a`` +========= ============= ============== + + .. _list_software_R-tesseract_1101: *R-tesseract* @@ -32238,15 +32842,16 @@ version toolchain *RASPA2* ++++++++ -A general purpose classical simulation package that can be used for the simulation of molecules in gases, fluids, zeolites, aluminosilicates, metal-organic frameworks, carbon nanotubes and external fields. +RASPA is a software package for simulating adsorption and diffusion of molecules in flexible nanoporous materials. -*homepage*: https://github.com/numat/RASPA2 +*homepage*: https://iraspa.org/raspa/ -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``2.0.3`` ``-Python-2.7.12`` ``intel/2016b`` -========= ================== =============== +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``2.0.3`` ``-Python-2.7.12`` ``intel/2016b`` +``2.0.41`` ``foss/2020b`` +========== ================== =============== .. _list_software_rasterio_873: @@ -32281,6 +32886,22 @@ version versionsuffix toolchain ========== ================= ============== +.. _list_software_Ratatosk_841: + +*Ratatosk* +++++++++++ + +Phased hybrid error correction of long reads using colored de Bruijn graphs + +*homepage*: https://github.com/DecodeGenetics/Ratatosk + +======= ============== +version toolchain +======= ============== +``0.4`` ``GCC/10.2.0`` +======= ============== + + .. _list_software_RAxML_420: *RAxML* @@ -32448,6 +33069,7 @@ RDFLib is a Python library for working with RDF, a simple yet powerful language version toolchain ========= ================================= ``4.2.2`` ``GCCcore/8.3.0``, ``foss/2019a`` +``5.0.0`` ``GCCcore/10.2.0`` ========= ================================= @@ -32607,6 +33229,8 @@ version toolchain ``3.2`` ``system`` ``3.3`` ``system`` ``3.4.1`` ``system`` +``3.5.0`` ``system`` +``3.5.1`` ``system`` ========= ========== @@ -32751,6 +33375,22 @@ version versionsuffix toolchain ========= ============= =============================== +.. _list_software_RevBayes_801: + +*RevBayes* +++++++++++ + +RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics. + +*homepage*: https://revbayes.github.io/ + +========= ============== +version toolchain +========= ============== +``1.1.1`` ``GCC/10.2.0`` +========= ============== + + .. _list_software_rgdal_522: *rgdal* @@ -33002,12 +33642,13 @@ version versionsuffix toolchain rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software. -*homepage*: http://cab.spbu.ru/software/rnaquast/ +*homepage*: https://cab.spbu.ru/software/rnaquast/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.5.2`` ``-Python-2.7.15`` ``foss/2018b`` +``2.2.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ============== @@ -33365,6 +34006,7 @@ version toolchain ``2.6.1`` ``GCCcore/7.3.0`` ``2.6.3`` ``GCCcore/8.2.0`` ``2.7.1`` ``GCCcore/8.3.0`` +``2.7.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= ================================================ @@ -33416,7 +34058,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -33635,10 +34277,27 @@ version versionsuffix toolchain ``1.8`` ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.10`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` -``1.11`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``1.11`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` +``1.12`` ``GCC/10.2.0``, ``GCC/9.3.0`` ========== ================= ======================================================================================================================================= +.. _list_software_sansa_534: + +*sansa* ++++++++ + +Structural variant (SV) annotation, a companion to the 'dolly' tool. + +*homepage*: https://github.com/dellytools/sansa/ + +========= =============== +version toolchain +========= =============== +``0.0.7`` ``gompi/2020b`` +========= =============== + + .. _list_software_SAS_231: *SAS* @@ -33764,6 +34423,7 @@ version versionsuffix toolchain ``2.0.2`` ``-OpenBLAS-0.3.5`` ``gompi/2019a``, ``gompic/2019a`` ``2.1.0`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b`` ``2.1.0`` ``-bf`` ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020b`` +``2.1.0`` ``-bl`` ``gompi/2020b`` ``2.2`` ``-amd`` ``gompi/2020a`` ========= ================================= ============================================================================================================================================ @@ -33884,6 +34544,22 @@ version versionsuffix toolchain ========== ================= ================================== +.. _list_software_scikit-cuda_1105: + +*scikit-cuda* ++++++++++++++ + +SciKit-cuda, a.k.a. skcuda, provides Python interfaces to many of the functions in the CUDA device/runtime, CUBLAS, CUFFT, and CUSOLVER libraries distributed as part of NVIDIA's CUDA Programming Toolkit. + +*homepage*: https://github.com/lebedov/scikit-cuda + +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``0.5.3`` ``-Python-3.7.4`` ``fosscuda/2019b`` +========= ================= ================== + + .. _list_software_scikit-image_1207: *scikit-image* @@ -33910,6 +34586,7 @@ version versionsuffix toolchain ``0.15.0`` ``-Python-3.7.2`` ``foss/2019a`` ``0.16.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``0.17.1`` ``-Python-3.8.2`` ``foss/2020a`` +``0.18.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ========== ================== =================================================== @@ -34297,6 +34974,7 @@ version toolchain ``2.0.8`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``2.0.9`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.0.10`` ``GCCcore/8.3.0`` +``2.0.14`` ``GCCcore/10.2.0`` ========== ====================================================================== @@ -34371,6 +35049,7 @@ version versionsuffix toolchain ``0.9.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``0.9.1`` ``-Python-2.7.16`` ``foss/2019b`` ``0.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.10.1`` ``intel/2020b`` ``0.10.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``0.11.1`` ``intel/2020b`` ========== ================== ========================================================================================= @@ -34408,6 +35087,22 @@ version versionsuffix toolchain ========== ================== ============== +.. _list_software_Seeder_600: + +*Seeder* +++++++++ + +Seeder is a framework for DNA motif discovery. + +*homepage*: https://metacpan.org/pod/Seeder + +======== ================ ================= +version versionsuffix toolchain +======== ================ ================= +``0.01`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +======== ================ ================= + + .. _list_software_segemehl_842: *segemehl* @@ -34707,6 +35402,7 @@ version versionsuffix toolchain ``2.3.4`` ``-R-3.5.1`` ``foss/2018b`` ``3.1.2`` ``-R-3.6.0`` ``foss/2019a`` ``3.1.5`` ``-R-4.0.0`` ``foss/2020a`` +``4.0.1`` ``-R-4.0.3`` ``foss/2020b`` ============ ============= =============== @@ -35023,6 +35719,7 @@ The silx project provides a collection of Python packages to support the develo version versionsuffix toolchain ========== ================= ================================== ``0.13.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``0.14.0`` ``foss/2020b`` ========== ================= ================================== @@ -35048,15 +35745,16 @@ version versionsuffix toolchain *SIMPLE* ++++++++ -Single-particle IMage Processing Linux Engine is a program package for cryo-EM image processing, focusing on ab initio 3D reconstruction of low-symmetry single-particles. +Single-particle IMage Processing Linux Engine SIMPLE is an open-source software package for analysis of cryogenic transmission electron microscopy (cryo-EM) movies of single-particles (Single-Particle Analysis, SPA). -*homepage*: http://simplecryoem.com/ +*homepage*: https://simplecryoem.com/ -======= ============== -version toolchain -======= ============== -``2.5`` ``foss/2018a`` -======= ============== +========= ============== +version toolchain +========= ============== +``2.5`` ``foss/2018a`` +``3.0.0`` ``foss/2020b`` +========= ============== .. _list_software_SimpleElastix_1348: @@ -35303,6 +36001,7 @@ version versionsuffix toolchain ``3.11.0`` ``foss/2018b`` ``3.12.2`` ``-Python-2.7.16`` ``intel/2019b`` ``3.12.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.12.2`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ================== =============================== @@ -35716,11 +36415,11 @@ SOCI is a database access library for C++ that makes the illusion of embedding S *homepage*: http://soci.sourceforge.net/ -========= ================= -version toolchain -========= ================= -``4.0.1`` ``GCCcore/9.3.0`` -========= ================= +========= ================================= +version toolchain +========= ================================= +``4.0.1`` ``GCC/10.2.0``, ``GCCcore/9.3.0`` +========= ================================= .. _list_software_SolexaQA++_852: @@ -35843,6 +36542,7 @@ version versionsuffix toolchain ``3.14.0`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` ``3.14.0`` ``-Python-3.7.4`` ``GCC/8.3.0`` ``3.14.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``3.15.2`` ``GCC/10.2.0`` ========== ================= ============================================== @@ -35892,6 +36592,7 @@ version versionsuffix toolchain ``2.4.0`` ``-Python-3.6.6`` ``intel/2018b`` ``2.4.5`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` ``3.0.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``3.1.1`` ``fosscuda/2020b`` ========= =========================================== =============================== @@ -35909,7 +36610,7 @@ version toolchain ========= ============================================================================================================================== ``2.0.2`` ``foss/2016a`` ``2.0.3`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``intel/2017a`` -``2.0.4`` ``GCCcore/9.3.0`` +``2.0.4`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================================== @@ -35971,12 +36672,13 @@ Spglib is a library for finding and handling crystal symmetries written in C. *homepage*: https://atztogo.github.io/spglib/ -========= ========================= -version toolchain -========= ========================= -``1.9.2`` ``intel/2016.02-GCC-4.9`` -``1.9.9`` ``intel/2017b`` -========= ========================= +========== ========================= +version toolchain +========== ========================= +``1.9.2`` ``intel/2016.02-GCC-4.9`` +``1.9.9`` ``intel/2017b`` +``1.16.1`` ``GCCcore/10.2.0`` +========== ========================= .. _list_software_spglib-python_1360: @@ -35988,18 +36690,18 @@ Spglib for Python. Spglib is a library for finding and handling crystal symmetri *homepage*: https://pypi.python.org/pypi/spglib -================ ================== =============================== -version versionsuffix toolchain -================ ================== =============================== -``1.9.4.2`` ``-Python-2.7.12`` ``intel/2016b`` -``1.9.5`` ``-Python-2.7.12`` ``intel/2016b`` -``1.9.9.38`` ``-Python-2.7.13`` ``intel/2017a`` -``1.10.0.2`` ``-Python-2.7.14`` ``intel/2017b`` -``1.10.0.2`` ``-Python-3.6.3`` ``intel/2017b`` -``1.14.1.post0`` ``-Python-3.7.2`` ``intel/2019a`` -``1.16.0`` ``foss/2020b``, ``intel/2020b`` -``1.16.0`` ``-Python-3.8.2`` ``intel/2020a`` -================ ================== =============================== +================ ================== =================================================== +version versionsuffix toolchain +================ ================== =================================================== +``1.9.4.2`` ``-Python-2.7.12`` ``intel/2016b`` +``1.9.5`` ``-Python-2.7.12`` ``intel/2016b`` +``1.9.9.38`` ``-Python-2.7.13`` ``intel/2017a`` +``1.10.0.2`` ``-Python-2.7.14`` ``intel/2017b`` +``1.10.0.2`` ``-Python-3.6.3`` ``intel/2017b`` +``1.14.1.post0`` ``-Python-3.7.2`` ``intel/2019a`` +``1.16.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``1.16.0`` ``-Python-3.8.2`` ``intel/2020a`` +================ ================== =================================================== .. _list_software_Sphinx_634: @@ -36263,6 +36965,7 @@ version versionsuffix toolchain ``2.10.4`` ``gompi/2019b`` ``2.10.5`` ``-centos_linux64`` ``system`` ``2.10.8`` ``gompi/2020a`` +``2.10.9`` ``gompi/2020b`` =========== =================== =============== @@ -36462,6 +37165,7 @@ version toolchain ``2.7.5b`` ``GCC/9.3.0`` ``2.7.6a`` ``GCC/10.2.0``, ``GCC/9.3.0`` ``2.7.7a`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``2.7.8a`` ``GCC/10.2.0`` ========== ============================================================== @@ -36554,7 +37258,7 @@ version versionsuffix toolchain ``0.10.1`` ``foss/2019a`` ``0.11.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``0.11.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``0.12.1`` ``intel/2020b`` +``0.12.1`` ``foss/2020b``, ``intel/2020b`` ========== ================== =============================== @@ -36682,6 +37386,22 @@ version toolchain ========= ===================================================================================== +.. _list_software_suave_548: + +*suave* ++++++++ + +suave is an interactive web application to visualize read depth ratios between two samples and the structural variants of one of the samples (typically the "case" sample in a case/control setup such as tumor/normal comparison). + +*homepage*: https://github.com/dellytools/suave + +============ ============== +version toolchain +============ ============== +``20160529`` ``foss/2020b`` +============ ============== + + .. _list_software_Subread_710: *Subread* @@ -36829,6 +37549,7 @@ version toolchain ``2.6.2`` ``intel/2016b``, ``intel/2018b`` ``2.7.0`` ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``5.1.0`` ``foss/2019b``, ``intel/2019b`` +``5.7.0`` ``foss/2020b``, ``intel/2020b`` ========= ================================================================================================================================== @@ -36862,7 +37583,7 @@ version toolchain ========= =============================== ``5.1.1`` ``foss/2016a``, ``intel/2016a`` ``5.2.1`` ``foss/2017b``, ``intel/2017b`` -``5.2.2`` ``intel/2020a`` +``5.2.2`` ``foss/2020a``, ``intel/2020a`` ========= =============================== @@ -37116,6 +37837,7 @@ version versionsuffix toolchain ``1.4`` ``foss/2019a``, ``intel/2019a`` ``1.5.1`` ``-Python-3.7.4`` ``foss/2019b`` ``1.6.2`` ``-Python-3.8.2`` ``foss/2020a`` +``1.7.1`` ``foss/2020b`` ========= ================== =============================== @@ -37426,11 +38148,12 @@ Tensorboard for PyTorch. *homepage*: https://github.com/lanpa/tensorboardX -======= ================= ============== -version versionsuffix toolchain -======= ================= ============== -``2.0`` ``-Python-3.7.4`` ``foss/2019b`` -======= ================= ============== +======= ================== ================== +version versionsuffix toolchain +======= ================== ================== +``2.0`` ``-Python-3.7.4`` ``foss/2019b`` +``2.1`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` +======= ================== ================== .. _list_software_TensorFlow_1043: @@ -37502,11 +38225,12 @@ TensorFlow Probability (TFP) is a library for probabilistic reasoning and statis *homepage*: https://www.tensorflow.org/probability -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``0.9.0`` ``-Python-3.7.4`` ``foss/2019b`` -========= ================= ============== +========== ================= ================================== +version versionsuffix toolchain +========== ================= ================================== +``0.9.0`` ``-Python-3.7.4`` ``foss/2019b`` +``0.12.1`` ``foss/2020b``, ``fosscuda/2020b`` +========== ================= ================================== .. _list_software_TensorRT_801: @@ -37650,16 +38374,16 @@ Texinfo is the official documentation format of the GNU project. *homepage*: https://www.gnu.org/software/texinfo/ -========= ==================================== -version toolchain -========= ==================================== -``4.13a`` ``system`` -``5.2`` ``GCC/4.8.2`` -``6.4`` ``GCCcore/5.4.0`` -``6.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``6.6`` ``GCCcore/8.2.0`` -``6.7`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ==================================== +========= ======================================================== +version toolchain +========= ======================================================== +``4.13a`` ``system`` +``5.2`` ``GCC/4.8.2`` +``6.4`` ``GCCcore/5.4.0`` +``6.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``6.6`` ``GCCcore/8.2.0`` +``6.7`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================== .. _list_software_texlive_769: @@ -37724,7 +38448,7 @@ version versionsuffix toolchain ``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` ``1.0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``1.0.4`` ``-Python-3.8.2`` ``foss/2020a`` -``1.1.2`` ``-PyMC`` ``intel/2020b`` +``1.1.2`` ``-PyMC`` ``fosscuda/2020b``, ``intel/2020b`` ========= ================== =================================================== @@ -37851,12 +38575,12 @@ The `time' command runs another program, then displays information about the res *homepage*: https://www.gnu.org/software/time/ -======= ==================================== -version toolchain -======= ==================================== -``1.7`` ``system`` -``1.9`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ==================================== +======= ======================================================= +version toolchain +======= ======================================================= +``1.7`` ``system`` +``1.9`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ======================================================= .. _list_software_TINKER_461: @@ -37969,9 +38693,9 @@ version toolchain *tmux* ++++++ -tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal. +tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal. -*homepage*: http://tmux.sourceforge.net/ +*homepage*: https://github.com/tmux/tmux ======== ============================== version toolchain @@ -37979,6 +38703,7 @@ version toolchain ``1.9a`` ``GCC/4.9.2`` ``2.2`` ``GCCcore/4.9.3`` ``2.3`` ``GCC/5.4.0-2.26``, ``system`` +``3.1c`` ``GCCcore/8.3.0`` ======== ============================== @@ -38077,12 +38802,12 @@ Data loaders and abstractions for text and NLP *homepage*: https://github.com/pytorch/text -========= =============================== ================== -version versionsuffix toolchain -========= =============================== ================== -``0.5.0`` ``-PyTorch-1.4.0-Python-3.7.4`` ``fosscuda/2019b`` -``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b`` -========= =============================== ================== +========= =============================== ================================== +version versionsuffix toolchain +========= =============================== ================================== +``0.5.0`` ``-PyTorch-1.4.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` +========= =============================== ================================== .. _list_software_torchvision_1208: @@ -38950,6 +39675,7 @@ version versionsuffix toolchain ``5.2.236`` ``-i86linux32`` ``system`` ``5.2.236-6.1.544`` ``-i86linux32`` ``system`` ``6.1.544`` ``-i86linux32`` ``system`` +``11.0.667`` ``-i86linux32`` ``system`` =================== =============== ========== @@ -39023,7 +39749,7 @@ version toolchain --- -:ref:`list_software_V8_142` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VMD_231` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` +:ref:`list_software_V8_142` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VMD_231` - :ref:`list_software_voltools_898` - :ref:`list_software_vorbis-tools_1267` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` .. _list_software_V8_142: @@ -39060,7 +39786,7 @@ version toolchain ``3.11.0`` ``foss/2016a``, ``intel/2016a`` ``3.13.0`` ``foss/2017b``, ``foss/2018a``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.14.0`` ``foss/2018b`` -``3.16.1`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2020a`` +``3.16.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020a`` ========== ================================================================================= @@ -39236,16 +39962,16 @@ The aim of VCFtools is to provide easily accessible methods for working with c *homepage*: https://vcftools.github.io -========== ================ ===================================================== -version versionsuffix toolchain -========== ================ ===================================================== -``0.1.14`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` -``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` -``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` -``0.1.16`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` -``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` -========== ================ ===================================================== +========== ================ ===================================================================== +version versionsuffix toolchain +========== ================ ===================================================================== +``0.1.14`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` +``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` +``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` +``0.1.16`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` +``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` +========== ================ ===================================================================== .. _list_software_VEGAS_374: @@ -39440,6 +40166,38 @@ version versionsuffix toolchain ============ ================== =============================== +.. _list_software_voltools_898: + +*voltools* +++++++++++ + +CUDA-accelerated numpy 3D affine transformations + +*homepage*: https://github.com/the-lay/voltools + +========= ============== +version toolchain +========= ============== +``0.4.2`` ``foss/2020b`` +========= ============== + + +.. _list_software_vorbis-tools_1267: + +*vorbis-tools* +++++++++++++++ + +Command-line tools for creating and playing Ogg Vorbis files. + +*homepage*: https://xiph.org/vorbis/ + +========= ================== +version toolchain +========= ================== +``1.4.2`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_Voro++_508: *Voro++* @@ -39639,6 +40397,7 @@ version versionsuffix toolchain ``8.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``8.2.0`` ``-Python-3.7.4`` ``foss/2019b`` ``8.2.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` +``9.0.1`` ``foss/2020b`` ========= ================== =================================================== @@ -39671,6 +40430,7 @@ version toolchain ``2019_update2`` ``system`` ``2019_update3`` ``system`` ``2019_update5`` ``system`` +``2020_update3`` ``system`` ================= ========== @@ -40312,23 +41072,23 @@ xarray (formerly xray) is an open source project and Python package that aims to *homepage*: https://github.com/pydata/xarray -========== ================== =============================== -version versionsuffix toolchain -========== ================== =============================== -``0.9.5`` ``-Python-2.7.13`` ``intel/2017a`` -``0.9.5`` ``-Python-3.6.1`` ``intel/2017a`` -``0.9.6`` ``-Python-2.7.13`` ``intel/2017a`` -``0.10.0`` ``-Python-2.7.14`` ``intel/2017b`` -``0.10.0`` ``-Python-3.6.3`` ``intel/2017b`` -``0.10.3`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.4`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.8`` ``-Python-3.6.4`` ``intel/2018a`` -``0.12.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` -``0.15.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``0.16.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``0.16.2`` ``intel/2020b`` -========== ================== =============================== +========== ================== =================================== +version versionsuffix toolchain +========== ================== =================================== +``0.9.5`` ``-Python-2.7.13`` ``intel/2017a`` +``0.9.5`` ``-Python-3.6.1`` ``intel/2017a`` +``0.9.6`` ``-Python-2.7.13`` ``intel/2017a`` +``0.10.0`` ``-Python-2.7.14`` ``intel/2017b`` +``0.10.0`` ``-Python-3.6.3`` ``intel/2017b`` +``0.10.3`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.4`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.8`` ``-Python-3.6.4`` ``intel/2018a`` +``0.12.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` +``0.15.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.16.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.16.2`` ``fosscuda/2020b``, ``intel/2020b`` +========== ================== =================================== .. _list_software_xbitmaps_872: @@ -40653,6 +41413,7 @@ version versionsuffix toolchain ``2.0200`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` ``2.0201`` ``GCCcore/8.3.0`` ``2.0205`` ``GCCcore/9.3.0`` +``2.0206`` ``GCCcore/10.2.0`` ========== ================ =============================== @@ -40777,6 +41538,7 @@ version versionsuffix toolchain ``1.2.2`` ``-X11-20180131`` ``GCCcore/6.4.0`` ``1.2.3`` ``GCCcore/7.3.0`` ``1.2.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.2.5`` ``GCCcore/10.2.0`` ========= ================= ======================================================================================================================= @@ -40908,7 +41670,23 @@ version versionsuffix toolchain --- -:ref:`list_software_Yade_387` - :ref:`list_software_yaff_422` - :ref:`list_software_Yambo_504` - :ref:`list_software_YANK_307` - :ref:`list_software_YAPS_317` - :ref:`list_software_Yasm_410` - :ref:`list_software_YAXT_326` +:ref:`list_software_YACS_304` - :ref:`list_software_Yade_387` - :ref:`list_software_yaff_422` - :ref:`list_software_Yambo_504` - :ref:`list_software_YANK_307` - :ref:`list_software_YAPS_317` - :ref:`list_software_Yasm_410` - :ref:`list_software_YAXT_326` + + +.. _list_software_YACS_304: + +*YACS* +++++++ + +YACS was created as a lightweight library to define and manage system configurations, such as those commonly found in software designed for scientific experimentation. These "configurations" typically cover concepts like hyperparameters used in training a machine learning model or configurable model hyperparameters, such as the depth of a convolutional neural network. + +*homepage*: https://github.com/rbgirshick/yacs + +========= ===================================== +version toolchain +========= ===================================== +``0.1.8`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +========= ===================================== .. _list_software_Yade_387: @@ -41057,11 +41835,12 @@ Z3 is a theorem prover from Microsoft Research. *homepage*: https://github.com/Z3Prover/z3 -========= ==================================== -version toolchain -========= ==================================== -``4.8.9`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ==================================== +========== ==================================== +version toolchain +========== ==================================== +``4.8.9`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.8.10`` ``GCCcore/10.2.0`` +========== ==================================== .. _list_software_zarr_447: diff --git a/docs/version-specific/easyconfig_constants.rst b/docs/version-specific/easyconfig_constants.rst index 96f44a1f..e04a2e19 100644 --- a/docs/version-specific/easyconfig_constants.rst +++ b/docs/version-specific/easyconfig_constants.rst @@ -19,6 +19,6 @@ Constant name Constant value ``OS_TYPE`` ``Darwin`` System type (e.g. 'Linux' or 'Darwin') ``OS_VERSION`` ``UNKNOWN`` System version ``SYSTEM`` ``{'name': 'system', 'version': 'system'}`` System toolchain -``SYS_PYTHON_VERSION`` ``3.9.0`` System Python version (platform.python_version()) +``SYS_PYTHON_VERSION`` ``3.9.2`` System Python version (platform.python_version()) ====================== ============================================================= ================================================================================ diff --git a/docs/version-specific/easyconfig_parameters.rst b/docs/version-specific/easyconfig_parameters.rst index 566fd2ca..bac34327 100644 --- a/docs/version-specific/easyconfig_parameters.rst +++ b/docs/version-specific/easyconfig_parameters.rst @@ -149,6 +149,7 @@ modules parameters **Parameter name** **Description** **Default value** ============================== =========================================================================================================== ================= ``allow_prepend_abs_path`` Allow specifying absolute paths to prepend in modextrapaths False +``citing`` Free-form text that describes how the software should be cited in publications None ``docpaths`` List of paths for documentation relative to installation directory None ``examples`` Free-form text with examples on using the software None ``include_modpath_extensions`` Include $MODULEPATH extensions specified by module naming scheme. True diff --git a/docs/version-specific/easyconfig_templates.rst b/docs/version-specific/easyconfig_templates.rst index f248f8c0..d9452410 100644 --- a/docs/version-specific/easyconfig_templates.rst +++ b/docs/version-specific/easyconfig_templates.rst @@ -136,5 +136,11 @@ Constant Template value ``SOURCELOWER_XZ`` Source .xz bundle with lowercase name ``%(namelower)s-%(version)s.xz`` ``SOURCE_TAR_Z`` Source .tar.Z bundle ``%(name)s-%(version)s.tar.Z`` ``SOURCELOWER_TAR_Z`` Source .tar.Z bundle with lowercase name ``%(namelower)s-%(version)s.tar.Z`` +``SOURCE_WHL`` Generic (non-compiled) Python 2 & Python 3 wheel package ``%(name)s-%(version)s-py2.py3-none-any.whl`` +``SOURCELOWER_WHL`` Generic (non-compiled) Python 2 & Python 3 wheel package with lowercase name ``%(namelower)s-%(version)s-py2.py3-none-any.whl`` +``SOURCE_PY2_WHL`` Generic (non-compiled) Python 2 wheel package ``%(name)s-%(version)s-py2-none-any.whl`` +``SOURCELOWER_PY2_WHL`` Generic (non-compiled) Python 2 wheel package with lowercase name ``%(namelower)s-%(version)s-py2-none-any.whl`` +``SOURCE_PY3_WHL`` Generic (non-compiled) Python 3 wheel package ``%(name)s-%(version)s-py3-none-any.whl`` +``SOURCELOWER_PY3_WHL`` Generic (non-compiled) Python 3 wheel package with lowercase name ``%(namelower)s-%(version)s-py3-none-any.whl`` ======================= ============================================================================================================= ======================================================================================== diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index 1cdeaaae..c514848b 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -335,43 +335,45 @@ Build a Python package and module with cmake. Extra easyconfig parameters specific to ``CMakePythonPackage`` easyblock ------------------------------------------------------------------------ -======================== ================================================================================================================================================================================================== ================== -easyconfig parameter description default value -======================== ================================================================================================================================================================================================== ================== -``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` -``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` -``build_cmd`` Build command to use ``"make"`` -``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` -``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``configure_cmd`` Configure command to use ``"cmake"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``generator`` Build file generator to use. None to use CMakes default ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed ``False`` -``separate_build_dir`` Perform build in a separate directory ``True`` -``srcdir`` Source directory location to provide to cmake command ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``unpack_sources`` Unpack sources prior to build/install ``True`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== ================================================================================================================================================================================================== ================== +======================== ================================================================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== ================================================================================================================================================================================================== ======================================================================= +``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` +``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` +``build_cmd`` Build command to use ``"make"`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` +``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``configure_cmd`` Configure command to use ``"cmake"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``generator`` Build file generator to use. None to use CMakes default ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Build command to use ``"make install"`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``separate_build_dir`` Perform build in a separate directory ``True`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``srcdir`` Source directory location to provide to cmake command ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``unpack_sources`` Unpack sources prior to build/install ``True`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` +``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` +======================== ================================================================================================================================================================================================== ======================================================================= Customised steps in ``CMakePythonPackage`` easyblock ---------------------------------------------------- @@ -532,37 +534,39 @@ Build a Python package and module with 'python configure/make/make install'. Extra easyconfig parameters specific to ``ConfigureMakePythonPackage`` easyblock -------------------------------------------------------------------------------- -======================== =================================================================================================================================================================================================== ================== -easyconfig parameter description default value -======================== =================================================================================================================================================================================================== ================== -``build_cmd`` Build command to use ``"make"`` -``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``configure_cmd`` Configure command to use ``"./configure"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed ``False`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``unpack_sources`` Unpack sources prior to build/install ``True`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== =================================================================================================================================================================================================== ================== +======================== =================================================================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== =================================================================================================================================================================================================== ======================================================================= +``build_cmd`` Build command to use ``"make"`` +``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``configure_cmd`` Configure command to use ``"./configure"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Build command to use ``"make install"`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``unpack_sources`` Unpack sources prior to build/install ``True`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` +``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` +======================== =================================================================================================================================================================================================== ======================================================================= Customised steps in ``ConfigureMakePythonPackage`` easyblock ------------------------------------------------------------ @@ -640,29 +644,31 @@ Extends PythonPackage to add a Fortran compiler to the make call Extra easyconfig parameters specific to ``FortranPythonPackage`` easyblock -------------------------------------------------------------------------- -======================== ========================================================================================================= ============= -easyconfig parameter description default value -======================== ========================================================================================================= ============= -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed ``False`` -``unpack_sources`` Unpack sources prior to build/install ``True`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== ========================================================================================================= ============= +======================== =============================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== =============================================================================================================================== ======================================================================= +``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install ``True`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` +``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` +======================== =============================================================================================================================== ======================================================================= Customised steps in ``FortranPythonPackage`` easyblock ------------------------------------------------------ @@ -927,34 +933,36 @@ Bundle of modules: only generate module files, nothing to build/install Extra easyconfig parameters specific to ``PythonBundle`` easyblock ------------------------------------------------------------------ -=========================== ========================================================================================================= ============= -easyconfig parameter description default value -=========================== ========================================================================================================= ============= -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed ``False`` -``unpack_sources`` Unpack sources prior to build/install ``True`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -=========================== ========================================================================================================= ============= +=========================== =============================================================================================================================== ======================================================================= +easyconfig parameter description default value +=========================== =============================================================================================================================== ======================================================================= +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install ``True`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` +``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` +=========================== =============================================================================================================================== ======================================================================= .. _PythonPackage: @@ -968,29 +976,31 @@ Builds and installs a Python package, and provides a dedicated module file. Extra easyconfig parameters specific to ``PythonPackage`` easyblock ------------------------------------------------------------------- -======================== ========================================================================================================= ============= -easyconfig parameter description default value -======================== ========================================================================================================= ============= -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed ``False`` -``unpack_sources`` Unpack sources prior to build/install ``True`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== ========================================================================================================= ============= +======================== =============================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== =============================================================================================================================== ======================================================================= +``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install ``True`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` +``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` +======================== =============================================================================================================================== ======================================================================= Customised steps in ``PythonPackage`` easyblock ----------------------------------------------- @@ -1269,29 +1279,31 @@ Support for install VSC Python packages. Extra easyconfig parameters specific to ``VSCPythonPackage`` easyblock ---------------------------------------------------------------------- -======================== ========================================================================================================= ============= -easyconfig parameter description default value -======================== ========================================================================================================= ============= -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed ``False`` -``unpack_sources`` Unpack sources prior to build/install ``True`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== ========================================================================================================= ============= +======================== =============================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== =============================================================================================================================== ======================================================================= +``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install ``True`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` +``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` +======================== =============================================================================================================================== ======================================================================= .. _VersionIndependentPythonPackage: @@ -1305,29 +1317,31 @@ Support for building/installing python packages without requiring a specific pyt Extra easyconfig parameters specific to ``VersionIndependentPythonPackage`` easyblock ------------------------------------------------------------------------------------- -======================== ========================================================================================================= ============= -easyconfig parameter description default value -======================== ========================================================================================================= ============= -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed ``False`` -``unpack_sources`` Unpack sources prior to build/install ``True`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== ========================================================================================================= ============= +======================== =============================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== =============================================================================================================================== ======================================================================= +``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install ``True`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` +``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` +======================== =============================================================================================================================== ======================================================================= Customised steps in ``VersionIndependentPythonPackage`` easyblock ----------------------------------------------------------------- diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index 56939da5..09bd7371 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -248,7 +248,8 @@ Override options ========================================================================= ================================================================================================================================================================================================================================================================================ Option flag Option description ========================================================================= ================================================================================================================================================================================================================================================================================ -``--accept-eula=ACCEPT-EULA`` Accept EULA for specified software (type comma-separated list; default: ) +``--accept-eula=ACCEPT-EULA`` Accept EULA for specified software [DEPRECATED, use --accept-eula-for instead!] (type comma-separated list; default: ) +``--accept-eula-for=ACCEPT-EULA-FOR`` Accept EULA for specified software (type comma-separated list; default: ) ``--add-dummy-to-minimal-toolchains`` Include dummy toolchain in minimal toolchain searches [DEPRECATED, use --add-system-to-minimal-toolchains instead!) (default: False) ``--add-system-to-minimal-toolchains`` Include system toolchain in minimal toolchain searches (default: False) ``--allow-loaded-modules=ALLOW-LOADED-MODULES`` List of software names for which to allow loaded modules in initial environment (type comma-separated list; default: EasyBuild) @@ -262,6 +263,8 @@ Option flag Opt ``--consider-archived-easyconfigs`` Also consider archived easyconfigs (default: False) ``-C, --containerize`` Generate container recipe/image (default: False) ``--copy-ec`` Copy specified easyconfig(s) to specified location (default: False) +``--cuda-cache-dir=PATH`` Path to CUDA cache dir to use if enabled. Defaults to a path inside the build dir. (type ) +``--cuda-cache-maxsize=CUDA-CACHE-MAXSIZE`` Maximum size of the CUDA cache (in MiB) used for JIT compilation of PTX code. Leave value empty to let EasyBuild choose a value or '0' to disable the cache (type ) ``--cuda-compute-capabilities=CUDA-COMPUTE-CAPABILITIES`` List of CUDA compute capabilities to use when building GPU software; values should be specified as digits separated by a dot, for example: 3.5,5.0,7.2 (type comma-separated list) ``--debug-lmod`` Run Lmod modules tool commands in debug module (default: False) ``--default-opt-level=DEFAULT-OPT-LEVEL`` Specify default optimisation level (type choice; default: defaultopt) (choices: noopt, lowopt, defaultopt, opt) @@ -272,6 +275,7 @@ Option flag Opt ``--dump-autopep8`` Reformat easyconfigs using autopep8 when dumping them (default: False) ``-e CLASS, --easyblock=CLASS`` easyblock to use for processing the spec file or dumping the options ``--enforce-checksums`` Enforce availability of checksums for all sources/patches, so they can be verified (default: False) +``--env-for-shebang=ENV-FOR-SHEBANG`` Define the env command to use when fixing shebangs (default: /usr/bin/env) ``--experimental`` Allow experimental code (with behaviour that can be changed/removed at any given time). (default: False) ``--extra-modules=EXTRA-MODULES`` List of extra modules to load after setting up the build environment (type comma-separated list) ``--fetch`` Allow downloading sources ignoring OS and modules tool dependencies, implies --stop=fetch, --ignore-osdeps and ignore modules tool (default: False) diff --git a/docs/version-specific/toolchain_opts.rst b/docs/version-specific/toolchain_opts.rst index 861c3fa7..f7f2f419 100644 --- a/docs/version-specific/toolchain_opts.rst +++ b/docs/version-specific/toolchain_opts.rst @@ -5,7 +5,7 @@ Available toolchain options (by toolchain) *(see also* ``eb --avail-toolchain-opts `` *)* -ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ +ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iiblf_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ .. _ClangGCC: @@ -1591,6 +1591,52 @@ option description ========================= ======================================================================= ========= +.. _gofbf: + +Available options for gofbf toolchain +------------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``f2c`` Generate code compatible with f2c and f77 ``False`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``loop`` Automatic loop parallellisation ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``lto`` Enable Link Time Optimization ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + .. _golf: Available options for golf toolchain @@ -2369,6 +2415,52 @@ option description ========================= ======================================================================= ========= +.. _iiblf: + +Available options for iiblf toolchain +------------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``intel-static`` Link Intel provided libraries statically ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``no-icc`` Don't set Intel specific macros ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + .. _iimkl: Available options for iimkl toolchain diff --git a/docs/version-specific/toolchains.rst b/docs/version-specific/toolchains.rst index baeed5cb..83746c36 100644 --- a/docs/version-specific/toolchains.rst +++ b/docs/version-specific/toolchains.rst @@ -39,6 +39,7 @@ Name Compiler(s) MPI Linear algebra **goalf** GCC OpenMPI ATLAS, ScaLAPACK FFTW **gobff** GCC OpenMPI BLIS, libFLAME, ScaLAPACK FFTW **goblf** GCC OpenMPI BLIS, LAPACK, ScaLAPACK FFTW +**gofbf** GCC OpenMPI FlexiBLAS, ScaLAPACK FFTW **golf** GCC *(none)* OpenBLAS FFTW **golfc** GCC, CUDA *(none)* OpenBLAS FFTW **gomkl** GCC OpenMPI imkl imkl @@ -56,6 +57,7 @@ Name Compiler(s) MPI Linear algebra **iccifortcuda** icc, ifort, CUDA *(none)* *(none)* *(none)* **ictce** icc, ifort impi imkl imkl **iibff** icc, ifort impi BLIS, libFLAME, ScaLAPACK FFTW +**iiblf** icc, ifort impi BLIS, LAPACK, ScaLAPACK FFTW **iimkl** icc, ifort *(none)* imkl imkl **iimklc** icc, ifort, CUDA *(none)* imkl imkl **iimpi** icc, ifort impi *(none)* *(none)* From ec53366689760e1ebbcc368515e73b7101c4fdbc Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 8 Apr 2021 10:06:19 +0800 Subject: [PATCH 124/286] update release notes and changelog for EasyBuild v4.3.4 + bump version to 4.3.4 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 155 +++++++++++++++++++++++++++++++++++++++++ docs/conf.py | 4 +- 3 files changed, 158 insertions(+), 2 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 89557958..c43a1949 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20210409.01** (`Apr 9th 2021`): update release notes for EasyBuild v4.3.4 (see :ref:`release_notes_eb434`) * **release 20210223.01** (`Feb 23rd 2021`): update release notes for EasyBuild v4.3.3 (see :ref:`release_notes_eb433`) * **release 20201210.01** (`Dec 10th 2020`): update release notes for EasyBuild v4.3.2 (see :ref:`release_notes_eb432`) * **release 20201029.01** (`Oct 29th 2020`): update release notes for EasyBuild v4.3.1 (see :ref:`release_notes_eb431`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 84d8f3df..8abde325 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -9,6 +9,161 @@ alongside 11,475 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb434: + +EasyBuild v4.3.4 (Apr 9th 2021) +------------------------------- + +bugfix/update release + +**framework** + +* various enhancements, including: + + * add support for filtering dependencies by using ``False`` as version (`#3506 `_) + * add ``create_unused_dir`` function to create a directory which does not yet exist (`#3551 `_) + * avoid running expensive ``module use`` and ``module unuse`` commands when using Lmod as modules tool, update ``$MODULEPATH`` directly instead (`#3557 `_, `#3633 `_) + * create CUDA cache (for JIT compiled PTX code) in build dir instead of ``$HOME`` (`#3569 `_) + * add "Citing" section to module files (`#3596 `_) + * add support for using fallback ``arch=*`` key in dependency version specified as arch->version mapping (`#3600 `_) + * also check for pending change requests and mergeable_state in ``check_pr_eligible_to_merge`` (`#3604 `_) + * ignore undismissed ``changes requested`` review if there is an ``approved`` review by the same user (`#3607 `_, `#3608 `_) + * sort output of ``eb --search`` in natural order (respecting numbers) (`#3609 `_) + * enhance ``eb`` command to ensure that ``easybuild.main`` can be imported before settling on python* command to use (`#3610 `_) + * add ``--env-for-shebang`` configuration option to define the ``env`` command to use for shebangs (`#3613 `_) + * add templates for architecture independent Python wheels (`#3618 `_) + * mention easyblocks PR in gist when uploading test report for it + fix ``clean_gists.py`` script (`#3622 `_) + * also accept regular expression value for ``--accept-eula-for`` (`#3630 `_) + * update ``validate_github_token`` function to accept GitHub token in new format (`#3632 `_) + +* various bug fixes, including: + + * fix ``$BLAS_LIB_MT`` for OpenBLAS, ensure ``-lpthread`` is included (`#3584 `_) + * use ``--opt=val`` for passing settings from config file to option parser to avoid error for values starting with ``-`` or ``--`` (`#3594 `_) + * avoid raised exception when getting output from interactive command in ``run_cmd_qa`` (`#3599 `_) + * add option to write file from file-like object and use in ``download_file`` (`#3614 `_) + * make sure that path to ``eb`` is always found by tests (`#3617 `_) + +* other changes: + + * add ``pick_default_branch`` function to clean up duplicate code in ``tools/github.py`` (`#3592 `_) + * refactor the CI configuration to use inclusion instead of exclusion (`#3616 `_) + * use develop branch when testing push access in ``--check-github`` (`#3629 `_) + * deprecate ``--accept-eula``, rename to ``--accept-eula-for`` (`#3630 `_) + +**easyblocks** + +* minor enhancements, including: + + * make OpenCV easyblock aware of protobuf, libwebp and OpenEXR dependencies provided via EasyBuild (`#2346 `_) + * update CP2K easyblock w.r.t. running regtest for CP2K v8.1 (`#2350 `_) + * update GROMACS easyblock for GROMACS/2021 with CUDA (`#2353 `_) + * adjust call to ``python-config`` for Python >= 3.8 in VMD easyblock (`#2355 `_) + * enhance cuDNN and CUDA easyblocks to support ``aarch64`` (`#2356 `_) + * pass down compiler flags provided by EasyBuild in g2clib easyblock (`#2357 `_) + * update VTune easyblock for version 2020 (`#2359 `_) + * make WRF and WPS easyblocks aware of ``(pre)configopts`` (`#2361 `_) + * add Clang version 12.0.0 for AOCC 3.0.0 to mapping in custom easyblock for AOCC (`#2362 `_) + * use ``PYPI_SOURCE`` as the default for source_urls of PythonPackage (`#2364 `_, `#2370 `_) + * enhance PythonPackage easyblock to catch faulty version (0.0.0) for installed Python packages (`#2367 `_, `#2377 `_) + * enhance BWA easyblock: pass compiler flags + use ``filetools`` functions (`#2368 `_) + +* various bug fixes, including: + + * set ``$R_LIBS_SITE`` rather than ``$R_LIBS`` when installing R packages (`#2326 `_) + * update PETSc easyblock to take into account that ScaLAPACK installation may not have header files + fix building in parallel (`#2348 `_) + * disable CMake user package repository in CMakeMake generic easyblock (`#2351 `_) + * update LAPACK easyblock to keep control of compiler options for versions >= 3.9.0 (`#2358 `_) + * also set ``$TORCH_CUDA_ARCH_LIST`` for PyTorch tests (`#2363 `_) + * enhance Hadoop easyblock to avoid copying same native library twice (`#2371 `_) + * fix pip extension download pattern for PythonPackage easyblock (`#2372 `_) + * make the CUDA stub libs take preference over system libs when linking (`#2373 `_) + * improve Python package version check and add ``unversioned_packages`` easyconfig parameter (`#2377 `_) + +**easyconfigs** + +* added easyconfig for goblf/2020b toolchain (`#12381 `_, `#12535 `_) + +* added example easyconfig files for 41 new software packages: + + * amplimap (`#12205 `_), BEEF (`#12104 `_), bpp (`#12036 `_), Brotli (`#11651 `_), CDAT (`#12322 `_), cicero (`#12252 `_), + CIF2Cell (`#12258 `_), CompareM (`#9377 `_), DL_POLY_4 (`#12324 `_), DMCfun (`#12412 `_), ESMPy (`#12339 `_), FLAC (`#12300 `_), + gdbm (`#12322 `_), GPyOpt (`#12524 `_), json-c (`#12344 `_), libcdms (`#12322 `_), libdrs (`#12322 `_), libogg (`#12285 `_), + libvorbis (`#12300 `_), LncLOOM (`#12287 `_), LPJmL (`#12344 `_), maze (`#12354 `_), MetaEuk (`#12188 `_), mrcfile (`#12497 `_), + Myokit (`#12261 `_), NCCL-tests (`#12415 `_), pyABC (`#12329 `_), PyCifRW (`#12258 `_), PyOD (`#12507 `_), pyro-api (`#12447 `_), + pyro-ppl (`#12447 `_), R-opencv (`#12226 `_), Ratatosk (`#12443 `_), RevBayes (`#12419 `_), sansa (`#12354 `_), scikit-cuda (`#12352 `_), + Seeder (`#9057 `_), suave (`#12354 `_), voltools (`#12497 `_), vorbis-tools (`#12300 `_), YACS (`#12309 `_) + +* added additional easyconfigs for various supported software packages, including: + + * AOCC 3.0.0, Arriba 2.1.0, ArviZ 0.11.1, arpack-ng 3.8.0 BCFtools 1.12, BEDTools 2.30.0, BUSCO 5.0.0, BioPerl 1.7.8, + Blosc 1.21.0, Boost.Python 1.74.0, bitarray 1.2.1, bokeh 2.2.3, CP2K 8.1, CUDAcore 11.2.2, CellRanger 6.0.0, + Clang 11.0.1, DIAMOND 2.0.7, Delly 0.8.7, dask 2021.2.0, dm-tree 0.1.5, Elk 7.0.12, Extrae 3.8.0, FLUENT 2021R1, + FabIO 0.11.0, Fiji 20201104, Flye 2.8.3, FreeSurfer 7.1.1, GDAL 3.2.1, GEOS 3.9.1, GLFW 3.3.3, + GMAP-GSNAP 2020-12-17, GROMACS 2021, GetOrganelle 1.7.4, gmsh 4.7.1, HTSeq 0.11.3, HTSlib 1.12, Hypre 2.20.0, + hyperopt 0.2.5, iVar 1.3.1, igraph 0.9.1, Jansson 2.13.1, Kent_tools 411, LAPACK 3.9.1, LAST 1179, LibSoup 2.72.0, + libxc 5.1.3, MAFFT 7.475, MCR R2020a.6 + R2020b.5 + R2021a.0.eb, MDTraj 1.9.5, MUMPS 5.3.5, MaSuRCA 4.0.1, + Mercurial 5.7.1, Monocle3 0.2.3, NGS 2.10.9, NVHPC 21.2, NetLogo 6.2.0, Nextflow 21.03.0, ncbi-vdb 2.10.9, + OSU-Micro-Benchmarks 5.7, OpenCV 4.5.1, OpenEXR 2.5.5, OptiX 7.2.0, PETSc 3.14.4, PLUMED 2.7.0, PROJ 7.2.1, + PyAMG 4.0.0, PyCUDA 2020.1, PyCairo 1.20.0, PyOpenCL 2021.1.2, PyTorch-Geometric 1.6.3, p7zip 17.03, pFUnit 4.2.0, + picard 2.25.1, pocl 1.6, preCICE 2.2.0, protobuf 2.5.0, pymatgen 2022.0.4, python-igraph 0.9.0, Qtconsole 5.0.2, + R 4.0.4, RASPA2 2.0.41, RDFlib 5.0.0, ReFrame 3.5.1, Ruby 2.7.2, rnaQUAST 2.2.0, SAMtools 1.12, SDL2 2.0.14, + SIMPLE 3.0.0, SPAdes 3.15.2, SUNDIALS 5.7.0, Seurat 4.0.1, Spark 3.1.1, scikit-image 0.18.1, silx 0.14.0, + spglib 1.16.1, sympy 1.7.1, tensorboardX 2.1, tensorflow-probability 0.12.1, tmux 3.1c, USEARCH 11.0.667, + VTK 9.0.1, VTune 2020_update3 + +* minor enhancements, including: + + * verify checksum of all patch files in easyconfigs test suite (`#12221 `_) + * add libwebp and OpenEXR dependencies for OpenCV 4.2.0 easyconfig with foss/2020a (`#12227 `_) + * add sanity check commands for vorbis-tools (`#12304 `_) + * add extensions to R-bundle-Bioconductor 3.12: motifmatchr (`#12390 `_), OUTRIDER + FRASER (`#12510 `_) + * add DMCfun extension for R v4.0.3 + v4.0.4 (`#12409 `_) + +* various bug fixes, including: + + * add missing GNU time dependency to WRF 4.0.2 built with foss/2018b (`#12179 `_) + * add archive ``source_urls`` for Hadoop and Spark (`#12220 `_) + * add missing Python build dep for SeqAn 2.4.0 (`#12222 `_) + * add missing pkg-config build dependency to VCFtools 0.1.16 (`#12245 `_), GObject-Introspection-1.64.0 (`#12298 `_), libsndfile (`#12303 `_) + * set ``$HTSLIB_DIR`` in HTSlib for use by EnsEMBLCoreAPI & Bio-DB-HTS (`#12253 `_) + * bump JasPer version to latest 2.0.24 for 2020b generation of easyconfigs + remove easyconfigs for ancient JasPer 2.0.1.4 with GCCcore/10.2.0 (`#12277 `_, `#12288 `_) + * bump pip to 20.3.4 in Python 2.7.18 easyconfig to fix unicode error (`#12293 `_) + * skip sanity check test in IPython-7.18.1-GCCcore-10.2.0.eb (`#12294 `_) + * add missing Perl and Autotools build dependencies in recent WRF easyconfigs (`#12301 `_) + * add missing groff build dependency for Perl 5.30.0 and 5.32.0 (`#12307 `_) + * add linkcomm + rnetcarto extensions to R v4.0.3 (`#12311 `_) + * add dependency on Flask in all ASE v3.21.1 easyconfigs (`#12312 `_) + * remove hard-coded ``-xHost`` from MMseqs2-11-e1a1c (`#12317 `_) + * revised outdated easyconfigs for libcerf + replaced obsolete homepages and source urls (`#12323 `_) + * consistently include ``new_archive`` source URL in Qt5 easyconfigs + add missing checksums (`#12325 `_, `#12426 `_) + * fix source URL and add alternate checksum for Hypre 2.14.0 (`#12337 `_) + * add patch for recent netCDF easyconfigs to fix MPI_Info_f2c issue with OpenMPI (`#12340 `_) + * add SourceForge fallback source URL for recent freetype easyconfigs (`#12341 `_) + * revert to Seaborn 0.10.1 as dependency for NanoPlot 1.33.0 (`#12345 `_) + * use ``-D_USE_METIS_5p1`` in OpenSees v3.2.0 patch to correctly build on top of METIS v5.1.0 (`#12403 `_) + * make sure that path to ``eb`` is always found by tests (`#12436 `_) + * stop tests changing the EasyBuild easyconfigs (`#12454 `_) + * use pip to install pkgconfig 1.5.1 (`#12455 `_) + * add CI test checking if the Python default ``source_urls`` are used and fix CI check where ``use_pip=False`` was ignored (`#12456 `_, `#12471 `_) + * fix source URLs in Arrow 0.x easyconfigs (`#12475 `_) + * fix numpy tests for recent SciPy-bundle easyconfig on POWER (`#12481 `_) + * don't download hwloc during FIRESTARTER build (`#12482 `_) + * avoid 0.0.0 install version for various Python apps (`#12519 `_, `#12522 `_) + * enable USER_SDPD package and disable building docs in LAMMPS 3Mar2020 (`#12527 `_) + * update ``$R_LIBS_SITE`` rather than ``$R_LIBS`` in easyconfigs installing R packages (`#12534 `_) + * add Python 3 build dep for HMMER 3.3.x test step (`#12536 `_) + +* other changes: + + * rename opencv_contrib and update to OpenCV v3.4.1 with contrib ``versionsuffix`` (`#12229 `_) + * fix minor style issues in POV-Ray v3.7.0.8 easyconfigs (`#12342 `_) + * enable ``-fPIC`` for g2clib (`#12349 `_) + * consistently include Keras-Applications and Keras-Preprocessing extensions in Keras 2.3.1 easyconfigs (`#12375 `_) + * remove ``PYPI_SOURCE`` source URL from easyconfigs using PythonPackage or PythonBundle (`#12541 `_, `#12452 `_, `#12453 `_) + * require ``sanity_pip_check`` for all Python package/bundles (`#12464 `_) + + .. _release_notes_eb433: EasyBuild v4.3.3 (Feb 23rd 2021) diff --git a/docs/conf.py b/docs/conf.py index 3f7e0859..1c5ccc08 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.3.3' # this is meant to reference the version of EasyBuild +version = '4.3.4' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20210223.0' # this is meant to reference the version of the documentation itself +release = '20210409.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From f36510d7ab598d99894f1c9d262591b0697b9d3d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 9 Apr 2021 14:48:35 +0800 Subject: [PATCH 125/286] bump version to 4.3.4 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 7ddfc0f1..d7fef477 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.3.3' +VERSION = '4.3.4' # Utility function to read README file From 5090e679e0768fc7b6b15ac080d6ac389e8ec8ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Apr 2021 09:58:58 +0200 Subject: [PATCH 126/286] make sure that release notes are in place for current EasyBuild version --- .github/workflows/doc_build.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/doc_build.yml b/.github/workflows/doc_build.yml index 9b4d04f1..b039f279 100644 --- a/.github/workflows/doc_build.yml +++ b/.github/workflows/doc_build.yml @@ -31,6 +31,11 @@ jobs: pip install sphinx # This test is weak, options -nWT would make it stronger but we have many warnings... READTHEDOCS=1 sphinx-build docs build + - name: Check release notes + run: | + # make sure release notes are in place for current version + ebver=$(grep '^VERSION' setup.py | sed "s/VERSION = '\([0-9.]*\)'/\1/g") + grep "^EasyBuild v${ebver}" docs/Release_notes.rst - name: Test installation run: | pip install . From d9e15822b822bb67271e430ce43273747a0742dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Apr 2021 10:33:05 +0200 Subject: [PATCH 127/286] update counts in release notes --- docs/Release_notes.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 626352eb..9913d02e 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,9 +3,9 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,248** different software packages, +The latest version of EasyBuild provides support for building and installing **2,288** different software packages, including 33 different (compiler) toolchains. It contains 229 software-specific easyblocks and 37 generic easyblocks, -alongside 11,475 easyconfig files. +alongside 11,784 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. From d8f09a8082252811ab42a073094b0997163e4e77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 10 Apr 2021 10:17:36 +0200 Subject: [PATCH 128/286] update setup.py to indicate compatibility with Python 3.8 and 3.9 --- setup.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/setup.py b/setup.py index d7fef477..b9dc29c1 100644 --- a/setup.py +++ b/setup.py @@ -74,6 +74,8 @@ def read(fname): "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", "Topic :: Scientific/Engineering", "Topic :: Software Development :: Build Tools", ], From 00d86d8361e55590a53cb58eeb0aa17b98c36f19 Mon Sep 17 00:00:00 2001 From: Ryan Pepper Date: Tue, 13 Apr 2021 14:44:29 +0100 Subject: [PATCH 129/286] Change unified diff command --- docs/Writing_easyconfig_files.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index e7fddef5..2080ba30 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -125,7 +125,7 @@ Remarks: is used for downloading (since EasyBuild v2.0) * patches need to be EasyBuild-compatible - * unified diff format (``diff -ru``) + * unified diff format (``diff -ruN``) * patched locations relative to unpacked sources * see :ref:`common_easyconfig_param_sources_checksums` for more information on ``checksums`` From 3f6ad610f6315ce8c76b85c739b1e00c63facd96 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 28 Apr 2021 15:50:51 +0200 Subject: [PATCH 130/286] Update Installing-Lmod-without-root-permissions.rst updated instructions to work for lmod 8.4 bumped because the current instructions don't work for bootstrap: `easybuild.tools.build_log.EasyBuildError: 'EasyBuild requires Lmod >= v6.5.1, found v6.1` --- ...stalling-Lmod-without-root-permissions.rst | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/docs/Installing-Lmod-without-root-permissions.rst b/docs/Installing-Lmod-without-root-permissions.rst index c2bd9cdc..f898aebe 100644 --- a/docs/Installing-Lmod-without-root-permissions.rst +++ b/docs/Installing-Lmod-without-root-permissions.rst @@ -6,6 +6,7 @@ Installing Lmod without root permissions This short guide will show how to install Lmod (and Lua, on which it depends) on Linux, without requiring root permissions. +Installing lua using the steps below does require rsync, make and gcc Lua ~~~ @@ -50,12 +51,14 @@ unexpected ``readline`` or ``ncurses`` libraries: Lmod ~~~~ +Dependencies: building Lmod using the steps below requires tcl, tcl-dev(el) make and bzip2 + **Step 1**: Download and unpack the latest available Lmod version, -`Lmod-6.1.tar.bz2`_ at the time of writing. +`Lmod-8.4.tar.bz2`_ at the time of writing. .. code:: bash - tar xfvj Lmod-6.1.tar.bz2 && cd Lmod-6.1 + tar xfvj Lmod-8.4.tar.bz2 && cd Lmod-8.4 **Step 2**: Configure, build and install Lmod build, in a custom prefix: @@ -68,7 +71,7 @@ Lmod .. code:: bash - export PATH=$HOME/lmod/6.1/libexec:$PATH + export PATH=$HOME/lmod/8.4/libexec:$PATH Optionally, give it a spin: @@ -76,7 +79,7 @@ Optionally, give it a spin: $ lmod --version - Modules based on Lua: Version 6.1 2016-02-05 16:31 + Modules based on Lua: Version 8.4 2020-07-31 12:25 -05:00 by Robert McLay mclay@tacc.utexas.edu **Step 4**: Define ``module`` function to use ``lmod`` (optional for use @@ -84,10 +87,10 @@ with EasyBuild): .. code:: bash - source $HOME/lmod/6.1/init/bash - export LMOD_CMD=$HOME/lmod/6.1/libexec/lmod + source $HOME/lmod/8.4/init/bash + export LMOD_CMD=$HOME/lmod/8.4/libexec/lmod .. _`http://sourceforge.net/projects/lmod/files/`: http://sourceforge.net/projects/lmod/files/ -.. _lua-5.1.4.8.tar.gz: http://sourceforge.net/projects/lmod/files/lua-5.1.4.8.tar.gz/download -.. _Lmod-6.1.tar.bz2: http://sourceforge.net/projects/lmod/files/Lmod-6.1.tar.bz2/download +.. _lua-5.1.4.8.tar.gz: https://sourceforge.net/projects/lmod/files/lua-5.1.4.8.tar.gz/download +.. _Lmod-8.4.tar.bz2: https://sourceforge.net/projects/lmod/files/Lmod-8.4.tar.bz2/download From 67e7d0edebebf4c5aef25f3ac8fa2f5538656aba Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 28 Apr 2021 15:52:40 +0200 Subject: [PATCH 131/286] Update Installing-Lmod-without-root-permissions.rst --- docs/Installing-Lmod-without-root-permissions.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Installing-Lmod-without-root-permissions.rst b/docs/Installing-Lmod-without-root-permissions.rst index f898aebe..c67f60f7 100644 --- a/docs/Installing-Lmod-without-root-permissions.rst +++ b/docs/Installing-Lmod-without-root-permissions.rst @@ -51,7 +51,7 @@ unexpected ``readline`` or ``ncurses`` libraries: Lmod ~~~~ -Dependencies: building Lmod using the steps below requires tcl, tcl-dev(el) make and bzip2 +Dependencies: building Lmod using the steps below requires tcl, tcl-dev(el), make and bzip2 **Step 1**: Download and unpack the latest available Lmod version, `Lmod-8.4.tar.bz2`_ at the time of writing. From 69c89be13d39d24ea325a27926bde12da1bedb0f Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Fri, 30 Apr 2021 15:08:30 +0200 Subject: [PATCH 132/286] Update Packaging_support.rst --- docs/Packaging_support.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Packaging_support.rst b/docs/Packaging_support.rst index 2973ba1a..c6722eac 100644 --- a/docs/Packaging_support.rst +++ b/docs/Packaging_support.rst @@ -20,7 +20,7 @@ Prerequisites EasyBuild leverages `FPM `_ to create binary packages (RPMs, Debian files, etc.). Hence, FPM must be available in some way or another. One way is via EasyBuild, for example by installing a module -for FPM using once of the available easyconfig files. +for FPM using one of the available easyconfig files. EasyBuild will also take care of installing Ruby for you (which is required for FPM itself):: From af583fb770345768a627f996cc095e01da9de277 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 May 2021 12:00:16 +0200 Subject: [PATCH 133/286] stop testing with Travis CI --- .travis.yml | 22 ---------------------- 1 file changed, 22 deletions(-) delete mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index eac21d13..00000000 --- a/.travis.yml +++ /dev/null @@ -1,22 +0,0 @@ -language: python -jobs: - include: - - python: "2.7" - - python: "3.6" - - python: "3.8" -# command to install dependencies -install: - - pip install codespell flake8 sphinx -# command to run tests -script: - # it is (currently) impossible to dismiss ignored suggestions but these are - # still added to the exit code (which is a just a count of spelling - # suggestions). Since we know we have one of these, we allow for that. - # see https://github.com/easybuilders/easybuild/pull/485 for details - - codespell --skip=".git,version-specific,scripts" --ignore-words-list=atleast,ninjs,simpy,proovread,namd --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo "Got one expected warning, so success!"; else $(exit $retVal); fi; - - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - - READTHEDOCS=1 sphinx-build docs build - # test installation too (using options that don't require to have a modules tool installed) - - pip install $TRAVIS_BUILD_DIR - - eb --list-easyblocks | grep EB_bzip2 - - eb --fetch bzip2-1.0.6.eb From b5f361cd0918a593d3423e24003adacb71044802 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 17 May 2021 14:07:37 +0200 Subject: [PATCH 134/286] Fix doku about Github tokens --- docs/Integration_with_GitHub.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Integration_with_GitHub.rst b/docs/Integration_with_GitHub.rst index e347128a..a0956258 100644 --- a/docs/Integration_with_GitHub.rst +++ b/docs/Integration_with_GitHub.rst @@ -93,11 +93,11 @@ Installing a GitHub token (``--install-github-token``) .. note:: *requires*: GitHub username + ``keyring`` Python package -A GitHub token is a string of 40 hexadecimal (lowercase) characters that is tied to your GitHub account, +A GitHub token is a string of 40 characters that is tied to your GitHub account, allowing you to access the GitHub API authenticated. Using a GitHub token is beneficial with respect to rate limitations, and enables write permissions on GitHub -(e.g., posting comments, creating gists, opening pull requests, etc.). +(e.g. posting comments, creating gists, opening pull requests). To obtain a GitHub token: From 42c4702b279a666da59a587d73476f21c25a515d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Jun 2021 16:49:16 +0200 Subject: [PATCH 135/286] auto-update docs for EasyBuild v4.4.0 --- docs/version-specific/Supported_software.rst | 3171 ++++++++++++----- docs/version-specific/easyblocks.rst | 4 + .../version-specific/easyconfig_constants.rst | 3 +- .../easyconfig_parameters.rst | 131 +- docs/version-specific/generic_easyblocks.rst | 271 +- docs/version-specific/help.rst | 9 +- docs/version-specific/toolchain_opts.rst | 130 +- docs/version-specific/toolchains.rst | 3 + 8 files changed, 2552 insertions(+), 1170 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 86facbf3..0bf9413a 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2287 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2349 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -97,23 +97,24 @@ ABINIT is a package whose main program allows one to find the total energy, cha *homepage*: https://www.abinit.org/ -========== ======================== =============================== -version versionsuffix toolchain -========== ======================== =============================== -``7.0.3`` ``-x86_64_linux_gnu4.5`` ``system`` -``7.0.5`` ``-x86_64_linux_gnu4.5`` ``system`` -``7.2.1`` ``-x86_64_linux_gnu4.5`` ``system`` -``7.10.5`` ``intel/2016.02-GCC-4.9`` -``7.10.5`` ``-libxc`` ``intel/2016.02-GCC-4.9`` -``8.0.8`` ``intel/2016a`` -``8.0.8b`` ``foss/2016b``, ``intel/2016b`` -``8.2.2`` ``foss/2016b``, ``intel/2016b`` -``8.4.4`` ``intel/2017b`` -``8.6.3`` ``intel/2018a`` -``8.10.2`` ``intel/2018b`` -``8.10.3`` ``intel/2018b`` -``9.2.1`` ``intel/2020a`` -========== ======================== =============================== +========== ======================== ================================ +version versionsuffix toolchain +========== ======================== ================================ +``7.0.3`` ``-x86_64_linux_gnu4.5`` ``system`` +``7.0.5`` ``-x86_64_linux_gnu4.5`` ``system`` +``7.2.1`` ``-x86_64_linux_gnu4.5`` ``system`` +``7.10.5`` ``intel/2016.02-GCC-4.9`` +``7.10.5`` ``-libxc`` ``intel/2016.02-GCC-4.9`` +``8.0.8`` ``intel/2016a`` +``8.0.8b`` ``foss/2016b``, ``intel/2016b`` +``8.2.2`` ``foss/2016b``, ``intel/2016b`` +``8.4.4`` ``intel/2017b`` +``8.6.3`` ``intel/2018a`` +``8.10.2`` ``intel/2018b`` +``8.10.3`` ``intel/2018b`` +``9.2.1`` ``intel/2020a`` +``9.4.1`` ``intel/2020a``, ``intel/2020b`` +========== ======================== ================================ .. _list_software_ABRA2_328: @@ -885,6 +886,7 @@ version toolchain ``0.921`` ``foss/2018a`` ``0.925`` ``foss/2018b`` ``0.933`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``0.935`` ``GCC/10.2.0`` ========= ====================================== @@ -1074,12 +1076,12 @@ Convert various sequence formats to FASTA *homepage*: https://github.com/tseemann/any2fasta -========= ================ ================= -version versionsuffix toolchain -========= ================ ================= -``0.4.2`` ``GCCcore/8.3.0`` -``0.4.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -========= ================ ================= +========= ================ ==================================== +version versionsuffix toolchain +========= ================ ==================================== +``0.4.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.4.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +========= ================ ==================================== .. _list_software_AOCC_278: @@ -1087,16 +1089,16 @@ version versionsuffix toolchain *AOCC* ++++++ -AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 11.0 +AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0 *homepage*: https://developer.amd.com/amd-aocc/ -========= ===================================== -version toolchain -========= ===================================== -``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.0.0`` ``GCCcore/10.2.0`` -========= ===================================== +========= ====================================== +version toolchain +========= ====================================== +``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.0.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_APBS_294: @@ -1128,6 +1130,7 @@ A PyTorch Extension: Tools for easy mixed precision and distributed training in version versionsuffix toolchain ============ ================= ================== ``20200325`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``20210420`` ``fosscuda/2020b`` ============ ================= ================== @@ -1229,6 +1232,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_Archive-Zip_1058: + +*Archive-Zip* ++++++++++++++ + +Provide an interface to ZIP archive files. + +*homepage*: https://metacpan.org/pod/Archive::Zip + +======== ================== +version toolchain +======== ================== +``1.68`` ``GCCcore/10.2.0`` +======== ================== + + .. _list_software_archspec_841: *archspec* @@ -1511,6 +1530,7 @@ version versionsuffix toolchain ``3.10.10`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.11.10`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``3.12.2`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` +``3.12.7`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` =========== ================= ================================================ @@ -1667,6 +1687,7 @@ version versionsuffix toolchain ``2.0.14`` ``foss/2019a`` ``4.0.1`` ``-Python-3.7.4`` ``foss/2019b`` ``4.0.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``4.2.1`` ``intelcuda/2020b`` ========== ================== =============================== @@ -1905,7 +1926,7 @@ version toolchain ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= ``2.68`` ``foss/2016b`` ``2.69`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.71`` ``system`` +``2.71`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``system`` ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= @@ -1992,6 +2013,7 @@ version toolchain ``1.15.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ``1.16.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ``1.16.2`` ``GCCcore/10.2.0`` +``1.16.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -2044,6 +2066,7 @@ version toolchain ``20170619`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` ``20180311`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ``20200321`` ``GCCcore/10.2.0`` +``20210128`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -2074,7 +2097,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` +:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` .. _list_software_Bader_478: @@ -2577,7 +2600,7 @@ version versionsuffix toolchain *bcolz* +++++++ -bcolz provides columnar, chunked data containers that can be compressed either in-memory and on-disk. Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, but it also comes with support for import/export facilities to/from HDF5/PyTables tables and pandas dataframes. +bcolz provides columnar, chunked data containers that can be compressed either in-memory and on-disk. Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, but it also comes with support for import/export facilities to/from HDF5/PyTables tables and pandas dataframes. *homepage*: https://bcolz.blosc.org/en/latest/ @@ -2585,6 +2608,7 @@ bcolz provides columnar, chunked data containers that can be compressed either i version versionsuffix toolchain ========= ================== ============== ``1.1.1`` ``-Python-2.7.13`` ``foss/2017a`` +``1.2.1`` ``foss/2020b`` ``1.2.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ============== @@ -2722,11 +2746,11 @@ BEEF is a library-based implementation of the Bayesian Error Estimation Function *homepage*: https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software -========= ======================= -version toolchain -========= ======================= -``0.1.1`` ``iccifort/2020.4.304`` -========= ======================= +========= ================================================ +version toolchain +========= ================================================ +``0.1.1`` ``iccifort/2019.5.281``, ``iccifort/2020.4.304`` +========= ================================================ .. _list_software_behave_619: @@ -2902,6 +2926,7 @@ version toolchain ``2.32`` ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` ``2.34`` ``GCCcore/10.1.0``, ``GCCcore/9.3.0``, ``system`` ``2.35`` ``GCCcore/10.2.0``, ``system`` +``2.36.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``system`` ========== ======================================================================================================================================================================================== @@ -3076,7 +3101,8 @@ version versionsuffix toolchain ``1.74`` ``foss/2019a`` ``1.75`` ``-Python-2.7.16`` ``foss/2019b`` ``1.75`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``1.78`` ``foss/2020b``, ``intel/2020b`` +``1.76`` ``-Python-2.7.18`` ``foss/2020b`` +``1.78`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.78`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ======== ================== =================================================== @@ -3097,6 +3123,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_BirdNET_616: + +*BirdNET* ++++++++++ + +BirdNET is a research platform that aims at recognizing birds by sound at scale. We support various hardware and operating systems such as Arduino microcontrollers, the Raspberry Pi, smartphones, web browsers, workstation PCs, and even cloud services. BirdNET is a citizen science platform as well as an analysis software for extremely large collections of audio. BirdNET aims to provide innovative tools for conservationists, biologists, and birders alike. + +*homepage*: https://birdnet.cornell.edu/ + +============ ================= ================== +version versionsuffix toolchain +============ ================= ================== +``20201214`` ``-Python-3.7.4`` ``fosscuda/2019b`` +============ ================= ================== + + .. _list_software_biscuit_755: *biscuit* @@ -3153,6 +3195,7 @@ version toolchain ``3.5.3`` ``GCCcore/9.3.0``, ``system`` ``3.6.1`` ``GCCcore/10.1.0`` ``3.7.1`` ``GCCcore/10.2.0``, ``system`` +``3.7.6`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``system`` ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -3240,6 +3283,7 @@ version versionsuffix toolchain ``2.8.1`` ``-Linux_x86_64`` ``system`` ``2.10.0`` ``-Linux_x86_64`` ``system`` ``2.10.1`` ``-Linux_x86_64`` ``system`` +``2.11.0`` ``-Linux_x86_64`` ``system`` ========== ================= ========== @@ -3320,6 +3364,7 @@ version versionsuffix toolchain ``0.3.2`` ``GCC/7.3.0-2.30`` ``0.6.0`` ``GCC/8.3.0-2.32`` ``0.8.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``0.8.1`` ``GCCcore/10.3.0`` ``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` ``2.2`` ``-amd`` ``GCCcore/9.3.0`` ========= ============= ===================================== @@ -3389,11 +3434,11 @@ Best Match Tagger for removing human reads from metagenomics datasets *homepage*: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/ -========= =============================== -version toolchain -========= =============================== -``3.101`` ``foss/2018b``, ``gompi/2019a`` -========= =============================== +========= ================================================ +version toolchain +========= ================================================ +``3.101`` ``foss/2018b``, ``gompi/2019a``, ``gompi/2020b`` +========= ================================================ .. _list_software_bnpy_441: @@ -3485,6 +3530,7 @@ version versionsuffix toolchain ``0.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``0.3.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``0.3.5`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``0.3.8`` ``fosscuda/2020b`` ========= ================= ================================== @@ -3572,7 +3618,7 @@ version versionsuffix toolchain ``1.69.0`` ``intel/2019.01`` ``1.70.0`` ``gompi/2019a``, ``gompic/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` ``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` -``1.72.0`` ``gompi/2020a``, ``iimpi/2020a`` +``1.72.0`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a`` ``1.72.0`` ``-no_mpi`` ``GCCcore/9.3.0`` ``1.74.0`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` ========== ================== ==================================================================== @@ -3598,7 +3644,7 @@ version versionsuffix toolchain ``1.67.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.70.0`` ``gompi/2019a``, ``gompic/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` ``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` -``1.72.0`` ``gompi/2020a``, ``iimpi/2020a`` +``1.72.0`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a`` ``1.74.0`` ``GCC/10.2.0`` ========== ================== ==================================================================== @@ -3636,7 +3682,7 @@ version toolchain ``1.2.1.1`` ``foss/2016b``, ``intel/2017b`` ``1.2.2`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ``1.2.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` -``1.3.0`` ``GCC/9.3.0`` +``1.3.0`` ``GCC/10.2.0``, ``GCC/9.3.0`` =========== ===================================================================================================================================== @@ -3887,11 +3933,11 @@ This module sets a group of environment variables for compilers, linkers, maths *homepage*: None -=========== ============================================================================================================================================================================================================================================================================================== -version toolchain -=========== ============================================================================================================================================================================================================================================================================================== -``default`` ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b`` -=========== ============================================================================================================================================================================================================================================================================================== +=========== ================================================================================================================================================================================================================================================================================================================================ +version toolchain +=========== ================================================================================================================================================================================================================================================================================================================================ +``default`` ``FCC/4.5.0``, ``Fujitsu/21.05``, ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b`` +=========== ================================================================================================================================================================================================================================================================================================================================ .. _list_software_Bullet_616: @@ -3927,6 +3973,7 @@ version versionsuffix toolchain ``3.0.2`` ``-Python-2.7.15`` ``intel/2018b`` ``4.0.5`` ``-Python-3.7.4`` ``foss/2019b`` ``5.0.0`` ``foss/2020b`` +``5.1.2`` ``foss/2020b`` ========= ================== =============== @@ -3939,11 +3986,11 @@ bustools is a program for manipulating BUS files for single cell RNA-Seq dataset *homepage*: https://github.com/BUStools/bustools -========== ============== -version toolchain -========== ============== -``0.40.0`` ``foss/2018b`` -========== ============== +========== ================================= +version toolchain +========== ================================= +``0.40.0`` ``GCCcore/9.3.0``, ``foss/2018b`` +========== ================================= .. _list_software_BWA_218: @@ -4116,7 +4163,7 @@ bzip2 is a freely available, patent free, high-quality data compressor. It typi version toolchain ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.0.6`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -4126,7 +4173,7 @@ version toolchain --- -:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_C3D_186: @@ -4205,16 +4252,16 @@ Cairo is a 2D graphics library with support for multiple output devices. Curren *homepage*: https://cairographics.org -=========== ================ =========================================================================== -version versionsuffix toolchain -=========== ================ =========================================================================== -``1.14.6`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``1.14.6`` ``-GLib-2.48.0`` ``foss/2016a``, ``intel/2016a`` -``1.14.8`` ``intel/2017a`` -``1.14.10`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017b`` -``1.14.12`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.16.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -=========== ================ =========================================================================== +=========== ================ =============================================================================================== +version versionsuffix toolchain +=========== ================ =============================================================================================== +``1.14.6`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``1.14.6`` ``-GLib-2.48.0`` ``foss/2016a``, ``intel/2016a`` +``1.14.8`` ``intel/2017a`` +``1.14.10`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017b`` +``1.14.12`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.16.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +=========== ================ =============================================================================================== .. _list_software_cairomm_744: @@ -4296,16 +4343,17 @@ Canu is a fork of the Celera Assembler designed for high-noise single-molecule s *homepage*: https://canu.readthedocs.io -======= ================ =============================== -version versionsuffix toolchain -======= ================ =============================== -``1.4`` ``foss/2016b`` -``1.7`` ``intel/2018a`` -``1.8`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``1.8`` ``-Perl-5.28.0`` ``foss/2018b`` -``1.8`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -``1.9`` ``-Java-11`` ``GCCcore/8.3.0`` -======= ================ =============================== +========= ================ =============================== +version versionsuffix toolchain +========= ================ =============================== +``1.4`` ``foss/2016b`` +``1.7`` ``intel/2018a`` +``1.8`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``1.8`` ``-Perl-5.28.0`` ``foss/2018b`` +``1.8`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``1.9`` ``-Java-11`` ``GCCcore/8.3.0`` +``2.1.1`` ``GCCcore/10.2.0`` +========= ================ =============================== .. _list_software_Canvas_604: @@ -4388,6 +4436,7 @@ carputils is a Python framework for generating and running openCARP examples. version versionsuffix toolchain ============ ================= ============== ``20200915`` ``-Python-3.8.2`` ``foss/2020a`` +``20210513`` ``foss/2020b`` ============ ================= ============== @@ -4433,12 +4482,13 @@ CastXML is a C-family abstract syntax tree XML output tool. *homepage*: https://github.com/CastXML/CastXML -============ ============== -version toolchain -============ ============== -``20160617`` ``foss/2016a`` -``20180806`` ``foss/2018a`` -============ ============== +============ ================= +version toolchain +============ ================= +``0.4.3`` ``GCCcore/8.3.0`` +``20160617`` ``foss/2016a`` +``20180806`` ``foss/2018a`` +============ ================= .. _list_software_Catch2_533: @@ -4577,7 +4627,7 @@ version toolchain *ccache* ++++++++ -Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again +Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again *homepage*: https://ccache.dev/ @@ -4589,6 +4639,7 @@ version versionsuffix toolchain ``3.3.3`` ``system`` ``3.3.4`` ``-f90`` ``system`` ``3.7.11`` ``system`` +``4.2.1`` ``system`` ========== ============= ========== @@ -4751,16 +4802,17 @@ CDO is a collection of command line Operators to manipulate and analyse Climate *homepage*: https://code.zmaw.de/projects/cdo -========= ================================================= -version toolchain -========= ================================================= -``1.7.2`` ``intel/2016b`` -``1.8.1`` ``intel/2017a`` -``1.9.1`` ``intel/2017b`` -``1.9.2`` ``intel/2017b`` -``1.9.5`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``1.9.8`` ``intel/2019b`` -========= ================================================= +========== ================================================= +version toolchain +========== ================================================= +``1.7.2`` ``intel/2016b`` +``1.8.1`` ``intel/2017a`` +``1.9.1`` ``intel/2017b`` +``1.9.2`` ``intel/2017b`` +``1.9.5`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +``1.9.8`` ``intel/2019b`` +``1.9.10`` ``gompi/2020b`` +========== ================================================= .. _list_software_cdsapi_628: @@ -4781,6 +4833,22 @@ version versionsuffix toolchain ========= ================= ================= +.. _list_software_cell2location_1323: + +*cell2location* ++++++++++++++++ + +Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model) + +*homepage*: https://github.com/BayraktarLab/cell2location/ + +============== ================== +version toolchain +============== ================== +``0.05-alpha`` ``fosscuda/2020b`` +============== ================== + + .. _list_software_CellMix_686: *CellMix* @@ -4816,6 +4884,7 @@ version toolchain ``5.0.0`` ``system`` ``5.0.1`` ``system`` ``6.0.0`` ``system`` +``6.0.1`` ``system`` ========= ========== @@ -5165,6 +5234,7 @@ version versionsuffix toolchain ``1.0.13`` ``-Python-2.7.15`` ``foss/2018b`` ``1.0.13`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.0.18`` ``-Python-2.7.15`` ``foss/2019a`` +``1.0.18`` ``-Python-2.7.18`` ``foss/2020b`` ``1.1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``1.1.3`` ``-Python-3.8.2`` ``intel/2020a`` ========== ================== =============================== @@ -5367,6 +5437,7 @@ version versionsuffix toolchain ========= ================== =============== ``2.3.2`` ``-Python-2.7.14`` ``intel/2017b`` ``2.3.3`` ``-Python-2.7.14`` ``intel/2018a`` +``2.3.8`` ``-Python-2.7.18`` ``foss/2020b`` ========= ================== =============== @@ -5531,6 +5602,7 @@ version toolchain ``2.4.0.0`` ``intel/2017b`` ``2.4.1.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018b`` ``2.4.1.3`` ``foss/2019b``, ``foss/2020a`` +``2.4.4.0`` ``GCC/10.2.0`` =========== ================================================================ @@ -5710,6 +5782,7 @@ version toolchain ``3.15.3`` ``GCCcore/8.3.0`` ``3.16.4`` ``GCCcore/9.3.0`` ``3.18.4`` ``GCCcore/10.2.0`` +``3.20.1`` ``GCCcore/10.3.0`` ========== ================================================================================================================================================= @@ -5736,7 +5809,7 @@ version toolchain A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing. -*homepage*: http://github.com/etal/cnvkit +*homepage*: https://github.com/etal/cnvkit ========= ========================= =============== version versionsuffix toolchain @@ -5744,6 +5817,7 @@ version versionsuffix toolchain ``0.9.2`` ``-Python-2.7.14`` ``intel/2017b`` ``0.9.3`` ``-Python-3.6.4`` ``intel/2018a`` ``0.9.6`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` +``0.9.8`` ``-R-4.0.3`` ``foss/2020b`` ========= ========================= =============== @@ -5897,7 +5971,7 @@ version versionsuffix toolchain *CONCOCT* +++++++++ -Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. +Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. *homepage*: https://concoct.readthedocs.io @@ -5908,6 +5982,7 @@ version versionsuffix toolchain ``1.0.0`` ``-Python-2.7.15`` ``foss/2018b`` ``1.0.0`` ``-Python-3.6.3`` ``foss/2017b`` ``1.1.0`` ``-Python-2.7.15`` ``foss/2019a`` +``1.1.0`` ``-Python-2.7.18`` ``foss/2020b`` ========= ================== ============== @@ -6367,6 +6442,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_cryoDRGN_744: + +*cryoDRGN* +++++++++++ + +cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous reconstruction. CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume. + +*homepage*: https://cb.csail.mit.edu/cb/cryodrgn/ + +========= ================== +version toolchain +========= ================== +``0.3.2`` ``fosscuda/2020b`` +========= ================== + + .. _list_software_CryptoMiniSat_1334: *CryptoMiniSat* @@ -6461,7 +6552,7 @@ Program for finding CTFs of electron micrographs. version toolchain ========== ====================================================== ``4.1.13`` ``foss/2019a``, ``fosscuda/2019a``, ``fosscuda/2019b`` -``4.1.14`` ``foss/2019b``, ``fosscuda/2019b`` +``4.1.14`` ``foss/2019b``, ``fosscuda/2019b``, ``fosscuda/2020b`` ========== ====================================================== @@ -6579,6 +6670,8 @@ version toolchain ``11.1.1`` ``system`` ``11.2.1`` ``system`` ``11.2.2`` ``system`` +``11.3.0`` ``system`` +``11.3.1`` ``system`` ========== ========== @@ -6632,7 +6725,7 @@ Transcript assembly, differential expression, and differential regulation for RN version toolchain ============ ================================================================================================= ``2.2.1`` ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``gompi/2019b``, ``intel/2017b``, ``intel/2018a`` -``20190706`` ``gompi/2019a`` +``20190706`` ``GCC/10.2.0``, ``gompi/2019a`` ============ ================================================================================================= @@ -6665,6 +6758,7 @@ CuPy is an open-source array library accelerated with NVIDIA CUDA. version versionsuffix toolchain ========= ================= ================== ``8.2.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``8.5.0`` ``fosscuda/2020b`` ========= ================= ================== @@ -6699,6 +6793,7 @@ version toolchain ``7.66.0`` ``GCCcore/8.3.0`` ``7.69.1`` ``GCCcore/9.3.0`` ``7.72.0`` ``GCCcore/10.2.0`` +``7.76.0`` ``GCCcore/10.3.0`` ========== =================================================================================== @@ -6739,6 +6834,7 @@ version versionsuffix toolchain ``1.16`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.18`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``1.18`` ``-Python-2.7.15`` ``foss/2018b`` +``1.18`` ``-Python-2.7.18`` ``GCC/10.2.0`` ``1.18`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``2.1`` ``-Python-3.6.6`` ``foss/2018b`` ``2.7`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` @@ -6839,9 +6935,9 @@ version versionsuffix toolchain *Cython* ++++++++ -The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. +Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). -*homepage*: https://pypi.python.org/pypi/Cython/ +*homepage*: https://cython.org/ =========== ================== =============================== version versionsuffix toolchain @@ -6853,6 +6949,7 @@ version versionsuffix toolchain ``0.27.3`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``0.29.10`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``0.29.10`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``0.29.22`` ``GCCcore/10.2.0`` =========== ================== =============================== @@ -6912,7 +7009,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` .. _list_software_dadi_402: @@ -7112,7 +7209,7 @@ version toolchain ``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` ``18.1.25`` ``GCCcore/7.3.0`` ``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``18.1.40`` ``GCCcore/10.2.0`` +``18.1.40`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` =========== ======================================================= @@ -7184,19 +7281,19 @@ D-Bus is a message bus system, a simple way for applications to talk to one ano *homepage*: http://dbus.freedesktop.org/ -=========== ==================================== -version toolchain -=========== ==================================== -``1.10.8`` ``foss/2016a``, ``intel/2016a`` -``1.10.12`` ``intel/2016b`` -``1.10.20`` ``GCCcore/6.4.0`` -``1.11.20`` ``intel/2017a`` -``1.13.0`` ``intel/2017b`` -``1.13.6`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.13.8`` ``GCCcore/8.2.0`` -``1.13.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.13.18`` ``GCCcore/10.2.0`` -=========== ==================================== +=========== ====================================== +version toolchain +=========== ====================================== +``1.10.8`` ``foss/2016a``, ``intel/2016a`` +``1.10.12`` ``intel/2016b`` +``1.10.20`` ``GCCcore/6.4.0`` +``1.11.20`` ``intel/2017a`` +``1.13.0`` ``intel/2017b`` +``1.13.6`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.13.8`` ``GCCcore/8.2.0`` +``1.13.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.13.18`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +=========== ====================================== .. _list_software_dbus-glib_889: @@ -7451,6 +7548,7 @@ version versionsuffix toolchain ``4.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2019a`` ``4.4.0`` ``-Python-2.7.15`` ``intel/2018b`` ``4.5.2`` ``GCCcore/10.2.0`` +``4.5.2`` ``-Python-2.7.18`` ``GCCcore/10.2.0`` ========= ================== ======================================================================== @@ -7495,11 +7593,12 @@ Python library for modeling DFAs, Moore Machines, and Transition Systems. *homepage*: https://github.com/mvcisback/dfa -========= ================= ================= -version versionsuffix toolchain -========= ================= ================= -``0.3.4`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -========= ================= ================= +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``0.3.4`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``2.1.2`` ``GCCcore/10.2.0`` +========= ================= ================== .. _list_software_DFT-D3_386: @@ -7648,11 +7747,12 @@ dill extends python's pickle module for serializing and de-serializing python ob *homepage*: https://pypi.org/project/dill/ -========= ================= -version toolchain -========= ================= -``0.3.0`` ``GCCcore/8.2.0`` -========= ================= +========= ===================================== +version toolchain +========= ===================================== +``0.3.0`` ``GCCcore/8.2.0`` +``0.3.3`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +========= ===================================== .. _list_software_DIRAC_355: @@ -7724,6 +7824,22 @@ version versionsuffix toolchain ======== ================= =============================== +.. _list_software_dm-reverb_900: + +*dm-reverb* ++++++++++++ + +Reverb is an efficient and easy-to-use data storage and transport system designed for machine learning research. Reverb is primarily used as an experience replay system for distributed reinforcement learning algorithms but the system also supports multiple data structure representations such as FIFO, LIFO, and priority queues. + +*homepage*: https://github.com/deepmind/reverb + +========= ============== +version toolchain +========= ============== +``0.2.0`` ``foss/2020b`` +========= ============== + + .. _list_software_dm-tree_686: *dm-tree* @@ -7852,13 +7968,13 @@ Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles *homepage*: https://github.com/google/double-conversion -========= ===================================== -version toolchain -========= ===================================== -``3.0.3`` ``foss/2018a`` -``3.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========= ===================================== +========= ========================================================= +version toolchain +========= ========================================================= +``3.0.3`` ``foss/2018a`` +``3.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +========= ========================================================= .. _list_software_DoubletFinder_1319: @@ -7882,9 +7998,9 @@ version versionsuffix toolchain *Doxygen* +++++++++ -Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. +Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. -*homepage*: http://www.doxygen.org +*homepage*: https://www.doxygen.org =========== ======================================================================================================================================================= version toolchain @@ -7898,6 +8014,7 @@ version toolchain ``1.8.16`` ``GCCcore/8.3.0`` ``1.8.17`` ``GCCcore/9.3.0`` ``1.8.20`` ``GCCcore/10.2.0`` +``1.9.1`` ``GCCcore/10.3.0`` =========== ======================================================================================================================================================= @@ -7917,6 +8034,22 @@ version versionsuffix toolchain ========= ============= ========== +.. _list_software_DROP_309: + +*DROP* +++++++ + +Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders + +*homepage*: https://gagneurlab-drop.readthedocs.io + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``1.0.3`` ``-R-4.0.3`` ``foss/2020b`` +========= ============= ============== + + .. _list_software_dropEst_737: *dropEst* @@ -8180,6 +8313,7 @@ version toolchain ``4.3.1`` ``system`` ``4.3.2`` ``system`` ``4.3.3`` ``system`` +``4.3.4`` ``system`` ========== ========== @@ -8333,6 +8467,7 @@ version toolchain ``3.3.5`` ``system`` ``3.3.7`` ``GCCcore/9.3.0``, ``system`` ``3.3.8`` ``GCCcore/10.2.0`` +``3.3.9`` ``GCCcore/10.3.0`` ========== =========================================== @@ -8380,11 +8515,12 @@ The elfutils project provides libraries and tools for ELF files and DWARF data. *homepage*: https://elfutils.org/ -========= ================= -version toolchain -========= ================= -``0.182`` ``GCCcore/9.3.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``0.182`` ``GCCcore/9.3.0`` +``0.183`` ``GCCcore/10.2.0`` +========= ================== .. _list_software_Elk_284: @@ -8689,7 +8825,7 @@ version versionsuffix toolchain ``7.0.2`` ``intel/2017b`` ``7.1.0r`` ``foss/2018b``, ``foss/2019a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``8.0.0`` ``foss/2019b``, ``intel/2019b`` -``8.0.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a`` +``8.0.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` ============ ================ ================================================================================= @@ -8706,6 +8842,7 @@ Earth System Modeling Framework (ESMF) Python Interface version versionsuffix toolchain ========= ================= =============== ``8.0.0`` ``-Python-3.7.4`` ``intel/2019b`` +``8.0.1`` ``intel/2020b`` ========= ================= =============== @@ -8771,6 +8908,7 @@ version versionsuffix toolchain ============ ================== =============== ``3.0.0b36`` ``-Python-2.7.12`` ``intel/2016b`` ``3.1.1`` ``-Python-3.6.6`` ``foss/2018b`` +``3.1.2`` ``-Python-3.8.2`` ``foss/2020a`` ============ ================== =============== @@ -8907,7 +9045,7 @@ version toolchain ``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.2.6`` ``GCCcore/8.2.0`` ``2.2.7`` ``GCCcore/8.3.0`` -``2.2.9`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.2.9`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ========= ========================================================================================================================= @@ -8967,7 +9105,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -9100,6 +9238,22 @@ version toolchain =========== ============== +.. _list_software_fastahack_934: + +*fastahack* ++++++++++++ + +Utilities for indexing and sequence extraction from FASTA files. + +*homepage*: https://github.com/ekg/fastahack + +========= ================= +version toolchain +========= ================= +``1.0.0`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_FastaIndex_999: *FastaIndex* @@ -9132,6 +9286,7 @@ version toolchain ``1.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``1.3`` ``iccifort/2019.5.281`` ``1.31`` ``iccifort/2020.1.217`` +``1.33`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` ======== ============================================================== @@ -9356,12 +9511,12 @@ FastTree infers approximately-maximum-likelihood phylogenetic trees from alignme *homepage*: http://www.microbesonline.org/fasttree/ -========== ================================================================= -version toolchain -========== ================================================================= -``2.1.10`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``2.1.11`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ================================================================= +========== =========================================================================== +version toolchain +========== =========================================================================== +``2.1.10`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``2.1.11`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== =========================================================================== .. _list_software_FastViromeExplorer_1873: @@ -9428,6 +9583,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_FCC_204: + +*FCC* ++++++ + +Fujitsu Compiler based compiler toolchain. + +*homepage*: (none) + +========= ========== +version toolchain +========= ========== +``4.5.0`` ``system`` +========= ========== + + .. _list_software_FCM_214: *FCM* @@ -9517,6 +9688,22 @@ version toolchain ======== ================= +.. _list_software_fermi-lite_1006: + +*fermi-lite* +++++++++++++ + +Standalone C library for assembling Illumina short reads in small regions. + +*homepage*: https://github.com/lh3/fermi-lite + +============ ================= +version toolchain +============ ================= +``20190320`` ``GCCcore/9.3.0`` +============ ================= + + .. _list_software_Ferret_616: *Ferret* @@ -9632,6 +9819,22 @@ version toolchain =========== =================================================== +.. _list_software_ffmpi_530: + +*ffmpi* ++++++++ + +Fujitsu Compiler based compiler toolchain, including Fujitsu MPI for MPI support. + +*homepage*: (none) + +========= ========== +version toolchain +========= ========== +``4.5.0`` ``system`` +========= ========== + + .. _list_software_ffnet_531: *ffnet* @@ -9676,6 +9879,7 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT ========= ============= ======================================================================================================================================================================================================================================================================================================================= version versionsuffix toolchain ========= ============= ======================================================================================================================================================================================================================================================================================================================= +``1.0.0`` ``-fujitsu`` ``FCC/4.5.0`` ``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` ``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` ``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` @@ -9685,6 +9889,7 @@ version versionsuffix toolchain ``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``iomkl/2018b`` ``3.3.8`` ``-amd`` ``gompi/2020a`` ``3.3.8`` ``-serial`` ``GCC/9.3.0`` +``3.3.9`` ``gompi/2021a`` ========= ============= ======================================================================================================================================================================================================================================================================================================================= @@ -9826,6 +10031,22 @@ version toolchain ======== ==================================== +.. _list_software_filevercmp_1069: + +*filevercmp* +++++++++++++ + +filevercmp function as in sort --version-sort. + +*homepage*: https://github.com/ekg/filevercmp + +============ ================= +version toolchain +============ ================= +``20141119`` ``GCCcore/9.3.0`` +============ ================= + + .. _list_software_Filtlong_831: *Filtlong* @@ -10045,11 +10266,11 @@ FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but l *homepage*: https://xiph.org/flac/ -========= ================== -version toolchain -========= ================== -``1.3.3`` ``GCCcore/10.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.3.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_FLAIR_366: @@ -10189,7 +10410,7 @@ version toolchain ``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``2.6.2`` ``intel/2016b`` ``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` -``2.6.4`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` +``2.6.4`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` ========== ======================================================================================================================================================================================================================================================================================================================================================================================= @@ -10209,6 +10430,22 @@ version toolchain ========= ============== +.. _list_software_FlexiBLAS_794: + +*FlexiBLAS* ++++++++++++ + +FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it. + +*homepage*: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release + +========= ============== +version toolchain +========= ============== +``3.0.4`` ``GCC/10.3.0`` +========= ============== + + .. _list_software_FlexiDot_799: *FlexiDot* @@ -10307,15 +10544,16 @@ Flye is a de novo assembler for long and noisy reads, such as those produced by *homepage*: https://github.com/fenderglass/Flye -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``2.4`` ``-Python-2.7.15`` ``intel/2018b`` -``2.6`` ``-Python-3.7.2`` ``foss/2019a`` -``2.6`` ``-Python-3.7.4`` ``intel/2019b`` -``2.8.1`` ``-Python-3.8.2`` ``intel/2020a`` -``2.8.2`` ``-Python-3.8.2`` ``foss/2020a`` -========= ================== =============== +========= ================== ======================================= +version versionsuffix toolchain +========= ================== ======================================= +``2.4`` ``-Python-2.7.15`` ``intel/2018b`` +``2.6`` ``-Python-3.7.2`` ``foss/2019a`` +``2.6`` ``-Python-3.7.4`` ``intel/2019b`` +``2.8.1`` ``-Python-3.8.2`` ``intel/2020a`` +``2.8.2`` ``-Python-3.8.2`` ``foss/2020a`` +``2.8.3`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +========= ================== ======================================= .. _list_software_FMILibrary_945: @@ -10410,6 +10648,7 @@ version versionsuffix toolchain ``2.13.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.13.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.13.92`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.13.93`` ``GCCcore/10.3.0`` =========== ================== ====================================================================================== @@ -10456,6 +10695,7 @@ version toolchain ``2019b`` ``system`` ``2020a`` ``system`` ``2020b`` ``system`` +``2021a`` ``system`` =========== ========== @@ -10571,11 +10811,11 @@ FragGeneScan is an application for finding (fragmented) genes in short reads. *homepage*: http://omics.informatics.indiana.edu/FragGeneScan/ -======== ================================= -version toolchain -======== ================================= -``1.31`` ``GCCcore/8.2.0``, ``foss/2018b`` -======== ================================= +======== ===================================================== +version toolchain +======== ===================================================== +``1.31`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``foss/2018b`` +======== ===================================================== .. _list_software_FRANz_417: @@ -10626,7 +10866,7 @@ version versionsuffix toolchain ========= ================ ====================================================================================================================================================================================== ``3.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` -``3.2.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``3.2.1`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ================ ====================================================================================================================================================================================== @@ -10708,9 +10948,26 @@ version versionsuffix toolchain ``2.9.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.10.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.10.3`` ``GCCcore/10.2.0`` +``2.10.4`` ``GCCcore/10.3.0`` ========== ================== ====================================================================== +.. _list_software_freetype-py_1146: + +*freetype-py* ++++++++++++++ + +Python binding for the freetype library + +*homepage*: https://github.com/rougier/freetype-py + +========= ================= ================= +version versionsuffix toolchain +========= ================= ================= +``2.2.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +========= ================= ================= + + .. _list_software_FreeXL_550: *FreeXL* @@ -10824,6 +11081,22 @@ version versionsuffix toolchain ========== ================== =============== +.. _list_software_fsom_437: + +*fsom* +++++++ + +A tiny C library for managing SOM (Self-Organizing Maps) neural networks. + +*homepage*: https://github.com/ekg/fsom + +============ ================= +version toolchain +============ ================= +``20141119`` ``GCCcore/9.3.0`` +============ ================= + + .. _list_software_FTGL_301: *FTGL* @@ -10840,6 +11113,22 @@ version toolchain ============= ====================================================================================== +.. _list_software_Fujitsu_746: + +*Fujitsu* ++++++++++ + +Toolchain using Fujitsu compilers and libraries. + +*homepage*: (none) + +========= ========== +version toolchain +========= ========== +``21.05`` ``system`` +========= ========== + + .. _list_software_fullrmc_757: *fullrmc* @@ -10964,7 +11253,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -11117,6 +11406,22 @@ version toolchain ======== =============== +.. _list_software_garnett_757: + +*garnett* ++++++++++ + +Garnett is a software package that faciliates automated cell type classification from single-cell expression data. + +*homepage*: https://cole-trapnell-lab.github.io/garnett + +========== ============= ============== +version versionsuffix toolchain +========== ============= ============== +``0.1.20`` ``-R-4.0.3`` ``foss/2020b`` +========== ============= ============== + + .. _list_software_GAT_220: *GAT* @@ -11166,43 +11471,45 @@ The Genome Analysis Toolkit or GATK is a software package developed at the Broad *homepage*: https://www.broadinstitute.org/gatk/ -============ =================== ================= -version versionsuffix toolchain -============ =================== ================= -``1.0.5083`` ``system`` -``2.5-2`` ``-Java-1.7.0_10`` ``system`` -``2.6-5`` ``-Java-1.7.0_10`` ``system`` -``2.7-4`` ``system`` -``2.7-4`` ``-Java-1.7.0_10`` ``system`` -``2.8-1`` ``-Java-1.7.0_10`` ``system`` -``3.0-0`` ``-Java-1.7.0_10`` ``system`` -``3.3-0`` ``-Java-1.7.0_21`` ``system`` -``3.3-0`` ``-Java-1.7.0_80`` ``system`` -``3.3-0`` ``-Java-1.8.0_66`` ``system`` -``3.5`` ``-Java-1.8.0_66`` ``system`` -``3.5`` ``-Java-1.8.0_74`` ``system`` -``3.6`` ``-Java-1.8.0_92`` ``system`` -``3.7`` ``-Java-1.8.0_112`` ``system`` -``3.8-0`` ``-Java-1.8.0_144`` ``system`` -``4.0.1.2`` ``-Java-1.8`` ``system`` -``4.0.4.0`` ``-Python-2.7.14`` ``intel/2018a`` -``4.0.4.0`` ``-Python-3.6.4`` ``intel/2018a`` -``4.0.5.1`` ``-Python-3.6.4`` ``foss/2018a`` -``4.0.7.0`` ``-Python-2.7.14`` ``intel/2018a`` -``4.0.7.0`` ``-Python-3.6.4`` ``intel/2018a`` -``4.0.8.1`` ``-Python-2.7.15`` ``foss/2018b`` -``4.0.8.1`` ``-Python-3.6.6`` ``foss/2018b`` -``4.0.10.0`` ``-Python-3.6.6`` ``foss/2018b`` -``4.0.12.0`` ``-Python-3.6.6`` ``foss/2018b`` -``4.1.0.0`` ``-Python-3.6.6`` ``foss/2018b`` -``4.1.2.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` -``4.1.3.0`` ``-Java-1.8`` ``GCCcore/8.3.0`` -``4.1.4.1`` ``-Java-1.8`` ``GCCcore/8.3.0`` -``4.1.4.1`` ``-Java-11`` ``GCCcore/8.3.0`` -``4.1.5.0`` ``-Java-1.8`` ``GCCcore/9.3.0`` -``4.1.5.0`` ``-Java-11`` ``GCCcore/9.3.0`` -``4.1.8.1`` ``-Java-1.8`` ``GCCcore/9.3.0`` -============ =================== ================= +============ =================== ================== +version versionsuffix toolchain +============ =================== ================== +``1.0.5083`` ``system`` +``2.5-2`` ``-Java-1.7.0_10`` ``system`` +``2.6-5`` ``-Java-1.7.0_10`` ``system`` +``2.7-4`` ``system`` +``2.7-4`` ``-Java-1.7.0_10`` ``system`` +``2.8-1`` ``-Java-1.7.0_10`` ``system`` +``3.0-0`` ``-Java-1.7.0_10`` ``system`` +``3.3-0`` ``-Java-1.7.0_21`` ``system`` +``3.3-0`` ``-Java-1.7.0_80`` ``system`` +``3.3-0`` ``-Java-1.8.0_66`` ``system`` +``3.5`` ``-Java-1.8.0_66`` ``system`` +``3.5`` ``-Java-1.8.0_74`` ``system`` +``3.6`` ``-Java-1.8.0_92`` ``system`` +``3.7`` ``-Java-1.8.0_112`` ``system`` +``3.8-0`` ``-Java-1.8.0_144`` ``system`` +``4.0.1.2`` ``-Java-1.8`` ``system`` +``4.0.4.0`` ``-Python-2.7.14`` ``intel/2018a`` +``4.0.4.0`` ``-Python-3.6.4`` ``intel/2018a`` +``4.0.5.1`` ``-Python-3.6.4`` ``foss/2018a`` +``4.0.7.0`` ``-Python-2.7.14`` ``intel/2018a`` +``4.0.7.0`` ``-Python-3.6.4`` ``intel/2018a`` +``4.0.8.1`` ``-Python-2.7.15`` ``foss/2018b`` +``4.0.8.1`` ``-Python-3.6.6`` ``foss/2018b`` +``4.0.10.0`` ``-Python-3.6.6`` ``foss/2018b`` +``4.0.12.0`` ``-Python-3.6.6`` ``foss/2018b`` +``4.1.0.0`` ``-Python-3.6.6`` ``foss/2018b`` +``4.1.2.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` +``4.1.3.0`` ``-Java-1.8`` ``GCCcore/8.3.0`` +``4.1.4.1`` ``-Java-1.8`` ``GCCcore/8.3.0`` +``4.1.4.1`` ``-Java-11`` ``GCCcore/8.3.0`` +``4.1.5.0`` ``-Java-1.8`` ``GCCcore/9.3.0`` +``4.1.5.0`` ``-Java-11`` ``GCCcore/9.3.0`` +``4.1.8.1`` ``-Java-1.8`` ``GCCcore/9.3.0`` +``4.2.0.0`` ``-Java-1.8`` ``GCCcore/10.2.0`` +``4.2.0.0`` ``-Java-11`` ``GCCcore/10.2.0`` +============ =================== ================== .. _list_software_Gaussian_827: @@ -11222,6 +11529,22 @@ version versionsuffix toolchain =========== ============= ========== +.. _list_software_gawk_426: + +*gawk* +++++++ + +The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code. + +*homepage*: https://www.gnu.org/software/gawk + +========= ============== +version toolchain +========= ============== +``5.1.0`` ``GCC/10.2.0`` +========= ============== + + .. _list_software_Gblocks_709: *Gblocks* @@ -11372,6 +11695,8 @@ version versionsuffix toolchain ``9.3.0`` ``system`` ``10.1.0`` ``system`` ``10.2.0`` ``system`` +``10.3.0`` ``system`` +``11.1.0`` ``system`` ``system`` ``system`` ``system`` ``-2.29`` ``system`` ========== =================== ========== @@ -11412,6 +11737,8 @@ version toolchain ``9.3.0`` ``system`` ``10.1.0`` ``system`` ``10.2.0`` ``system`` +``10.3.0`` ``system`` +``11.1.0`` ``system`` ``system`` ``system`` ========== ========== @@ -11552,6 +11879,7 @@ version versionsuffix toolchain ``8.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``9.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``10.1`` ``GCCcore/10.2.0`` +``10.2`` ``GCCcore/10.3.0`` ========== ================== =============================== @@ -11592,7 +11920,7 @@ version toolchain *gdc-client* ++++++++++++ -The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS. +The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS. *homepage*: https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool @@ -11602,6 +11930,7 @@ version versionsuffix toolchain ``1.0.1`` ``-Python-2.7.12`` ``intel/2016b`` ``1.3.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` ``1.3.0`` ``-Python-2.7.15`` ``foss/2018b`` +``1.6.0`` ``GCCcore/10.2.0`` ========= ================== =============================== @@ -11707,12 +12036,13 @@ A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. *homepage*: https://github.com/NVIDIA/gdrcopy -======= ================ ================== -version versionsuffix toolchain -======= ================ ================== -``2.1`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` -``2.1`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` -======= ================ ================== +======= ================ ====================================== +version versionsuffix toolchain +======= ================ ====================================== +``2.1`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` +``2.1`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` +``2.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +======= ================ ====================================== .. _list_software_Geant4_547: @@ -11736,6 +12066,7 @@ version toolchain ``10.5`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018b`` ``10.6`` ``foss/2019b`` ``10.6.2`` ``foss/2020a`` +``10.7.1`` ``GCC/10.2.0`` ============= ================================================================ @@ -11752,6 +12083,7 @@ Datasets for Geant4. version toolchain ============ ========== ``20201103`` ``system`` +``20210510`` ``system`` ============ ========== @@ -11804,6 +12136,22 @@ version toolchain ========== ============================== +.. _list_software_gemmi_527: + +*gemmi* ++++++++ + +Gemmi is a library, accompanied by a set of programs, developed primarily for use in macromolecular crystallography (MX). For working with: macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files), refinement restraints (CIF files), reflection data (MTZ and mmCIF formats), data on a 3D grid (electron density maps, masks, MRC/CCP4 format) crystallographic symmetry. Parts of this library can be useful in structural bioinformatics (for symmetry- aware analysis of protein models), and in other molecular-structure sciences that use CIF files (we have the fastest open-source CIF parser). + +*homepage*: https://gemmi.readthedocs.io/ + +========= ================== +version toolchain +========= ================== +``0.4.5`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_gencore_variant_detection_2645: *gencore_variant_detection* @@ -11829,12 +12177,13 @@ Eukaryotic gene prediction suite with automatic training *homepage*: http://exon.gatech.edu/GeneMark -======== ================= -version toolchain -======== ================= -``4.38`` ``GCCcore/8.2.0`` -``4.57`` ``GCCcore/8.3.0`` -======== ================= +======== ================== +version toolchain +======== ================== +``4.38`` ``GCCcore/8.2.0`` +``4.57`` ``GCCcore/8.3.0`` +``4.65`` ``GCCcore/10.2.0`` +======== ================== .. _list_software_gengetopt_973: @@ -11846,11 +12195,11 @@ Gengetopt is a tool to write command line option parsing code for C programs. *homepage*: https://www.gnu.org/software/gengetopt/gengetopt.html -======== ================= -version toolchain -======== ================= -``2.23`` ``GCCcore/9.3.0`` -======== ================= +======== ===================================== +version toolchain +======== ===================================== +``2.23`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +======== ===================================== .. _list_software_Genome_Profiler_1533: @@ -12021,6 +12370,22 @@ version versionsuffix toolchain ========== ================= =============== +.. _list_software_georges_748: + +*georges* ++++++++++ + +Georges the lemur opinionated particle accelerator modeling Python package. Also a thin wrapper over MAD-X/PTC, BDSim and G4Beamline. + +*homepage*: https://github.com/ULB-Metronu/georges + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``2019.2`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== + + .. _list_software_GEOS_302: *GEOS* @@ -12121,7 +12486,7 @@ version versionsuffix toolchain ``0.19.8.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` ``0.19.8.1`` ``-libxml2-2.9.7`` ``GCCcore/6.4.0`` ``0.20.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` -``0.21`` ``GCCcore/10.2.0``, ``system`` +``0.21`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``system`` ============ ================== =================================================================================================== @@ -12132,15 +12497,15 @@ version versionsuffix toolchain GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files. -*homepage*: https://github.com/gpertea/gffcompare +*homepage*: https://ccb.jhu.edu/software/stringtie/gffcompare.shtml -========== ================= -version toolchain -========== ================= -``0.10.1`` ``foss/2016b`` -``0.10.6`` ``GCCcore/7.3.0`` -``0.11.6`` ``GCCcore/8.3.0`` -========== ================= +========== ==================================== +version toolchain +========== ==================================== +``0.10.1`` ``foss/2016b`` +``0.10.6`` ``GCCcore/7.3.0`` +``0.11.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ==================================== .. _list_software_gffread_719: @@ -12152,13 +12517,13 @@ GFF/GTF parsing utility providing format conversions, region filtering, FASTA se *homepage*: https://github.com/gpertea/gffread -========== ================= -version toolchain -========== ================= -``0.9.12`` ``foss/2016b`` -``0.10.6`` ``GCCcore/7.3.0`` -``0.11.6`` ``GCCcore/8.3.0`` -========== ================= +========== ==================================== +version toolchain +========== ==================================== +``0.9.12`` ``foss/2016b`` +``0.10.6`` ``GCCcore/7.3.0`` +``0.11.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ==================================== .. _list_software_gflags_628: @@ -12263,12 +12628,12 @@ giflib is a library for reading and writing gif images. It is API and ABI compat *homepage*: http://giflib.sourceforge.net/ -========= ======================================================== -version toolchain -========= ======================================================== -``5.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``5.2.1`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ======================================================== +========= ============================================================================ +version toolchain +========= ============================================================================ +``5.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``5.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ============================================================================ .. _list_software_gifsicle_838: @@ -12488,6 +12853,7 @@ version versionsuffix toolchain ``3.0.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``3.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``3.1.9`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``3.1.14`` ``GCCcore/10.2.0`` ========== ================= =============================== @@ -12566,15 +12932,18 @@ version versionsuffix toolchain *glew* ++++++ -The OpenGL Extension Wrangler Library The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. OpenGL core and extension functionality is exposed in a single header file. GLEW has been tested on a variety of operating systems, including Windows, Linux, Mac OS X, FreeBSD, Irix, and Solaris. +The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. -*homepage*: http://glew.sourceforge.net/ +*homepage*: https://github.com/nigels-com/glew -========= ======================================================================= -version toolchain -========= ======================================================================= -``2.1.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b`` -========= ======================================================================= +========= ============= =========================================================================================== +version versionsuffix toolchain +========= ============= =========================================================================================== +``2.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b`` +``2.2.0`` ``-egl`` ``GCCcore/10.2.0`` +``2.2.0`` ``-glx`` ``GCCcore/10.2.0`` +``2.2.0`` ``-osmesa`` ``GCCcore/10.2.0`` +========= ============= =========================================================================================== .. _list_software_GLFW_304: @@ -12620,6 +12989,7 @@ version toolchain ``2.62.0`` ``GCCcore/8.3.0`` ``2.64.1`` ``GCCcore/9.3.0`` ``2.66.1`` ``GCCcore/10.2.0`` +``2.68.2`` ``GCCcore/10.3.0`` ========== ================================================= @@ -12699,14 +13069,14 @@ OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics s *homepage*: https://github.com/g-truc/glm -=========== ==================================== -version toolchain -=========== ==================================== -``0.9.7.6`` ``intel/2016a`` -``0.9.8.3`` ``GCCcore/5.4.0``, ``GCCcore/7.3.0`` -``0.9.9.0`` ``GCCcore/6.4.0`` -``0.9.9.8`` ``GCCcore/8.3.0`` -=========== ==================================== +=========== ===================================== +version toolchain +=========== ===================================== +``0.9.7.6`` ``intel/2016a`` +``0.9.8.3`` ``GCCcore/5.4.0``, ``GCCcore/7.3.0`` +``0.9.9.0`` ``GCCcore/6.4.0`` +``0.9.9.8`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +=========== ===================================== .. _list_software_GlobalArrays_1219: @@ -12795,6 +13165,7 @@ version toolchain ``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` ``4.61`` ``intel/2017a`` ``4.65`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``5.0`` ``GCCcore/10.3.0`` ======== ================================================================================================================= @@ -12872,6 +13243,7 @@ version toolchain ``6.1.1`` ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``6.1.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b`` ``6.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``6.2.1`` ``GCCcore/10.3.0`` ========== ===================================================================================================================================================== @@ -13086,6 +13458,7 @@ version toolchain ``1.13.1`` ``system`` ``1.14`` ``system`` ``1.14.1`` ``system`` +``1.16.3`` ``system`` ========== ================= @@ -13203,6 +13576,7 @@ version toolchain ``2019a`` ``system`` ``2020a`` ``system`` ``2020b`` ``system`` +``2021a`` ``system`` ========= ========== @@ -13233,6 +13607,7 @@ version versionsuffix toolchain ``2019b`` ``system`` ``2020a`` ``system`` ``2020b`` ``system`` +``2021a`` ``system`` ``system`` ``-2.29`` ``system`` =========== ============= ========== @@ -13289,7 +13664,7 @@ version toolchain ========== ===================================================================== ``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b`` ``1.8.1`` ``GCCcore/8.2.0`` -``1.10.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.10.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ===================================================================== @@ -13375,12 +13750,12 @@ GNU gperf is a perfect hash function generator. For a given list of strings, it *homepage*: https://www.gnu.org/software/gperf/ -========= ========================================================================================================================= -version toolchain -========= ========================================================================================================================= -``3.0.4`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``3.1`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ========================================================================================================================= +========= ===================================================================================================================================== +version toolchain +========= ===================================================================================================================================== +``3.0.4`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``3.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ===================================================================================================================================== .. _list_software_gperftools_1093: @@ -13415,10 +13790,27 @@ dstat-like utilization monitor for NVIDIA GPUs version versionsuffix toolchain ========= ================== ================== ``0.5.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``0.6.0`` ``gcccuda/2020b`` ``0.6.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ================== ================== +.. _list_software_GPyOpt_579: + +*GPyOpt* +++++++++ + +GPyOpt is a Python open-source library for Bayesian Optimization + +*homepage*: https://sheffieldml.github.io/GPyOpt + +========= =============== +version toolchain +========= =============== +``1.2.6`` ``intel/2020b`` +========= =============== + + .. _list_software_GPyTorch_784: *GPyTorch* @@ -13623,6 +14015,7 @@ version versionsuffix toolchain ``2.42.2`` ``-Python-3.7.4`` ``foss/2019b`` ``2.44.1`` ``-Java-11`` ``GCCcore/9.3.0`` ``2.44.1`` ``-Java-11-Python-3.8.2`` ``GCCcore/9.3.0`` +``2.47.0`` ``-Java-11`` ``GCCcore/10.2.0`` ========== ========================= =============================== @@ -13787,11 +14180,11 @@ Groff (GNU troff) is a typesetting system that reads plain text mixed with forma *homepage*: https://www.gnu.org/software/groff -========== ======================================================== -version toolchain -========== ======================================================== -``1.22.4`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ======================================================== +========== =========================================================================================== +version toolchain +========== =========================================================================================== +``1.22.4`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== =========================================================================================== .. _list_software_GroIMP_526: @@ -13851,6 +14244,7 @@ version versionsuffix toolchain ``2020.4`` ``-Python-3.8.2`` ``foss/2020a`` ``2020.5`` ``-Python-3.8.2`` ``fosscuda/2020a`` ``2021`` ``foss/2020b``, ``fosscuda/2020b`` +``2021.2`` ``fosscuda/2020b`` ========== ================= ============================================================================================================ @@ -14006,6 +14400,7 @@ version toolchain ``1.8.3`` ``foss/2016a`` ``1.16.0`` ``GCC/8.2.0-2.31.1`` ``1.16.2`` ``GCC/8.3.0`` +``1.18.4`` ``GCC/10.2.0`` =========== ================================================================================================================== @@ -14027,6 +14422,7 @@ version toolchain ``1.15.1`` ``fosscuda/2018b`` ``1.16.0`` ``GCC/8.2.0-2.31.1`` ``1.16.2`` ``GCC/8.3.0`` +``1.18.4`` ``GCC/10.2.0`` =========== ================================================================================================================== @@ -14046,6 +14442,7 @@ version versionsuffix toolchain ``0.3.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ``1.0.2`` ``-Python-3.7.4`` ``intel/2019b`` ``1.3.0`` ``-Python-3.8.2`` ``intel/2020a`` +``1.5.0`` ``intel/2020b`` ========= ================== =============================== @@ -14195,7 +14592,7 @@ version toolchain *Gurobi* ++++++++ -The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. +The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. *homepage*: https://www.gurobi.com @@ -14212,8 +14609,10 @@ version versionsuffix toolchain ``9.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``9.0.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``9.0.1`` ``system`` +``9.0.3`` ``GCCcore/10.2.0``, ``system`` ``9.1.0`` ``system`` ``9.1.1`` ``GCCcore/10.2.0`` +``9.1.2`` ``GCCcore/10.2.0``, ``system`` ========= ================= =============================== @@ -14226,13 +14625,13 @@ gzip (GNU zip) is a popular data compression program as a replacement for compre *homepage*: http://www.gnu.org/software/gzip/ -======== =========================================================================== -version toolchain -======== =========================================================================== -``1.8`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``1.9`` ``GCCcore/7.3.0`` -``1.10`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======== =========================================================================== +======== =============================================================================================== +version toolchain +======== =============================================================================================== +``1.8`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``1.9`` ``GCCcore/7.3.0`` +``1.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======== =============================================================================================== .. _list_software_letter_h: @@ -14241,7 +14640,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -14332,18 +14731,19 @@ Hadoop MapReduce by Cloudera *homepage*: https://archive.cloudera.com/cdh5/cdh/5/ -=================== ========================== ===================================== -version versionsuffix toolchain -=================== ========================== ===================================== -``2.4.0`` ``-seagate-722af1-native`` ``system`` -``2.5.0-cdh5.3.1`` ``-native`` ``system`` -``2.6.0-cdh5.4.5`` ``-native`` ``system`` -``2.6.0-cdh5.7.0`` ``-native`` ``system`` -``2.6.0-cdh5.8.0`` ``-native`` ``system`` -``2.6.0-cdh5.12.0`` ``-native`` ``system`` -``2.9.2`` ``-native`` ``GCCcore/7.3.0`` -``2.10.0`` ``-native`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` -=================== ========================== ===================================== +=================== ========================== ================== +version versionsuffix toolchain +=================== ========================== ================== +``2.4.0`` ``-seagate-722af1-native`` ``system`` +``2.5.0-cdh5.3.1`` ``-native`` ``system`` +``2.6.0-cdh5.4.5`` ``-native`` ``system`` +``2.6.0-cdh5.7.0`` ``-native`` ``system`` +``2.6.0-cdh5.8.0`` ``-native`` ``system`` +``2.6.0-cdh5.12.0`` ``-native`` ``system`` +``2.9.2`` ``-native`` ``GCCcore/7.3.0`` +``2.10.0`` ``-native`` ``GCCcore/8.3.0`` +``2.10.0`` ``-native-Java-1.8`` ``GCCcore/10.2.0`` +=================== ========================== ================== .. _list_software_hanythingondemand_1808: @@ -14570,6 +14970,7 @@ version versionsuffix toolchain ``1.10.1`` ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2017b``, ``iomkl/2018a`` ``1.10.2`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``1.10.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompic/2019a``, ``gompic/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpic/2019a``, ``iimpic/2019b``, ``iompi/2019b`` +``1.10.5`` ``-serial`` ``GCCcore/8.3.0`` ``1.10.6`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpic/2020a`` ``1.10.7`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpic/2020b`` ``1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` @@ -14694,6 +15095,7 @@ version toolchain ``1.47.12`` ``GCCcore/9.3.0`` ``1.47.15`` ``GCCcore/10.1.0`` ``1.47.16`` ``GCCcore/10.2.0`` +``1.48.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0`` =========== ================================================================================================================================================================================== @@ -14763,6 +15165,22 @@ version versionsuffix toolchain ========= ========================= ============== +.. _list_software_hifiasm_737: + +*hifiasm* ++++++++++ + +Hifiasm: a haplotype-resolved assembler for accurate Hifi reads. + +*homepage*: https://github.com/chhylp123/hifiasm + +========== ================= +version toolchain +========== ================= +``0.15.2`` ``GCCcore/9.3.0`` +========== ================= + + .. _list_software_HIPS_308: *HIPS* @@ -14847,7 +15265,7 @@ version toolchain ``3.1b2`` ``GCC/6.4.0-2.28``, ``foss/2016a``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a``, ``intel/2018a`` ``3.2.1`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iimpi/2019b``, ``intel/2018b`` ``3.3.1`` ``gompi/2020a``, ``iimpi/2020a`` -``3.3.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b`` +``3.3.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020b`` ========= ============================================================================================================================================ @@ -14909,21 +15327,23 @@ Horovod is a distributed training framework for TensorFlow. *homepage*: https://github.com/uber/horovod -========== =================================== ================== -version versionsuffix toolchain -========== =================================== ================== -``0.9.10`` ``-Python-3.6.3`` ``intel/2017b`` -``0.18.1`` ``-Python-3.7.2`` ``foss/2019a`` -``0.18.2`` ``-TensorFlow-1.15.0-Python-3.7.4`` ``fosscuda/2019b`` -``0.18.2`` ``-TensorFlow-1.15.2-Python-3.7.4`` ``fosscuda/2019b`` -``0.18.2`` ``-TensorFlow-2.0.0-Python-3.7.4`` ``fosscuda/2019b`` -``0.19.1`` ``-TensorFlow-2.1.0-Python-3.7.4`` ``fosscuda/2019b`` -``0.19.5`` ``-TensorFlow-2.2.0-Python-3.7.4`` ``fosscuda/2019b`` -``0.20.3`` ``-TensorFlow-2.3.1-Python-3.7.4`` ``fosscuda/2019b`` -``0.21.1`` ``-PyTorch-1.7.1-Python-3.7.4`` ``fosscuda/2019b`` -``0.21.1`` ``-TensorFlow-2.4.1`` ``fosscuda/2020b`` -``0.21.1`` ``-TensorFlow-2.4.1-Python-3.7.4`` ``fosscuda/2019b`` -========== =================================== ================== +========== =================================== ================================== +version versionsuffix toolchain +========== =================================== ================================== +``0.9.10`` ``-Python-3.6.3`` ``intel/2017b`` +``0.18.1`` ``-Python-3.7.2`` ``foss/2019a`` +``0.18.2`` ``-TensorFlow-1.15.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.18.2`` ``-TensorFlow-1.15.2-Python-3.7.4`` ``fosscuda/2019b`` +``0.18.2`` ``-TensorFlow-2.0.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.19.1`` ``-TensorFlow-2.1.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.19.5`` ``-TensorFlow-2.2.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.20.3`` ``-TensorFlow-2.3.1-Python-3.7.4`` ``fosscuda/2019b`` +``0.21.1`` ``-PyTorch-1.7.1-Python-3.7.4`` ``fosscuda/2019b`` +``0.21.1`` ``-TensorFlow-2.4.1`` ``fosscuda/2020b`` +``0.21.1`` ``-TensorFlow-2.4.1-Python-3.7.4`` ``fosscuda/2019b`` +``0.21.3`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` +``0.21.3`` ``-TensorFlow-2.3.1-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +========== =================================== ================================== .. _list_software_horton_666: @@ -15005,7 +15425,7 @@ version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020a``, ``intel/2020b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -15148,6 +15568,7 @@ version toolchain ``2.0.3`` ``GCCcore/8.3.0`` ``2.1.0`` ``GCCcore/9.2.0`` ``2.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.4.1`` ``GCCcore/10.3.0`` =========== ===================================================================================================================================================================================================================================================== @@ -15253,6 +15674,8 @@ version versionsuffix toolchain ``5.6.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``5.41.2`` ``GCCcore/10.2.0`` ``5.41.5`` ``GCCcore/10.2.0`` +``6.7.0`` ``GCCcore/10.2.0`` +``6.13.1`` ``GCCcore/10.3.0`` ========== ================= ================================== @@ -15282,7 +15705,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -15536,11 +15959,11 @@ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequen *homepage*: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/ -========= =================================================================== -version toolchain -========= =================================================================== -``1.1.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``foss/2018a``, ``foss/2018b`` -========= =================================================================== +========= ================================================================================================== +version toolchain +========= ================================================================================================== +``1.1.3`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` +========= ================================================================================================== .. _list_software_ieeg-cli_767: @@ -15648,7 +16071,7 @@ version toolchain ``0.8.0`` ``foss/2019b`` ``0.8.2`` ``foss/2020a`` ``0.8.5`` ``foss/2020b`` -``0.9.1`` ``fosscuda/2020b`` +``0.9.1`` ``foss/2020b``, ``fosscuda/2020b`` ========= ================================================ @@ -15668,6 +16091,7 @@ version versionsuffix toolchain ``2.3.80`` ``-Java-1.7.0_80`` ``system`` ``2.5.0`` ``-Java-11`` ``system`` ``2.8.0`` ``-Java-11`` ``system`` +``2.9.4`` ``-Java-11`` ``system`` ========== ================== ========== @@ -15779,8 +16203,10 @@ version versionsuffix toolchain ``2019b`` ``system`` ``2020.00`` ``system`` ``2020.06-impi-18.5`` ``system`` +``2020.12`` ``system`` ``2020a`` ``system`` ``2020b`` ``system`` +``2021a`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ===================== ==================== ========== @@ -15934,12 +16360,12 @@ imake is a Makefile-generator that is intended to make it easier to develop soft *homepage*: https://www.x.org/ -========= ================== -version toolchain -========= ================== -``1.0.7`` ``intel/2016a`` -``1.0.8`` ``GCCcore/10.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.0.7`` ``intel/2016a`` +``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_IMB_216: @@ -16002,9 +16428,9 @@ version versionsuffix toolchain *imkl* ++++++ -Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. +Intel oneAPI Math Kernel Library -*homepage*: https://software.intel.com/mkl +*homepage*: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html ============== ============= ====================================================================================================================================================================================================================================================================== version versionsuffix toolchain @@ -16033,6 +16459,8 @@ version versionsuffix toolchain ``2020.0.166`` ``iimpi/2020.00`` ``2020.1.217`` ``gompi/2020a``, ``iimpi/2020.06-impi-18.5``, ``iimpi/2020a``, ``iimpic/2020a``, ``iompi/2020a`` ``2020.4.304`` ``gompi/2020b``, ``iimpi/2020b``, ``iimpic/2020b``, ``iompi/2020b`` +``2021.1.1`` ``iimpi/2020.12`` +``2021.2.0`` ``gompi/2021a``, ``iimpi/2021a`` ============== ============= ====================================================================================================================================================================================================================================================================== @@ -16093,44 +16521,46 @@ The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing librar *homepage*: http://software.intel.com/en-us/intel-mpi-library/ -============== ============= ================================================================================================================================================================================================================================ -version versionsuffix toolchain -============== ============= ================================================================================================================================================================================================================================ -``3.2.2.006`` ``system`` -``4.0.0.028`` ``system`` -``4.0.0.028`` ``-32bit`` ``system`` -``4.0.2.003`` ``system`` -``4.1.0.027`` ``system`` -``4.1.0.030`` ``system`` -``4.1.1.036`` ``system`` -``4.1.2.040`` ``system`` -``4.1.3.045`` ``system`` -``4.1.3.049`` ``GCC/4.8.3``, ``system`` -``5.0.3.048`` ``GCC/4.9.3`` -``5.1.1.109`` ``iccifort/2016.0.109-GCC-4.9.3-2.25`` -``5.1.2.150`` ``iccifort/2016.1.150-GCC-4.9.3-2.25`` -``5.1.3.181`` ``iccifort/2016.2.181-GCC-4.9.3-2.25``, ``iccifort/2016.2.181-GCC-5.3.0-2.26``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.3.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``iccifortcuda/2016.10`` -``2017.0.098`` ``iccifort/2017.0.098-GCC-5.4.0-2.26`` -``2017.1.132`` ``GCC/5.4.0-2.26``, ``iccifort/2017.1.132-GCC-5.4.0-2.26``, ``iccifort/2017.1.132-GCC-6.3.0-2.27`` -``2017.2.174`` ``iccifort/2017.2.174-GCC-6.3.0-2.27`` -``2017.3.196`` ``GCC/6.4.0-2.28``, ``gcccuda/2017b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifortcuda/2017.4.196-GCC-6.4.0-2.28`` -``2017.4.239`` ``iccifort/2017.5.239-GCC-6.4.0-2.28`` -``2018.0.128`` ``iccifort/2018.0.128-GCC-6.4.0-2.28`` -``2018.1.163`` ``GCC/6.4.0-2.28``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` -``2018.2.199`` ``iccifort/2018.2.199-GCC-6.4.0-2.28`` -``2018.3.222`` ``GCC/7.3.0-2.30``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` -``2018.4.274`` ``iccifort/2018.5.274-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifortcuda/2019a`` -``2018.5.288`` ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifortcuda/2019b`` -``2019.0.117`` ``iccifort/2019.0.117-GCC-8.2.0-2.31.1`` -``2019.1.144`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2019.2.187`` ``iccifort/2019.2.187-GCC-8.2.0-2.31.1`` -``2019.3.199`` ``iccifort/2019.3.199-GCC-8.3.0-2.32`` -``2019.6.166`` ``iccifort/2020.0.166-GCC-9.2.0`` -``2019.7.217`` ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` -``2019.9.304`` ``iccifort/2020.4.304``, ``iccifortcuda/2020b`` -``2021.1.1`` ``intel-compilers/2021.1.2`` -``system`` ``iccifort/system-GCC-system-2.29`` -============== ============= ================================================================================================================================================================================================================================ +=============== ============= ================================================================================================================================================================================================================================ +version versionsuffix toolchain +=============== ============= ================================================================================================================================================================================================================================ +``3.2.2.006`` ``system`` +``4.0.0.028`` ``system`` +``4.0.0.028`` ``-32bit`` ``system`` +``4.0.2.003`` ``system`` +``4.1.0.027`` ``system`` +``4.1.0.030`` ``system`` +``4.1.1.036`` ``system`` +``4.1.2.040`` ``system`` +``4.1.3.045`` ``system`` +``4.1.3.049`` ``GCC/4.8.3``, ``system`` +``5.0.3.048`` ``GCC/4.9.3`` +``5.1.1.109`` ``iccifort/2016.0.109-GCC-4.9.3-2.25`` +``5.1.2.150`` ``iccifort/2016.1.150-GCC-4.9.3-2.25`` +``5.1.3.181`` ``iccifort/2016.2.181-GCC-4.9.3-2.25``, ``iccifort/2016.2.181-GCC-5.3.0-2.26``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.3.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``iccifortcuda/2016.10`` +``2017.0.098`` ``iccifort/2017.0.098-GCC-5.4.0-2.26`` +``2017.1.132`` ``GCC/5.4.0-2.26``, ``iccifort/2017.1.132-GCC-5.4.0-2.26``, ``iccifort/2017.1.132-GCC-6.3.0-2.27`` +``2017.2.174`` ``iccifort/2017.2.174-GCC-6.3.0-2.27`` +``2017.3.196`` ``GCC/6.4.0-2.28``, ``gcccuda/2017b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifortcuda/2017.4.196-GCC-6.4.0-2.28`` +``2017.4.239`` ``iccifort/2017.5.239-GCC-6.4.0-2.28`` +``2018.0.128`` ``iccifort/2018.0.128-GCC-6.4.0-2.28`` +``2018.1.163`` ``GCC/6.4.0-2.28``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` +``2018.2.199`` ``iccifort/2018.2.199-GCC-6.4.0-2.28`` +``2018.3.222`` ``GCC/7.3.0-2.30``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` +``2018.4.274`` ``iccifort/2018.5.274-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifortcuda/2019a`` +``2018.5.288`` ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifortcuda/2019b`` +``2019.0.117`` ``iccifort/2019.0.117-GCC-8.2.0-2.31.1`` +``2019.1.144`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2019.2.187`` ``iccifort/2019.2.187-GCC-8.2.0-2.31.1`` +``2019.3.199`` ``iccifort/2019.3.199-GCC-8.3.0-2.32`` +``2019.6.166`` ``iccifort/2020.0.166-GCC-9.2.0`` +``2019.7.217`` ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` +``2019.9.304`` ``iccifort/2020.4.304``, ``iccifortcuda/2020b`` +``2019.12.320`` ``iccifort/2020.4.304`` +``2021.1.1`` ``intel-compilers/2021.1.2`` +``2021.2.0`` ``intel-compilers/2021.2.0`` +``system`` ``iccifort/system-GCC-system-2.29`` +=============== ============= ================================================================================================================================================================================================================================ .. _list_software_IMPUTE2_518: @@ -16349,8 +16779,10 @@ version versionsuffix toolchain ``2019b`` ``system`` ``2020.00`` ``system`` ``2020.06-impi-18.5`` ``system`` +``2020.12`` ``system`` ``2020a`` ``system`` ``2020b`` ``system`` +``2021a`` ``system`` ===================== ============= ========== @@ -16367,6 +16799,7 @@ Intel C, C++ & Fortran compilers (classic and oneAPI) version toolchain ============ ========== ``2021.1.2`` ``system`` +``2021.2.0`` ``system`` ============ ========== @@ -16458,6 +16891,22 @@ version toolchain ============= =============== +.. _list_software_intervaltree_1301: + +*intervaltree* +++++++++++++++ + +An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. + +*homepage*: https://github.com/ekg/intervaltree + +======= ================= +version toolchain +======= ================= +``0.1`` ``GCCcore/9.3.0`` +======= ================= + + .. _list_software_intltool_885: *intltool* @@ -16467,18 +16916,18 @@ intltool is a set of tools to centralize translation of many different file for *homepage*: http://freedesktop.org/wiki/Software/intltool/ -========== ================ ====================================================================================== -version versionsuffix toolchain -========== ================ ====================================================================================== -``0.51.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.51.0`` ``-Perl-5.20.3`` ``intel/2016a`` -``0.51.0`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` -``0.51.0`` ``-Perl-5.24.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` -``0.51.0`` ``-Perl-5.24.1`` ``GCCcore/6.3.0``, ``intel/2017a`` -``0.51.0`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` -``0.51.0`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``0.51.0`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -========== ================ ====================================================================================== +========== ================ =============================================================================================== +version versionsuffix toolchain +========== ================ =============================================================================================== +``0.51.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.51.0`` ``-Perl-5.20.3`` ``intel/2016a`` +``0.51.0`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` +``0.51.0`` ``-Perl-5.24.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` +``0.51.0`` ``-Perl-5.24.1`` ``GCCcore/6.3.0``, ``intel/2017a`` +``0.51.0`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` +``0.51.0`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``0.51.0`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +========== ================ =============================================================================================== .. _list_software_io_lib_622: @@ -16807,7 +17256,7 @@ version toolchain ``0.15`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a`` ``0.16`` ``GCC/4.9.3-2.25`` ``0.17`` ``foss/2016a`` -``0.23`` ``GCCcore/10.2.0`` +``0.23`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ======== ====================================================== @@ -16964,12 +17413,12 @@ JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian *homepage*: http://mcmc-jags.sourceforge.net/ -========= =============================================================================================== -version toolchain -========= =============================================================================================== -``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` -``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2017b`` -========= =============================================================================================== +========= =============================================================================================================== +version toolchain +========= =============================================================================================================== +``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` +``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2017b`` +========= =============================================================================================================== .. _list_software_Jansson_732: @@ -17007,6 +17456,7 @@ version toolchain ``2.0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.0.16`` ``GCCcore/9.3.0`` ``2.0.24`` ``GCCcore/10.2.0`` +``2.0.28`` ``GCCcore/10.3.0`` =========== ========================================================================================================================================================== @@ -17322,6 +17772,7 @@ version versionsuffix toolchain ``1.4.2`` ``-linux-x86_64`` ``system`` ``1.5.1`` ``-linux-x86_64`` ``system`` ``1.5.3`` ``-linux-x86_64`` ``system`` +``1.6.1`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -17471,7 +17922,7 @@ version toolchain ``0.45.0`` ``foss/2018b`` ``0.45.1`` ``foss/2019a`` ``0.46.0`` ``intel/2019a`` -``0.46.1`` ``foss/2019b`` +``0.46.1`` ``foss/2019b``, ``iimpi/2020a``, ``iimpi/2020b`` ``0.46.2`` ``foss/2020b`` ========== ================================================ @@ -17551,7 +18002,7 @@ version versionsuffix toolchain *Keras* +++++++ -Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano. +Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow. *homepage*: https://keras.io/ @@ -17578,6 +18029,7 @@ version versionsuffix toolchain ``2.2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``2.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.3.1`` ``-Python-3.8.2`` ``foss/2020a`` +``2.4.3`` ``foss/2020b``, ``fosscuda/2020b`` ========= ================== ================================== @@ -17724,16 +18176,16 @@ Kraken is a system for assigning taxonomic labels to short DNA sequences, usual *homepage*: https://ccb.jhu.edu/software/kraken/ -=============== ================ ================= -version versionsuffix toolchain -=============== ================ ================= -``0.10.5-beta`` ``-Perl-5.22.1`` ``foss/2016a`` -``0.10.5-beta`` ``-Perl-5.24.0`` ``foss/2016b`` -``1.0`` ``-Perl-5.26.1`` ``intel/2018a`` -``1.1`` ``-Perl-5.28.0`` ``foss/2018b`` -``1.1.1`` ``GCCcore/9.3.0`` -``1.1.1`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -=============== ================ ================= +=============== ================ ===================================== +version versionsuffix toolchain +=============== ================ ===================================== +``0.10.5-beta`` ``-Perl-5.22.1`` ``foss/2016a`` +``0.10.5-beta`` ``-Perl-5.24.0`` ``foss/2016b`` +``1.0`` ``-Perl-5.26.1`` ``intel/2018a`` +``1.1`` ``-Perl-5.28.0`` ``foss/2018b`` +``1.1.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.1.1`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +=============== ================ ===================================== .. _list_software_Kraken2_654: @@ -17743,7 +18195,7 @@ version versionsuffix toolchain Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. -*homepage*: http://www.ccb.jhu.edu/software/kraken2/ +*homepage*: https://github.com/DerrickWood/kraken2/wiki ============== ================ =============== version versionsuffix toolchain @@ -17753,6 +18205,7 @@ version versionsuffix toolchain ``2.0.8-beta`` ``-Perl-5.30.0`` ``gompi/2019b`` ``2.0.9-beta`` ``-Perl-5.28.0`` ``foss/2018b`` ``2.0.9-beta`` ``-Perl-5.30.2`` ``gompi/2020a`` +``2.1.1`` ``gompi/2020b`` ============== ================ =============== @@ -17781,12 +18234,13 @@ Krona Tools is a set of scripts to create Krona charts from several Bioinformat *homepage*: https://github.com/marbl/Krona/wiki/KronaTools -========= ================= -version toolchain -========= ================= -``2.7`` ``GCCcore/7.3.0`` -``2.7.1`` ``GCCcore/8.2.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``2.7`` ``GCCcore/7.3.0`` +``2.7.1`` ``GCCcore/8.2.0`` +``2.8`` ``GCCcore/10.2.0`` +========= ================== .. _list_software_kwant_549: @@ -17859,7 +18313,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -18016,6 +18470,23 @@ version toolchain ======== ================= +.. _list_software_LDC_211: + +*LDC* ++++++ + +The LLVM-based D Compiler + +*homepage*: https://wiki.dlang.org/LDC + +========== ============= ================== +version versionsuffix toolchain +========== ============= ================== +``0.17.6`` ``-x86_64`` ``system`` +``1.25.1`` ``GCCcore/10.2.0`` +========== ============= ================== + + .. _list_software_LeadIT_531: *LeadIT* @@ -18041,12 +18512,12 @@ Implementation of the Leiden algorithm for various quality functions to be used *homepage*: https://github.com/vtraag/leidenalg -========= ================= ================== -version versionsuffix toolchain -========= ================= ================== -``0.8.2`` ``-Python-3.8.2`` ``foss/2020a`` -``0.8.3`` ``fosscuda/2020b`` -========= ================= ================== +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``0.8.2`` ``-Python-3.8.2`` ``foss/2020a`` +``0.8.3`` ``foss/2020b``, ``fosscuda/2020b`` +========= ================= ================================== .. _list_software_LEMON_379: @@ -18165,6 +18636,7 @@ version toolchain ``3.4.0`` ``GCCcore/8.2.0`` ``3.4.2`` ``GCCcore/9.3.0`` ``3.4.3`` ``GCCcore/10.2.0`` +``3.5.1`` ``GCCcore/10.3.0`` ========= ================== @@ -18381,7 +18853,7 @@ version versionsuffix toolchain *libdeflate* ++++++++++++ -Generic PCI access library. +Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. *homepage*: https://github.com/ebiggers/libdeflate @@ -18389,6 +18861,7 @@ Generic PCI access library. version toolchain ======= ================= ``1.5`` ``GCCcore/7.3.0`` +``1.7`` ``GCCcore/9.3.0`` ======= ================= @@ -18415,6 +18888,7 @@ version toolchain ``2.4.99`` ``GCCcore/8.3.0`` ``2.4.100`` ``GCCcore/9.3.0`` ``2.4.102`` ``GCCcore/10.2.0`` +``2.4.106`` ``GCCcore/10.3.0`` =========== ================================================== @@ -18520,7 +18994,7 @@ version toolchain ``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` ``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` ``2.1.11`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.1.12`` ``GCCcore/10.2.0`` +``2.1.12`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========== ====================================================================================== @@ -18539,6 +19013,7 @@ version toolchain ``1.9.1`` ``GCCcore/9.3.0`` ``1.10.1`` ``GCCcore/9.3.0`` ``1.11.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.12.1`` ``GCCcore/10.3.0`` ========== ===================================== @@ -18572,7 +19047,7 @@ The libffi library provides a portable, high level programming interface to var version toolchain ========= ============================================================================================================================================================================================================================================================================================================= ``3.2.1`` ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``system`` -``3.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================================================================================================================================================================================================================= @@ -18615,18 +19090,18 @@ version toolchain *libgcrypt* +++++++++++ -Libgpg-error is a small library that defines common error values for all GnuPG components. +Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG *homepage*: https://gnupg.org/related_software/libgcrypt/index.html -========= ==================================== -version toolchain -========= ==================================== -``1.6.5`` ``intel/2016a`` -``1.8.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.8.5`` ``GCCcore/8.3.0`` -``1.9.2`` ``GCCcore/10.2.0`` -========= ==================================== +========= ====================================== +version toolchain +========= ====================================== +``1.6.5`` ``intel/2016a`` +``1.8.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.8.5`` ``GCCcore/8.3.0`` +``1.9.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_libgd_514: @@ -18692,12 +19167,12 @@ libgit2 is a portable, pure C implementation of the Git core methods provided as *homepage*: https://libgit2.org/ -========= ===================================== -version toolchain -========= ===================================== -``1.0.0`` ``GCCcore/8.3.0`` -``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========= ===================================== +========= ========================================================= +version toolchain +========= ========================================================= +``1.0.0`` ``GCCcore/8.3.0`` +``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +========= ========================================================= .. _list_software_libglade_820: @@ -18730,7 +19205,7 @@ version versionsuffix toolchain ========= ================ =========================================================================================================================================================================================================================================================================================================================================== ``9.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b``, ``iomkl/2018a`` ``9.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` -``9.0.1`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``9.0.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ================ =========================================================================================================================================================================================================================================================================================================================================== @@ -18748,6 +19223,7 @@ version toolchain ========= ======================================================= ``1.2.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.3.2`` ``GCCcore/10.2.0`` +``1.3.3`` ``GCCcore/10.3.0`` ========= ======================================================= @@ -18768,6 +19244,7 @@ version toolchain ``1.36`` ``GCCcore/8.2.0`` ``1.38`` ``GCCcore/8.3.0`` ``1.41`` ``GCCcore/10.2.0`` +``1.42`` ``GCCcore/10.3.0`` ======== ================== @@ -18897,12 +19374,12 @@ Libiconv converts from one character encoding to another through Unicode convers *homepage*: https://www.gnu.org/software/libiconv -======== =========================================================================== -version toolchain -======== =========================================================================== -``1.15`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``1.16`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======== =========================================================================== +======== =============================================================================================== +version toolchain +======== =============================================================================================== +``1.15`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``1.16`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======== =============================================================================================== .. _list_software_libidn_626: @@ -18920,10 +19397,26 @@ version toolchain ``1.32`` ``GCCcore/5.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` ``1.34`` ``GCCcore/6.4.0`` ``1.35`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.36`` ``GCCcore/10.2.0`` +``1.36`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ======== ====================================================================================== +.. _list_software_libidn2_676: + +*libidn2* ++++++++++ + +GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn's purpose is to encode and decode internationalized domain names. + +*homepage*: https://www.gnu.org/software/libidn + +========= ===================================================================================================================================== +version toolchain +========= ===================================================================================================================================== +``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ===================================================================================================================================== + + .. _list_software_Libint_610: *Libint* @@ -18985,6 +19478,7 @@ version versionsuffix toolchain ``2.0.3`` ``GCCcore/8.3.0`` ``2.0.4`` ``GCCcore/9.3.0`` ``2.0.5`` ``GCCcore/10.2.0`` +``2.0.6`` ``GCCcore/10.3.0`` ========= ================= ================================================================== @@ -19045,11 +19539,12 @@ GNU libmicrohttpd is a small C library that is supposed to make it easy to run *homepage*: https://www.gnu.org/software/libmicrohttpd/ -========== ================= -version toolchain -========== ================= -``0.9.71`` ``GCCcore/9.3.0`` -========== ================= +========== ================== +version toolchain +========== ================== +``0.9.71`` ``GCCcore/9.3.0`` +``0.9.73`` ``GCCcore/10.2.0`` +========== ================== .. _list_software_libmo_unpack_1268: @@ -19093,11 +19588,11 @@ Ogg is a multimedia container format, and the native file and stream format for *homepage*: https://xiph.org/ogg/ -========= ================== -version toolchain -========= ================== -``1.3.4`` ``GCCcore/10.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.3.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_libosmium_977: @@ -19126,11 +19621,11 @@ Library for portable access to PCI bus configuration registers from PCI Utils. *homepage*: https://github.com/pciutils/pciutils -========= ===================================== -version toolchain -========= ===================================== -``3.7.0`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0`` -========= ===================================== +========= ========================================================= +version toolchain +========= ========================================================= +``3.7.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0`` +========= ========================================================= .. _list_software_libpciaccess_1253: @@ -19147,7 +19642,7 @@ version toolchain ========== ============================================================================================= ``0.13.4`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.16`` ``GCCcore/10.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``0.16`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ========== ============================================================================================= @@ -19160,23 +19655,23 @@ libpng is the official PNG reference library *homepage*: http://www.libpng.org/pub/png/libpng.html -========== ===================================================================== -version toolchain -========== ===================================================================== -``1.2.58`` ``system`` -``1.2.59`` ``system`` -``1.6.21`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``1.6.23`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``1.6.24`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` -``1.6.26`` ``foss/2016b``, ``intel/2016b`` -``1.6.27`` ``intel/2016b`` -``1.6.28`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``gimkl/2017a`` -``1.6.29`` ``GCCcore/6.3.0`` -``1.6.32`` ``GCCcore/6.4.0`` -``1.6.34`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.6.36`` ``GCCcore/8.2.0`` -``1.6.37`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ===================================================================== +========== ============================================================================ +version toolchain +========== ============================================================================ +``1.2.58`` ``system`` +``1.2.59`` ``system`` +``1.6.21`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``1.6.23`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` +``1.6.24`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` +``1.6.26`` ``foss/2016b``, ``intel/2016b`` +``1.6.27`` ``intel/2016b`` +``1.6.28`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``gimkl/2017a`` +``1.6.29`` ``GCCcore/6.3.0`` +``1.6.32`` ``GCCcore/6.4.0`` +``1.6.34`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.6.36`` ``GCCcore/8.2.0`` +``1.6.37`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ============================================================================ .. _list_software_libpsl_646: @@ -19288,7 +19783,7 @@ version versionsuffix toolchain The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. -*homepage*: http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html +*homepage*: https://tiswww.case.edu/php/chet/readline/rltop.html ======= =================================================================================================================================================================================================================================================================================================================================================================================== version toolchain @@ -19296,6 +19791,7 @@ version toolchain ``6.3`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``7.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``8.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +``8.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` ======= =================================================================================================================================================================================================================================================================================================================================================================================== @@ -19308,11 +19804,44 @@ The routines supporting the distribution and special functions in R and a few ot *homepage*: https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library -========= ============== -version toolchain -========= ============== -``3.6.0`` ``foss/2018b`` -========= ============== +========= ================= +version toolchain +========= ================= +``3.6.0`` ``foss/2018b`` +``4.0.0`` ``GCCcore/9.3.0`` +========= ================= + + +.. _list_software_librosa_748: + +*librosa* ++++++++++ + +Python module for audio and music processing + +*homepage*: https://librosa.github.io + +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``0.7.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +========= ================= ================================== + + +.. _list_software_librsb_638: + +*librsb* +++++++++ + +A shared memory parallel sparse matrix computations library for the Recursive Sparse Blocks format + +*homepage*: https://sourceforge.net/projects/librsb/ + +=========== ============== +version toolchain +=========== ============== +``1.2.0.9`` ``GCC/10.2.0`` +=========== ============== .. _list_software_librsvg_761: @@ -19412,6 +19941,7 @@ Libsndfile is a C library for reading and writing files containing sampled sound version toolchain ========== ================================================================================================================================== ``1.0.28`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a`` +``1.0.31`` ``GCCcore/10.3.0`` ========== ================================================================================================================================== @@ -19536,6 +20066,7 @@ version toolchain ======== ================================ ``3.22`` ``intel/2016b``, ``intel/2017b`` ``3.23`` ``foss/2018b``, ``intel/2018b`` +``3.24`` ``GCCcore/9.3.0`` ======== ================================ @@ -19592,6 +20123,7 @@ version toolchain ``4.0.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018b`` ``4.0.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``4.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.2.0`` ``GCCcore/10.3.0`` ========== ========================================================================================================= @@ -19622,13 +20154,13 @@ GNU libtool is a generic library support script. Libtool hides the complexity of *homepage*: http://www.gnu.org/software/libtool -========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain -========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` -``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` -``2.4.6`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +========= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +version toolchain +========= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` +``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``2.4.6`` ``FCC/4.5.0``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +========= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= .. _list_software_libunistring_1306: @@ -19665,7 +20197,8 @@ version toolchain ``1.1`` ``GCC/4.9.2``, ``foss/2016a``, ``intel/2016b`` ``1.2.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016b`` ``1.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.4.0`` ``GCCcore/10.2.0`` +``1.4.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.5.0`` ``GCCcore/10.3.0`` ========= ======================================================================= @@ -19726,12 +20259,12 @@ libvdwxc is a general library for evaluating energy and potential for exchange-c *homepage*: https://libvdwxc.org -========= ============================================== -version toolchain -========= ============================================== -``0.3.2`` ``foss/2018b`` -``0.4.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020b`` -========= ============================================== +========= ============================================================== +version toolchain +========= ============================================================== +``0.3.2`` ``foss/2018b`` +``0.4.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b`` +========= ============================================================== .. _list_software_libvorbis_972: @@ -19743,11 +20276,11 @@ Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-pu *homepage*: https://xiph.org/vorbis/ -========= ================== -version toolchain -========= ================== -``1.3.7`` ``GCCcore/10.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.3.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_libwebp_741: @@ -19765,6 +20298,7 @@ version toolchain ``1.0.0`` ``foss/2018b`` ``1.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.2.0`` ``GCCcore/10.3.0`` ========= ======================================================== @@ -19821,6 +20355,7 @@ version toolchain ``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` ``4.3.4`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` ``5.1.2`` ``GCC/10.2.0`` +``5.1.3`` ``GCC/10.2.0`` ========= ======================================================================================================================================================================================= @@ -20044,7 +20579,7 @@ version versionsuffix toolchain ``2.9.7`` ``GCCcore/6.4.0`` ``2.9.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.9.9`` ``GCCcore/8.3.0`` -``2.9.10`` ``GCCcore/10.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``2.9.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ========== ================== ================================================================================================================================================================================== @@ -20238,7 +20773,7 @@ version toolchain ``0.1.7`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``system`` ``0.2.1`` ``GCCcore/7.3.0``, ``system`` ``0.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.2.5`` ``GCCcore/10.2.0`` +``0.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= =================================================================== @@ -20267,12 +20802,12 @@ libzip is a C library for reading, creating, and modifying zip archives. *homepage*: https://libzip.org/ -========= ================== -version toolchain -========= ================== -``1.5.2`` ``GCCcore/8.2.0`` -``1.7.3`` ``GCCcore/10.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.5.2`` ``GCCcore/8.2.0`` +``1.7.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_lifelines_955: @@ -20377,6 +20912,22 @@ version toolchain ========= ============== +.. _list_software_line_profiler_1386: + +*line_profiler* ++++++++++++++++ + +line_profiler is a module for doing line-by-line profiling of functions. kernprof is a convenient script for running either line_profiler or the Python standard library's cProfile or profile modules, depending on what is available. + +*homepage*: https://github.com/pyutils/line_profiler + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``3.1.0`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_Lingeling_921: *Lingeling* @@ -20458,6 +21009,7 @@ version toolchain ``10.0.0`` ``GCCcore/8.3.0`` ``10.0.1`` ``GCCcore/10.2.0`` ``11.0.0`` ``GCCcore/10.2.0`` +``11.1.0`` ``GCCcore/10.3.0`` ========== ======================================================================== @@ -20478,6 +21030,7 @@ version toolchain ``0.9.22`` ``GCCcore/7.3.0`` ``0.9.23`` ``GCCcore/8.2.0`` ``0.9.24`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.9.28`` ``GCCcore/10.3.0`` ========== ======================================================== @@ -20490,14 +21043,14 @@ Lmfit provides a high-level interface to non-linear optimization and curve fitti *homepage*: https://lmfit.github.io/lmfit-py -========== ================== =============== -version versionsuffix toolchain -========== ================== =============== -``0.9.9`` ``-Python-3.6.4`` ``intel/2018a`` -``0.9.14`` ``-Python-2.7.15`` ``intel/2018b`` -``1.0.0`` ``-Python-3.7.4`` ``intel/2019b`` -``1.0.1`` ``-Python-3.8.2`` ``foss/2020a`` -========== ================== =============== +========== ================== =============================== +version versionsuffix toolchain +========== ================== =============================== +``0.9.9`` ``-Python-3.6.4`` ``intel/2018a`` +``0.9.14`` ``-Python-2.7.15`` ``intel/2018b`` +``1.0.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.0.1`` ``-Python-3.8.2`` ``foss/2020a`` +========== ================== =============================== .. _list_software_Lmod_396: @@ -20660,6 +21213,22 @@ version toolchain ========= ===================================== +.. _list_software_loompy_672: + +*loompy* +++++++++ + +Python implementation of the Loom file format, an efficient file format for large omics datasets + +*homepage*: https://loompy.org/ + +========= =============== +version toolchain +========= =============== +``3.0.6`` ``intel/2020b`` +========= =============== + + .. _list_software_LPJmL_415: *LPJmL* @@ -20845,6 +21414,7 @@ A probabilistic framework for structural variant discovery. version toolchain ========== ============== ``0.2.13`` ``foss/2016b`` +``0.3.1`` ``foss/2020b`` ========== ============== @@ -20940,6 +21510,7 @@ version toolchain ``1.9.0`` ``GCCcore/7.3.0`` ``1.9.1`` ``GCCcore/8.2.0`` ``1.9.2`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.9.3`` ``GCCcore/10.3.0`` ========= ======================================================== @@ -20952,12 +21523,12 @@ Portable lossless data compression library *homepage*: http://www.oberhumer.com/opensource/lzo/ -======== ====================================================================================================================================================================================================================================== -version toolchain -======== ====================================================================================================================================================================================================================================== -``2.09`` ``intel/2016b``, ``intel/2017b`` -``2.10`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` -======== ====================================================================================================================================================================================================================================== +======== ========================================================================================================================================================================================================================================================== +version toolchain +======== ========================================================================================================================================================================================================================================================== +``2.09`` ``intel/2016b``, ``intel/2017b`` +``2.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` +======== ========================================================================================================================================================================================================================================================== .. _list_software_letter_m: @@ -20966,7 +21537,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -20983,7 +21554,7 @@ version toolchain ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.4.16`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.4.18`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` +``1.4.18`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -21103,16 +21674,16 @@ The MAGMA project aims to develop a dense linear algebra library similar to LAP *homepage*: https://icl.cs.utk.edu/magma/ -========= ================ ============================================================================== -version versionsuffix toolchain -========= ================ ============================================================================== -``2.3.0`` ``fosscuda/2017b``, ``intelcuda/2017b`` -``2.3.0`` ``-CUDA-9.1.85`` ``foss/2018a`` -``2.4.0`` ``fosscuda/2018b`` -``2.5.0`` ``fosscuda/2018b`` -``2.5.1`` ``fosscuda/2019a``, ``fosscuda/2019b`` -``2.5.4`` ``fosscuda/2019a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b`` -========= ================ ============================================================================== +========= ================ ======================================================================================================================== +version versionsuffix toolchain +========= ================ ======================================================================================================================== +``2.3.0`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``2.3.0`` ``-CUDA-9.1.85`` ``foss/2018a`` +``2.4.0`` ``fosscuda/2018b`` +``2.5.0`` ``fosscuda/2018b`` +``2.5.1`` ``fosscuda/2019a``, ``fosscuda/2019b`` +``2.5.4`` ``fosscuda/2019a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intelcuda/2019b``, ``intelcuda/2020b`` +========= ================ ======================================================================================================================== .. _list_software_MagresPython_1249: @@ -21172,14 +21743,14 @@ GNU version of make utility *homepage*: https://www.gnu.org/software/make/make.html -========= ===================================== -version toolchain -========= ===================================== -``3.82`` ``GCC/4.8.2`` -``4.1`` ``GCC/4.9.2`` -``4.2.1`` ``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` -``4.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========= ===================================== +========= ========================================================= +version toolchain +========= ========================================================= +``3.82`` ``GCC/4.8.2`` +``4.1`` ``GCC/4.9.2`` +``4.2.1`` ``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` +``4.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +========= ========================================================= .. _list_software_makedepend_1038: @@ -21224,11 +21795,11 @@ makeinfo is part of the Texinfo project, the official documentation format of th *homepage*: https://www.gnu.org/software/texinfo/ -======= ======================================================== -version toolchain -======= ======================================================== -``6.7`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ======================================================== +======= =========================================================================================== +version toolchain +======= =========================================================================================== +``6.7`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= =========================================================================================== .. _list_software_Mako_392: @@ -21253,6 +21824,7 @@ version versionsuffix toolchain ``1.1.0`` ``GCCcore/8.3.0`` ``1.1.2`` ``GCCcore/9.3.0`` ``1.1.3`` ``GCCcore/10.2.0`` +``1.1.4`` ``GCCcore/10.3.0`` ========= ================== ================================================================================================================================================================= @@ -21492,7 +22064,7 @@ version toolchain MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. -*homepage*: https://www.mathworks.com/products/matlab.html +*homepage*: https://www.mathworks.com/products/matlab ========= ========== version toolchain @@ -21504,6 +22076,9 @@ version toolchain ``2017a`` ``system`` ``2018b`` ``system`` ``2019b`` ``system`` +``2020a`` ``system`` +``2020b`` ``system`` +``2021a`` ``system`` ========= ========== @@ -21567,7 +22142,7 @@ version versionsuffix toolchain ``2.2.4`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` ``2.2.4`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``2.2.5`` ``-Python-2.7.16`` ``foss/2019b`` -``2.2.5`` ``-Python-2.7.18`` ``foss/2020a``, ``intel/2020a`` +``2.2.5`` ``-Python-2.7.18`` ``foss/2020a``, ``foss/2020b``, ``fosscuda/2020a``, ``intel/2020a`` ``3.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` ``3.0.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` @@ -21653,14 +22228,15 @@ version toolchain *MaxBin* ++++++++ -MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. +MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. -*homepage*: https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html +*homepage*: https://sourceforge.net/projects/maxbin/ ========= ================ ==================== version versionsuffix toolchain ========= ================ ==================== ``2.2.6`` ``-Perl-5.28.0`` ``foss/2018b`` +``2.2.7`` ``gompi/2020b`` ``2.2.7`` ``-Perl-5.28.1`` ``GCC/8.2.0-2.31.1`` ========= ================ ==================== @@ -21921,15 +22497,15 @@ Read, write and analyze MD trajectories with only a few lines of Python code. *homepage*: https://mdtraj.org -========= ================= =============================== -version versionsuffix toolchain -========= ================= =============================== -``1.9.1`` ``-Python-3.6.3`` ``intel/2017b`` -``1.9.2`` ``-Python-3.6.6`` ``intel/2018b`` -``1.9.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.9.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.9.5`` ``foss/2020b``, ``intel/2020b`` -========= ================= =============================== +========= ================= =================================================== +version versionsuffix toolchain +========= ================= =================================================== +``1.9.1`` ``-Python-3.6.3`` ``intel/2017b`` +``1.9.2`` ``-Python-3.6.6`` ``intel/2018b`` +``1.9.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.9.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.9.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +========= ================= =================================================== .. _list_software_medaka_611: @@ -22053,6 +22629,7 @@ version versionsuffix toolchain ``1.1.4`` ``-Python-3.6.6`` ``foss/2018b`` ``1.2.8`` ``GCCcore/8.2.0`` ``1.2.9`` ``GCCcore/9.3.0``, ``foss/2018b`` +``1.2.9`` ``-Python-2.7.18`` ``GCCcore/10.2.0`` ========= ================== ================================= @@ -22186,6 +22763,7 @@ version versionsuffix toolchain ========= ================== ================== ``3.8.3`` ``-Python-2.7.11`` ``foss/2016a`` ``5.7.1`` ``GCCcore/10.2.0`` +``5.7.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ================== ================== @@ -22214,6 +22792,7 @@ version toolchain ``19.2.1`` ``GCCcore/8.3.0`` ``20.0.2`` ``GCCcore/9.3.0`` ``20.2.1`` ``GCCcore/10.2.0`` +``21.1.1`` ``GCCcore/10.3.0`` ========== ==================================================================== @@ -22230,6 +22809,7 @@ Graphical program for display time dependent data on 3D finite elment meshes version versionsuffix toolchain ======= ================= ============== ``2.0`` ``-Python-3.8.2`` ``foss/2020a`` +``2.2`` ``foss/2020b`` ======= ================= ============== @@ -22260,11 +22840,11 @@ Meshtool is a comand-line tool written in C++. It is designed to apply various m *homepage*: https://bitbucket.org/aneic/meshtool -======= ============= -version toolchain -======= ============= -``16`` ``GCC/9.3.0`` -======= ============= +======= ============================= +version toolchain +======= ============================= +``16`` ``GCC/10.2.0``, ``GCC/9.3.0`` +======= ============================= .. _list_software_Meson_514: @@ -22289,6 +22869,7 @@ version versionsuffix toolchain ``0.53.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``0.55.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``0.55.3`` ``GCCcore/10.2.0`` +``0.58.0`` ``GCCcore/10.3.0`` ========== ================= ================================== @@ -22338,6 +22919,7 @@ version versionsuffix toolchain ========== ================== =============== ``2.12.1`` ``-Python-2.7.15`` ``foss/2018b`` ``2.14`` ``gompi/2019a`` +``2.15`` ``-Python-2.7.18`` ``gompi/2020b`` ========== ================== =============== @@ -22451,6 +23033,7 @@ version versionsuffix toolchain ========= ================== ============== ``2.7.8`` ``-Python-2.7.12`` ``foss/2016b`` ``2.7.8`` ``-Python-3.6.6`` ``foss/2018b`` +``2.7.8`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ============== @@ -22459,7 +23042,7 @@ version versionsuffix toolchain *metaWRAP* ++++++++++ -MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. +MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. *homepage*: https://github.com/bxlab/metaWRAP @@ -22468,6 +23051,7 @@ version versionsuffix toolchain ========= ================== ============== ``1.2`` ``-Python-2.7.15`` ``foss/2018b`` ``1.2.2`` ``-Python-2.7.15`` ``foss/2019a`` +``1.3`` ``-Python-2.7.18`` ``foss/2020b`` ========= ================== ============== @@ -22777,6 +23361,7 @@ version toolchain ``2.12`` ``foss/2018a`` ``2.13`` ``foss/2018b`` ``2.17`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/9.3.0`` +``2.18`` ``GCCcore/10.2.0`` ========== ====================================================== @@ -23052,6 +23637,22 @@ version toolchain ============ ================================ +.. _list_software_mmtf-cpp_804: + +*mmtf-cpp* +++++++++++ + +The Macromolecular Transmission Format (MMTF) is a new compact binary format to transmit and store biomolecular structures for fast 3D visualization and analysis. + +*homepage*: https://mmtf.rcsb.org/ + +========= ================== +version toolchain +========= ================== +``1.0.0`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_MOABS_370: *MOABS* @@ -23109,16 +23710,17 @@ version versionsuffix toolchain Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac -*homepage*: https://www.cmbi.ru.nl/molden/ +*homepage*: https://www3.cmbi.umcn.nl/molden -======= ================= -version toolchain -======= ================= -``5.6`` ``foss/2016a`` -``5.7`` ``intel/2016b`` -``5.8`` ``foss/2018a`` -``6.1`` ``GCCcore/8.2.0`` -======= ================= +======= ===================================== +version toolchain +======= ===================================== +``5.6`` ``foss/2016a`` +``5.7`` ``intel/2016b`` +``5.8`` ``foss/2018a`` +``6.1`` ``GCCcore/8.2.0`` +``6.8`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +======= ===================================== .. _list_software_Molekel_713: @@ -23181,6 +23783,24 @@ version versionsuffix toolchain ============= ======================== ========== +.. _list_software_mongolite_974: + +*mongolite* ++++++++++++ + +High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'. Includes support for aggregation, indexing, map-reduce, streaming, encryption, enterprise authentication, and GridFS. The online user manual provides an overview of the available methods in the package: . + +*homepage*: https://cran.r-project.org/web/packages/mongolite + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``2.3.0`` ``-R-4.0.0`` ``foss/2020a`` +``2.3.0`` ``-R-4.0.3`` ``foss/2020b`` +``2.3.0`` ``-R-4.0.4`` ``foss/2020b`` +========= ============= ============== + + .. _list_software_Mono_409: *Mono* @@ -23332,13 +23952,14 @@ MotionCor2 correct anisotropic image motion at the single pixel level across the *homepage*: https://msg.ucsf.edu/ -========= ================= -version toolchain -========= ================= -``1.2.6`` ``GCCcore/8.2.0`` -``1.3.1`` ``GCCcore/8.3.0`` -``1.3.2`` ``GCCcore/8.3.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``1.2.6`` ``GCCcore/8.2.0`` +``1.3.1`` ``GCCcore/8.3.0`` +``1.3.2`` ``GCCcore/8.3.0`` +``1.4.2`` ``GCCcore/10.2.0`` +========= ================== .. _list_software_motionSegmentation_1924: @@ -23398,14 +24019,14 @@ Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily h *homepage*: http://www.multiprecision.org/ -========= =============== =============================== -version versionsuffix toolchain -========= =============== =============================== -``1.0.3`` ``intel/2017a`` -``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` -``1.1.0`` ``GCC/8.3.0``, ``GCC/9.3.0`` -``1.2.1`` ``GCCcore/10.2.0`` -========= =============== =============================== +========= =============== ====================================== +version versionsuffix toolchain +========= =============== ====================================== +``1.0.3`` ``intel/2017a`` +``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` +``1.1.0`` ``GCC/8.3.0``, ``GCC/9.3.0`` +``1.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= =============== ====================================== .. _list_software_MPFR_309: @@ -23426,7 +24047,7 @@ version toolchain ``3.1.6`` ``GCCcore/6.4.0`` ``4.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``4.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.1.0`` ``GCCcore/10.2.0`` +``4.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ================================================================ @@ -23660,6 +24281,22 @@ version versionsuffix toolchain =================== ================== =============== +.. _list_software_msgpack-c_886: + +*msgpack-c* ++++++++++++ + +MessagePack is an efficient binary serialization format, which lets you exchange data among multiple languages like JSON, except that it's faster and smaller. Small integers are encoded into a single byte while typical short strings require only one extra byte in addition to the strings themselves. + +*homepage*: http://msgpack.org/ + +========= ================== +version toolchain +========= ================== +``3.3.0`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_MSM_237: *MSM* @@ -23725,6 +24362,22 @@ version toolchain ============ ========== +.. _list_software_multichoose_1196: + +*multichoose* ++++++++++++++ + +generate multiset combinations (n multichoose k). + +*homepage*: https://github.com/ekg/multichoose + +========= ================= +version toolchain +========= ================= +``1.0.3`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_MultiNest_933: *MultiNest* @@ -23829,12 +24482,12 @@ muParser is an extensible high performance math expression parser library writt *homepage*: https://beltoforion.de/article.php?a=muparser -========= ================= -version toolchain -========= ================= -``2.2.5`` ``GCCcore/6.4.0`` -``2.3.2`` ``GCCcore/9.3.0`` -========= ================= +========= ===================================== +version toolchain +========= ===================================== +``2.2.5`` ``GCCcore/6.4.0`` +``2.3.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========= ===================================== .. _list_software_MuPeXI_536: @@ -24083,11 +24736,11 @@ Myokit is an open-source Python-based toolkit that facilitates modeling and simu *homepage*: http://myokit.org -========== ============== -version toolchain -========== ============== -``1.32.0`` ``foss/2020b`` -========== ============== +========== ================================== +version toolchain +========== ================================== +``1.32.0`` ``foss/2020b``, ``fosscuda/2020b`` +========== ================================== .. _list_software_mypy_463: @@ -24162,7 +24815,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -24423,7 +25076,7 @@ version toolchain ``2.13.01`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``2.13.03`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.14.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.15.05`` ``GCCcore/10.2.0`` +``2.15.05`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` =========== ==================================================================================== @@ -24606,13 +25259,13 @@ NCL is an interpreted language designed specifically for scientific data analysi *homepage*: https://www.ncl.ucar.edu -========= ================================================================= -version toolchain -========= ================================================================= -``6.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``6.5.0`` ``intel/2018a`` -``6.6.2`` ``foss/2018b``, ``intel/2018b``, ``intel/2019b``, ``intel/2020a`` -========= ================================================================= +========= ================================================================================= +version toolchain +========= ================================================================================= +``6.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +``6.5.0`` ``intel/2018a`` +``6.6.2`` ``foss/2018b``, ``foss/2020a``, ``intel/2018b``, ``intel/2019b``, ``intel/2020a`` +========= ================================================================================= .. _list_software_ncl_317: @@ -24687,7 +25340,7 @@ version toolchain ``5.9`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25``, ``gimkl/2.11.5``, ``system`` ``6.0`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``6.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` -``6.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0``, ``system`` +``6.2`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``system`` ======= ============================================================================================================================================================================================================================================================================================================================================================================= @@ -24696,7 +25349,7 @@ version toolchain *ncview* ++++++++ -Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. +Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. *homepage*: http://meteora.ucsd.edu/~pierce/ncview_home_page.html @@ -24704,6 +25357,7 @@ Ncview is a visual browser for netCDF format files. Typically you would use ncvi version toolchain ========= ====================================================================================================================================================================================== ``2.1.7`` ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``gompi/2019a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b``, ``iomkl/2018b`` +``2.1.8`` ``gompi/2020a`` ========= ====================================================================================================================================================================================== @@ -24845,7 +25499,7 @@ version versionsuffix toolchain ``4.6.1`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``4.6.2`` ``gompi/2019a``, ``iimpi/2019a`` ``4.7.1`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` -``4.7.4`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020a``, ``iimpi/2020b`` +``4.7.4`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2020b`` =========== ================ ========================================================================================================================== @@ -24880,7 +25534,7 @@ version versionsuffix toolchain ``4.3.0`` ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``4.3.0`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.3.0`` ``-HDF5-1.8.19`` ``intel/2017b`` -``4.3.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2019b``, ``iimpi/2020a`` +``4.3.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b`` ========= ================ ====================================================================================================================================================== @@ -24903,8 +25557,8 @@ version versionsuffix toolchain ``4.4.4`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.4.4`` ``-HDF5-1.8.19`` ``foss/2017b``, ``intel/2017b`` ``4.4.5`` ``gompi/2019a``, ``iimpi/2019a`` -``4.5.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` -``4.5.3`` ``gompi/2020b``, ``iimpi/2020b`` +``4.5.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` +``4.5.3`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b`` ========= ================ ==================================================================================================================================================================================================================================================================================================================================== @@ -25026,13 +25680,14 @@ version toolchain NetPIPE is a protocol independent communication performance benchmark that visually represents the network performance under a variety of conditions. -*homepage*: http://netpipe.cs.ksu.edu/ +*homepage*: https://netpipe.cs.ksu.edu/ -======= =============== -version toolchain -======= =============== -``5.1`` ``intel/2018a`` -======= =============== +========= ================================ +version toolchain +========= ================================ +``5.1`` ``intel/2018a`` +``5.1.4`` ``gompi/2020b``, ``iimpi/2020b`` +========= ================================ .. _list_software_nettle_652: @@ -25054,9 +25709,26 @@ version toolchain ``3.4.1`` ``GCCcore/8.2.0`` ``3.5.1`` ``GCCcore/8.3.0`` ``3.6`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.7.2`` ``GCCcore/10.3.0`` ========= =========================================================================================================================================== +.. _list_software_networkTools_1307: + +*networkTools* +++++++++++++++ + +Dynamical Network Analysis is a method of characterizing allosteric signalling through biomolecular complexes. + +*homepage*: http://faculty.scs.illinois.edu/schulten/software/networkTools/ + +======= ============= +version toolchain +======= ============= +``2`` ``GCC/9.3.0`` +======= ============= + + .. _list_software_networkx_898: *networkx* @@ -25119,6 +25791,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_NewHybrids_1023: + +*NewHybrids* +++++++++++++ + +This implements a Gibbs sampler to estimate the posterior probability that genetically sampled individuals fall into each of a set of user-defined hybrid categories. + +*homepage*: https://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm#NewHybs + +============= ============== +version toolchain +============= ============== +``1.1_Beta3`` ``GCC/10.2.0`` +============= ============== + + .. _list_software_Nextflow_855: *Nextflow* @@ -25321,6 +26009,7 @@ version versionsuffix toolchain ``2.5.1`` ``-Python-3.6.6`` ``foss/2018b`` ``3.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.2.0`` ``-Python-3.8.2`` ``foss/2020a`` +``3.2.1`` ``foss/2020b`` ========= ================================= =============================== @@ -25372,6 +26061,7 @@ version versionsuffix toolchain ``0.5.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``0.5.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``0.7.0`` ``-Python-3.8.2`` ``foss/2020a`` +``0.7.1`` ``foss/2020b`` ========= ================== =============================== @@ -25384,13 +26074,14 @@ Nim is a systems and applications programming language. *homepage*: https://nim-lang.org/ -========== ================= -version toolchain -========== ================= -``0.18.0`` ``GCCcore/6.4.0`` -``0.19.2`` ``GCCcore/7.3.0`` -``1.0.0`` ``GCCcore/8.3.0`` -========== ================= +========== ================== +version toolchain +========== ================== +``0.18.0`` ``GCCcore/6.4.0`` +``0.19.2`` ``GCCcore/7.3.0`` +``1.0.0`` ``GCCcore/8.3.0`` +``1.4.6`` ``GCCcore/10.2.0`` +========== ================== .. _list_software_NIMBLE_439: @@ -25425,6 +26116,7 @@ version toolchain ``1.9.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` ``1.10.0`` ``GCCcore/9.3.0`` ``1.10.1`` ``GCCcore/10.2.0`` +``1.10.2`` ``GCCcore/10.3.0`` ========== ==================================================================================== @@ -25477,6 +26169,7 @@ version toolchain ``2.4.2`` ``GCC/5.4.0-2.26``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``iomkl/2018a`` ``2.6.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.6.2`` ``GCCcore/10.2.0`` +``2.7.0`` ``GCCcore/10.3.0`` ========= =================================================================================================================================================================================================================================================== @@ -25687,6 +26380,7 @@ version toolchain ``4.21`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``4.25`` ``GCCcore/9.3.0`` ``4.29`` ``GCCcore/10.2.0`` +``4.30`` ``GCCcore/10.3.0`` ======== ==================================== @@ -25707,6 +26401,7 @@ version toolchain ``3.45`` ``GCCcore/8.3.0`` ``3.51`` ``GCCcore/9.3.0`` ``3.57`` ``GCCcore/10.2.0`` +``3.65`` ``GCCcore/10.3.0`` ========== ==================================== @@ -25807,6 +26502,7 @@ version toolchain ``2.0.11`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.3.0-2.26``, ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``GCC/6.2.0-2.27``, ``GCC/6.3.0-2.27``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` ``2.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.0.13`` ``GCCcore/10.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``2.0.14`` ``GCCcore/10.3.0`` ========== ============================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -25933,7 +26629,7 @@ version toolchain NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. -*homepage*: http://www.nwchem-sw.org +*homepage*: https://www.nwchem-sw.org ===================== ============================================== ================================ version versionsuffix toolchain @@ -25942,6 +26638,7 @@ version versionsuffix toolc ``6.6.revision27746`` ``-2015-10-20-patches-20170814-Python-2.7.13`` ``intel/2017a`` ``6.8.revision47`` ``-2017-12-14-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` ``7.0.0`` ``-Python-3.7.4`` ``intel/2019b`` +``7.0.2`` ``-Python-3.7.4`` ``intel/2019b`` ===================== ============================================== ================================ @@ -25967,7 +26664,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -26074,6 +26771,23 @@ version versionsuffix toolchain ========= ============= ================================================ +.. _list_software_Octopus-vcf_1113: + +*Octopus-vcf* ++++++++++++++ + +Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities in a sequential manner. This allows octopus to implicitly consider all possible haplotypes at a given loci in reasonable time. + +*homepage*: https://github.com/luntergroup/octopus + +========= ============== +version toolchain +========= ============== +``0.7.1`` ``foss/2020b`` +``0.7.2`` ``foss/2020b`` +========= ============== + + .. _list_software_OMA_221: *OMA* @@ -26090,6 +26804,22 @@ version toolchain ========= ========== +.. _list_software_onedrive_860: + +*onedrive* +++++++++++ + +A free Microsoft OneDrive Client which supports OneDrive Personal, OneDrive for Business, OneDrive for Office365 and SharePoint. + +*homepage*: https://abraunegg.github.io/ + +========== ================== +version toolchain +========== ================== +``2.4.11`` ``GCCcore/10.2.0`` +========== ================== + + .. _list_software_OOMPA_380: *OOMPA* @@ -26209,6 +26939,7 @@ version versionsuffix toolchain ``0.3.8`` ``GCC/9.2.0`` ``0.3.9`` ``GCC/9.3.0`` ``0.3.12`` ``GCC/10.2.0`` +``0.3.15`` ``GCC/10.3.0`` ========== ================= ========================================================== @@ -26225,6 +26956,7 @@ openCARP is an open cardiac electrophysiology simulator for in-silico experiment version versionsuffix toolchain ======= ================= ============== ``3.2`` ``-Python-3.8.2`` ``foss/2020a`` +``6.0`` ``foss/2020b`` ======= ================= ============== @@ -26313,6 +27045,7 @@ version toolchain ``2.4.0`` ``GCCcore/8.3.0`` ``2.4.1`` ``GCCcore/9.3.0`` ``2.5.5`` ``GCCcore/10.2.0`` +``3.0.1`` ``GCCcore/10.3.0`` ========= ================================ @@ -26421,14 +27154,14 @@ OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been d *homepage*: https://www.openjpeg.org/ -========= ===================================== -version toolchain -========= ===================================== -``2.1`` ``GCCcore/6.4.0`` -``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2.4.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========= ===================================== +========= ========================================================= +version toolchain +========= ========================================================= +``2.1`` ``GCCcore/6.4.0`` +``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.4.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +========= ========================================================= .. _list_software_OpenKIM-API_890: @@ -26473,13 +27206,15 @@ OpenMM is a toolkit for molecular simulation. *homepage*: http://openmm.org -========= ================= =============================== -version versionsuffix toolchain -========= ================= =============================== -``7.1.1`` ``-Python-3.6.3`` ``intel/2017b`` -``7.4.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``7.4.2`` ``-Python-3.8.2`` ``intel/2020a`` -========= ================= =============================== +========= ================= =================================== +version versionsuffix toolchain +========= ================= =================================== +``7.1.1`` ``-Python-3.6.3`` ``intel/2017b`` +``7.4.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``7.4.2`` ``-Python-3.8.2`` ``intel/2020a`` +``7.5.0`` ``foss/2020b``, ``intel/2020b`` +``7.5.0`` ``-Python-3.8.2`` ``fosscuda/2020a``, ``intel/2020a`` +========= ================= =================================== .. _list_software_OpenMMTools_1085: @@ -26507,12 +27242,13 @@ OpenMolcas is a quantum chemistry software package *homepage*: https://gitlab.com/Molcas/OpenMolcas -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``18.09`` ``-Python-3.6.6`` ``intel/2018b`` -``20.10`` ``-Python-3.8.2`` ``intel/2020a`` -========= ================= =============== +========= ====================== =============== +version versionsuffix toolchain +========= ====================== =============== +``18.09`` ``-Python-3.6.6`` ``intel/2018b`` +``20.10`` ``-Python-3.8.2`` ``intel/2020a`` +``20.10`` ``-Python-3.8.2-noGA`` ``intel/2020a`` +========= ====================== =============== .. _list_software_OpenMPI_632: @@ -26561,6 +27297,7 @@ version versionsuffix toolchain ``4.0.3`` ``GCC/9.3.0``, ``gcccuda/2020a``, ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` ``4.0.5`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` ``4.1.0`` ``GCC/10.2.0`` +``4.1.1`` ``GCC/10.3.0`` ``system`` ``GCC/system-2.29`` ========== ============= ==================================================================================================================== @@ -26726,11 +27463,13 @@ The OpenSSL Project is a collaborative effort to develop a robust, commercial-gr ========== ===================================================================== version toolchain ========== ===================================================================== +``1.0`` ``system`` ``1.0.1f`` ``GCC/4.8.2`` ``1.0.1k`` ``GCC/4.9.2`` ``1.0.1s`` ``foss/2016a``, ``intel/2016a`` ``1.0.2g`` ``GCCcore/4.9.3`` ``1.0.2h`` ``foss/2016.04``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` +``1.1`` ``system`` ``1.1.0c`` ``GCC/5.4.0-2.26`` ``1.1.0e`` ``intel/2016b`` ``1.1.0h`` ``GCCcore/7.3.0`` @@ -26738,6 +27477,7 @@ version toolchain ``1.1.1d`` ``GCCcore/8.3.0`` ``1.1.1e`` ``GCCcore/9.3.0`` ``1.1.1h`` ``GCCcore/10.2.0`` +``1.1.1k`` ``GCCcore/10.3.0`` ========== ===================================================================== @@ -26938,7 +27678,7 @@ version toolchain OSU Micro-Benchmarks -*homepage*: https://mvapich.cse.ohio-state.edu/benchmarks/ +*homepage*: http://mvapich.cse.ohio-state.edu/benchmarks/ ========= ============================================================================================================================================================================================= version toolchain @@ -26946,7 +27686,8 @@ version toolchain ``5.3.2`` ``foss/2016a``, ``foss/2017a`` ``5.6.2`` ``gompi/2019a`` ``5.6.3`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2019b``, ``iimpic/2020a`` -``5.7`` ``gompi/2020b``, ``gompic/2020b`` +``5.7`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b`` +``5.7.1`` ``ffmpi/4.5.0``, ``gompi/2021a`` ========= ============================================================================================================================================================================================= @@ -27006,7 +27747,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -27025,6 +27766,22 @@ version toolchain ========== ====================================================================== +.. _list_software_p4-phylogenetics_1615: + +*p4-phylogenetics* +++++++++++++++++++ + +A Python phyloinformatic toolkit, and an implementation of tree-heterogeneous models of evolution. + +*homepage*: http://p4.nhm.ac.uk/ + +================ ================= ============== +version versionsuffix toolchain +================ ================= ============== +``1.4-20210322`` ``-Python-3.7.4`` ``foss/2019b`` +================ ================= ============== + + .. _list_software_p4est_496: *p4est* @@ -27074,6 +27831,7 @@ version toolchain ``9.38.1`` ``GCC/4.9.2``, ``system`` ``16.02`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2018a`` ``17.03`` ``GCCcore/10.2.0`` +``17.04`` ``GCCcore/10.3.0`` ========== =========================================================================== @@ -27096,6 +27854,22 @@ version toolchain =========== =============================== +.. _list_software_pagmo_532: + +*pagmo* ++++++++ + +pagmo is a C++ scientific library for massively parallel optimization. + +*homepage*: https://esa.github.io/pagmo2 + +========== ============== +version toolchain +========== ============== +``2.17.0`` ``foss/2020b`` +========== ============== + + .. _list_software_PAML_298: *PAML* @@ -27188,6 +27962,7 @@ version toolchain ``2.1.3`` ``system`` ``2.5`` ``system`` ``2.10`` ``system`` +``2.13`` ``system`` ========= ========== @@ -27265,6 +28040,7 @@ version toolchain ``20190922`` ``GCCcore/8.3.0`` ``20200422`` ``GCCcore/9.3.0`` ``20200522`` ``GCCcore/9.3.0`` +``20210322`` ``GCCcore/10.2.0`` ============ =============================== @@ -27316,6 +28092,7 @@ version toolchain ``2.4`` ``foss/2018b`` ``2.4.1`` ``GCC/8.3.0``, ``intel/2019b`` ``2.4.2`` ``iccifort/2020.1.217`` +``2.4.3`` ``GCC/10.2.0`` ========= ============================== @@ -27526,6 +28303,7 @@ PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computatio version versionsuffix toolchain =========== ============= ========== ``4.0a166`` ``-centos64`` ``system`` +``4.0a168`` ``-centos64`` ``system`` =========== ============= ========== @@ -27749,7 +28527,7 @@ version toolchain ``8.41`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``8.42`` ``GCCcore/6.4.0`` ``8.43`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``8.44`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``8.44`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ======== ================================================================================== @@ -27770,6 +28548,7 @@ version toolchain ``10.33`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``10.34`` ``GCCcore/9.3.0`` ``10.35`` ``GCCcore/10.2.0`` +``10.36`` ``GCCcore/10.3.0`` ========= ==================================== @@ -27871,6 +28650,7 @@ version versionsuffix toolchain ``5.30.0`` ``GCCcore/8.3.0`` ``5.30.2`` ``GCCcore/9.3.0`` ``5.32.0`` ``GCCcore/10.2.0`` +``5.32.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` ========== ============= ========================================================================================= @@ -28199,6 +28979,7 @@ version versionsuffix toolchain ``1.14.2`` ``-Python-2.7.15`` ``intel/2018b`` ``2.0.0`` ``-Python-2.7.14`` ``intel/2018a`` ``2.2.0`` ``-Python-3.7.2`` ``intel/2019a`` +``2.7.1`` ``-Python-3.7.4`` ``intel/2019b`` ``2.7.1`` ``-Python-3.8.2`` ``intel/2020a`` ============= ================== =============================== @@ -28346,7 +29127,7 @@ version versionsuffix toolchain *pigz* ++++++ -pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. +pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. *homepage*: https://zlib.net/pigz/ @@ -28356,6 +29137,7 @@ version toolchain ``2.3.3`` ``foss/2016b`` ``2.3.4`` ``GCCcore/6.4.0`` ``2.4`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` +``2.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ================================================================================================================================= @@ -28647,7 +29429,7 @@ version toolchain ``0.34.0`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``0.38.0`` ``GCCcore/8.2.0`` ``0.38.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.40.0`` ``GCCcore/10.2.0`` +``0.40.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========== ============================================================================================================================================ @@ -28676,14 +29458,14 @@ pkg-config is a helper tool used when compiling applications and libraries. It *homepage*: http://www.freedesktop.org/wiki/Software/pkg-config/ -========== ==================================================================================================================================================================================== -version toolchain -========== ==================================================================================================================================================================================== -``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` -``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``0.29.2`` ``GCCcore/10.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a``, ``system`` -========== ==================================================================================================================================================================================== +========== ======================================================================================================================================================================================================== +version toolchain +========== ======================================================================================================================================================================================================== +``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` +``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``0.29.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a``, ``system`` +========== ======================================================================================================================================================================================================== .. _list_software_pkgconfig_952: @@ -29042,6 +29824,7 @@ version toolchain ``3.1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``3.1.4`` ``GCCcore/8.3.0`` ``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.2.3`` ``GCCcore/10.3.0`` ========= ======================================================= @@ -29054,14 +29837,14 @@ Parallel netCDF: A Parallel I/O Library for NetCDF File Access *homepage*: https://trac.mcs.anl.gov/projects/parallel-netcdf -========== ================================ -version toolchain -========== ================================ -``1.8.1`` ``intel/2017a`` -``1.9.0`` ``intel/2018a`` -``1.10.0`` ``foss/2018b``, ``intel/2018b`` -``1.12.1`` ``gompi/2020a``, ``iimpi/2020a`` -========== ================================ +========== ================================================== +version toolchain +========== ================================================== +``1.8.1`` ``intel/2017a`` +``1.9.0`` ``intel/2018a`` +``1.10.0`` ``foss/2018b``, ``intel/2018b`` +``1.12.1`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a`` +========== ================================================== .. _list_software_pocl_430: @@ -29073,15 +29856,15 @@ Pocl is a portable open source (MIT-licensed) implementation of the OpenCL stand *homepage*: https://portablecl.org -======= ======================================= -version toolchain -======= ======================================= -``1.2`` ``GCC/7.3.0-2.30`` -``1.3`` ``GCC/8.2.0-2.31.1``, ``gcccuda/2019a`` -``1.4`` ``GCC/8.3.0``, ``gcccuda/2019b`` -``1.5`` ``GCC/9.3.0`` -``1.6`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -======= ======================================= +======= ========================================================== +version toolchain +======= ========================================================== +``1.2`` ``GCC/7.3.0-2.30`` +``1.3`` ``GCC/8.2.0-2.31.1``, ``gcccuda/2019a`` +``1.4`` ``GCC/8.3.0``, ``gcccuda/2019b`` +``1.5`` ``GCC/9.3.0`` +``1.6`` ``GCC/10.2.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` +======= ========================================================== .. _list_software_poetry_675: @@ -29483,13 +30266,14 @@ version toolchain Primer3 is a widely used program for designing PCR primers (PCR = 'Polymerase Chain Reaction'). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers. -*homepage*: http://primer3.sourceforge.net +*homepage*: https://primer3.org/ ========= ========================================================= version toolchain ========= ========================================================= ``2.3.7`` ``intel/2017b`` ``2.4.0`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` +``2.5.0`` ``GCC/9.3.0`` ========= ========================================================= @@ -29550,11 +30334,11 @@ Tool for genome-wide association analysis of imputed genetic data. *homepage*: http://www.genabel.org/packages/ProbABEL -========= ========== -version toolchain -========= ========== -``0.5.0`` ``system`` -========= ========== +========= ============================= +version toolchain +========= ============================= +``0.5.0`` ``GCCcore/9.3.0``, ``system`` +========= ============================= .. _list_software_prodigal_850: @@ -29621,15 +30405,15 @@ Prokka is a software tool for the rapid annotation of prokaryotic genomes. *homepage*: https://www.vicbioinformatics.com/software.prokka.shtml -========== ================== ================================ -version versionsuffix toolchain -========== ================== ================================ -``1.11`` ``-BioPerl-1.7.0`` ``foss/2016b`` -``1.13`` ``-BioPerl-1.7.2`` ``intel/2018a`` -``1.13.4`` ``foss/2018b`` -``1.13.7`` ``gompi/2019a`` -``1.14.5`` ``gompi/2019a``, ``gompi/2019b`` -========== ================== ================================ +========== ================== ================================================= +version versionsuffix toolchain +========== ================== ================================================= +``1.11`` ``-BioPerl-1.7.0`` ``foss/2016b`` +``1.13`` ``-BioPerl-1.7.2`` ``intel/2018a`` +``1.13.4`` ``foss/2018b`` +``1.13.7`` ``gompi/2019a`` +``1.14.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020b`` +========== ================== ================================================= .. _list_software_prompt-toolkit_1493: @@ -29808,6 +30592,7 @@ version toolchain ========== ================= ``2.2.12`` ``GCCcore/8.3.0`` ``2.3.1`` ``GCCcore/9.3.0`` +``2.3.3`` ``GCCcore/9.3.0`` ========== ================= @@ -30114,11 +30899,12 @@ A python library for manipulating sequential and combinatorial circuits. This mo *homepage*: https://github.com/mvcisback/py-aiger -========= ================= ================= -version versionsuffix toolchain -========= ================= ================= -``6.1.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -========= ================= ================= +========== ================= ================== +version versionsuffix toolchain +========== ================= ================== +``6.1.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``6.1.14`` ``GCCcore/10.2.0`` +========== ================= ================== .. _list_software_py-aiger-bdd_1141: @@ -30219,6 +31005,7 @@ version versionsuffix toolchain ``0.8.0`` ``foss/2019a``, ``intel/2019a`` ``0.8.1`` ``foss/2019b`` ``0.8.2`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``0.8.2`` ``-Python-2.7.18`` ``GCC/10.2.0`` ========== ================== ======================================= @@ -30273,6 +31060,7 @@ version versionsuffix toolchain ``2.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``2.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``2.6.0`` ``GCCcore/10.2.0`` +``2.6.2`` ``GCCcore/10.3.0`` ========= ================= ================== @@ -30314,6 +31102,7 @@ version toolchain ============ ========== ``2017.2.3`` ``system`` ``2019.3.1`` ``system`` +``2021.1.1`` ``system`` ============ ========== @@ -30495,14 +31284,15 @@ Pure python package for DICOM medical file reading and writing. *homepage*: https://pydicom.github.io/ -========= ================== ================= -version versionsuffix toolchain -========= ================== ================= -``0.9.9`` ``-Python-2.7.11`` ``intel/2016a`` -``1.2.2`` ``GCCcore/8.2.0`` -``1.4.2`` ``GCCcore/8.3.0`` -``2.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -========= ================== ================= +========= ================== ================== +version versionsuffix toolchain +========= ================== ================== +``0.9.9`` ``-Python-2.7.11`` ``intel/2016a`` +``1.2.2`` ``GCCcore/8.2.0`` +``1.4.2`` ``GCCcore/8.3.0`` +``2.1.2`` ``GCCcore/10.2.0`` +``2.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +========= ================== ================== .. _list_software_pydlpoly_893: @@ -30535,6 +31325,7 @@ Python interface to Graphviz's Dot language. version toolchain ========= ================================= ``1.4.1`` ``GCCcore/9.3.0``, ``foss/2019b`` +``1.4.2`` ``GCCcore/10.2.0`` ========= ================================= @@ -30588,6 +31379,38 @@ version versionsuffix toolchain ========== ================= ================================== +.. _list_software_pyfaidx_757: + +*pyfaidx* ++++++++++ + +pyfaidx: efficient pythonic random access to fasta subsequences + +*homepage*: https://pypi.python.org/pypi/pyfaidx + +=========== ================== +version toolchain +=========== ================== +``0.5.9.5`` ``GCCcore/10.2.0`` +=========== ================== + + +.. _list_software_pyfasta_760: + +*pyfasta* ++++++++++ + +fast, memory-efficient, pythonic (and command-line) access to fasta sequence files + +*homepage*: https://pypi.org/project/pyfasta/ + +========= ============== +version toolchain +========= ============== +``0.5.2`` ``foss/2020b`` +========= ============== + + .. _list_software_PyFFmpeg_766: *PyFFmpeg* @@ -30739,6 +31562,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_pygmo_556: + +*pygmo* ++++++++ + +pygmo is a scientific Python library for massively parallel optimization. + +*homepage*: https://esa.github.io/pygmo2 + +========== ============== +version toolchain +========== ============== +``2.16.1`` ``foss/2020b`` +========== ============== + + .. _list_software_PyGObject_871: *PyGObject* @@ -30930,6 +31769,7 @@ version versionsuffix toolchain ``1.9.3`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``1.9.5`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``1.9.5`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +``2.7.4`` ``GCCcore/10.2.0`` ========= ================== ================================================ @@ -31185,13 +32025,14 @@ Python interface to PROJ4 library for cartographic transformations *homepage*: https://pyproj4.github.io/pyproj -=============== ================= ================= -version versionsuffix toolchain -=============== ================= ================= -``2.1.3`` ``GCCcore/8.2.0`` -``2.4.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``2.6.1.post1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -=============== ================= ================= +=============== ================= ================== +version versionsuffix toolchain +=============== ================= ================== +``2.1.3`` ``GCCcore/8.2.0`` +``2.4.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.6.1.post1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``3.0.1`` ``GCCcore/10.2.0`` +=============== ================= ================== .. _list_software_pyqstem_787: @@ -31404,6 +32245,7 @@ version versionsuffix toolchain ``0.15.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``0.15.3`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ``0.16.0.1`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` +``0.16.0.1`` ``-Python-2.7.18`` ``GCC/10.2.0`` ============ ================== ============================================================================================== @@ -31414,13 +32256,14 @@ version versionsuffix toolchain PySAT is a Python toolkit, which aims at providing a simple and unified interface to a number of state-of-art Boolean satisfiability (SAT) solvers as well as to a variety of cardinality and pseudo-Boolean encodings. -*homepage*: https://github.com/mvcisback/py-aiger +*homepage*: https://pysathq.github.io/ -=============== ================= ============= -version versionsuffix toolchain -=============== ================= ============= -``0.1.6.dev11`` ``-Python-3.8.2`` ``GCC/9.3.0`` -=============== ================= ============= +=============== ================= ============== +version versionsuffix toolchain +=============== ================= ============== +``0.1.6.dev11`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``0.1.7.dev1`` ``GCC/10.2.0`` +=============== ================= ============== .. _list_software_pyScaf_614: @@ -31471,6 +32314,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_pysheds_768: + +*pysheds* ++++++++++ + +Simple and fast watershed delineation in python. + +*homepage*: https://mattbartos.com/pysheds/ + +=========== ============== +version toolchain +=========== ============== +``0.2.7.1`` ``foss/2020b`` +=========== ============== + + .. _list_software_pyshp_564: *pyshp* @@ -31705,6 +32564,7 @@ version versionsuffix toolchain ``2.7.15`` ``-bare`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``2.7.16`` ``GCCcore/8.3.0`` ``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.7.18`` ``-bare`` ``GCCcore/10.3.0`` ``3.5.1`` ``foss/2016a``, ``intel/2016a`` ``3.5.2`` ``foss/2016.04``, ``foss/2016b``, ``intel/2016b`` ``3.5.2`` ``-bare`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` @@ -31718,6 +32578,7 @@ version versionsuffix toolchain ``3.7.4`` ``GCCcore/8.3.0`` ``3.8.2`` ``GCCcore/9.3.0`` ``3.8.6`` ``GCCcore/10.2.0`` +``3.9.5`` ``GCCcore/10.3.0`` ========== ================= ================================================================================================================================================================= @@ -31746,14 +32607,14 @@ Python interface to the igraph high performance graph library, primarily aimed a *homepage*: https://igraph.org/python -=============== ================== ============================== -version versionsuffix toolchain -=============== ================== ============================== -``0.7.1.post6`` ``-Python-2.7.14`` ``intel/2017b`` -``0.7.1.post6`` ``-Python-3.6.6`` ``foss/2018b`` -``0.8.0`` ``foss/2019b``, ``foss/2020a`` -``0.9.0`` ``fosscuda/2020b`` -=============== ================== ============================== +=============== ================== ================================== +version versionsuffix toolchain +=============== ================== ================================== +``0.7.1.post6`` ``-Python-2.7.14`` ``intel/2017b`` +``0.7.1.post6`` ``-Python-3.6.6`` ``foss/2018b`` +``0.8.0`` ``foss/2019b``, ``foss/2020a`` +``0.9.0`` ``foss/2020b``, ``fosscuda/2020b`` +=============== ================== ================================== .. _list_software_python-Levenshtein_1876: @@ -31789,6 +32650,7 @@ version versionsuffix toolchain ``1.1.16`` ``-Python-3.6.6`` ``foss/2018b`` ``1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``1.2.2`` ``-Python-3.8.2`` ``intel/2020a`` +``1.2.4`` ``fosscuda/2020b`` ========== ================== =================================================== @@ -31850,6 +32712,7 @@ version versionsuffix toolchain ``1.6.0`` ``-Python-3.7.4-imkl`` ``fosscuda/2019b`` ``1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` ``1.7.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.8.1`` ``foss/2020b`` ========= ============================= ================================== @@ -32283,6 +33146,7 @@ version toolchain ``5.13.1`` ``GCCcore/8.3.0`` ``5.14.1`` ``GCCcore/9.3.0`` ``5.14.2`` ``GCCcore/10.2.0`` +``5.15.2`` ``GCCcore/10.3.0`` ========== ==================================================================================== @@ -32426,22 +33290,22 @@ Quantum ESPRESSO is an integrated suite of computer codes for electronic-struc *homepage*: https://www.quantum-espresso.org -========= ============= ================================================ -version versionsuffix toolchain -========= ============= ================================================ -``5.3.0`` ``intel/2016.02-GCC-4.9`` -``5.4.0`` ``intel/2016.02-GCC-4.9`` -``5.4.0`` ``-hybrid`` ``foss/2016b`` -``6.0`` ``intel/2016b`` -``6.1`` ``intel/2017a`` -``6.2`` ``intel/2017b`` -``6.2.1`` ``iomkl/2017b`` -``6.3`` ``foss/2018b``, ``intel/2018b`` -``6.4.1`` ``intel/2019a`` -``6.5`` ``intel/2019a``, ``intel/2019b`` -``6.6`` ``foss/2019b``, ``foss/2020b``, ``intel/2019b`` -``6.7`` ``foss/2019b``, ``intel/2019b``, ``iomkl/2019b`` -========= ============= ================================================ +========= ============= =============================================================== +version versionsuffix toolchain +========= ============= =============================================================== +``5.3.0`` ``intel/2016.02-GCC-4.9`` +``5.4.0`` ``intel/2016.02-GCC-4.9`` +``5.4.0`` ``-hybrid`` ``foss/2016b`` +``6.0`` ``intel/2016b`` +``6.1`` ``intel/2017a`` +``6.2`` ``intel/2017b`` +``6.2.1`` ``iomkl/2017b`` +``6.3`` ``foss/2018b``, ``intel/2018b`` +``6.4.1`` ``intel/2019a`` +``6.5`` ``intel/2019a``, ``intel/2019b`` +``6.6`` ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2019b`` +``6.7`` ``foss/2019b``, ``intel/2019b``, ``iomkl/2019b`` +========= ============= =============================================================== .. _list_software_QUAST_398: @@ -32449,7 +33313,7 @@ version versionsuffix toolchain *QUAST* +++++++ -QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. +QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. *homepage*: https://github.com/ablab/quast @@ -32459,6 +33323,7 @@ version versionsuffix toolchain ``4.6.0`` ``-Python-3.5.2`` ``foss/2016b`` ``4.6.3`` ``-Python-3.6.4`` ``foss/2018a`` ``5.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` +``5.0.2`` ``-Python-2.7.18`` ``foss/2020b`` ``5.0.2`` ``-Python-3.7.2`` ``foss/2019a`` ``5.0.2`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ============================== @@ -32590,7 +33455,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -32656,6 +33521,22 @@ version versionsuffix toolchain ======== ============= =============================== +.. _list_software_R-INLA_419: + +*R-INLA* +++++++++ + +R-INLA is a package in R that do approximate Bayesian inference for Latent Gaussian Models. + +*homepage*: https://www.r-inla.org + +============ ============= ============== +version versionsuffix toolchain +============ ============= ============== +``21.05.02`` ``-R-4.0.4`` ``foss/2020b`` +============ ============= ============== + + .. _list_software_R-keras_661: *R-keras* @@ -32671,6 +33552,7 @@ version versionsuffix toolchain ``2.1.6`` ``-R-3.4.4`` ``foss/2018a`` ``2.2.5.0`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a``, ``fosscuda/2019a`` ``2.2.5.0`` ``-Python-3.7.4-R-3.6.2`` ``foss/2019b``, ``fosscuda/2019b`` +``2.4.0`` ``-R-4.0.4`` ``foss/2020b``, ``fosscuda/2020b`` =========== ========================= ================================== @@ -32867,6 +33749,7 @@ Rasterio reads and writes geospatial raster data. version versionsuffix toolchain ========= ================= ============== ``1.1.7`` ``-Python-3.8.2`` ``foss/2020a`` +``1.2.3`` ``foss/2020b`` ========= ================= ============== @@ -32911,17 +33794,17 @@ RAxML search algorithm for maximum likelihood based inference of phylogenetic tr *homepage*: https://github.com/stamatak/standard-RAxML -========== ================ ================================================= -version versionsuffix toolchain -========== ================ ================================================= -``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` -``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` -``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` -``8.2.12`` ``-hybrid-avx2`` ``iimpi/2019b``, ``intel/2018b``, ``intel/2019a`` -========== ================ ================================================= +========== ================ ================================================================== +version versionsuffix toolchain +========== ================ ================================================================== +``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` +``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` +``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` +``8.2.12`` ``-hybrid-avx2`` ``gompi/2020a``, ``iimpi/2019b``, ``intel/2018b``, ``intel/2019a`` +========== ================ ================================================================== .. _list_software_RAxML-NG_614: @@ -32938,6 +33821,7 @@ version toolchain ========= ============================== ``0.9.0`` ``GCC/8.3.0``, ``gompi/2019b`` ``1.0.1`` ``gompi/2019b`` +``1.0.2`` ``gompi/2020b`` ========= ============================== @@ -33016,11 +33900,12 @@ Rclone is a command line program to sync files and directories to and from a va *homepage*: https://rclone.org/ -======== ============= ========== -version versionsuffix toolchain -======== ============= ========== -``1.42`` ``-amd64`` ``system`` -======== ============= ========== +========== ============= ========== +version versionsuffix toolchain +========== ============= ========== +``1.42`` ``-amd64`` ``system`` +``1.54.1`` ``-amd64`` ``system`` +========== ============= ========== .. _list_software_Rcorrector_1061: @@ -33142,6 +34027,7 @@ version toolchain ``1.2.1`` ``GCCcore/8.3.0`` ``1.3`` ``GCCcore/9.3.0`` ``2.0.3`` ``GCCcore/10.2.0`` +``2.1.1`` ``GCCcore/10.3.0`` ========= ================== @@ -33231,9 +34117,26 @@ version toolchain ``3.4.1`` ``system`` ``3.5.0`` ``system`` ``3.5.1`` ``system`` +``3.5.2`` ``system`` ========= ========== +.. _list_software_RegTools_815: + +*RegTools* +++++++++++ + +RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. + +*homepage*: https://regtools.readthedocs.org + +========= ============== +version toolchain +========= ============== +``0.5.2`` ``foss/2020b`` +========= ============== + + .. _list_software_RELION_457: *RELION* @@ -33339,6 +34242,22 @@ version versionsuffix toolchain ============ ====================== ========================================================== +.. _list_software_request_777: + +*request* ++++++++++ + +Request is designed to be the simplest way possible to make http calls. It supports HTTPS and follows redirects by default. + +*homepage*: https://github.com/request/request/ + +========== =================== ================== +version versionsuffix toolchain +========== =================== ================== +``2.88.1`` ``-nodejs-12.19.0`` ``fosscuda/2020b`` +========== =================== ================== + + .. _list_software_requests_892: *requests* @@ -33515,9 +34434,26 @@ Rmath is the standalone version of the R math library. Rmath can be used in you version toolchain ========= =============== ``3.3.1`` ``intel/2016b`` +``4.0.4`` ``foss/2020b`` ========= =============== +.. _list_software_rMATS-turbo_1024: + +*rMATS-turbo* ++++++++++++++ + +rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net). + +*homepage*: https://github.com/Xinglab/rmats-turbo + +========= ============== +version toolchain +========= ============== +``4.1.1`` ``foss/2020b`` +========= ============== + + .. _list_software_RMBlast_661: *RMBlast* @@ -34049,6 +34985,7 @@ version toolchain ``1.35.0`` ``GCCcore/8.2.0`` ``1.37.0`` ``GCCcore/8.3.0`` ``1.42.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.52.1`` ``GCCcore/10.3.0`` ========== ========================================================================== @@ -34058,7 +34995,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -34194,12 +35131,13 @@ Sambamba is a high performance modern robust and fast tool (and library), writt *homepage*: https://lomereiter.github.io/sambamba/ -========= ========== -version toolchain -========= ========== -``0.6.6`` ``system`` -``0.7.1`` ``system`` -========= ========== +========= ============== +version toolchain +========= ============== +``0.6.6`` ``system`` +``0.7.1`` ``system`` +``0.8.0`` ``GCC/10.2.0`` +========= ============== .. _list_software_samblaster_1070: @@ -34215,6 +35153,7 @@ samblaster is a fast and flexible program for marking duplicates in read-id gro version toolchain ========== ============== ``0.1.24`` ``foss/2018b`` +``0.1.26`` ``GCC/10.2.0`` ========== ============== @@ -34239,15 +35178,16 @@ version toolchain *samclip* +++++++++ -Filter SAM file for soft and hard clipped alignments +Filter SAM file for soft and hard clipped alignments. *homepage*: https://github.com/tseemann/samclip -======= ================ ================= -version versionsuffix toolchain -======= ================ ================= -``0.2`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -======= ================ ================= +========= ================ ================= +version versionsuffix toolchain +========= ================ ================= +``0.2`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``0.4.0`` ``GCCcore/9.3.0`` +========= ================ ================= .. _list_software_SAMtools_786: @@ -34424,6 +35364,7 @@ version versionsuffix toolchain ``2.1.0`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b`` ``2.1.0`` ``-bf`` ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020b`` ``2.1.0`` ``-bl`` ``gompi/2020b`` +``2.1.0`` ``-fb`` ``gompi/2021a`` ``2.2`` ``-amd`` ``gompi/2020a`` ========= ================================= ============================================================================================================================================ @@ -34461,6 +35402,22 @@ version toolchain ======= ============= +.. _list_software_scanpy_654: + +*scanpy* +++++++++ + +Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. + +*homepage*: https://scanpy.readthedocs.io/en/stable/ + +========= ============== +version toolchain +========= ============== +``1.7.2`` ``foss/2020b`` +========= ============== + + .. _list_software_sciClone_816: *sciClone* @@ -34498,7 +35455,7 @@ version versionsuffix toolchain *scikit-allel* ++++++++++++++ -This package provides utilities for exploratory analysis of large scale genetic variation data. It is based on numpy, scipy and other general-purpose Python scientific libraries. +This package provides utilities for exploratory analysis of large scale genetic variation data. It is based on numpy, scipy and other general-purpose Python scientific libraries. *homepage*: https://scikit-allel.readthedocs.io/en/latest/ @@ -34507,6 +35464,7 @@ version versionsuffix toolchain ========= ================== ============== ``1.1.8`` ``-Python-2.7.13`` ``foss/2017a`` ``1.2.1`` ``-Python-3.8.2`` ``foss/2020a`` +``1.3.2`` ``foss/2020b`` ========= ================== ============== @@ -34535,13 +35493,13 @@ Scikit-Build, or skbuild, is an improved build system generator for CPython C/C+ *homepage*: https://scikit-build.readthedocs.io/en/latest -========== ================= ================================== -version versionsuffix toolchain -========== ================= ================================== -``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` -``0.11.1`` ``foss/2020b``, ``fosscuda/2020b`` -========== ================= ================================== +========== ================= ======================================================================== +version versionsuffix toolchain +========== ================= ======================================================================== +``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``0.11.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +========== ================= ======================================================================== .. _list_software_scikit-cuda_1105: @@ -34625,6 +35583,7 @@ version versionsuffix toolchain ``0.20.2`` ``-Python-3.6.6`` ``foss/2018b`` ``0.20.3`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``0.20.4`` ``-Python-2.7.16`` ``intel/2019b`` +``0.20.4`` ``-Python-2.7.18`` ``foss/2020b`` ``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``0.23.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``0.23.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` @@ -34732,9 +35691,11 @@ version versionsuffix toolchain ``2019.10`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``2019.10`` ``-Python-3.7.2`` ``intel/2019a`` ``2019.10`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` -``2020.03`` ``-Python-2.7.18`` ``foss/2020a``, ``intel/2020a`` +``2020.03`` ``-Python-2.7.18`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` ``2020.03`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``2020.11`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +``2020.11`` ``-Python-2.7.18`` ``foss/2020b`` +``2021.05`` ``foss/2021a`` =========== ================== ======================================================================== @@ -34779,27 +35740,28 @@ SCons is a software construction tool. *homepage*: https://www.scons.org/ -========= ======================= ================================================================================= -version versionsuffix toolchain -========= ======================= ================================================================================= -``2.4.1`` ``-Python-2.7.11`` ``foss/2016a`` -``2.5.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.5.1`` ``intel/2017a`` -``2.5.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.5.1`` ``-Python-2.7.13`` ``intel/2017a`` -``3.0.1`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a``, ``iomkl/2018a`` -``3.0.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` -``3.0.1`` ``-Python-2.7.15-bare`` ``GCCcore/7.3.0`` -``3.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``3.0.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``3.0.4`` ``-Python-2.7.15`` ``foss/2018b`` -``3.0.5`` ``GCCcore/8.2.0`` -``3.0.5`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` -``3.0.5`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``3.1.1`` ``GCCcore/8.3.0`` -``3.1.2`` ``GCCcore/9.3.0`` -``4.0.1`` ``GCCcore/10.2.0`` -========= ======================= ================================================================================= +=============== ======================= ================================================================================= +version versionsuffix toolchain +=============== ======================= ================================================================================= +``2.4.1`` ``-Python-2.7.11`` ``foss/2016a`` +``2.5.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``2.5.1`` ``intel/2017a`` +``2.5.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``2.5.1`` ``-Python-2.7.13`` ``intel/2017a`` +``3.0.1`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a``, ``iomkl/2018a`` +``3.0.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` +``3.0.1`` ``-Python-2.7.15-bare`` ``GCCcore/7.3.0`` +``3.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``3.0.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``3.0.4`` ``-Python-2.7.15`` ``foss/2018b`` +``3.0.5`` ``GCCcore/8.2.0`` +``3.0.5`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``3.0.5`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``3.1.1`` ``GCCcore/8.3.0`` +``3.1.2`` ``GCCcore/9.3.0`` +``4.0.1`` ``GCCcore/10.2.0`` +``4.1.0.post1`` ``GCCcore/10.2.0`` +=============== ======================= ================================================================================= .. _list_software_SCOOP_388: @@ -35031,9 +35993,9 @@ version toolchain *Seaborn* +++++++++ -Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. +Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. -*homepage*: https://stanford.edu/~mwaskom/software/seaborn/ +*homepage*: https://seaborn.pydata.org/ ========== ================== ========================================================================================= version versionsuffix toolchain @@ -35048,10 +36010,11 @@ version versionsuffix toolchain ``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``0.9.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``0.9.1`` ``-Python-2.7.16`` ``foss/2019b`` +``0.9.1`` ``-Python-2.7.18`` ``foss/2020b`` ``0.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``0.10.1`` ``intel/2020b`` ``0.10.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``0.11.1`` ``intel/2020b`` +``0.11.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ========== ================== ========================================================================================= @@ -35116,7 +36079,7 @@ segemehl is a software to map short sequencer reads to reference genomes. Unli version toolchain ========= ================================================ ``0.2.0`` ``foss/2016b``, ``intel/2017b``, ``intel/2018a`` -``0.3.4`` ``GCC/8.3.0``, ``foss/2018b`` +``0.3.4`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``foss/2018b`` ========= ================================================ @@ -35260,13 +36223,13 @@ SeqAn is an open source C++ library of efficient algorithms and data structures *homepage*: https://www.seqan.de/ -========= ============= =========================================================================================== -version versionsuffix toolchain -========= ============= =========================================================================================== -``1.4.2`` ``-library`` ``system`` -``2.3.2`` ``foss/2016b`` -``2.4.0`` ``GCC/8.2.0-2.31.1``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2018b`` -========= ============= =========================================================================================== +========= ============= =============================================================================================================== +version versionsuffix toolchain +========= ============= =============================================================================================================== +``1.4.2`` ``-library`` ``system`` +``2.3.2`` ``foss/2016b`` +``2.4.0`` ``GCC/8.2.0-2.31.1``, ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2018b`` +========= ============= =============================================================================================================== .. _list_software_SeqAn3_523: @@ -35302,6 +36265,22 @@ version toolchain ========== ========== +.. _list_software_SeqLib_576: + +*SeqLib* +++++++++ + +C++ interface to HTSlib, BWA-MEM and Fermi. + +*homepage*: https://github.com/walaj/SeqLib + +========= ============= +version toolchain +========= ============= +``1.2.0`` ``GCC/9.3.0`` +========= ============= + + .. _list_software_Seqmagick_917: *Seqmagick* @@ -35406,6 +36385,38 @@ version versionsuffix toolchain ============ ============= =============== +.. _list_software_SeuratData_1006: + +*SeuratData* +++++++++++++ + +SeuratData is a mechanism for distributing datasets in the form of Seurat objects using R's internal package and data management systems. + +*homepage*: https://github.com/satijalab/seurat-data + +============ ============= ============== +version versionsuffix toolchain +============ ============= ============== +``20210514`` ``-R-4.0.3`` ``foss/2020b`` +============ ============= ============== + + +.. _list_software_SeuratWrappers_1480: + +*SeuratWrappers* +++++++++++++++++ + +SeuratWrappers is a collection of community-provided methods and extensions for Seurat + +*homepage*: https://github.com/satijalab/seurat-wrappers + +============ ============= ============== +version versionsuffix toolchain +============ ============= ============== +``20210528`` ``-R-4.0.3`` ``foss/2020b`` +============ ============= ============== + + .. _list_software_sf_217: *sf* @@ -36119,6 +37130,22 @@ version toolchain ============ ============== +.. _list_software_smithwaterman_1412: + +*smithwaterman* ++++++++++++++++ + +smith-waterman-gotoh alignment algorithm. + +*homepage*: https://github.com/ekg/smithwaterman + +============ ================= +version toolchain +============ ================= +``20160702`` ``GCCcore/9.3.0`` +============ ================= + + .. _list_software_Smoldyn_742: *Smoldyn* @@ -36168,6 +37195,7 @@ version versionsuffix toolchain ``5.2.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``5.7.1`` ``-Python-3.7.2`` ``foss/2019a`` ``5.26.1`` ``-Python-3.8.2`` ``intel/2020a`` +``6.1.0`` ``foss/2020b`` ========== ================= =============================== @@ -36252,7 +37280,7 @@ version toolchain ``1.1.3`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25`` ``1.1.6`` ``system`` ``1.1.7`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``intel/2017b`` -``1.1.8`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.1.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================ @@ -36272,6 +37300,22 @@ version versionsuffix toolchain ========= ================ ============== +.. _list_software_snp-sites_934: + +*snp-sites* ++++++++++++ + +Finds SNP sites from a multi-FASTA alignment file. + +*homepage*: https://sanger-pathogens.github.io/snp-sites/ + +========= ================= +version toolchain +========= ================= +``2.5.1`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_snpEff_610: *snpEff* @@ -36530,20 +37574,21 @@ Genome assembler for single-cell and isolates data sets *homepage*: http://bioinf.spbau.ru/en/spades -========== ================= ============================================== -version versionsuffix toolchain -========== ================= ============================================== -``3.9.0`` ``foss/2016a``, ``foss/2016b`` -``3.10.1`` ``foss/2016b``, ``foss/2017a`` -``3.11.1`` ``foss/2017b``, ``foss/2018a`` -``3.12.0`` ``foss/2016b``, ``foss/2018a``, ``foss/2018b`` -``3.13.0`` ``foss/2018b`` -``3.13.1`` ``GCC/8.2.0-2.31.1`` -``3.14.0`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` -``3.14.0`` ``-Python-3.7.4`` ``GCC/8.3.0`` -``3.14.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` -``3.15.2`` ``GCC/10.2.0`` -========== ================= ============================================== +========== ================== ============================================== +version versionsuffix toolchain +========== ================== ============================================== +``3.9.0`` ``foss/2016a``, ``foss/2016b`` +``3.10.1`` ``foss/2016b``, ``foss/2017a`` +``3.11.1`` ``foss/2017b``, ``foss/2018a`` +``3.12.0`` ``foss/2016b``, ``foss/2018a``, ``foss/2018b`` +``3.13.0`` ``foss/2018b`` +``3.13.1`` ``GCC/8.2.0-2.31.1`` +``3.14.0`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` +``3.14.0`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``3.14.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``3.15.2`` ``GCC/10.2.0`` +``3.15.2`` ``-Python-2.7.18`` ``GCC/10.2.0`` +========== ================== ============================================== .. _list_software_spaln_542: @@ -36593,6 +37638,7 @@ version versionsuffix toolchain ``2.4.5`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` ``3.0.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``3.1.1`` ``fosscuda/2020b`` +``3.1.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= =========================================== =============================== @@ -36700,6 +37746,7 @@ version versionsuffix toolchain ``1.10.0.2`` ``-Python-3.6.3`` ``intel/2017b`` ``1.14.1.post0`` ``-Python-3.7.2`` ``intel/2019a`` ``1.16.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``1.16.0`` ``-Python-3.7.4`` ``intel/2019b`` ``1.16.0`` ``-Python-3.8.2`` ``intel/2020a`` ================ ================== =================================================== @@ -36923,6 +37970,7 @@ version toolchain ``3.29.0`` ``GCCcore/8.3.0`` ``3.31.1`` ``GCCcore/9.3.0`` ``3.33.0`` ``GCCcore/10.2.0`` +``3.35.4`` ``GCCcore/10.3.0`` ============ ==================================================================================================================================================================== @@ -36978,12 +38026,13 @@ Single Read Paired Read Indel Substitution Minimizer *homepage*: https://github.com/ncbi/SRPRISM -========= ============= ================= -version versionsuffix toolchain -========= ============= ================= -``3.0.0`` ``foss/2018b`` -``3.1.1`` ``-Java-11`` ``GCCcore/8.2.0`` -========= ============= ================= +========= ============= ================== +version versionsuffix toolchain +========= ============= ================== +``3.0.0`` ``foss/2018b`` +``3.1.1`` ``-Java-11`` ``GCCcore/8.2.0`` +``3.1.2`` ``GCCcore/10.2.0`` +========= ============= ================== .. _list_software_SSAHA2_418: @@ -37036,6 +38085,22 @@ version versionsuffix toolchain ========= ================ =============== +.. _list_software_SSW_253: + +*SSW* ++++++ + +SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically. + +*homepage*: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library + +======= ================= +version toolchain +======= ================= +``1.1`` ``GCCcore/9.3.0`` +======= ================= + + .. _list_software_Stack_502: *Stack* @@ -37245,21 +38310,21 @@ Statsmodels is a Python module that provides classes and functions for the esti *homepage*: https://www.statsmodels.org -========== ================== =============================== -version versionsuffix toolchain -========== ================== =============================== -``0.6.1`` ``-Python-2.7.13`` ``foss/2017a`` -``0.6.1`` ``-Python-3.5.1`` ``intel/2016a`` -``0.6.1`` ``-Python-3.5.2`` ``intel/2016b`` -``0.8.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``0.9.0`` ``-Python-2.7.16`` ``intel/2019b`` -``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.10.1`` ``foss/2019a`` -``0.11.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``0.11.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``0.12.1`` ``foss/2020b``, ``intel/2020b`` -========== ================== =============================== +========== ================== =================================================== +version versionsuffix toolchain +========== ================== =================================================== +``0.6.1`` ``-Python-2.7.13`` ``foss/2017a`` +``0.6.1`` ``-Python-3.5.1`` ``intel/2016a`` +``0.6.1`` ``-Python-3.5.2`` ``intel/2016b`` +``0.8.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.9.0`` ``-Python-2.7.16`` ``intel/2019b`` +``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.10.1`` ``foss/2019a`` +``0.11.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.11.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.12.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +========== ================== =================================================== .. _list_software_STEAK_376: @@ -37549,7 +38614,7 @@ version toolchain ``2.6.2`` ``intel/2016b``, ``intel/2018b`` ``2.7.0`` ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``5.1.0`` ``foss/2019b``, ``intel/2019b`` -``5.7.0`` ``foss/2020b``, ``intel/2020b`` +``5.7.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ========= ================================================================================================================================== @@ -37854,7 +38919,7 @@ Szip compression software, providing lossless compression of scientific data version toolchain ========= ============================================================================================================================================================================================================================================================================================= ``2.1`` ``GCC/4.8.1``, ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``gmpolf/2017.10``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================================================================================================================================================================================================= @@ -37864,7 +38929,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_typing-extensions_1816` +:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_typing-extensions_1816` .. _list_software_tabix_536: @@ -37883,6 +38948,22 @@ version toolchain ========= ========================================================================================================= +.. _list_software_tabixpp_760: + +*tabixpp* ++++++++++ + +C++ wrapper to tabix indexer + +*homepage*: https://github.com/ekg/tabixpp + +========= ============= +version toolchain +========= ============= +``1.1.0`` ``GCC/9.3.0`` +========= ============= + + .. _list_software_taco_423: *taco* @@ -37899,6 +38980,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_TagDust_700: + +*TagDust* ++++++++++ + +Raw sequences produced by next generation sequencing (NGS) machines may contain adapter, linker, barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences to be mapped in downstream pipelines. + +*homepage*: http://tagdust.sourceforge.net/ + +======== ===================================== +version toolchain +======== ===================================== +``2.33`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +======== ===================================== + + .. _list_software_TagLib_563: *TagLib* @@ -37931,6 +39028,22 @@ version versionsuffix toolchain ================== =============================== ================================== +.. _list_software_TALON_382: + +*TALON* ++++++++ + +TALON is a Python package for identifying and quantifying known and novel genes/isoforms in long-read transcriptome data sets. TALON is technology-agnostic in that it works from mapped SAM files, allowing data from different sequencing platforms (i.e. PacBio and Oxford Nanopore) to be analyzed side by side. + +*homepage*: https://github.com/mortazavilab/TALON + +======= ============== +version toolchain +======= ============== +``5.0`` ``foss/2020b`` +======= ============== + + .. _list_software_TAMkin_548: *TAMkin* @@ -37959,11 +39072,11 @@ A set of programs for the taxonomic analysis of nucleotide sequence data *homepage*: https://github.com/fungs/taxator-tk -========= =============================== -version toolchain -========= =============================== -``1.3.3`` ``foss/2018b``, ``gompi/2019a`` -========= =============================== +========= =============================================== +version toolchain +========= =============================================== +``1.3.3`` ``GCC/10.2.0``, ``foss/2018b``, ``gompi/2019a`` +========= =============================================== .. _list_software_tbb_312: @@ -38054,6 +39167,7 @@ version toolchain ``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``8.6.10`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``8.6.11`` ``GCCcore/10.3.0`` ========== ========================================================================================================================================================================= @@ -38070,6 +39184,7 @@ TCLAP is a small, flexible library that provides a simple interface for defining version toolchain ========= ================= ``1.2.2`` ``GCCcore/8.3.0`` +``1.2.4`` ``GCCcore/9.3.0`` ========= ================= @@ -38088,6 +39203,7 @@ version toolchain ``6.19.00`` ``intel/2016a`` ``6.20.00`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``6.22.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``6.22.03`` ``GCCcore/10.2.0`` =========== ======================================================= @@ -38209,6 +39325,7 @@ version versionsuffix toolchain ``2.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.2.2`` ``-Python-3.7.4`` ``foss/2019b`` ``2.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.3.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` ``2.4.1`` ``foss/2020b``, ``fosscuda/2020b`` @@ -38448,7 +39565,7 @@ version versionsuffix toolchain ``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` ``1.0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``1.0.4`` ``-Python-3.8.2`` ``foss/2020a`` -``1.1.2`` ``-PyMC`` ``fosscuda/2020b``, ``intel/2020b`` +``1.1.2`` ``-PyMC`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ========= ================== =================================================== @@ -38575,12 +39692,12 @@ The `time' command runs another program, then displays information about the res *homepage*: https://www.gnu.org/software/time/ -======= ======================================================= -version toolchain -======= ======================================================= -``1.7`` ``system`` -``1.9`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ======================================================= +======= =========================================================================== +version toolchain +======= =========================================================================== +``1.7`` ``system`` +``1.9`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= =========================================================================== .. _list_software_TINKER_461: @@ -38659,7 +39776,7 @@ version versionsuffix toolchain ``2.7.15`` ``GCCcore/8.2.0`` ``2.7.15`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.7.16`` ``GCCcore/8.3.0`` -``2.7.18`` ``GCCcore/9.3.0`` +``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``3.6.1`` ``-Python-3.6.1`` ``foss/2017a``, ``intel/2017a`` ``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` ``3.6.3`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` @@ -38688,23 +39805,40 @@ version toolchain ============ =============================== +.. _list_software_tMAE_327: + +*tMAE* +++++++ + +Package containing functions to: perform a negative binomial test on allele-specific counts add gnomAD minor allele frequencies MAplot (FC vs total counts) of allele-specific counts and results allelic counts (ALT vs REF) + +*homepage*: https://github.com/mumichae/tMAE + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``1.0.0`` ``-R-4.0.3`` ``foss/2020b`` +========= ============= ============== + + .. _list_software_tmux_462: *tmux* ++++++ -tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal. +tmux is a terminal multiplexer: it enables a number of terminals to be created, accessed, and controlled from a single screen. tmux may be detached from a screen and continue running in the background, then later reattached. -*homepage*: https://github.com/tmux/tmux +*homepage*: https://github.com/tmux/tmux/ -======== ============================== -version toolchain -======== ============================== -``1.9a`` ``GCC/4.9.2`` -``2.2`` ``GCCcore/4.9.3`` -``2.3`` ``GCC/5.4.0-2.26``, ``system`` -``3.1c`` ``GCCcore/8.3.0`` -======== ============================== +======== ===================================== +version toolchain +======== ===================================== +``1.9a`` ``GCC/4.9.2`` +``2.2`` ``GCCcore/4.9.3`` +``2.3`` ``GCC/5.4.0-2.26``, ``system`` +``3.1c`` ``GCCcore/8.3.0`` +``3.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +======== ===================================== .. _list_software_ToFu_382: @@ -38774,6 +39908,7 @@ version versionsuffix toolchain ``2.1.0`` ``-Python-2.7.14`` ``intel/2018a`` ``2.1.1`` ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``2.1.2`` ``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` +``2.1.2`` ``-Python-2.7.18`` ``GCC/10.2.0`` ========= ================== ================================================================================ @@ -38831,6 +39966,7 @@ version versionsuffix toolchain ``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` ``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0-imkl`` ``fosscuda/2019b`` ``0.8.2`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` +``0.8.2`` ``-Python-3.7.4-PyTorch-1.7.1`` ``fosscuda/2019b`` ========= ==================================== ================================== @@ -38873,6 +40009,7 @@ version versionsuffix toolchain ``4.47.0`` ``GCCcore/9.3.0`` ``4.51.0`` ``-Python-3.8.2`` ``intel/2020a`` ``4.56.2`` ``GCCcore/10.2.0`` +``4.60.0`` ``GCCcore/10.2.0`` ========== ================== =============================== @@ -38892,6 +40029,22 @@ version toolchain ========= ================= +.. _list_software_TranscriptClean_1549: + +*TranscriptClean* ++++++++++++++++++ + +TranscriptClean is a Python program that corrects mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome. + +*homepage*: https://github.com/mortazavilab/TranscriptClean + +========= ============== +version toolchain +========= ============== +``2.0.2`` ``foss/2020b`` +========= ============== + + .. _list_software_TransDecoder_1214: *TransDecoder* @@ -39010,15 +40163,16 @@ version versionsuffix toolchain *TRF* +++++ -Tandem repeats finder: a program to analyze DNA sequences. Legacy version. +Tandem Repeats Finder: a program to analyze DNA sequences. *homepage*: https://tandem.bu.edu/trf/trf.html -======== ============= ========== -version versionsuffix toolchain -======== ============= ========== -``4.09`` ``-linux64`` ``system`` -======== ============= ========== +========== ============= ===================================== +version versionsuffix toolchain +========== ============= ===================================== +``4.09`` ``-linux64`` ``system`` +``4.09.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========== ============= ===================================== .. _list_software_Triangle_822: @@ -39079,6 +40233,7 @@ version versionsuffix toolchain ``0.6.2`` ``-Python-2.7.15`` ``foss/2018b`` ``0.6.2`` ``-Python-3.6.6`` ``foss/2018b`` ``0.6.5`` ``-Java-11-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.6.6`` ``-Python-2.7.18`` ``GCC/10.2.0`` ``0.6.6`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ========================= =============================== @@ -39092,11 +40247,11 @@ A tool for automated alignment trimming in large-scale phylogenetic analyses *homepage*: http://trimal.cgenomics.org/ -========= ===================================== -version toolchain -========= ===================================== -``1.4.1`` ``GCC/8.2.0-2.31.1``, ``intel/2018a`` -========= ===================================== +========= ======================================================== +version toolchain +========= ======================================================== +``1.4.1`` ``GCC/8.2.0-2.31.1``, ``GCCcore/9.3.0``, ``intel/2018a`` +========= ======================================================== .. _list_software_Trimmomatic_1158: @@ -39385,7 +40540,7 @@ version versionsuffix toolchain --- -:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` +:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` .. _list_software_UCLUST_480: @@ -39425,6 +40580,7 @@ version versionsuffix toolchain ``1.8.0`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` ``1.9.0`` ``GCCcore/10.2.0`` ``1.9.0`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` +``1.10.0`` ``GCCcore/10.3.0`` ============ ================ ======================================================= @@ -39480,6 +40636,22 @@ version versionsuffix toolchain ============ ================= ============== +.. _list_software_umap-learn_1010: + +*umap-learn* +++++++++++++ + +Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction. + +*homepage*: https://pypi.org/project/umap-learn/ + +========= ================== +version toolchain +========= ================== +``0.4.6`` ``fosscuda/2020b`` +========= ================== + + .. _list_software_UMI-tools_841: *UMI-tools* @@ -39637,11 +40809,11 @@ UnZip is an extraction utility for archives compressed in .zip format (also call *homepage*: http://www.info-zip.org/UnZip.html -======= ================================================================================================================= -version toolchain -======= ================================================================================================================= -``6.0`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ================================================================================================================= +======= ===================================================================================================================================== +version toolchain +======= ===================================================================================================================================== +``6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ===================================================================================================================================== .. _list_software_UQTk_357: @@ -39722,25 +40894,25 @@ Set of Linux utilities *homepage*: https://www.kernel.org/pub/linux/utils/util-linux -========== ==================================== -version toolchain -========== ==================================== -``2.27.1`` ``foss/2016a``, ``intel/2016a`` -``2.28`` ``foss/2016a``, ``intel/2016a`` -``2.28.1`` ``intel/2016b`` -``2.29`` ``foss/2016b``, ``intel/2016b`` -``2.29.2`` ``GCCcore/6.3.0``, ``intel/2017a`` -``2.30`` ``GCCcore/6.4.0`` -``2.30.1`` ``GCCcore/6.3.0``, ``foss/2017a`` -``2.31`` ``GCCcore/6.4.0`` -``2.31.1`` ``GCCcore/6.4.0`` -``2.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.32.1`` ``GCCcore/7.3.0`` -``2.33`` ``GCCcore/8.2.0`` -``2.34`` ``GCCcore/8.3.0`` -``2.35`` ``GCCcore/9.3.0`` -``2.36`` ``GCCcore/10.2.0`` -========== ==================================== +========== ====================================== +version toolchain +========== ====================================== +``2.27.1`` ``foss/2016a``, ``intel/2016a`` +``2.28`` ``foss/2016a``, ``intel/2016a`` +``2.28.1`` ``intel/2016b`` +``2.29`` ``foss/2016b``, ``intel/2016b`` +``2.29.2`` ``GCCcore/6.3.0``, ``intel/2017a`` +``2.30`` ``GCCcore/6.4.0`` +``2.30.1`` ``GCCcore/6.3.0``, ``foss/2017a`` +``2.31`` ``GCCcore/6.4.0`` +``2.31.1`` ``GCCcore/6.4.0`` +``2.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.32.1`` ``GCCcore/7.3.0`` +``2.33`` ``GCCcore/8.2.0`` +``2.34`` ``GCCcore/8.3.0`` +``2.35`` ``GCCcore/9.3.0`` +``2.36`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========== ====================================== .. _list_software_letter_v: @@ -39749,7 +40921,7 @@ version toolchain --- -:ref:`list_software_V8_142` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VMD_231` - :ref:`list_software_voltools_898` - :ref:`list_software_vorbis-tools_1267` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` +:ref:`list_software_V8_142` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcflib_630` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VMD_231` - :ref:`list_software_voltools_898` - :ref:`list_software_vorbis-tools_1267` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` .. _list_software_V8_142: @@ -39787,6 +40959,7 @@ version toolchain ``3.13.0`` ``foss/2017b``, ``foss/2018a``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.14.0`` ``foss/2018b`` ``3.16.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020a`` +``3.17.0`` ``gompi/2021a`` ========== ================================================================================= @@ -39937,6 +41110,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_vcflib_630: + +*vcflib* +++++++++ + +vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals. + +*homepage*: https://github.com/vcflib/vcflib + +========= ================= ============= +version versionsuffix toolchain +========= ================= ============= +``1.0.2`` ``-Python-3.8.2`` ``GCC/9.3.0`` +========= ================= ============= + + .. _list_software_vcfnp_541: *vcfnp* @@ -40191,11 +41380,11 @@ Command-line tools for creating and playing Ogg Vorbis files. *homepage*: https://xiph.org/vorbis/ -========= ================== -version toolchain -========= ================== -``1.4.2`` ``GCCcore/10.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_Voro++_508: @@ -40363,11 +41552,11 @@ A tool set for short variant discovery in genetic sequence data. *homepage*: http://genome.sph.umich.edu/wiki/Vt -=========== ============== -version toolchain -=========== ============== -``0.57721`` ``foss/2018b`` -=========== ============== +=========== ============================= +version toolchain +=========== ============================= +``0.57721`` ``GCC/9.3.0``, ``foss/2018b`` +=========== ============================= .. _list_software_VTK_245: @@ -40508,7 +41697,7 @@ version versionsuffix toolchain ``2.0.1.1`` ``-abinit`` ``intel/2018b`` ``2.1.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``3.0.0`` ``intel/2018b`` -``3.1.0`` ``foss/2020b``, ``intel/2020b`` +``3.1.0`` ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` =========== ============= ================================================ @@ -40517,14 +41706,15 @@ version versionsuffix toolchain *WannierTools* ++++++++++++++ -an open-source software package for novel topological materials +WannierTools is an open source software that studies the physical properties of given tight-binding model. -*homepage*: http://www.wanniertools.com/ +*homepage*: http://www.wanniertools.com ========= =============== version toolchain ========= =============== ``2.3.0`` ``intel/2018a`` +``2.5.1`` ``intel/2020b`` ========= =============== @@ -40645,6 +41835,7 @@ version toolchain ``1.19.4`` ``GCCcore/6.4.0`` ``1.20.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ``1.20.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.21.1`` ``GCCcore/10.3.0`` ========== ===================================== @@ -40842,16 +42033,16 @@ The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale *homepage*: http://www.wrf-model.org -=========== ============= ================================ -version versionsuffix toolchain -=========== ============= ================================ -``3.8.0`` ``-dmpar`` ``intel/2016a``, ``intel/2016b`` -``3.9.1.1`` ``-dmpar`` ``foss/2020a``, ``intel/2020a`` -``4.0.1`` ``-dmpar`` ``intel/2018b`` -``4.0.2`` ``-dmpar`` ``foss/2018b`` -``4.1.3`` ``-dm+sm`` ``intel/2019b`` -``4.1.3`` ``-dmpar`` ``foss/2019b``, ``intel/2019b`` -=========== ============= ================================ +=========== ============= ================================================================ +version versionsuffix toolchain +=========== ============= ================================================================ +``3.8.0`` ``-dmpar`` ``intel/2016a``, ``intel/2016b`` +``3.9.1.1`` ``-dmpar`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` +``4.0.1`` ``-dmpar`` ``intel/2018b`` +``4.0.2`` ``-dmpar`` ``foss/2018b`` +``4.1.3`` ``-dm+sm`` ``intel/2019b`` +``4.1.3`` ``-dmpar`` ``foss/2019b``, ``intel/2019b`` +=========== ============= ================================================================ .. _list_software_WRF-Fire_674: @@ -40958,6 +42149,7 @@ version toolchain ``3.0.3`` ``foss/2018a`` ``3.0.4`` ``GCC/8.2.0-2.31.1`` ``3.1.3`` ``GCC/8.3.0`` +``3.1.4`` ``GCC/10.2.0`` ========= ==================== @@ -40967,7 +42159,7 @@ version toolchain --- -:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_XZ_178` +:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_XZ_178` .. _list_software_X11_186: @@ -40992,6 +42184,7 @@ version toolchain ``20190717`` ``GCCcore/8.3.0`` ``20200222`` ``GCCcore/9.3.0`` ``20201008`` ``GCCcore/10.2.0`` +``20210518`` ``GCCcore/10.3.0`` ============ ================================================== @@ -41021,6 +42214,7 @@ version toolchain ``20190925`` ``GCCcore/8.3.0`` ``20191217`` ``GCCcore/9.3.0`` ``20201026`` ``GCCcore/10.2.0`` +``20210414`` ``GCCcore/10.3.0`` ============ ================================= @@ -41044,6 +42238,7 @@ version toolchain ``3.0`` ``GCCcore/8.2.0`` ``3.2`` ``GCCcore/8.3.0`` ``3.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.5`` ``GCCcore/10.3.0`` ======= ===================================== @@ -41265,14 +42460,30 @@ Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerce *homepage*: https://xerces.apache.org/xerces-c/ -========= ==================================== -version toolchain -========= ==================================== -``3.1.4`` ``GCCcore/6.4.0`` -``3.2.0`` ``GCCcore/7.3.0`` -``3.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.2.3`` ``GCCcore/9.3.0`` -========= ==================================== +========= ===================================== +version toolchain +========= ===================================== +``3.1.4`` ``GCCcore/6.4.0`` +``3.2.0`` ``GCCcore/7.3.0`` +``3.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.2.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========= ===================================== + + +.. _list_software_xESMF_419: + +*xESMF* ++++++++ + +xESMF: Universal Regridder for Geospatial Data + +*homepage*: https://xesmf.readthedocs.io + +========= =============== +version toolchain +========= =============== +``0.3.0`` ``intel/2020b`` +========= =============== .. _list_software_xextproto_1021: @@ -41361,6 +42572,22 @@ version toolchain ======== =============================== +.. _list_software_XlsxWriter_1068: + +*XlsxWriter* +++++++++++++ + +A Python module for creating Excel XLSX files + +*homepage*: https://xlsxwriter.readthedocs.io/ + +========= ================== +version toolchain +========= ================== +``1.4.0`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_XMDS2_366: *XMDS2* @@ -41519,6 +42746,7 @@ version toolchain ``1.19.0`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``1.19.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.19.2`` ``GCCcore/10.2.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``1.19.3`` ``GCCcore/10.3.0`` ========== ==================================================================================================================================== @@ -41551,13 +42779,13 @@ X protocol and ancillary headers *homepage*: https://www.freedesktop.org/wiki/Software/xlibs -========== ============================================================================================= -version toolchain -========== ============================================================================================= -``7.0.28`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``7.0.29`` ``intel/2016a`` -``7.0.31`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ============================================================================================= +========== ===================================================================================================================================== +version toolchain +========== ===================================================================================================================================== +``7.0.28`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``7.0.29`` ``intel/2016a`` +``7.0.31`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ===================================================================================================================================== .. _list_software_XSD_239: @@ -41660,7 +42888,7 @@ version versionsuffix toolchain ``5.2.2`` ``-gettext-0.19.7`` ``foss/2016a``, ``intel/2016a`` ``5.2.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``gimkl/2017a`` ``5.2.4`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` -``5.2.5`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``5.2.5`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ========= =================== =========================================================================================================================================================== @@ -41792,11 +43020,11 @@ Yasm: Complete rewrite of the NASM assembler with BSD license *homepage*: http://www.tortall.net/projects/yasm/ -========= ======================================================================================================================================================================================================================================================= -version toolchain -========= ======================================================================================================================================================================================================================================================= -``1.3.0`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -========= ======================================================================================================================================================================================================================================================= +========= =========================================================================================================================================================================================================================================================================== +version toolchain +========= =========================================================================================================================================================================================================================================================================== +``1.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +========= =========================================================================================================================================================================================================================================================================== .. _list_software_YAXT_326: @@ -41814,6 +43042,7 @@ version toolchain ``0.5.1`` ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``0.6.0`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``0.6.2`` ``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` +``0.9.0`` ``gompi/2020b`` ========= ================================================= @@ -41848,7 +43077,7 @@ version toolchain *zarr* ++++++ -Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing. +Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing. *homepage*: https://zarr.readthedocs.io/en/stable/ @@ -41857,6 +43086,7 @@ version versionsuffix toolchain ========= ================== ============== ``2.1.4`` ``-Python-2.7.13`` ``foss/2017a`` ``2.4.0`` ``-Python-3.8.2`` ``foss/2020a`` +``2.8.1`` ``foss/2020b`` ========= ================== ============== @@ -41907,11 +43137,11 @@ Zip is a compression and file packaging/archive utility. Although highly compati *homepage*: http://www.info-zip.org/Zip.html -======= =========================================================================== -version toolchain -======= =========================================================================== -``3.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= =========================================================================== +======= =============================================================================================== +version toolchain +======= =============================================================================================== +``3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= =============================================================================================== .. _list_software_zlib_433: @@ -41929,7 +43159,7 @@ version toolchain ``1.2.7`` ``GCC/4.8.1``, ``GCC/4.8.2`` ``1.2.8`` ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.2.10`` ``system`` -``1.2.11`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` +``1.2.11`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -42000,5 +43230,6 @@ version toolchain ``1.4.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2018b`` ``1.4.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.4.5`` ``GCCcore/10.2.0`` +``1.4.9`` ``GCCcore/10.3.0`` ========= ==================================================== diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index 1e04d258..59509f14 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -48,6 +48,7 @@ * BuildEnv * CrayToolchain + * EB_OpenSSL_wrapper * PythonBundle * SystemCompiler * SystemMPI @@ -73,6 +74,7 @@ * EB_Doxygen * EB_Eigen * EB_ELSI + * EB_FlexiBLAS * EB_GATE * EB_Geant4 * EB_GROMACS @@ -256,6 +258,7 @@ * ConfigureMakePythonPackage * EB_cryptography + * EB_dm_minus_reverb * EB_EasyBuildMeta * EB_EggLib * EB_libxml2 @@ -388,6 +391,7 @@ * ConfigureMakePythonPackage * EB_cryptography + * EB_dm_minus_reverb * EB_EasyBuildMeta * EB_EggLib * EB_libxml2 diff --git a/docs/version-specific/easyconfig_constants.rst b/docs/version-specific/easyconfig_constants.rst index e04a2e19..ec6d4bf5 100644 --- a/docs/version-specific/easyconfig_constants.rst +++ b/docs/version-specific/easyconfig_constants.rst @@ -8,6 +8,7 @@ Constants that can be used in easyconfigs ====================== ============================================================= ================================================================================ Constant name Constant value Description ====================== ============================================================= ================================================================================ +``ARCH`` ``x86_64`` CPU architecture of current system (aarch64, x86_64, ppc64le, ...) ``EXTERNAL_MODULE`` ``EXTERNAL_MODULE`` External module marker ``HOME`` ``/home/example`` Home directory ($HOME) ``OS_NAME`` ``UNKNOWN`` System name (e.g. 'fedora' or 'RHEL') @@ -19,6 +20,6 @@ Constant name Constant value ``OS_TYPE`` ``Darwin`` System type (e.g. 'Linux' or 'Darwin') ``OS_VERSION`` ``UNKNOWN`` System version ``SYSTEM`` ``{'name': 'system', 'version': 'system'}`` System toolchain -``SYS_PYTHON_VERSION`` ``3.9.2`` System Python version (platform.python_version()) +``SYS_PYTHON_VERSION`` ``3.9.5`` System Python version (platform.python_version()) ====================== ============================================================= ================================================================================ diff --git a/docs/version-specific/easyconfig_parameters.rst b/docs/version-specific/easyconfig_parameters.rst index bac34327..439022f4 100644 --- a/docs/version-specific/easyconfig_parameters.rst +++ b/docs/version-specific/easyconfig_parameters.rst @@ -38,45 +38,48 @@ toolchain parameters build parameters ---------------- -============================= ===================================================================================================================== ================= -**Parameter name** **Description** **Default value** -============================= ===================================================================================================================== ================= -``bitbucket_account`` Bitbucket account name to be used to resolve template values in source URLs "%(namelower)s" -``buildopts`` Extra options passed to make step (default already has -j X) "" -``checksums`` Checksums for sources and patches [] -``configopts`` Extra options passed to configure (default already has --prefix) "" -``cuda_compute_capabilities`` List of CUDA compute capabilities to build with (if supported) [] -``easyblock`` EasyBlock to use for building; if set to None, an easyblock is selected based on the software name None -``easybuild_version`` EasyBuild-version this spec-file was written for None -``enhance_sanity_check`` Indicate that additional sanity check commands & paths should enhance the existin sanity check, not replace it False -``fix_perl_shebang_for`` List of files for which Perl shebang should be fixed to '#!/usr/bin/env perl' (glob patterns supported) None -``fix_python_shebang_for`` List of files for which Python shebang should be fixed to '#!/usr/bin/env python' (glob patterns supported) None -``github_account`` GitHub account name to be used to resolve template values in source URLs "%(namelower)s" -``hidden`` Install module file as 'hidden' by prefixing its version with '.' False -``installopts`` Extra options for installation "" -``maxparallel`` Max degree of parallelism None -``parallel`` Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit) None -``patches`` List of patches to apply [] -``postinstallcmds`` Commands to run after the install step. [] -``prebuildopts`` Extra options pre-passed to build command. "" -``preconfigopts`` Extra options pre-passed to configure. "" -``preinstallopts`` Extra prefix options for installation. "" -``pretestopts`` Extra prefix options for test. "" -``runtest`` Indicates if a test should be run after make; should specify argument after make (for e.g.,"test" for make test) None -``sanity_check_commands`` format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h') [] -``sanity_check_paths`` List of files and directories to check (format: {'files':, 'dirs':}) {} -``skip`` Skip existing software False -``skipsteps`` Skip these steps [] -``source_urls`` List of URLs for source files [] -``sources`` List of source files [] -``stop`` Keyword to halt the build process after a certain step. None -``testopts`` Extra options for test. "" -``tests`` List of test-scripts to run after install. A test script should return a non-zero exit status to fail [] -``unpack_options`` Extra options for unpacking source "" -``unwanted_env_vars`` List of environment variables that shouldn't be set during build [] -``versionprefix`` Additional prefix for software version (placed before version and toolchain name) "" -``versionsuffix`` Additional suffix for software version (placed after toolchain name) "" -============================= ===================================================================================================================== ================= +=============================== ========================================================================================================================================= ================= +**Parameter name** **Description** **Default value** +=============================== ========================================================================================================================================= ================= +``banned_linked_shared_libs`` List of shared libraries (names, file names, or paths) which are not allowed to be linked in any installed binary/library [] +``bin_lib_subdirs`` List of subdirectories for binaries and libraries, which is used during sanity check to check RPATH linking and banned/required libraries [] +``bitbucket_account`` Bitbucket account name to be used to resolve template values in source URLs "%(namelower)s" +``buildopts`` Extra options passed to make step (default already has -j X) "" +``checksums`` Checksums for sources and patches [] +``configopts`` Extra options passed to configure (default already has --prefix) "" +``cuda_compute_capabilities`` List of CUDA compute capabilities to build with (if supported) [] +``easyblock`` EasyBlock to use for building; if set to None, an easyblock is selected based on the software name None +``easybuild_version`` EasyBuild-version this spec-file was written for None +``enhance_sanity_check`` Indicate that additional sanity check commands & paths should enhance the existin sanity check, not replace it False +``fix_perl_shebang_for`` List of files for which Perl shebang should be fixed to '#!/usr/bin/env perl' (glob patterns supported) None +``fix_python_shebang_for`` List of files for which Python shebang should be fixed to '#!/usr/bin/env python' (glob patterns supported) None +``github_account`` GitHub account name to be used to resolve template values in source URLs "%(namelower)s" +``hidden`` Install module file as 'hidden' by prefixing its version with '.' False +``installopts`` Extra options for installation "" +``maxparallel`` Max degree of parallelism None +``parallel`` Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit) None +``patches`` List of patches to apply [] +``postinstallcmds`` Commands to run after the install step. [] +``prebuildopts`` Extra options pre-passed to build command. "" +``preconfigopts`` Extra options pre-passed to configure. "" +``preinstallopts`` Extra prefix options for installation. "" +``pretestopts`` Extra prefix options for test. "" +``required_linked_shared_libs`` List of shared libraries (names, file names, or paths) which must be linked in all installed binaries/libraries [] +``runtest`` Indicates if a test should be run after make; should specify argument after make (for e.g.,"test" for make test) None +``sanity_check_commands`` format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h') [] +``sanity_check_paths`` List of files and directories to check (format: {'files':, 'dirs':}) {} +``skip`` Skip existing software False +``skipsteps`` Skip these steps [] +``source_urls`` List of URLs for source files [] +``sources`` List of source files [] +``stop`` Keyword to halt the build process after a certain step. None +``testopts`` Extra options for test. "" +``tests`` List of test-scripts to run after install. A test script should return a non-zero exit status to fail [] +``unpack_options`` Extra options for unpacking source "" +``unwanted_env_vars`` List of environment variables that shouldn't be set during build [] +``versionprefix`` Additional prefix for software version (placed before version and toolchain name) "" +``versionsuffix`` Additional suffix for software version (placed after toolchain name) "" +=============================== ========================================================================================================================================= ================= file-management parameters @@ -145,31 +148,31 @@ extensions parameters modules parameters ------------------ -============================== =========================================================================================================== ================= -**Parameter name** **Description** **Default value** -============================== =========================================================================================================== ================= -``allow_prepend_abs_path`` Allow specifying absolute paths to prepend in modextrapaths False -``citing`` Free-form text that describes how the software should be cited in publications None -``docpaths`` List of paths for documentation relative to installation directory None -``examples`` Free-form text with examples on using the software None -``include_modpath_extensions`` Include $MODULEPATH extensions specified by module naming scheme. True -``modaliases`` Aliases to be defined in module file {} -``modaltsoftname`` Module name to use (rather than using software name None -``modextrapaths`` Extra paths to be prepended in module file {} -``modextravars`` Extra environment variables to be added to module file {} -``modloadmsg`` Message that should be printed when generated module is loaded {} -``modluafooter`` Footer to include in generated module file (Lua syntax) "" -``modtclfooter`` Footer to include in generated module file (Tcl syntax) "" -``module_depends_on`` Use depends_on (Lmod 7.6.1+) for dependencies in generated module (implies recursive unloading of modules). False -``moduleclass`` Module class to be used for this software "base" -``moduleforceunload`` Force unload of all modules when loading the extension False -``moduleloadnoconflict`` Don't check for conflicts, unload other versions instead False -``recursive_module_unload`` Recursive unload of all dependencies when unloading module False -``site_contacts`` String/list of strings with site contacts for the software None -``upstream_contacts`` String/list of strings with upstream contact addresses (e.g., support e-mail, mailing list, bugtracker) None -``usage`` Usage instructions for the software None -``whatis`` List of brief (one line) description entries for the software None -============================== =========================================================================================================== ================= +============================== ================================================================================================================================================================================== ================= +**Parameter name** **Description** **Default value** +============================== ================================================================================================================================================================================== ================= +``allow_prepend_abs_path`` Allow specifying absolute paths to prepend in modextrapaths False +``citing`` Free-form text that describes how the software should be cited in publications None +``docpaths`` List of paths for documentation relative to installation directory None +``examples`` Free-form text with examples on using the software None +``include_modpath_extensions`` Include $MODULEPATH extensions specified by module naming scheme. True +``modaliases`` Aliases to be defined in module file {} +``modaltsoftname`` Module name to use (rather than using software name None +``modextrapaths`` Extra paths to be prepended in module file {} +``modextravars`` Extra environment variables to be added to module file {} +``modloadmsg`` Message that should be printed when generated module is loaded {} +``modluafooter`` Footer to include in generated module file (Lua syntax) "" +``modtclfooter`` Footer to include in generated module file (Tcl syntax) "" +``module_depends_on`` Use depends_on (Lmod 7.6.1+) for dependencies in generated module (implies recursive unloading of modules). False +``moduleclass`` Module class to be used for this software "base" +``moduleforceunload`` Force unload of all modules when loading the extension False +``moduleloadnoconflict`` Don't check for conflicts, unload other versions instead False +``recursive_module_unload`` Recursive unload of all dependencies when unloading module (True/False to hard enable/disable; None implies honoring the --recursive-module-unload EasyBuild configuration setting None +``site_contacts`` String/list of strings with site contacts for the software None +``upstream_contacts`` String/list of strings with upstream contact addresses (e.g., support e-mail, mailing list, bugtracker) None +``usage`` Usage instructions for the software None +``whatis`` List of brief (one line) description entries for the software None +============================== ================================================================================================================================================================================== ================= other parameters diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index c514848b..45addaba 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -354,6 +354,7 @@ easyconfig parameter description ``install_target`` Option to pass to setup.py ``"install"`` ``options`` Dictionary with extension options. ``{}`` ``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` ``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` ``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` @@ -363,7 +364,7 @@ easyconfig parameter description ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` ``srcdir`` Source directory location to provide to cmake command ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``unpack_sources`` Unpack sources prior to build/install ``True`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` ``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` @@ -549,6 +550,7 @@ easyconfig parameter description ``install_target`` Option to pass to setup.py ``"install"`` ``options`` Dictionary with extension options. ``{}`` ``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` ``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` ``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` @@ -556,7 +558,7 @@ easyconfig parameter description ``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``unpack_sources`` Unpack sources prior to build/install ``True`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` ``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` ``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` @@ -644,31 +646,32 @@ Extends PythonPackage to add a Fortran compiler to the make call Extra easyconfig parameters specific to ``FortranPythonPackage`` easyblock -------------------------------------------------------------------------- -======================== =============================================================================================================================== ======================================================================= -easyconfig parameter description default value -======================== =============================================================================================================================== ======================================================================= -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install ``True`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== =============================================================================================================================== ======================================================================= +======================== ========================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== ========================================================================================================================================================== ======================================================================= +``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` +``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` +======================== ========================================================================================================================================================== ======================================================================= Customised steps in ``FortranPythonPackage`` easyblock ------------------------------------------------------ @@ -933,36 +936,37 @@ Bundle of modules: only generate module files, nothing to build/install Extra easyconfig parameters specific to ``PythonBundle`` easyblock ------------------------------------------------------------------ -=========================== =============================================================================================================================== ======================================================================= -easyconfig parameter description default value -=========================== =============================================================================================================================== ======================================================================= -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install ``True`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -=========================== =============================================================================================================================== ======================================================================= +=========================== ========================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +=========================== ========================================================================================================================================================== ======================================================================= +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` +``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` +=========================== ========================================================================================================================================================== ======================================================================= .. _PythonPackage: @@ -976,31 +980,32 @@ Builds and installs a Python package, and provides a dedicated module file. Extra easyconfig parameters specific to ``PythonPackage`` easyblock ------------------------------------------------------------------- -======================== =============================================================================================================================== ======================================================================= -easyconfig parameter description default value -======================== =============================================================================================================================== ======================================================================= -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install ``True`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== =============================================================================================================================== ======================================================================= +======================== ========================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== ========================================================================================================================================================== ======================================================================= +``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` +``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` +======================== ========================================================================================================================================================== ======================================================================= Customised steps in ``PythonPackage`` easyblock ----------------------------------------------- @@ -1279,31 +1284,32 @@ Support for install VSC Python packages. Extra easyconfig parameters specific to ``VSCPythonPackage`` easyblock ---------------------------------------------------------------------- -======================== =============================================================================================================================== ======================================================================= -easyconfig parameter description default value -======================== =============================================================================================================================== ======================================================================= -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install ``True`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== =============================================================================================================================== ======================================================================= +======================== ========================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== ========================================================================================================================================================== ======================================================================= +``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` +``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` +======================== ========================================================================================================================================================== ======================================================================= .. _VersionIndependentPythonPackage: @@ -1317,31 +1323,32 @@ Support for building/installing python packages without requiring a specific pyt Extra easyconfig parameters specific to ``VersionIndependentPythonPackage`` easyblock ------------------------------------------------------------------------------------- -======================== =============================================================================================================================== ======================================================================= -easyconfig parameter description default value -======================== =============================================================================================================================== ======================================================================= -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install ``True`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== =============================================================================================================================== ======================================================================= +======================== ========================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== ========================================================================================================================================================== ======================================================================= +``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` +``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` +======================== ========================================================================================================================================================== ======================================================================= Customised steps in ``VersionIndependentPythonPackage`` easyblock ----------------------------------------------------------------- diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index 09bd7371..97f0b758 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -113,7 +113,7 @@ Option flag Option desc ``--sourcepath=SOURCEPATH`` Path(s) to where sources should be downloaded (string, colon-separated) (default: /home/example/.local/easybuild/sources) ``--subdir-modules=SUBDIR-MODULES`` Installpath subdir for modules (default: modules) ``--subdir-software=SUBDIR-SOFTWARE`` Installpath subdir for software (default: software) -``--subdir-user-modules=SUBDIR-USER-MODULES`` Base path of user-specific modules relative to --envvar-user-modules +``--subdir-user-modules=SUBDIR-USER-MODULES`` Base path of user-specific modules relative to --envvars-user-modules ``--suffix-modules-path=SUFFIX-MODULES-PATH`` Suffix for module files install path (default: all) ``--testoutput=TESTOUTPUT`` Path to where a job should place the output (to be set within jobscript) ``--tmp-logdir=TMP-LOGDIR`` Log directory where temporary log files are stored @@ -164,7 +164,7 @@ Option flag Option description ``--close-pr-msg=CLOSE-PR-MSG`` Custom close message for pull request closed with --close-pr; (type ) ``--close-pr-reasons=CLOSE-PR-REASONS`` Close reason for pull request closed with --close-pr; supported values: archived, inactive, obsolete, retest (type ) ``--dump-test-report=DUMP-TEST-REPORT`` Dump test report to specified path (default: test_report.md) -``--from-pr=PR#`` Obtain easyconfigs from specified PR (type ) +``--from-pr=PR#`` Obtain easyconfigs from specified PR (type comma-separated list; default: ) ``--git-working-dirs-path=GIT-WORKING-DIRS-PATH`` Path to Git working directories for EasyBuild repositories (type ) ``--github-org=GITHUB-ORG`` GitHub organization (type ) ``--github-user=GITHUB-USER`` GitHub username (type ) @@ -256,6 +256,7 @@ Option flag Opt ``--allow-modules-tool-mismatch`` Allow mismatch of modules tool and definition of 'module' function (default: False) ``--allow-use-as-root-and-accept-consequences`` Allow using of EasyBuild as root (NOT RECOMMENDED!) (default: False) ``--backup-modules`` Back up an existing module file, if any. Only works when using --module-only +``--banned-linked-shared-libs=BANNED-LINKED-SHARED-LIBS`` Comma-separated list of shared libraries (names, file names, or paths) which are not allowed to be linked in any installed binary/library (type comma-separated list) ``--check-ebroot-env-vars=CHECK-EBROOT-ENV-VARS`` Action to take when defined $EBROOT* environment variables are found for which there is no matching loaded module; supported values: error, ignore, unset, warn (default: warn) ``--cleanup-builddir`` Cleanup build dir after successful installation. (default: True; disable with --disable-cleanup-builddir) ``--cleanup-tmpdir`` Cleanup tmp dir after successful run. (default: True; disable with --disable-cleanup-tmpdir) @@ -310,11 +311,15 @@ Option flag Opt ``-p, --pretend`` Does the build/installation in a test directory located in $HOME/easybuildinstall (default: False) ``--read-only-installdir`` Set read-only permissions on installation directory after installation (default: False) ``--remove-ghost-install-dirs`` Remove ghost installation directories when --force or --rebuild is used, rather than just warning about them (default: False) +``--required-linked-shared-libs=REQUIRED-LINKED-SHARED-LIBS`` Comma-separated list of shared libraries (names, file names, or paths) which must be linked in all installed binaries/libraries (type comma-separated list) ``--rpath`` Enable use of RPATH for linking with libraries (default: False) ``--rpath-filter=RPATH-FILTER`` List of regex patterns to use for filtering out RPATH paths (type comma-separated list) +``--rpath-override-dirs=RPATH-OVERRIDE-DIRS`` Path(s) to be prepended when linking with RPATH (string, colon-separated) +``--sanity-check-only`` Only run sanity check (module is expected to be installed already (default: False) ``--set-default-module`` Set the generated module as default (default: False) ``--set-gid-bit`` Set group ID bit on newly created directories (default: False) ``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` Silence specified deprecation warnings (type comma-separated list) +``--skip-extensions`` Skip installation of extensions (default: False) ``-t, --skip-test-cases`` Skip running test cases (default: False) ``--skip-test-step`` Skip running the test step (e.g. unit tests) (default: False) ``--sticky-bit`` Set sticky bit on newly created directories (default: False) diff --git a/docs/version-specific/toolchain_opts.rst b/docs/version-specific/toolchain_opts.rst index f7f2f419..cc8159a6 100644 --- a/docs/version-specific/toolchain_opts.rst +++ b/docs/version-specific/toolchain_opts.rst @@ -5,7 +5,7 @@ Available toolchain options (by toolchain) *(see also* ``eb --avail-toolchain-opts `` *)* -ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iiblf_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ +ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iiblf_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ .. _ClangGCC: @@ -231,6 +231,91 @@ option description ========================= =============================================================================================================================================================================================================================================================== ========= +.. _FCC: + +Available options for FCC toolchain +----------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + +.. _Fujitsu: + +Available options for Fujitsu toolchain +--------------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + .. _GCC: Available options for GCC toolchain @@ -720,6 +805,49 @@ option description ========================= ======================================================================= ========= +.. _ffmpi: + +Available options for ffmpi toolchain +------------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + .. _foss: Available options for foss toolchain diff --git a/docs/version-specific/toolchains.rst b/docs/version-specific/toolchains.rst index 83746c36..4a4780c5 100644 --- a/docs/version-specific/toolchains.rst +++ b/docs/version-specific/toolchains.rst @@ -17,8 +17,11 @@ Name Compiler(s) MPI Linear algebra **CrayGNU** PrgEnv-gnu cray-mpich cray-libsci *(none)* **CrayIntel** PrgEnv-intel cray-mpich cray-libsci *(none)* **CrayPGI** PrgEnv-pgi cray-mpich cray-libsci *(none)* +**FCC** lang *(none)* *(none)* *(none)* +**ffmpi** FCC *(none)* *(none)* *(none)* **foss** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW **fosscuda** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW +**Fujitsu** *(none)* *(none)* *(none)* FFTW **GCC** GCC *(none)* *(none)* *(none)* **GCCcore** GCCcore *(none)* *(none)* *(none)* **gcccuda** GCC, CUDA *(none)* *(none)* *(none)* From 8a8b598ee0153e87c59fdb1a1260fb32ad38dcc6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Jun 2021 08:44:28 +0200 Subject: [PATCH 136/286] update overview of common toolchains for foss/2021a + intel/2021a --- docs/Common-toolchains.rst | 68 +++++++++++++++++++++----------------- 1 file changed, 37 insertions(+), 31 deletions(-) diff --git a/docs/Common-toolchains.rst b/docs/Common-toolchains.rst index a2a203d5..92ff62d4 100644 --- a/docs/Common-toolchains.rst +++ b/docs/Common-toolchains.rst @@ -56,9 +56,11 @@ This toolchain consists of: * the Open MPI library (https://www.open-mpi.org/) -* the OpenBLAS (http://www.openblas.net/) + LAPACK (http://netlib.org/lapack) libraries +* the OpenBLAS (http://www.openblas.net/) + LAPACK (http://netlib.org/lapack) libraries (for ``foss`` < 2021a) - * the ScaLAPACK (http://netlib.org/scalapack) library is also included +* the FlexiBLAS library (https://www.mpi-magdeburg.mpg.de/projects/flexiblas), with OpenBLAS + LAPACK as backend (for ``foss`` >= 2021a) + +* the ScaLAPACK (http://netlib.org/scalapack) library is also included * the FFTW library (http://fftw.org/) @@ -149,35 +151,37 @@ Overview of common toolchains Component versions in ``foss`` toolchain ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ -| ``foss`` | *date* |*binutils* | *GCC* | *Open MPI* | *OpenBLAS* | *LAPACK* | *ScaLAPACK* | *FFTW* | -+================+=============+============+===========+============+============+=======================+==============+=============+ -| ``2014b`` | Jul '14 | '*(none)* | 4.8.3 | 1.8.1 | 0.2.9 | 3.5.0 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ -| ``2015a`` | Jan '15 | '*(none)* | 4.9.2 | 1.8.4 | 0.2.13 | 3.5.0 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ -| ``2015b`` | Jul '15 | 2.25 | 4.9.3 | 1.8.8 | 0.2.14 | 3.5.0 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ -| ``2016a`` | Jan '16 | 2.25 | 4.9.3 | 1.10.2 | 0.2.15 | 3.6.0 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ -| ``2016b`` | Jul '16 | 2.26 | 5.4.0 | 1.10.3 | 0.2.18 | 3.6.1 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ -| ``2017a`` | Jan '17 | 2.27 | 6.3.0 | 2.0.2 | 0.2.19 | 3.7.0 | 2.0.2 | 3.3.6(-pl2) | -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ -| ``2017b`` | Jul '17 | 2.28 | 6.4.0 | 2.1.1 | 0.2.20* | (incl. with OpenBLAS) | 2.0.2 | 3.3.6(-pl2) | -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ -| ``2018a`` | Jan '18 | 2.28 | 6.4.0 | 2.1.2 | 0.2.20* | (incl. with OpenBLAS) | 2.0.2 | 3.3.7 | -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ -| ``2018b`` | Jul '18 | 2.30 | 7.3.0 | 3.1.1 | 0.3.1 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ -| ``2019a`` | Jan '19 | 2.31.1 | 8.2.0 | 3.1.3 | 0.3.5 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ -| ``2019b`` | Sept '19 | 2.32 | 8.3.0 | 3.1.4 | 0.3.7 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ -| ``2020a`` | May '20 | 2.34 | 9.3.0 | 4.0.3 | 0.3.9 | (incl. with OpenBLAS) | 2.1.0 | 3.3.8 | -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ -| ``2020b`` | Nov '20 | 2.35 | 10.2.0 | 4.0.5 | 0.3.12 | (incl. with OpenBLAS) | 2.1.0 | 3.3.8 | -+----------------+-------------+------------+-----------+------------+------------+-----------------------+--------------+-------------+ ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``foss`` | *date* |*binutils* | *GCC* | *Open MPI* | *FlexiBLAS* | *OpenBLAS* | *LAPACK* | *ScaLAPACK* | *FFTW* | ++================+=============+============+===========+============+=============+============+=======================+==============+=============+ +| ``2014b`` | Jul '14 | '*(none)* | 4.8.3 | 1.8.1 | *(none)* | 0.2.9 | 3.5.0 | 2.0.2 | 3.3.4 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2015a`` | Jan '15 | '*(none)* | 4.9.2 | 1.8.4 | *(none)* | 0.2.13 | 3.5.0 | 2.0.2 | 3.3.4 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2015b`` | Jul '15 | 2.25 | 4.9.3 | 1.8.8 | *(none)* | 0.2.14 | 3.5.0 | 2.0.2 | 3.3.4 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2016a`` | Jan '16 | 2.25 | 4.9.3 | 1.10.2 | *(none)* | 0.2.15 | 3.6.0 | 2.0.2 | 3.3.4 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2016b`` | Jul '16 | 2.26 | 5.4.0 | 1.10.3 | *(none)* | 0.2.18 | 3.6.1 | 2.0.2 | 3.3.4 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2017a`` | Jan '17 | 2.27 | 6.3.0 | 2.0.2 | *(none)* | 0.2.19 | 3.7.0 | 2.0.2 | 3.3.6(-pl2) | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2017b`` | Jul '17 | 2.28 | 6.4.0 | 2.1.1 | *(none)* | 0.2.20* | (incl. with OpenBLAS) | 2.0.2 | 3.3.6(-pl2) | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2018a`` | Jan '18 | 2.28 | 6.4.0 | 2.1.2 | *(none)* | 0.2.20* | (incl. with OpenBLAS) | 2.0.2 | 3.3.7 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2018b`` | Jul '18 | 2.30 | 7.3.0 | 3.1.1 | *(none)* | 0.3.1 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2019a`` | Jan '19 | 2.31.1 | 8.2.0 | 3.1.3 | *(none)* | 0.3.5 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2019b`` | Sept '19 | 2.32 | 8.3.0 | 3.1.4 | *(none)* | 0.3.7 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2020a`` | May '20 | 2.34 | 9.3.0 | 4.0.3 | *(none)* | 0.3.9 | (incl. with OpenBLAS) | 2.1.0 | 3.3.8 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2020b`` | Nov '20 | 2.35 | 10.2.0 | 4.0.5 | *(none)* | 0.3.12 | (incl. with OpenBLAS) | 2.1.0 | 3.3.8 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2021a`` | May '21 | 2.36.1 | 10.3.0 | 4.1.1 | 3.0.4 | 0.3.15 | (incl. with OpenBLAS) | 2.1.0 | 3.3.9 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ *(components marked with* * *were patched)* @@ -216,6 +220,8 @@ Component versions in ``intel`` toolchain +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ | ``2020b`` | Nov'20 | 2.35 | 10.2.0 | 2020.4.304 | 2019.9.304 | 2020.4.304 | +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ +| ``2021a`` | May'21 | 2.36.1 | 10.3.0 | 2021.2.0 | 2021.2.0 | 2021.2.0 | ++----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ ``(*)``: This toolchain is deprecated, see :ref:`deprecated_easyconfigs_toolchains` for more information. From 00b3cf851bc85b0e5e1a10a12fa4fd717baed683 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 2 Jun 2021 17:06:34 +0800 Subject: [PATCH 137/286] update release notes and changelog for EasyBuild v4.4.0 + bump version to 4.4.0 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 243 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 243 insertions(+), 5 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index c43a1949..8f7d9101 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20210602.01** (`Jun 2nd 2021`): update release notes for EasyBuild v4.4.0 (see :ref:`release_notes_eb440`) * **release 20210409.01** (`Apr 9th 2021`): update release notes for EasyBuild v4.3.4 (see :ref:`release_notes_eb434`) * **release 20210223.01** (`Feb 23rd 2021`): update release notes for EasyBuild v4.3.3 (see :ref:`release_notes_eb433`) * **release 20201210.01** (`Dec 10th 2020`): update release notes for EasyBuild v4.3.2 (see :ref:`release_notes_eb432`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 9913d02e..04b02342 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,249 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,288** different software packages, -including 33 different (compiler) toolchains. It contains 229 software-specific easyblocks and 37 generic easyblocks, -alongside 11,784 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,349** different software packages, +including 36 different (compiler) toolchains. It contains 232 software-specific easyblocks and 37 generic easyblocks, +alongside 12,266 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb440: + +EasyBuild v4.4.0 (June 2nd 2021) +-------------------------------- + +feature release + +**framework** + +* various enhancements, including: + + * enhance ``apply_regex_substitutions`` to allow specifying action to take in case there are no matches (`#3440 `_) + * performance improvements for easyconfig parsing and eb startup (`#3555 `_) + * add support for downloading easyconfigs from multiple PRs with ``--from-pr`` (`#3605 `_, `#3707 `_, `#3708 `_) + * add support for prepending custom library paths in RPATH section via ``--rpath-override-dirs`` (`#3650 `_) + * allow amending easyconfig parameters which are not the default (`#3651 `_) + * update HierarchicalMNS for Intel OneAPI compilers (`#3653 `_) + * add support for ``--sanity-check-only`` (`#3655 `_) + * add support for running commands asynchronously via ``run_cmd`` + ``complete_cmd`` functions (`#3656 `_) + * add support for using oneAPI versions of 'intel' toolchain components (`#3665 `_) + * add toolchain definition for gofbf (foss with FlexiBLAS rather than OpenBLAS) (`#3666 `_) + * add support for using ``ARCH`` constant in easyconfig files (`#3670 `_) + * honor keyboard interrupt in ``eb`` command (`#3674 `_) + * add toolchain definition for Fujitsu toolchain (`#3677 `_, `#3704 `_, `#3712 `_, `#3713 `_, `#3714 `_, `#3717 `_) + * extend sanity check step to check whether specific libraries are not linked into installed binaries/libraries (`#3678 `_) + + * via ``banned-linked-shared-libs`` and ``required-linked-shared-libs`` EasyBuild configuration options + * via ``banned_linked_shared_libs`` and ``required_linked_shared_libs`` methods in toolchain support + * via ``banned_linked_shared_libs`` and ``required_linked_shared_libs`` methods in easyblock + * via ``banned_linked_shared_libs`` and ``required_linked_shared_libs`` easyconfig parameters + + * add ``locate_solib`` function to locate Linux shared libraries (`#3682 `_) + * add system agnostic function to locate shared libraries (`#3683 `_) + * add ``update_build_option`` function to update specific build options after initializing the EasyBuild configuration (`#3684 `_) + * allow opting out of recursively unloaded of modules via recursive_module_unload easyconfig parameter (`#3689 `_) + * check for correct version values when parsing easystack file (`#3693 `_) + * run post-install commands specified for a specific extension (`#3696 `_) + * add support for ``--skip-extensions`` (`#3702 `_) + * include PR title in output produced by ``--merge-pr`` (`#3706 `_) + +* various bug fixes, including: + + * avoid metadata greedy behaviour when probing for external module metadata (mostly relevant for integration with Cray Programming Environment) (`#3559 `_) + * catch problems early on if ``--github-user`` is not specified for ``--new-pr`` & co (`#3644 `_) + * re-enable write permissions when installing with ``read-only-installdir`` (`#3649 `_) + * also run sanity check for extensions when using ``--module-only`` (`#3655 `_) + * improve logging when failing to load class from ``exts_classmap`` (`#3657 `_) + * fix use of ``--module-only`` on existing installations without write permissions (`#3659 `_) + * correct help text for ``subdir-user-modules`` (`#3660 `_) + * avoid picking up easyblocks outside of sandbox in framework tests (`#3680 `_) + * use unload/load in ``ModuleGeneratorLua.swap_module``, since ``swap`` is not supported by Lmod (`#3685 `_) + * update HierarchicalMNS to also return 'Toolchain//' as ``$MODULEPATH`` extension for cpe* Cray toolchains (`#3686 `_) + * make ``EasyConfigParser.get_config_dict`` return a copy rather than a reference (`#3692 `_) + * make sure that ``$TAPE`` is unset when using piped tar (`#3698 `_) + * fix extending message for changed files in ``new_pr_from_branch`` (`#3699 `_) + * enhance ``sched_getaffinity`` function to avoid early crash when counting available cores on systems with more than 1024 cores (`#3701 `_) + * correctly strip extension from filename in ``extract_cmd`` and ``back_up_file`` functions (`#3705 `_) + +* other changes: + + * deprecate adding a non-existing path to ``$MODULEPATH`` (`#3637 `_) + * bump cryptography requirement from 3.2.1 to 3.3.2 (`#3643 `_, `#3648 `_) + * test bootstrap script in separate workflow, and limit test configurations a bit (`#3646 `_) + * update ``setup.py`` to indicate compatibility with Python 3.8 and 3.9 (`#3647 `_) + * replace ``log_error`` parameter of ``which()`` by ``on_error`` (`#3661 `_, `#3664 `_) + * don't skip sanity check for ``--module-only --rebuild`` (`#3645 `_) + * move ``disable_templating`` function into the EasyConfig class (`#3668 `_) + * pin GitPython version for Python<3.6, don't test bootstrap script against Python 3.8/3.9 (`#3675 `_) + * tweak foss toolchain definition to switch from OpenBLAS to FlexiBLAS in foss/2021a (`#3679 `_) + * suggest missing SSH key when not able to read from remote repository in ``--check-github`` (`#3681 `_) + * drop support for Python 2.6 (`#3715 `_) + +**easyblocks** + +* 3 new software-specific easyblocks: + + * FlexiBLAS (`#2369 `_, `#2422 `_, `#2424 `_, `#2426 `_) + * dm-reverb (`#2413 `_) + * custom easyblock to install OpenSSL wrapper for OpenSSL installed in OS, with fallback to build and install OpenSSL from source if not available in OS (`#2429 `_) + +* minor enhancements, including: + + * also add ``-pthread`` to ``prebuildopts`` of cryptography (`#2270 `_) + * don't unpack Python wheel (*.whl) files by default in generic PythonPackage easyblock (`#2366 `_, `#2442 `_) + * enable installation of samples for CUDA > 10.1 (`#2374 `_) + * add option to disable pip connecting to PyPi (enable use of ``--no-index``) (`#2390 `_) + * update MotionCor2 easyblock to handle new version and be aware of CUDAcore (`#2394 `_) + * make it possible to force disabling kernel features in Qt easyblock (`#2403 `_) + * update imkl easyblock to support oneAPI versions (>= 2021.x) (`#2407 `_) + * add``"gurobi_cl --help`` as default sanity check command for Gurobi (`#2411 `_) + * enhance BWA easyblock to copy includes and libraries (`#2417 `_) + * allow ``default`` versions to be defined by ModuleRC easyblock (`#2418 `_) + * enhance MesonNinja and CMakeMake easyblocks to create unused build dir when ``separate_build_dir`` is set (`#2419 `_) + * enable ``sanity_pip_check`` by default for Python easyconfigs if pip >= 9.0 will be installed (`#2423 `_) + * enhance FFTW easyblock to support SVE CPU feature and building with Fujitsu compiler (`#2425 `_) + * make ScaLAPACK easyblock aware of FlexiBLAS (`#2427 `_) + * update imkl easyblock to unpack example tarballs and set ``$MKL_EXAMPLES`` (+ some code cleanup) (`#2430 `_) + * update list of system libs for TensorFlow 2.5 (`#2432 `_) + * allow disabling MPI tests when installing Intel MPI (impi) via ``--disable-mpi-tests`` (`#2440 `_) + * exclude bottleneck tests in PyTorch (`#2450 `_) + +* various bug fixes, including: + + * ensure lib subdirectory is found in stage 2 of GCC installation + fall back to lib64 (`#2339 `_) + * fix permission on MATLAB installer config file so it can be written to (`#2385 `_) + * fix problem with installing older CUDA versions that uses the Perl based installer (`#2387 `_) + * enhance Python easyblock: add option to install pip with core Python, tweak defaults, create unversioned pip symlink (`#2388 `_) + * fix ``installopts`` before installing the extension in GROMACS easyblock (`#2391 `_) + * updated numpy easyblock to use ``read_file`` for patch (`#2395 `_) + * use explicit build toolset and compiler path in Boost easyblock (`#2402 `_) + * replace hardcoded ``2021.1.1`` with ``self.version`` in impi easyblock (`#2405 `_) + * set ``$SANDCASTLE`` when running PyTorch tests to disable some tests as-if we are on Facebook's CI (`#2412 `_) + * make GROMACS easyblock work with ``--module-only`` (`#2414 `_) + * make sure OpenFOAM sanity checks don't require builddir write permissions (`#2415 `_) + * make Tkinter easyblock work with ``--module-only`` (`#2416 `_) + * also disable altivec with FFTW 3.3.9 on POWER (`#2437 `_) + * make sure that ``self.python_cmd`` is set before using it in ``PythonPackage.sanity_check_step`` (`#2447 `_) + +* other changes, including: + + * update ``setup.py`` to indicate compatibility with Python 3.8 and 3.9 (`#2384 `_) + * use ``on_error`` rather than deprecated ``log_error`` named argument for ``which`` function (`#2406 `_) + * remove ``cuda_compute_capabilities`` from custom easyconfig parameters for Clang, LAMMPS and TensorFlow (now supported as general easyconfig parameter) (`#2433 `_) + +**easyconfigs** + +* added easyconfigs for new Fujitsu toolchain: FCC/4.5.0 (`#12999 `_, `#12995 `_, `#13007 `_), ffmpi/4.5.0 (`#13000 `_) and Fujitsu/21.05 (`#13001 `_, `#13007 `_) +* add easyconfigs for updates of common toolchains: foss/2021a (`#12867 `_, `#12975 `_), intel/2021a (`#12885 `_, `#12975 `_) + + * see also https://easybuild.readthedocs.io/en/latest/Common-toolchains.html + +* added easyconfig for gomkl/2021a toolchain (`#12987 `_) +* added example easyconfig files for 58 new software packages: + + * Archive-Zip (`#12651 `_), BirdNET (`#12737 `_, `#12712 `_, `#12737 `_), cell2location (`#12448 `_), cryoDRGN (`#12704 `_), + dm-reverb (`#12824 `_), DROP (`#12559 `_, `#12801 `_, `#12950 `_), fastahack (`#12841 `_), fermi-lite (`#12856 `_), filevercmp (`#12841 `_), + FlexiBLAS (`#12476 `_), freetype-py (`#12918 `_), fsom (`#12841 `_), garnett (`#12529 `_), gawk (`#12716 `_), gemmi (`#12855 `_), + georges (`#12570 `_), hifiasm (`#12897 `_), intervaltree (`#12838 `_), LDC (`#12671 `_), libidn2 (`#12670 `_), librosa (`#10477 `_), + librsb (`#12780 `_), line_profiler (`#12556 `_), loompy (`#12804 `_), mmtf-cpp (`#12580 `_), mongolite (`#12632 `_), msgpack-c (`#12580 `_), + multichoose (`#12839 `_), networkTools (`#12810 `_), NewHybrids (`#12528 `_), Octopus-vcf (`#12598 `_), onedrive (`#12671 `_), + p4-phylogenetics (`#12549 `_), pagmo (`#12678 `_), pyfaidx (`#12872 `_), pyfasta (`#12952 `_), pygmo (`#12678 `_), pysheds (`#12791 `_), + R-INLA (`#12955 `_, `#12927 `_, `#12955 `_), RegTools (`#12874 `_), request (`#12448 `_), rMATS-turbo (`#12982 `_), scanpy (`#12731 `_), + SeqLib (`#12856 `_), SeuratData (`#12993 `_), SeuratWrappers (`#12994 `_), smithwaterman (`#12841 `_), snp-sites (`#12900 `_), + SSW (`#12856 `_), tabixpp (`#12837 `_), TagDust (`#11599 `_), TALON (`#12963 `_), tMAE (`#12559 `_), TranscriptClean (`#12952 `_), + umap-learn (`#12448 `_), vcflib (`#12841 `_), xESMF (`#12799 `_), XlsxWriter (`#12820 `_) + +* added additional easyconfigs for various supported software packages, including: + + * ABINIT 9.4.1, apex 20210420, astropy 4.2.1, binutils 2.36.1, BLIS 0.8.1, Bonito 0.3.8, BUSCO 5.1.2, canu 2.1.1, + carputils 20210513, CastXML 0.4.3, ccache 4.2.1, CDO 1.9.10, CIRCexplorer2 2.3.8, CLHEP 2.4.4.0, CMake 3.20.1, + CNVkit 0.9.8, CUDA(core) 11.3.0, CuPy 8.5.0, cURL 7.76.0, DFA 2.1.2, Doxygen 1.9.1, Eigen 3.3.9, FastANI 1.33, + FFTW 3.3.9, GATK 4.2.0.0, GCC 10.3.0 + 11.1.0, GDB 10.2, gdc-client 1.6.0, GDRCopy 2.2, Geant4 10.7.1, + Geant4-data 20210510, GeneMark-ET 4.65, glew 2.2.0, GLib 2.68.2, GLPK 5.0, GMP 6.2.1, Go 1.16.3, Graphviz 2.47.0, + GROMACS 2021.2, GStreamer 1.18.4, GTDB-Tk 1.5.0, Gurobi 9.1.2, HMMER 3.3.2, Horovod 0.21.3, hwloc 2.4.1, + hypothesis 6.13.1, IGV 2.9.4, impi 2021.2.0, imkl 2021.2.0, intel-compilers 2021.2.0, JasPer 2.0.28, Julia 1.6.1, + Kraken2 2.1.1, KronaTools 2.8, libarchive 3.5.1, libdeflate 1.7, libdrm 2.4.106, libfabric 1.12.1, libreadline 8.1, + libRmath 4.0.0, libsndfile 1.0.31, LIBSVM 3.24, LibTIFF 4.2.0, libunwind 1.5.0, libwebp 1.2.0, LLVM 11.1.0, + LMDB 0.9.28, LUMPY 0.3.1, lz4 1.9.3, Mako 1.1.4, MATLAB 2021a, Mesa 21.1.1, meshalyzer 2.2, Meson 0.58.0, + MetaBAT 2.15, metaWRAP 1.3, minimap2 2.18, Molden 6.8, MotionCor2 1.4.2, ncview 2.1.8, NetPIPE 5.1.4, nettle 3.7.2, + NiBabel 3.2.1, Nilearn 0.7.1, Nim 1.4.6, Ninja 1.10.2, NLopt 2.7.0, NSS 3.65, numactl 2.0.14, NWChem 7.0.2, + OpenBLAS 0.3.15, openCARP 6.0, OpenEXR 3.0.1, OpenMM 7.5.0, OpenMPI 4.1.1, OpenSSL 1.1 (wrapper), + OSU-Micro-Benchmarks 5.7.1, Pandoc 2.13, parallel 20210322, parasail 2.4.3, PAUP 4.0a168, PCRE2 10.36, Perl 5.32.1, + pigz 2.6, PMIx 3.2.3, Primer3 2.5.0, PRSice 2.3.3, py-aiger 6.1.14, pybind11 2.6.2, PyCharm 2021.1.1, pydot 1.4.2, + pyproj 3.0.1, PySAT 0.1.7.dev1, PyTorch 1.8.1, python-parasail 1.2.4, Pylint 2.7.4, Python 3.9.5, Qt5 5.15.2, + R-keras 2.4.0, rasterio 1.2.3, RAxML-NG 1.0.2, rclone 1.54.1, re2c 2.1.1, ReFrame 3.5.2, Rmath 4.0.4, Rust 1.52.1, + Sambamba 0.8.0, samblaster 0.1.26, samclip 0.4.0, scikit-allel 1.3.2, SciPy-bundle 2021.05, SCons 4.1.0.post1, + snakemake 6.1.0, SQLite 3.35.4, SRPRISM 3.1.2, Tcl 8.6.11, TCLAP 1.2.4, tmux 3.2, tqdm 4.60.0, UCX 1.10.0, + Valgrind 3.17.0, WannierTools 2.5.1, wget 1.21.1, wxWidgets 3.1.4, X11 20210518, x264 20210414, x265 3.5, + xorg-macros 1.19.3, YAXT 0.9.0, zarr 2.8.1, zstd 1.4.9 + +* minor enhancements, including: + + * add additional extensions to R v4.0.3 and v4.0.4: miceadds, visdat, UpSetR, naniar, stringdist, + image.binarization (`#12735 `_), lassosum (`#12821 `_), lslx, regsem, semPLS (`#13005 `_) + * add GenABEL to R-bundle-Bioconductor (`#12822 `_) + +* various bug fixes, including: + + * disable automatic acceptance of NVHPC EULA (`#12014 `_) + * enhance RStudio-Server, add patch to inherit environment variables, add sanity check commands to verify installation (`#12544 `_) + * add fix to scipy to handle ``NaN`` arguments to ``vi`` function (`#12551 `_) + * copy all binaries + examples & co for PAML v4.9j (`#12567 `_) + * add patch to fix hardcoded ``num_cores`` in DMCfun extension included with R 4.0.x (`#12583 `_) + * backport Charm++ patch for NAMD/2.14 on intel/2020a to handle newer glibc (`#12594 `_) + * add setuptools_scm and pytest-runner extensions to Pylint easyconfigs (`#12599 `_) + * fix typo in Delly easyconfig to actually do parallel build (`#12633 `_) + * fix potential memory leak in OpenBLAS 0.3.12 (`#12649 `_) + * consistently use pip to install Python packages in recent Python easyconfigs (`#12650 `_) + * replace bintray source url for Groovy (`#12652 `_) + * add missing Python & Perl dependencies to AUGUSTUS v3.4.0 with foss/2020b (`#12662 `_) + * fix wget dependency: use libidn2 rather than libidn (`#12670 `_) + * fix source URLs for recent ELPA versions (`#12700 `_) + * override host compiler check in CUDAcore (`#12701 `_) + * add Python build dependency to libpsl 0.21.0 easyconfigs (`#12715 `_) + * fix error in libgpg-error 1.36 with gawk builtin (`#12716 `_) + * add libtool build dependency to leidenalg (`#12741 `_) + * fix source URLs for Boost 1.71.0 - 1.74.0 easyconfigs (`#12743 `_) and Boost.Python (`#12744 `_) + * add patches for PyTorch 1.7.1 avoiding failures on POWER and A100 (`#12753 `_) + * add patch for OpenPGM 5.2.122 eaysconfigs to fix non-existent directory in *.pc (pkgconfig) file (`#12774 `_) + * add missing Perl build dependency to recent wget easyconfigs (`#12787 `_) + * make sure Python dependency is used in preCICE 2.x easyconfigs (`#12793 `_) + * don't skip source step in FastTree easyconfigs + fix SHA256 checksum for FastTree 2.1.11 (`#12794 `_) + * add patch for rhdf5filters extension in Bioconductor 3.12 bundle to fix installation on aarch64 (`#12836 `_) + * add IceLake detection to OpenBLAS 0.3.12 and 0.3.15 (`#12865 `_) + * fix checksum for MaxBin 2.2.7 (`#12869 `_) + * run ``make clean`` before building FragGeneScan, to clean up object files included in source tarball (`#12870 `_) + * clean up install of KronaTools (`#12871 `_) + * add UCX dependency to OneAPI versions of impi (`#12873 `_) + * correct description in libdeflate easyconfig (`#12886 `_) + * override Makefile with hardcoded ``CC=cc`` in UnZip easyconfigs (`#12887 `_) + * fix compatibility of FLAIR v1.5.1-20200630 with rpy2 v3.x (`#12899 `_) + * fix test step for libxc 4.3.4 and 5.1.x when using RPATH linking (`#12912 `_) + * fix source URLs in BLAST 2.10.x easyconfigs (`#12914 `_) + * add missing xproto build dependency to imake easyconfig (`#12930 `_) + * add patch to fix GCC 10.2.0 rejecting valid code on PPC (`#12948 `_) + * in easyconfig tests, check version of dependencies named Python, not if dependencies with certain versions are named Python (`#12962 `_) + * update easyconfigs for binutils 2.35 to use binutils 2.35.2 source tarball instead to pick up bug fixes (`#12967 `_, `#12988 `_) + * fix download URL for DB 18.1.40 (`#12974 `_) + * fix test failure in TensorFlow 2.4.1 on recent CUDA drivers (`#12979 `_) + * fix error in ``configopts`` for netCDF and HDF5 and add missing dependencies of ABINIT 9.x (`#12981 `_) + * add patch to fix buffer overflow in OpenMPI 4.1.x (`#12983 `_) + +* other changes: + + * update ``setup.py`` to indicate compatibility with Python 3.8 and 3.9 (`#12565 `_) + * add ``-Java`` versionsuffix for Hadoop easyconfig using GCCcore/10.2.0 toolchain, since it depends on Java 1.8 (`#12709 `_) + * remove unnecessary workaround for missing version of OpenDataCube and Spyder for 2020+ toolchains (`#12757 `_) + * remove ``unpack_sources = False`` from recent easyconfigs that use a *.whl file as source (`#12783 `_) + * whitelist Seaborn 0.10.1 for NanoComp 1.13.1 and NanoPlot 1.33.0 (`#12790 `_) + * add check to make sure that source step is not being skipped (`#12807 `_) + * use ``EasyConfig.disable_templating`` method in test suite (`#12848 `_) + * disable usNIC by default in libfabric to avoid problems due to linking to both libnl and libnl-3 (`#12854 `_) + * use OpenSSL wrapper as dependency in easyconfigs using GCCcore/10.3.0 toolchain (`#12922 `_, `#12944 `_) + * dump easyconfig before initializing easyblock in order to compare it with original easyconfig (`#12925 `_) + * remove postinstallcmds from imkl 2020.x easyconfigs, easyblock now installs examples (`#12937 `_) + + .. _release_notes_eb434: EasyBuild v4.3.4 (Apr 9th 2021) diff --git a/docs/conf.py b/docs/conf.py index 1c5ccc08..ce6781aa 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.3.4' # this is meant to reference the version of EasyBuild +version = '4.4.0' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20210409.0' # this is meant to reference the version of the documentation itself +release = '20210602.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 5914cdcd169d6561402b709d01e7a86c091e58bc Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 2 Jun 2021 10:45:01 +0100 Subject: [PATCH 138/286] Python 2.6 support removed --- docs/Deprecated-functionality.rst | 16 ---------------- docs/Installation.rst | 4 ++-- docs/Python-2-3-compatibility.rst | 2 +- docs/Removed-functionality.rst | 14 ++++++++++++-- 4 files changed, 15 insertions(+), 21 deletions(-) diff --git a/docs/Deprecated-functionality.rst b/docs/Deprecated-functionality.rst index 5462b1ba..970085ec 100644 --- a/docs/Deprecated-functionality.rst +++ b/docs/Deprecated-functionality.rst @@ -27,7 +27,6 @@ for which support will be removed in EasyBuild version 5.0. For EasyBuild users: * :ref:`depr_lmod6` -* :ref:`depr_python26` For authors of easyconfig files: @@ -54,21 +53,6 @@ Support for using Lmod 6.x as modules tool with EasyBuild has been deprecated, and will be removed in a future version of EasyBuild. -.. _depr_python26: - -Support for running EasyBuild on top of Python 2.6 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -* *deprecated since:* EasyBuild v4.1.0 (Nov'19) -* *removed in:* EasyBuild v5.0 -* *alternative(s)*: **use Python 2.7 or 3.5+** - -Support for running EasyBuild on top of Python 2.6 has been deprecated, -and will be removed in a future version of EasyBuild. - -You should upgrade to a newer version of Python (see also :ref:`py2_py3_compatibility`). - - .. _depr_dummy_toolchain: ``dummy`` toolchain diff --git a/docs/Installation.rst b/docs/Installation.rst index 688eb38f..ee012cd9 100644 --- a/docs/Installation.rst +++ b/docs/Installation.rst @@ -31,7 +31,7 @@ The only strict requirements are: * **Python**: - * Python 2.6 or 2.7, or Python 3.x (>= 3.5) + * Python 2.7, or Python 3.x (>= 3.5) * **note**: only EasyBuild v4.0 (or newer) is compatible with Python 3, earlier EasyBuild releases require Python 2 @@ -387,7 +387,7 @@ Required dependencies * `Python `_: - * Python 2.6 or 2.7, or Python 3.x (>= 3.5) + * Python 2.7, or Python 3.x (>= 3.5) * no third-party Python packages are strictly required (the Python standard library is sufficient) diff --git a/docs/Python-2-3-compatibility.rst b/docs/Python-2-3-compatibility.rst index 6fe69a40..e00667a1 100644 --- a/docs/Python-2-3-compatibility.rst +++ b/docs/Python-2-3-compatibility.rst @@ -6,7 +6,7 @@ Compatibility with Python 2 and Python 3 Starting with EasyBuild v4.0, the EasyBuild framework and easyblocks are compatible with both Python versions 2 and 3. More specifically, the following Python versions are currently supported: -* Python 2.6.x +* Python 2.6.x (support was removed in EasyBuild v4.4.0) * Python 2.7.x * Python 3.5.x * Python 3.6.x diff --git a/docs/Removed-functionality.rst b/docs/Removed-functionality.rst index 1b2f9d72..74ae97c0 100644 --- a/docs/Removed-functionality.rst +++ b/docs/Removed-functionality.rst @@ -258,7 +258,7 @@ In EasyBuild v2.0, some intrusive changes were made that break backward compatib For EasyBuild users: -* :ref:`depr_python_version_compatibility_eb1` +* :ref:`depr_python_version_compatibility` * :ref:`depr_easybuild_configuration_eb1` * :ref:`depr_softroot_version_env_vars_eb1` @@ -283,11 +283,21 @@ For EasyBuild framework developers: backward-incompatible changes documented at :ref:`depr_ConfigureMake_fallback_eb1` and :ref:`depr_easyconfig_parameters_eb1`. See :ref:`fix_broken_easyconfigs_script` for more information. -.. _depr_python_version_compatibility_eb1: +.. _depr_python_version_compatibility: Python version compatibility ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +**Compatibility with Python 2.6 is removed.** + +* *deprecated since:* EasyBuild v4.1.0 (Nov'19) +* *removed in:* EasyBuild v4.4.0 +* *alternative(s)*: **upgrade to Python v2.7.x or v3.5+** + +Support for running EasyBuild on top of Python 2.6 was removed in EasyBuild version 4.4.0. + +You should upgrade to a newer version of Python (see also :ref:`py2_py3_compatibility`). + **Compatibility with Python 2.4 is removed.** * *deprecated since:* EasyBuild v1.14.0 (July'14) From f5c3db2526bde9d314baa150c67bfda928d9193d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 2 Jun 2021 19:47:05 +0800 Subject: [PATCH 139/286] bump version to 4.4.0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index b9dc29c1..13545939 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.3.4' +VERSION = '4.4.0' # Utility function to read README file From 09d31584c40c20077389d4a9d122b240eb1e995c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Jun 2021 15:13:58 +0200 Subject: [PATCH 140/286] fix status badge in README: use GitHub Actions workflow rather than Travis CI --- README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index c9d1d8b0..62687619 100644 --- a/README.rst +++ b/README.rst @@ -1,8 +1,8 @@ .. image:: https://easybuilders.github.io/easybuild/images/easybuild_logo_small.png :align: center -.. image:: https://travis-ci.org/easybuilders/easybuild.svg?branch=develop - :target: https://travis-ci.org/easybuilders/easybuild +.. image:: https://github.com/easybuilders/easybuild/actions/workflows/doc_build.yml/badge.svg + :target: https://github.com/easybuilders/easybuild/actions/workflows/doc_build.yml `EasyBuild `_ is a software build and installation framework that allows you to manage (scientific) software From f648497969fd1d1ddc98800abf9826f042c2d949 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Jun 2021 17:48:04 +0200 Subject: [PATCH 141/286] add @SebastianAchilles as EasyBuild maintainer --- docs/Maintainers.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/Maintainers.rst b/docs/Maintainers.rst index 19448cd4..213372a1 100644 --- a/docs/Maintainers.rst +++ b/docs/Maintainers.rst @@ -67,6 +67,10 @@ The EasyBuild maintainers all have admin access to the different EasyBuild GitHu (maintainers are listed in alphabetical order, by last name) +* **Sebastian Achilles** (`JSC `_) + + * GitHub: `@SebastianAchilles `_ - e-mail: ``s.achilles (at) fz-juelich.de`` - IRC/Slack: ``Sebastian Achilles`` + * **Damian Alvarez** (`JSC `_) * GitHub: `@damianam `_ - e-mail: ``d.alvarez (at) fz-juelich.de`` - IRC/Slack: ``dalvarez`` From 31f9f00503d54b52c21c1134c08e96545ee6af00 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Jun 2021 17:48:32 +0200 Subject: [PATCH 142/286] add @bedroge as EasyBuild maintainer --- docs/Maintainers.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/Maintainers.rst b/docs/Maintainers.rst index 19448cd4..d57c561c 100644 --- a/docs/Maintainers.rst +++ b/docs/Maintainers.rst @@ -83,6 +83,10 @@ The EasyBuild maintainers all have admin access to the different EasyBuild GitHu * GitHub: `@lexming `_ - e-mail: ``alex.domingo.toro (at) vub.be`` - IRC/Slack: ``lexming`` +* **Bob Dröge** (`University of Groning `_) + + * GitHub: `@bedroge `_ - e-mail: ``b.e.droge (at) rug.nl`` - IRC/Slack: ``Bob Dröge`` + * **Pablo Escobar** (`sciCORE, University of Basel `_) * GitHub: `@pescobar `_ - e-mail: ``pablo.escobarlopez (at) unibas.ch`` - IRC/Slack: ``pescobar`` From 2dcf0910447423b8207307a0722bf0d3e771a2e7 Mon Sep 17 00:00:00 2001 From: bartoldeman Date: Mon, 7 Jun 2021 14:37:28 -0400 Subject: [PATCH 143/286] Update docs/Maintainers.rst MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- docs/Maintainers.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Maintainers.rst b/docs/Maintainers.rst index d57c561c..9c7a82f7 100644 --- a/docs/Maintainers.rst +++ b/docs/Maintainers.rst @@ -83,7 +83,7 @@ The EasyBuild maintainers all have admin access to the different EasyBuild GitHu * GitHub: `@lexming `_ - e-mail: ``alex.domingo.toro (at) vub.be`` - IRC/Slack: ``lexming`` -* **Bob Dröge** (`University of Groning `_) +* **Bob Dröge** (`University of Groningen `_) * GitHub: `@bedroge `_ - e-mail: ``b.e.droge (at) rug.nl`` - IRC/Slack: ``Bob Dröge`` From d4d5178b7944018642adfeb2c2e40455bc180569 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 10 Jun 2021 16:19:45 +0200 Subject: [PATCH 144/286] Add docu and example for write-module-hook Also fix some typos and minor issues --- docs/Hooks.rst | 67 +++++++++++++++++++++++++++++++++----------------- 1 file changed, 44 insertions(+), 23 deletions(-) diff --git a/docs/Hooks.rst b/docs/Hooks.rst index 40653d0d..539e49c8 100644 --- a/docs/Hooks.rst +++ b/docs/Hooks.rst @@ -59,12 +59,14 @@ Available hooks Currently (since EasyBuild v3.7.0), three types of hooks are supported: * ``start_hook`` and ``end_hook``, which are triggered *once* before starting software installations, - and *once* right after completing all installations, respectfully; -* ``parse_hook``, which is triggered when an easyconfig file is being parsed; + and *once* right after completing all installations, respectively +* ``parse_hook``, which is triggered when an easyconfig file is being parsed +* ``module_write_hook``, which is triggered right before a module file is written. + This includes the temporary module files used for extensions, sanity checks and the devel module! * "*step*" hooks that are triggered before and after every step of each installation procedure that is performed, also aptly named '``pre``'- and '``post``'-hooks -The list of currently available hooks in order of exeuction, +The list of currently available hooks in order of execution, which can also be consulted using ``eb --avail-hooks``, is: * ``start_hook`` *(only called once in an EasyBuild session)* @@ -87,11 +89,12 @@ which can also be consulted using ``eb --avail-hooks``, is: * ``pre_package_hook``, ``post_package_hook`` * ``pre_testcases_hook``, ``post_testcases_hook`` * ``end_hook`` *(only called once in an EasyBuild session)* + * ``module_write_hook`` *(can be called anytime, available since EasyBuild v4.4.1)* All functions implemented in the provided Python module for which the name ends with ``_hook`` are considered. -If any ``*_hook`` functions are encountered that do not match with any of the available hooks, an error is reported. -EasyBuild will try to provide suggestions for available hooks that closely match with the encountered unknown hook. +If any ``*_hook`` functions are encountered that do not match any of the available hooks, an error is reported. +EasyBuild will try to provide suggestions for available hooks that closely match the encountered unknown hook. For example:: @@ -119,6 +122,12 @@ Do take into account the following: * for ``parse_hook``, one argument is provided: the ``EasyConfig`` instance that corresponds to the easyconfig file being parsed (usually referred to as ``ec``) +* for ``module_write_hook``, 3 arguments are provided: + * the ``EasyBlock`` instance used to perform the installation (usually referred to as ``self``) + * the filepath of the module that will be written + * the module text as a string + The return value of this hook (if any) will then be written into the file. + * for the step hooks, one argument is provided: the ``EasyBlock`` instance used to perform the installation (usually referred to as ``self``) @@ -133,7 +142,7 @@ avoids that your hook implementations may break when updating to future EasyBuil def pre_configure_hook(self, *args, **kwargs): ... -In hooks, you have access to the full functionality provided by the EasyBuild framework, +In hooks you have access to the full functionality provided by the EasyBuild framework, so do ``import`` from ``easybuild.tools.*`` (or other ``easybuild.*`` namespaces) to leverage those functions. @@ -147,7 +156,7 @@ before further parsing of some easyconfig parameters (like ``*dependencies``) in custom data structures is done. This is important since it allows to dynamically modify easyconfig files -while they are still "raw", i.e., when the easyconfig parameter values are +while they are still "raw", i.e. when the easyconfig parameter values are still basic Python data structures like lists, dictionaries, etc. that are easy to manipulate (see also :ref:`hooks_caveats_manipulating`). @@ -161,7 +170,8 @@ Caveats ------- Due to internal details of the EasyBuild framework, you may run into some surprises when -implementing hooks. Here are some things to take into account: +implementing hooks. +Here are some things to take into account: .. _hooks_caveats_template_values: @@ -173,9 +183,10 @@ In all *step* hooks, template values in easyconfig parameters will be resolved w That is, if the ``%(version)`` template is used in for example the ``sources`` easyconfig parameter, it will be replaced with the actual value of the ``version`` easyconfig parameter whenever the ``sources`` value is used. -This can be avoided by temporarily disabling templating via ``self.cfg.enable_templating``, should the need arise. +This can be avoided by temporarily disabling templating by wrapping the code in ``with self.cfg.disable_templating:``. -There is one notable exception to this: templates in easyconfig parameters are *not* resolved in ``parse_hook``, +There is one notable exception to this: +Templates in easyconfig parameters are *not* resolved in ``parse_hook``, because templating has been disabled explicitly before ``parse_hook`` is called; this helps significantly to simplify manipulating of easyconfig parameter values (see also :ref:`hooks_caveats_manipulating`). @@ -191,7 +202,7 @@ You may run into surprises when trying to manipulate easyconfig parameters, for First of all, the original easyconfig parameters may already be processed in another data structure which does not resemble the original format in which the parameter was defined in the easyconfig file. -Moreover, this processing could be done either "in place", i.e. by replacing the original easyconfig parameter value, +Moreover, this processing could be done either "in place", i.e. by replacing the original easyconfig parameter value or in a separate variable, which effectively means that any changes to the original easyconfig parameter value are simply ignored. @@ -209,8 +220,8 @@ More specifically, the following approach will *not* work in any of the (step) h self.cfg['patches'].append('example.patch') The problem here is that the value obtained via ``self.cfg['patches']`` is not a reference -to the actual easyconfig parameter value, but a reference to a temporary copy thereof; -hence, any updates on the copy are effectively lost immediately. +to the actual easyconfig parameter value but a reference to a temporary copy thereof; +hence any updates on the copy are effectively lost immediately. To achieve the intended effect, you can either: @@ -221,12 +232,10 @@ To achieve the intended effect, you can either: def pre_fetch_hook(self): "Example of pre-fetch hook to manipulate list of patches." # temporarily disable templating, so changes to 'patches' easyconfig parameter are picked up - orig_enable_templating = self.cfg.enable_templating - self.cfg.enable_templating = False - # add patch - self.cfg['patches'].append('example.patch') - # restore templating state - self.cfg.enable_templating = orig_enable_templating + with self.cfg.disable_templating: + # add patch + self.cfg['patches'].append('example.patch') + # templating state restored * or replace the original value entirely: @@ -240,7 +249,7 @@ To achieve the intended effect, you can either: A better approach for manipulating easyconfig parameters is to use the ``parse_hook`` that was introduced in EasyBuild v3.7.0 (see :ref:`hooks_parse_hook`), where these kind of surprises will not occur (because templating is automatically disabled -before ``parse_hook`` is called, and restored immediately afterwards). +before ``parse_hook`` is called and restored immediately afterwards). See also :ref:`hooks_examples_inject_patch`. .. _hooks_caveats_archived_easyconfig: @@ -249,12 +258,12 @@ Archived easyconfig file vs hooks +++++++++++++++++++++++++++++++++ EasyBuild archives the easyconfig file that was used for a particular installation: -a copy is stored both in the ``easybuild`` subdirectory of the software installation +A copy is stored both in the ``easybuild`` subdirectory of the software installation directory and in the easyconfigs repository (see :ref:`easyconfigs_repo`). If any changes were made to the easyconfig file via hooks, these changes will *not* be -reflected in these copies. The assumption here is that the hooks will also be in place -for future (re-)installations. +reflected in these copies. +The assumption here is that the hooks will also be in place for future (re-)installations. EasyBuild does however store an additional copy of the easyconfig file which includes any modifications that were done dynamically, for example by hooks. @@ -295,3 +304,15 @@ Example hook to inject a custom patch file patch_file = 'example.patch' ec.log.info("[parse hook] Injecting additional patch file '%s'", patch_file) ec['patches'].append(patch_file) + +Example hook to replace PYTHONPATH by EBPYTHONPREFIXES in (Lua) modules +++++++++++++++++++++++++++++++++++++++++++ + +.. code:: python + + def module_write_hook(self, filepath, module_txt, *args, **kwargs): + # Note: if `self.mod_filepath == filepath` => final module file + if 'Python' in (dep['name'] for dep in self.cfg.dependencies()): + search = r'prepend_path\("PYTHONPATH", pathJoin\(root, "lib/python\d.\d/site-packages"\)\)' + replace = 'prepend_path("EBPYTHONPREFIXES", root)' + return re.sub(search, replace, module_txt) From 7ed8a40c64aca072f8adebe3ffe3f1aff451d67d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Jun 2021 21:30:36 +0200 Subject: [PATCH 145/286] minor tweaks to hooks doc page --- docs/Hooks.rst | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/docs/Hooks.rst b/docs/Hooks.rst index 539e49c8..b14f60db 100644 --- a/docs/Hooks.rst +++ b/docs/Hooks.rst @@ -62,7 +62,8 @@ Currently (since EasyBuild v3.7.0), three types of hooks are supported: and *once* right after completing all installations, respectively * ``parse_hook``, which is triggered when an easyconfig file is being parsed * ``module_write_hook``, which is triggered right before a module file is written. - This includes the temporary module files used for extensions, sanity checks and the devel module! + This includes the temporary module file used when installing extensions and during the sanity check, + as well as the devel module. * "*step*" hooks that are triggered before and after every step of each installation procedure that is performed, also aptly named '``pre``'- and '``post``'-hooks @@ -89,7 +90,7 @@ which can also be consulted using ``eb --avail-hooks``, is: * ``pre_package_hook``, ``post_package_hook`` * ``pre_testcases_hook``, ``post_testcases_hook`` * ``end_hook`` *(only called once in an EasyBuild session)* - * ``module_write_hook`` *(can be called anytime, available since EasyBuild v4.4.1)* + * ``module_write_hook`` *(called multiple times per installation, available since EasyBuild v4.4.1)* All functions implemented in the provided Python module for which the name ends with ``_hook`` are considered. @@ -126,7 +127,7 @@ Do take into account the following: * the ``EasyBlock`` instance used to perform the installation (usually referred to as ``self``) * the filepath of the module that will be written * the module text as a string - The return value of this hook (if any) will then be written into the file. + The return value of this hook (if any) will then be appended to the contents of the module file. * for the step hooks, one argument is provided: the ``EasyBlock`` instance used to perform the installation (usually referred to as ``self``) @@ -202,7 +203,7 @@ You may run into surprises when trying to manipulate easyconfig parameters, for First of all, the original easyconfig parameters may already be processed in another data structure which does not resemble the original format in which the parameter was defined in the easyconfig file. -Moreover, this processing could be done either "in place", i.e. by replacing the original easyconfig parameter value +Moreover, this processing could be done either "in place" by replacing the original easyconfig parameter value, or in a separate variable, which effectively means that any changes to the original easyconfig parameter value are simply ignored. @@ -306,12 +307,12 @@ Example hook to inject a custom patch file ec['patches'].append(patch_file) Example hook to replace PYTHONPATH by EBPYTHONPREFIXES in (Lua) modules -++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ .. code:: python def module_write_hook(self, filepath, module_txt, *args, **kwargs): - # Note: if `self.mod_filepath == filepath` => final module file + # note: if `self.mod_filepath == filepath` => final module file if 'Python' in (dep['name'] for dep in self.cfg.dependencies()): search = r'prepend_path\("PYTHONPATH", pathJoin\(root, "lib/python\d.\d/site-packages"\)\)' replace = 'prepend_path("EBPYTHONPREFIXES", root)' From bfd9858f7d3d481e07f1c13e13a1202d80dc0616 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Jun 2021 21:42:41 +0200 Subject: [PATCH 146/286] fix typo in docs on deprecated functionality --- docs/Deprecated-functionality.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Deprecated-functionality.rst b/docs/Deprecated-functionality.rst index 970085ec..ec16bf8a 100644 --- a/docs/Deprecated-functionality.rst +++ b/docs/Deprecated-functionality.rst @@ -104,7 +104,7 @@ rid of, together with supporting a better alternative. ERROR: EasyBuild encountered an exception (at easybuild/framework/easyconfig/easyconfig.py:937 in process_easyconfig): Failed to process easyconfig /home/example/gzip-1.5-goolf-1.4.10.eb: DEPRECATED (since v2.0) functionality used: Easyconfig parameter 'makeopts' is deprecated, use 'buildopts' instead; - see http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html for more informatio + see http://easybuild.readthedocs.org/en/latest/Deprecated-functionality.html for more information. * the code supporting the deprecated functionality is *removed* in EasyBuild version ``X.(Y+1)`` (i.e., the first non-bugfix-only release after version ``X.Y``), see also :ref:`removed_functionality` From ae52922c4b23d88ffb0f90dd993ac27c1547c4e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Jun 2021 08:46:14 +0200 Subject: [PATCH 147/286] correct statement on return value of module write hook --- docs/Hooks.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Hooks.rst b/docs/Hooks.rst index b14f60db..c706c066 100644 --- a/docs/Hooks.rst +++ b/docs/Hooks.rst @@ -127,7 +127,7 @@ Do take into account the following: * the ``EasyBlock`` instance used to perform the installation (usually referred to as ``self``) * the filepath of the module that will be written * the module text as a string - The return value of this hook (if any) will then be appended to the contents of the module file. + The return value of this hook (if any) is used as contents for the module file that will be written. * for the step hooks, one argument is provided: the ``EasyBlock`` instance used to perform the installation (usually referred to as ``self``) From 644bd18cdfab1bd93d1caed973d43b8738356903 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Jun 2021 09:45:21 +0200 Subject: [PATCH 148/286] clarify return value of module write hook --- docs/Hooks.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Hooks.rst b/docs/Hooks.rst index c706c066..06ef0da1 100644 --- a/docs/Hooks.rst +++ b/docs/Hooks.rst @@ -127,7 +127,7 @@ Do take into account the following: * the ``EasyBlock`` instance used to perform the installation (usually referred to as ``self``) * the filepath of the module that will be written * the module text as a string - The return value of this hook (if any) is used as contents for the module file that will be written. + The return value of this hook, when set, will replace the original text that is then written to the module file. * for the step hooks, one argument is provided: the ``EasyBlock`` instance used to perform the installation (usually referred to as ``self``) From f7f3bbeb0d9772e9b348c947d77c964228afb54b Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 16 Jun 2021 14:27:32 +0100 Subject: [PATCH 149/286] use virtualenv for installation --- docs/Installation.rst | 307 ++++-------------------------------------- 1 file changed, 24 insertions(+), 283 deletions(-) diff --git a/docs/Installation.rst b/docs/Installation.rst index ee012cd9..6e7c4d21 100644 --- a/docs/Installation.rst +++ b/docs/Installation.rst @@ -5,12 +5,12 @@ Installing EasyBuild EasyBuild is Python software, so there are a couple of ways to install it. -We recommend using the **bootstrap** install procedure described at :ref:`bootstrapping`, because of various issues -with the different installation tools that are available for Python packages. +We recommend installing EasyBuild into a virtualenv, described at :ref:`virtualenv`. -Do take into account the required and optional dependencies (see :ref:`requirements` and :ref:`dependencies`). +It is also possible to install EasyBuild as a module. To do this, +use the 3-step procedure outlined at https://easybuilders.github.io/easybuild-tutorial/2021-lust/installation/#method-2-installing-easybuild-with-easybuild -For advanced options, see :ref:`bootstrap_advanced_options`. +Do take into account the required and optional dependencies (see :ref:`requirements` and :ref:`dependencies`). Notes on other ways of installing EasyBuild are available under section :ref:`alt_inst_methods`. @@ -49,82 +49,28 @@ The only strict requirements are: For more information on (optional) dependencies, see :ref:`dependencies`. -.. _bootstrapping: +.. _virtualenv: -Bootstrapping EasyBuild +EasyBuild in a VirtualEnv ----------------------- -Installing any Python package can be a real pain, and since EasyBuild is basically -a set of Python packages glued together, installing EasyBuild may (ironically) cause some headaches. - -To resolve this, we have created a bootstrap script that installs the -latest EasyBuild version for you together with an environment module for -it - and yes, we use EasyBuild for doing so. - -A demo of bootstrapping EasyBuild is available :ref:`here `. - - -Bootstrapping procedure -~~~~~~~~~~~~~~~~~~~~~~~ - -The easiest way (by far) to install EasyBuild is by bootstrapping it, -i.e., installing the latest EasyBuild release (obtained from PyPI) using EasyBuild itself. - -To bootstrap EasyBuild: - -* download the bootstrap script from https://raw.githubusercontent.com/easybuilders/easybuild-framework/develop/easybuild/scripts/bootstrap_eb.py -* execute it, and specify an installation prefix as an argument - -Yes, it's that easy! - -The bootstrap script will perform a 3-stage bootstrap procedure: - -* *stage 0:* download and install a specific version of the ``distribute`` Python package, which provides - the ``easy_install`` tool for installing Python software into a temporary directory -* *stage 1:* download and install the most recent version of EasyBuild from PyPI into a temporary location, using the - ``easy_install`` tool from stage 0 -* *stage 2:* install the most recent version of EasyBuild into the specified installation prefix, - using the temporary EasyBuild installation from stage 1 (inception!) - -This should result in an ``EasyBuild`` module that you can load to start using EasyBuild, after making sure the -module is available by updating ``$MODULEPATH``. More specifically, you need to include the ``modules/all`` -subdirectory of the specified installation prefix into ``$MODULEPATH``. - -For example:: - - # pick an installation prefix to install EasyBuild to (change this to your liking) - EASYBUILD_PREFIX=$HOME/.local/easybuild - - # download script - curl -O https://raw.githubusercontent.com/easybuilders/easybuild-framework/develop/easybuild/scripts/bootstrap_eb.py - - # bootstrap EasyBuild - python bootstrap_eb.py $EASYBUILD_PREFIX - - # update $MODULEPATH, and load the EasyBuild module - module use $EASYBUILD_PREFIX/modules/all - module load EasyBuild +The easiest way to install EasyBuild is in a virtualenv:: -.. note:: - - The path you specify to the bootstrap script is where EasyBuild should be installed. - If you also want software that is built/installed using EasyBuild to be located there, you will need - to configure EasyBuild accordingly (see :ref:`configuring_easybuild`), for example by - putting the definition for ``$EASYBUILD_PREFIX`` in your ``.bashrc``. - - See also :ref:`configuring_easybuild`. + # Create a virtualenv + python -m venv easybuild + + # Enter the virtualenv + source easybuild/bin/activate + + # Install EasyBuild + pip install easybuild -.. XXX - UPDATE BY VERSION - -.. tip:: +Then, when you wish to use EasyBuild again you need to do the ``source easybuild/bin/activate``. - The bootstrap script will only succeed if command ``module --version`` reports a sufficiently recent version - (e.g., environments-modules-c >=v3.2.10 or Lmod >= 5.6.3), because modules are applied throughout, - e.g., to resolve dependencies and detect already installed software. +The installation above will create the virtualenv in your current directory. You can instead specfiy an absolute path for the +location of the virtualenv. -Normally, only when the above fails to work for you for some reason, should you resort -to one of the alternative approaches documented at :ref:`alt_inst_methods` -(these are more involved but also they may give more control). +To leave the virtualenv, use ``deactivate``. Sanity check ~~~~~~~~~~~~ @@ -149,225 +95,20 @@ For example:: may make a big difference, if you have installed both versions 1.9.0 and 1.15.2, with respect to what is the version being loaded by default. -.. _install_running_unit_tests: - -Running unit tests -~~~~~~~~~~~~~~~~~~ - -After completion of the bootstrap procedure and loading the -``EasyBuild`` module, try running the EasyBuild unit tests:: - - # specify modules tool to use: Lmod *(default)*, EnvironmentModules, EnvironmentModulesC, or EnvironmentModulesTcl - # see also http://easybuild.readthedocs.org/en/latest/Configuration.html#modules-tool-modules-tool - export TEST_EASYBUILD_MODULES_TOOL=Lmod - - # run full unit test suite for EasyBuild framework - python -m test.framework.suite - -Keep in mind that this is just an example, more details about the EasyBuild unit tests are available at :ref:`unit_tests`. - -If this does not complete successfully, `please open an issue`_ to report it. - -.. _please open an issue: https://github.com/easybuilders/easybuild-framework/issues/new - - -Example bootstrap run -~~~~~~~~~~~~~~~~~~~~~ - -Example output for bootstrapping EasyBuild v1.16.1:: - - [[INFO]] Found module command 'lmod' (Lmod), so using it. - [[INFO]] - - +++ STAGE 0: installing distribute via included (patched) distribute_setup.py... - - - Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.34.tar.gz - Extracting in /tmp/tmpz0zyAG - Now working in /tmp/tmpz0zyAG/distribute-0.6.34 - Installing Distribute - [[INFO]] - - +++ STAGE 1: installing EasyBuild in temporary dir with easy_install... - - - Installing with setuptools.setup... - Installing version 1.16.1 - warning: install_lib: 'build/lib' does not exist -- no Python modules to install - - zip_safe flag not set; analyzing archive contents... - Installing with setuptools.setup... - Installing version 1.16.1 (API version 1) - Installing with setuptools.setup... - Installing version 1.16.1 (required versions: API >= 1) - Installing with setuptools.setup... - Installing version 1.16.1.0 (required versions: API >= 1, easyblocks >= 1.16) - warning: install_lib: 'build/lib' does not exist -- no Python modules to install +You can also run ``eb --show-config`` to see the default EasyBuild configuration. See the Configuring EasyBuild section +for more information :ref:`configuring_easybuild` - [[INFO]] - - +++ STAGE 2: installing EasyBuild in /home/example/.local/easybuild with EasyBuild from stage 1... - - - Couldn't import dot_parser, loading of dot files will not be possible. - == temporary log file in case of crash /tmp/easybuild-zql_Ft/easybuild-peQ8GA.log - == processing EasyBuild easyconfig /tmp/tmp_gzHPM/EasyBuild-1.16.1.eb - == building and installing EasyBuild/1.16.1... - == fetching files... - == creating build dir, resetting environment... - == unpacking... - == patching... - == preparing... - == configuring... - == building... - == testing... - == installing... - == taking care of extensions... - == packaging... - == postprocessing... - == sanity checking... - == cleaning up... - == creating module... - == COMPLETED: Installation ended successfully - == Results of the build can be found in the log file /home/example/.local/easybuild/software/EasyBuild/1.16.1/easybuild/easybuild-EasyBuild-1.16.1-20150220.210610.log - == Build succeeded for 1 out of 1 - == temporary log file /tmp/easybuild-zql_Ft/easybuild-peQ8GA.log has been removed. - == temporary directory /tmp/easybuild-zql_Ft has been removed. - [[INFO]] Done! - [[INFO]] - [[INFO]] EasyBuild v1.16.1 was installed to /home/example/.local/easybuild, so make sure your $MODULEPATH includes /home/example/.local/easybuild/modules/all - [[INFO]] - [[INFO]] Run 'module load EasyBuild', and run 'eb --help' to get help on using EasyBuild. - [[INFO]] Set $EASYBUILD_MODULES_TOOL to 'Lmod' to use the same modules tool as was used now. - [[INFO]] - [[INFO]] By default, EasyBuild will install software to $HOME/.local/easybuild. - [[INFO]] To install software with EasyBuild to /home/example/.local/easybuild, make sure $EASYBUILD_INSTALLPATH is set accordingly. - [[INFO]] See http://easybuild.readthedocs.org/en/latest/Configuration.html for details on configuring EasyBuild. - - -After the bootstrap completes, the installed ``EasyBuild`` module can be loaded:: - - $ module use $HOME/.local/easybuild/modules/all - $ module av - ------------------------- /home/example/.local/easybuild/modules/all -------------------------- - EasyBuild/1.16.1 - - $ module load EasyBuild - $ module list - Currently Loaded Modulefiles: - 1) EasyBuild/1.16.1 - - $ which eb - /home/example/.local/easybuild/software/EasyBuild/1.16.1/bin/eb - - $ eb --version - This is EasyBuild 1.16.1 (framework: 1.16.1, easyblocks: 1.16.1) on host example.local. - -Now, enjoy! - -.. _bootstrap_advanced_options: - -Advanced bootstrapping options ------------------------------- - -To use these advanced options, make sure you are using the latest version of the bootstrap script, available -at https://raw.githubusercontent.com/easybuilders/easybuild-framework/develop/easybuild/scripts/bootstrap_eb.py . - -Skipping the installation of ``easy_install`` (stage 0) -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -The first stage of the bootstrap procedure consists of installing a specific version of the -``distribute`` Python package, which provides the ``easy_install`` installation tool for Python software, -in a temporary location. The bootstrap script then tries to ensure this particular installation is used -during the other bootstrap stages. - -If you already have a version of ``easy_install`` on your system, and if you are confident that it behaves (in particular, -that it complies to the installation prefix specified via ``--prefix``), you can skip stage 0 of the bootstrap procedure. - -To do so, simply define the ``EASYBUILD_BOOTSTRAP_SKIP_STAGE0`` environment variable (the value doesn't matter):: - - $ export EASYBUILD_BOOTSTRAP_SKIP_STAGE0=1 - $ python bootstrap_eb.py $HOME/eb/test_nostage0 - ... - [[INFO]] Skipping stage0, using local distribute/setuptools providing easy_install - ... - - +++ STAGE 1: installing EasyBuild in temporary dir with easy_install... - - ... - -.. _bootstrap_offline: - -Offline bootstrapping using supplied source tarballs -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -By default, the bootstrap script will download the most recent (stable) EasyBuild version from PyPI, the Python Package -Index (https://pypi.python.org/pypi). - -Recent versions of the bootstrap script also allow to supply source tarballs for the different EasyBuild components -(framework, easyblocks, easyconfigs), and (optionally) the vsc-base and vsc-install libraries EasyBuild depends on. - -The source tarball filenames must match a pattern like ``*.tar.gz``, where ```` denotes the name of the -respective EasyBuild component: - - * ``vsc-install*.tar.gz`` (*must* be downloaded from PyPI, see note below) - * ``vsc-base*.tar.gz`` (*must* be downloaded from PyPI, see note below) - * ``easybuild-framework*.tar.gz`` - * ``easybuild-easyblocks*.tar.gz`` - * ``easybuild-easyconfigs*.tar.gz`` - -The location of the source tarballs can be specified using the ``$EASYBUILD_BOOTSTRAP_SOURCEPATH`` environment variable. - -.. note:: The source tarballs for ``vsc-base`` and ``vsc-install`` *must* be downloaded from PyPI rather than GitHub, - since the source tarballs published via PyPi are pre-processed, as opposed to the 'raw' source tarballs - that are available on GitHub. - - To download the source tarballs from PyPI, visit https://pypi.python.org/pypi/vsc-base or - https://pypi.python.org/pypi/vsc-install. Alternatively, you can download the source tarball for the - most recent version using pip, for example:: - - pip download vsc-base --no-deps - -Example usage, with the relevant output at the start of stage 1 of the bootstrap process:: - - $ export EASYBUILD_BOOTSTRAP_SOURCEPATH=/tmp/$USER - $ python bootstrap_eb.py $HOME/eb/test_tarballs - - +++ STAGE 0: installing distribute via included (patched) distribute_setup.py... - - ... - - +++ STAGE 1: installing EasyBuild in temporary dir with easy_install... - - [[INFO]] Fetching sources from /tmp/example... - [[INFO]] Found /tmp/example/vsc-install-0.10.21.tar.gz for vsc-install package - [[INFO]] Found /tmp/example/vsc-base-2.5.5.tar.gz for vsc-base package - [[INFO]] Found /tmp/example/easybuild-framework-3.0.2.tar.gz for easybuild-framework package - [[INFO]] Found /tmp/example/easybuild-easyblocks.tar.gz for easybuild-easyblocks package - [[INFO]] Found /tmp/example/easybuild-easyconfigs.tar.gz for easybuild-easyconfigs package - ... - -.. note:: Providing a source tarball for ``vsc-base`` and ``vsc-install` is *optional*. - If not specified, the most recent version available - on PyPI will be downloaded and installed automatically when the ``easybuild-framework`` package is installed. - Source tarballs for all three EasyBuild components *must* be provided when ``$EASYBUILD_BOOTSTRAP_SOURCEPATH`` - is defined, however. .. _updating: Updating an existing EasyBuild installation ------------------------------------------- -To upgrade to a newer EasyBuild version (say, |version|) than the one currently installed there are several options: - - * (re)bootstrap EasyBuild to obtain an ``EasyBuild`` module for version |version|, using the instructions above, see :ref:`bootstrapping`. - * install EasyBuild version |version| with a previous version of EasyBuild +To upgrade to a newer EasyBuild version (say, |version|) than the one currently installed: - * using ``eb --install-latest-eb-release`` (requires EasyBuild v2.9.0 or more recent), or - * using the easyconfig file available on the develop branch at Github `__ +* Activate your EasyBuild virtualenv - * install EasyBuild version |version| from PyPI, using one of the standard Python installation tools (``easy_install``, ``pip``, ...), see also :ref:`alt_inst_easy_install_pip` - * update the ``main`` branch of your Git working copies of the different EasyBuild repositories +* ``pip install --upgrade easybuild`` will upgrade EasyBuild to the latest release. .. _dependencies: From a3fef2362d3080a8897868e03ca5d6c36cf39011 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 16 Jun 2021 15:12:59 +0100 Subject: [PATCH 150/286] pull in sections from the tutorial install instructions --- docs/Installation.rst | 227 +++++++++++++++++++++++++++++++++++++----- 1 file changed, 204 insertions(+), 23 deletions(-) diff --git a/docs/Installation.rst b/docs/Installation.rst index 6e7c4d21..f78ed927 100644 --- a/docs/Installation.rst +++ b/docs/Installation.rst @@ -5,10 +5,10 @@ Installing EasyBuild EasyBuild is Python software, so there are a couple of ways to install it. -We recommend installing EasyBuild into a virtualenv, described at :ref:`virtualenv`. +We recommend installing EasyBuild using ``pip`, described at :ref:`pip`. It is also possible to install EasyBuild as a module. To do this, -use the 3-step procedure outlined at https://easybuilders.github.io/easybuild-tutorial/2021-lust/installation/#method-2-installing-easybuild-with-easybuild +use the 3-step procedure outlined at :ref:`eb_as_module`. Do take into account the required and optional dependencies (see :ref:`requirements` and :ref:`dependencies`). @@ -49,28 +49,22 @@ The only strict requirements are: For more information on (optional) dependencies, see :ref:`dependencies`. -.. _virtualenv: +.. _pip: -EasyBuild in a VirtualEnv +Using pip to Install EasyBuild ----------------------- -The easiest way to install EasyBuild is in a virtualenv:: +Since EasyBuild is released as a Python package on PyPI (https://pypi.org/project/easybuild) +you can install it using `pip`, the most commonly used tool for installing Python packages. - # Create a virtualenv - python -m venv easybuild - - # Enter the virtualenv - source easybuild/bin/activate - - # Install EasyBuild - pip install easybuild - -Then, when you wish to use EasyBuild again you need to do the ``source easybuild/bin/activate``. +Install EasyBuild with:: -The installation above will create the virtualenv in your current directory. You can instead specfiy an absolute path for the -location of the virtualenv. + pip install easybuild -To leave the virtualenv, use ``deactivate``. +.. note:: + There are various other ways of installing Python packages, which we won't cover here. + If you are familiar with other tools like `virtualenv` or `pipenv`, feel free to use those + instead to install EasyBuild. Sanity check ~~~~~~~~~~~~ @@ -98,18 +92,204 @@ For example:: You can also run ``eb --show-config`` to see the default EasyBuild configuration. See the Configuring EasyBuild section for more information :ref:`configuring_easybuild` - .. _updating: Updating an existing EasyBuild installation -------------------------------------------- +~~~~~~~~~~~~ To upgrade to a newer EasyBuild version (say, |version|) than the one currently installed: -* Activate your EasyBuild virtualenv - * ``pip install --upgrade easybuild`` will upgrade EasyBuild to the latest release. +.. _advancedpip: + +Advanced pip install options +~~~~~~~~~~~~ + +For the ``pip`` install, you may wish to slightly change this command depending on the context and your personal preferences: + +* To install EasyBuild *system-wide*, you can use ``sudo`` (if you have admin privileges): ``sudo pip install easybuild`` + +* To install EasyBuild *in your personal home directory*, you can use the ``--user`` option: ``pip install --user easybuild`` + This will result in an EasyBuild installation in ``$HOME/.local/``. + +* To install EasyBuild in a *specific directory* you can use the ``--prefix`` option: ``pip install --prefix _PREFIX_ easybuild`` + In this command, you should replace '``_PREFIX_``' with the location where you want to have EasyBuild installed + (for example, ``$HOME/tools`` or ``/tmp/$USER``). + +``pip`` vs ``pip3`` +~~~~~~~~~~~~ + +On systems where both Python 2 and Python 3 are installed you may also have different ``pip`` commands +available. Or maybe ``pip`` is not available at all, and only "versioned" ``pip`` commands like ``pip3`` are +available. + +If you (only) have ``pip3`` available, you can replace ``pip`` with ``pip3`` in any of the ``pip install`` commands +above. + +If you want to ensure that you are using the ``pip`` installation that corresponds to the Python 3 installation +that you intend to use, you can use ``python3 -m pip`` rather than ``pip3``. + +Updating your environment +~~~~~~~~~~~~ + +If you used the `--user` or `--prefix` option in the `pip install` command, +or if you installed EasyBuild with a `pip` version that does not correspond +to your default Python installation, +you will need to update your environment to make EasyBuild ready for use. +This is not required if you did a system-wide installation in a standard location with the default Python version. + +.. note:: + Keep in mind that you will have to make these environment changes again if you start a new shell session. + To avoid this, you can update one of the shell startup scripts in your home directory (`.bashrc` for example). + +Updating ``$PATH`` +~~~~~~~~~~~~ + +Update the ``$PATH`` environment variable to make sure the ``eb`` command is available:: + + export PATH=_PREFIX_/bin:$PATH + +**Replace '`_PREFIX_`' in this command** with the directory path where EasyBuild was installed into +(use `$HOME/.local` if you used `pip install --user`). + +This is not required if you installing EasyBuild in a standard system location. + +You can check with the ``which eb`` command to determine whether or not you need to update the ``$PATH`` environment variable. + +Updating ``$PYTHONPATH`` +~~~~~~~~~~~~ + +If you installed EasyBuild to a non-standard location using ``pip install --prefix``, +you also need to update the Python search path environment variable ``$PYTHONPATH`` to instruct Python where +it can find the EasyBuild Python packages. + +This is not required if you used the ``--user`` option, since Python will automatically consider +``$HOME/.local`` when searching for installed Python packages, or if you installed EasyBuild in a standard +system-wide location. + +Update ``$PYTHONPATH`` by running a command like:: + + export PYTHONPATH=_PREFIX_/lib/pythonX.Y/site-packages:$PYTHONPATH + +Here, you need to replace the ``X`` and ``Y`` with the major and minor version of your Python installation, +which you can determine by running ``python -V``. +For example, if you are using Python 3.6, make sure you are using ``/python3.6/`` in the command to update ``$PYTHONPATH``. + +And of course, you again need to **replace '``_PREFIX_``'** with the installation prefix where EasyBuild was installed +into. + +For example:: + + # update $PYTHONPATH if EasyBuild was installed in $HOME/tools with Python 3.6 + export PYTHONPATH=$HOME/tools/lib/python3.6/site-packages:$PYTHONPATH + + +Setting ``$EB_PYTHON`` +~~~~~~~~~~~~ + +If you want to control which Python version is used to run EasyBuild, +you can specify the name or the full path to the `python` command that should be used by the ``eb`` command +via the ``$EB_PYTHON`` environment variable. + +This may be required when you installing EasyBuild with a version of ``pip`` that does not correspond +with the default Python version. + +For example, to ensure that ``eb`` uses ``python3.6``:: + + export EB_PYTHON=python3.6 + + +Setting ``$EB_VERBOSE`` +~~~~~~~~~~~~ + +To determine which ``python`` commands are being considered by the ``eb`` command, +you can define the ``$EB_VERBOSE`` environment variable. For example:: + + $ EB_VERBOSE=1 eb --version + >> Considering 'python3.6'... + >> 'python3' version: 3.6.8, which matches Python 3 version requirement (>= 3.5) + >> Selected Python command: python3 (/usr/bin/python3.6) + >> python3.6 -m easybuild.main --version + This is EasyBuild 4.3.3 (framework: 4.3.3, easyblocks: 4.3.3) on host example + + +.. _eb_as_module: + +Installing EasyBuild with EasyBuild +----------------------- + +If you prefer having EasyBuild available through an environment module file, +you can consider installing EasyBuild with EasyBuild. This can be done in 3 steps: + +* Step 1: Installing EasyBuild with ``pip`` into a temporary location (only needed if EasyBuild is not installed yet) +* Step 2: Using EasyBuild to install EasyBuild as a module +* Step 3: Loading the EasyBuild module + +.. _eb_as_module_step1: + +Step 1: Installing EasyBuild into a temporary location +~~~~~~~~~~~~ + +If you don't have EasyBuild installed yet, you need to install it in a temporary location first. +The recommended way of doing this is using :ref:`pip`. + +For example, to install EasyBuild into a subdirectory ``/tmp/$USER`` using the default Python 3 version:: + + # pick installation prefix, and install EasyBuild into it + export EB_TMPDIR=/tmp/$USER/eb_tmp + python3 -m pip install --ignore-installed --prefix $EB_TMPDIR easybuild + + # update environment to use this temporary EasyBuild installation + export PATH=$EB_TMPDIR/bin:$PATH + export PYTHONPATH=$(/bin/ls -rtd -1 $EB_TMPDIR/lib*/python*/site-packages | tail -1):$PYTHONPATH + export EB_PYTHON=python3 + +.. _eb_as_module_step2: + +Step 2: Using EasyBuild to install EasyBuild +~~~~~~~~~~~~ + +Once you have a working (recent) temporary EasyBuild installation, you can use it to +install EasyBuild as a module. Usually this is done in the location where you would +like to install other software too. + +You can use the ``eb --install-latest-eb-release`` command for this, +combined with the ``--prefix`` option to control which directories are used by EasyBuild for the installation. + +For example, to install the latest version of EasyBuild as a module into ``$HOME/easybuild``:: + + eb --install-latest-eb-release --prefix $HOME/easybuild + +.. note:: + + You may see a harmless deprecation warning popping up when performing this installation, just ignore it. + +.. _eb_as_module_step3: + +Step 3: Loading the EasyBuild module +~~~~~~~~~~~~ + +Once :ref:`eb_as_module_step2` is completed, you should be able to load the module that was generated alongside +the EasyBuild installation. You will need to do this every time you start a new shell session. + +First, make the module available by running the following command (which will update the module search path +environment variable ``$MODULEPATH``):: + + module use _PREFIX_/modules/all + +**Replace '``_PREFIX_``'** with the path to the directory that you used when running :ref:`eb_as_module_step2` +(for example, ``$HOME/easybuild``). + +Then, load the EasyBuild module to update your environment and make EasyBuild available for use:: + + module load EasyBuild + +.. note:: + Note that in this case, we don't need to make any changes to our environment for EasyBuild to work correctly. + The environment module file that was generated by EasyBuild specifies all changes that need to be made. + + .. _dependencies: Dependencies @@ -128,7 +308,8 @@ Required dependencies * `Python `_: - * Python 2.7, or Python 3.x (>= 3.5) + * Python 2.7, or Python 3.x (>= 3.5). Since Python 2 is end-of-life (https://www.python.org/doc/sunset-python-2/) we recommend + using Python 3 if it is available * no third-party Python packages are strictly required (the Python standard library is sufficient) From 7743a4a9c0237fe2f6c6d4063d55f9d48dc79732 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 16 Jun 2021 15:15:23 +0100 Subject: [PATCH 151/286] missing ` --- docs/Installation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Installation.rst b/docs/Installation.rst index f78ed927..6f262274 100644 --- a/docs/Installation.rst +++ b/docs/Installation.rst @@ -5,7 +5,7 @@ Installing EasyBuild EasyBuild is Python software, so there are a couple of ways to install it. -We recommend installing EasyBuild using ``pip`, described at :ref:`pip`. +We recommend installing EasyBuild using ``pip``, described at :ref:`pip`. It is also possible to install EasyBuild as a module. To do this, use the 3-step procedure outlined at :ref:`eb_as_module`. From 22a257b746d1d314e0bc9acf608af25d9d759040 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 16 Jun 2021 15:49:25 +0100 Subject: [PATCH 152/286] minor clarifications and more ` --- docs/Installation.rst | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/docs/Installation.rst b/docs/Installation.rst index 6f262274..09794d91 100644 --- a/docs/Installation.rst +++ b/docs/Installation.rst @@ -5,9 +5,9 @@ Installing EasyBuild EasyBuild is Python software, so there are a couple of ways to install it. -We recommend installing EasyBuild using ``pip``, described at :ref:`pip`. +We recommend installing EasyBuild using ``pip``. This method is described at :ref:`pip`. -It is also possible to install EasyBuild as a module. To do this, +It is also possible to install EasyBuild as a module. To do this, use the 3-step procedure outlined at :ref:`eb_as_module`. Do take into account the required and optional dependencies (see :ref:`requirements` and :ref:`dependencies`). @@ -31,7 +31,8 @@ The only strict requirements are: * **Python**: - * Python 2.7, or Python 3.x (>= 3.5) + * Python 2.7, or Python 3.x (>= 3.5). Since Python 2 is end-of-life (https://www.python.org/doc/sunset-python-2/) we recommend + using Python 3 if it is available * **note**: only EasyBuild v4.0 (or newer) is compatible with Python 3, earlier EasyBuild releases require Python 2 @@ -55,7 +56,7 @@ Using pip to Install EasyBuild ----------------------- Since EasyBuild is released as a Python package on PyPI (https://pypi.org/project/easybuild) -you can install it using `pip`, the most commonly used tool for installing Python packages. +you can install it using ``pip``, the most commonly used tool for installing Python packages. Install EasyBuild with:: @@ -63,7 +64,7 @@ Install EasyBuild with:: .. note:: There are various other ways of installing Python packages, which we won't cover here. - If you are familiar with other tools like `virtualenv` or `pipenv`, feel free to use those + If you are familiar with other tools like ``virtualenv`` or ``pipenv``, feel free to use those instead to install EasyBuild. Sanity check @@ -97,7 +98,7 @@ for more information :ref:`configuring_easybuild` Updating an existing EasyBuild installation ~~~~~~~~~~~~ -To upgrade to a newer EasyBuild version (say, |version|) than the one currently installed: +To upgrade to a newer EasyBuild version than the one currently installed: * ``pip install --upgrade easybuild`` will upgrade EasyBuild to the latest release. @@ -133,15 +134,14 @@ that you intend to use, you can use ``python3 -m pip`` rather than ``pip3``. Updating your environment ~~~~~~~~~~~~ -If you used the `--user` or `--prefix` option in the `pip install` command, -or if you installed EasyBuild with a `pip` version that does not correspond -to your default Python installation, -you will need to update your environment to make EasyBuild ready for use. +If you used the ``--user`` or ``--prefix`` option in the ``pip install`` command, +or if you installed EasyBuild with a ``pip`` version that does not correspond +to your default Python installation, you will need to update your environment to make EasyBuild ready for use. This is not required if you did a system-wide installation in a standard location with the default Python version. .. note:: Keep in mind that you will have to make these environment changes again if you start a new shell session. - To avoid this, you can update one of the shell startup scripts in your home directory (`.bashrc` for example). + To avoid this, you can update one of the shell startup scripts in your home directory (``.bashrc`` for example). Updating ``$PATH`` ~~~~~~~~~~~~ @@ -150,8 +150,8 @@ Update the ``$PATH`` environment variable to make sure the ``eb`` command is ava export PATH=_PREFIX_/bin:$PATH -**Replace '`_PREFIX_`' in this command** with the directory path where EasyBuild was installed into -(use `$HOME/.local` if you used `pip install --user`). +**Replace '``_PREFIX_``' in this command** with the directory path where EasyBuild was installed into +(use ``$HOME/.local`` if you used ``pip install --user``). This is not required if you installing EasyBuild in a standard system location. @@ -189,7 +189,7 @@ Setting ``$EB_PYTHON`` ~~~~~~~~~~~~ If you want to control which Python version is used to run EasyBuild, -you can specify the name or the full path to the `python` command that should be used by the ``eb`` command +you can specify the name or the full path to the ``python`` command that should be used by the ``eb`` command via the ``$EB_PYTHON`` environment variable. This may be required when you installing EasyBuild with a version of ``pip`` that does not correspond From 9a227b68e66e19ca9dce84230e7345028b1e9863 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Jun 2021 11:34:53 +0200 Subject: [PATCH 153/286] some minor reformating in installation doc page --- docs/Installation.rst | 65 +++++++++++++++++++++++++++++++++---------- 1 file changed, 50 insertions(+), 15 deletions(-) diff --git a/docs/Installation.rst b/docs/Installation.rst index 09794d91..e7aab9a8 100644 --- a/docs/Installation.rst +++ b/docs/Installation.rst @@ -62,6 +62,8 @@ Install EasyBuild with:: pip install easybuild +You may need to tweak this command a bit, depending on your setup, see :ref:`more_pip`. + .. note:: There are various other ways of installing Python packages, which we won't cover here. If you are familiar with other tools like ``virtualenv`` or ``pipenv``, feel free to use those @@ -77,10 +79,10 @@ For example:: $ module list Currently Loaded Modules: - 1) EasyBuild/1.16.1 + 1) EasyBuild/4.4.0 $ eb --version - This is EasyBuild 1.16.1 (framework: 1.16.1, easyblocks: 1.16.1) on host example.local + This is EasyBuild 4.4.0 (framework: 4.4.0, easyblocks: 4.4.0) on host example.local .. tip:: @@ -90,8 +92,8 @@ For example:: may make a big difference, if you have installed both versions 1.9.0 and 1.15.2, with respect to what is the version being loaded by default. -You can also run ``eb --show-config`` to see the default EasyBuild configuration. See the Configuring EasyBuild section -for more information :ref:`configuring_easybuild` +You can also run ``eb --show-system-info`` to see system information relevant to EasyBuild, +or run``eb --show-config`` to see the default EasyBuild configuration (see also :ref:`configuring_easybuild`). .. _updating: @@ -102,22 +104,42 @@ To upgrade to a newer EasyBuild version than the one currently installed: * ``pip install --upgrade easybuild`` will upgrade EasyBuild to the latest release. -.. _advancedpip: +.. _more_pip: -Advanced pip install options +Additional pip install options ~~~~~~~~~~~~ For the ``pip`` install, you may wish to slightly change this command depending on the context and your personal preferences: -* To install EasyBuild *system-wide*, you can use ``sudo`` (if you have admin privileges): ``sudo pip install easybuild`` +* to install EasyBuild *system-wide*, you can use ``sudo`` (if you have admin privileges): + + .. code:: sh + + sudo pip install easybuild + +* To install EasyBuild *in your personal home directory*, you can use the ``--user`` option: + + .. code:: sh + + pip install --user easybuild -* To install EasyBuild *in your personal home directory*, you can use the ``--user`` option: ``pip install --user easybuild`` This will result in an EasyBuild installation in ``$HOME/.local/``. -* To install EasyBuild in a *specific directory* you can use the ``--prefix`` option: ``pip install --prefix _PREFIX_ easybuild`` +* To install EasyBuild in a *specific directory* you can use the ``--prefix`` option: + + .. code:: sh + + pip install --prefix _PREFIX_ easybuild + In this command, you should replace '``_PREFIX_``' with the location where you want to have EasyBuild installed (for example, ``$HOME/tools`` or ``/tmp/$USER``). +Keep in mind that you may need to update your environment too when using ``--user`` or ``--prefix``, +see :ref:`more_pip_env`. + + +.. _more_pip_pip3: + ``pip`` vs ``pip3`` ~~~~~~~~~~~~ @@ -126,11 +148,22 @@ available. Or maybe ``pip`` is not available at all, and only "versioned" ``pip` available. If you (only) have ``pip3`` available, you can replace ``pip`` with ``pip3`` in any of the ``pip install`` commands -above. +above: + +.. code:: sh + + pip3 install easybuild If you want to ensure that you are using the ``pip`` installation that corresponds to the Python 3 installation that you intend to use, you can use ``python3 -m pip`` rather than ``pip3``. +.. code:: sh + + python3.6 -m pip install easybuild + + +.. _more_pip_env: + Updating your environment ~~~~~~~~~~~~ @@ -278,7 +311,7 @@ environment variable ``$MODULEPATH``):: module use _PREFIX_/modules/all -**Replace '``_PREFIX_``'** with the path to the directory that you used when running :ref:`eb_as_module_step2` +**Replace** ``_PREFIX_`` with the path to the directory that you used when running :ref:`eb_as_module_step2` (for example, ``$HOME/easybuild``). Then, load the EasyBuild module to update your environment and make EasyBuild available for use:: @@ -308,12 +341,14 @@ Required dependencies * `Python `_: - * Python 2.7, or Python 3.x (>= 3.5). Since Python 2 is end-of-life (https://www.python.org/doc/sunset-python-2/) we recommend - using Python 3 if it is available + * Python 2.7, or Python 3.x (>= 3.5); + + * since Python 2 is end-of-life (https://www.python.org/doc/sunset-python-2/) we strongly recommend + using Python 3 if it is available; - * no third-party Python packages are strictly required (the Python standard library is sufficient) + * no third-party Python packages are strictly required (the Python standard library is sufficient); - * for some *specific* EasyBuild features additional Python packages are required however, see :ref:`optional_python_packages` + * for some *specific* EasyBuild features additional Python packages are required however, see :ref:`optional_python_packages`; * a **modules tool**: Tcl(/C) environment modules or Lmod From 3fe186b9681ad342db35584ea9c09fce829bd2fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Jun 2021 11:41:41 +0200 Subject: [PATCH 154/286] add ref to $EB_PYTHON section --- docs/Installation.rst | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/Installation.rst b/docs/Installation.rst index e7aab9a8..ae5c03b8 100644 --- a/docs/Installation.rst +++ b/docs/Installation.rst @@ -161,6 +161,8 @@ that you intend to use, you can use ``python3 -m pip`` rather than ``pip3``. python3.6 -m pip install easybuild +Note that you may also need to instruct the ``eb`` command to use the correct Python version at runtime, +via ``$EB_PYTHON`` (see :ref:`more_pip_env_EB_PYTHON`). .. _more_pip_env: @@ -176,6 +178,8 @@ This is not required if you did a system-wide installation in a standard locatio Keep in mind that you will have to make these environment changes again if you start a new shell session. To avoid this, you can update one of the shell startup scripts in your home directory (``.bashrc`` for example). +.. _more_pip_env_PATH: + Updating ``$PATH`` ~~~~~~~~~~~~ @@ -190,6 +194,8 @@ This is not required if you installing EasyBuild in a standard system location. You can check with the ``which eb`` command to determine whether or not you need to update the ``$PATH`` environment variable. +.. _more_pip_env_PYTHONPATH: + Updating ``$PYTHONPATH`` ~~~~~~~~~~~~ @@ -217,6 +223,7 @@ For example:: # update $PYTHONPATH if EasyBuild was installed in $HOME/tools with Python 3.6 export PYTHONPATH=$HOME/tools/lib/python3.6/site-packages:$PYTHONPATH +.. _more_pip_env_EB_PYTHON: Setting ``$EB_PYTHON`` ~~~~~~~~~~~~ @@ -233,6 +240,8 @@ For example, to ensure that ``eb`` uses ``python3.6``:: export EB_PYTHON=python3.6 +.. _more_pip_env_EB_VERBOSE: + Setting ``$EB_VERBOSE`` ~~~~~~~~~~~~ From d0d6d60b2f038bf2faba72276eb20a541de8964f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Jun 2021 11:57:40 +0200 Subject: [PATCH 155/286] fix formatting issue --- docs/Installation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Installation.rst b/docs/Installation.rst index ae5c03b8..a2ed485d 100644 --- a/docs/Installation.rst +++ b/docs/Installation.rst @@ -187,7 +187,7 @@ Update the ``$PATH`` environment variable to make sure the ``eb`` command is ava export PATH=_PREFIX_/bin:$PATH -**Replace '``_PREFIX_``' in this command** with the directory path where EasyBuild was installed into +**Replace** ``_PREFIX_`` **in this command** with the directory path where EasyBuild was installed into (use ``$HOME/.local`` if you used ``pip install --user``). This is not required if you installing EasyBuild in a standard system location. From d7607bfede9c066eac1fb5bc7ee99e6d8a7a4251 Mon Sep 17 00:00:00 2001 From: Will Furnass Date: Tue, 29 Jun 2021 18:18:07 +0100 Subject: [PATCH 156/286] Note that --try-update-deps requires --experimental --- docs/Experimental_features.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/Experimental_features.rst b/docs/Experimental_features.rst index dbca8a87..ec6cf97a 100644 --- a/docs/Experimental_features.rst +++ b/docs/Experimental_features.rst @@ -14,3 +14,4 @@ Currently enabled experimental features include: * support for easyconfig files in YAML syntax (see :ref:`easyconfig_yeb_format`) * support for generating container recipes & images (see :ref:`containers`) * support for using easystack files (see :ref:`easystack`) + * support for trying to update versions of the dependencies of an easyconfig based on what is available in the robot path (see :ref:`basic_usage_help`) From 6da45f8cfb125452bf02b2a2e161791880072119 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Jul 2021 09:26:21 +0200 Subject: [PATCH 157/286] add @hajgato to list of EasyBuild maintainers --- docs/Maintainers.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/Maintainers.rst b/docs/Maintainers.rst index 28a212f7..29563b5c 100644 --- a/docs/Maintainers.rst +++ b/docs/Maintainers.rst @@ -99,6 +99,10 @@ The EasyBuild maintainers all have admin access to the different EasyBuild GitHu * GitHub: `@fgeorgatos `_ - e-mail: ``kefalonia (at) gmail.com`` - IRC/Slack: ``fotis`` +* **Balázs Hajgató** (`HPC-UGent `_) + + * GitHub: `@hajgato `_ - e-mail: ``balazs.hajgato (at) ugent.be`` - IRC/Slack: ``hajgato`` + * **Kenneth Hoste** (`HPC-UGent `_) * GitHub: `@boegel `_ - e-mail: ``kenneth.hoste (at) ugent.be`` - IRC/Slack: ``boegel`` From ff031aae6ae03a960a7adf092a86a2102b150666 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 4 Jul 2021 15:06:48 +0200 Subject: [PATCH 158/286] auto-update documentation for EasyBuild v4.4.1 --- docs/version-specific/Supported_software.rst | 2184 ++++++++++++------ docs/version-specific/easyblocks.rst | 9 +- docs/version-specific/generic_easyblocks.rst | 10 + docs/version-specific/help.rst | 1 + docs/version-specific/toolchain_opts.rst | 45 +- docs/version-specific/toolchains.rst | 3 +- 6 files changed, 1558 insertions(+), 694 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 0bf9413a..411772aa 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2349 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2388 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -97,24 +97,24 @@ ABINIT is a package whose main program allows one to find the total energy, cha *homepage*: https://www.abinit.org/ -========== ======================== ================================ -version versionsuffix toolchain -========== ======================== ================================ -``7.0.3`` ``-x86_64_linux_gnu4.5`` ``system`` -``7.0.5`` ``-x86_64_linux_gnu4.5`` ``system`` -``7.2.1`` ``-x86_64_linux_gnu4.5`` ``system`` -``7.10.5`` ``intel/2016.02-GCC-4.9`` -``7.10.5`` ``-libxc`` ``intel/2016.02-GCC-4.9`` -``8.0.8`` ``intel/2016a`` -``8.0.8b`` ``foss/2016b``, ``intel/2016b`` -``8.2.2`` ``foss/2016b``, ``intel/2016b`` -``8.4.4`` ``intel/2017b`` -``8.6.3`` ``intel/2018a`` -``8.10.2`` ``intel/2018b`` -``8.10.3`` ``intel/2018b`` -``9.2.1`` ``intel/2020a`` -``9.4.1`` ``intel/2020a``, ``intel/2020b`` -========== ======================== ================================ +========== ======================== ================================================ +version versionsuffix toolchain +========== ======================== ================================================ +``7.0.3`` ``-x86_64_linux_gnu4.5`` ``system`` +``7.0.5`` ``-x86_64_linux_gnu4.5`` ``system`` +``7.2.1`` ``-x86_64_linux_gnu4.5`` ``system`` +``7.10.5`` ``intel/2016.02-GCC-4.9`` +``7.10.5`` ``-libxc`` ``intel/2016.02-GCC-4.9`` +``8.0.8`` ``intel/2016a`` +``8.0.8b`` ``foss/2016b``, ``intel/2016b`` +``8.2.2`` ``foss/2016b``, ``intel/2016b`` +``8.4.4`` ``intel/2017b`` +``8.6.3`` ``intel/2018a`` +``8.10.2`` ``intel/2018b`` +``8.10.3`` ``intel/2018b`` +``9.2.1`` ``intel/2020a`` +``9.4.1`` ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` +========== ======================== ================================================ .. _list_software_ABRA2_328: @@ -633,23 +633,25 @@ version toolchain *Amber* +++++++ -Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. +Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. *homepage*: http://ambermd.org/amber.html -======= ================================================= ======================================================================== -version versionsuffix toolchain -======= ================================================= ======================================================================== -``14`` ``-AmberTools-15-patchlevel-13-13`` ``intel/2016a`` -``16`` ``-AmberTools-16-patchlevel-5-14`` ``iomkl/2016.07`` -``16`` ``-AmberTools-16-patchlevel-5-14-CUDA`` ``iomkl/2016.09-GCC-4.9.3-2.25`` -``16`` ``-AmberTools-16-patchlevel-5-14-serial`` ``iomkl/2016.07`` -``16`` ``-AmberTools-17-patchlevel-10-15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``16`` ``-AmberTools-17-patchlevel-10-15-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``16`` ``-AmberTools-17-patchlevel-8-12`` ``intel/2017b`` -``18`` ``-AmberTools-18-patchlevel-10-8`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017b`` -``18`` ``-AmberTools-19-patchlevel-12-17-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b`` -======= ================================================= ======================================================================== +========= ================================================= ======================================================================== +version versionsuffix toolchain +========= ================================================= ======================================================================== +``14`` ``-AmberTools-15-patchlevel-13-13`` ``intel/2016a`` +``16`` ``-AmberTools-16-patchlevel-5-14`` ``iomkl/2016.07`` +``16`` ``-AmberTools-16-patchlevel-5-14-CUDA`` ``iomkl/2016.09-GCC-4.9.3-2.25`` +``16`` ``-AmberTools-16-patchlevel-5-14-serial`` ``iomkl/2016.07`` +``16`` ``-AmberTools-17-patchlevel-10-15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``16`` ``-AmberTools-17-patchlevel-10-15-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``16`` ``-AmberTools-17-patchlevel-8-12`` ``intel/2017b`` +``18`` ``-AmberTools-18-patchlevel-10-8`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017b`` +``18`` ``-AmberTools-19-patchlevel-12-17-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b`` +``20.11`` ``-AmberTools-20.15-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``20.11`` ``-AmberTools-21.3`` ``foss/2020b``, ``fosscuda/2020b`` +========= ================================================= ======================================================================== .. _list_software_AmberMini_884: @@ -753,6 +755,22 @@ version toolchain ========= ============== +.. _list_software_AMPHORA2_570: + +*AMPHORA2* +++++++++++ + +An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences. + +*homepage*: https://github.com/wu-lab-uva/AMPHORA2 + +============ ========================== =============== +version versionsuffix toolchain +============ ========================== =============== +``20190730`` ``-Java-13-pthreads-avx2`` ``gompi/2020b`` +============ ========================== =============== + + .. _list_software_AMPL-MP_500: *AMPL-MP* @@ -1101,6 +1119,22 @@ version toolchain ========= ====================================== +.. _list_software_AOMP_301: + +*AOMP* +++++++ + +AMD fork of LLVM, setup for OpenMP offloading to Accelerators + +*homepage*: https://github.com/ROCm-Developer-Tools/aomp + +========== ===================================== +version toolchain +========== ===================================== +``13.0-2`` ``GCCcore/10.2.0``, ``gcccuda/2020a`` +========== ===================================== + + .. _list_software_APBS_294: *APBS* @@ -1143,12 +1177,12 @@ Apache Portable Runtime (APR) libraries. *homepage*: https://apr.apache.org/ -========= ======================================================== -version toolchain -========= ======================================================== -``1.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``iomkl/2018a`` -``1.7.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` -========= ======================================================== +========= ============================================================================ +version toolchain +========= ============================================================================ +``1.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``iomkl/2018a`` +``1.7.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +========= ============================================================================ .. _list_software_APR-util_718: @@ -1160,11 +1194,11 @@ Apache Portable Runtime (APR) util libraries. *homepage*: http://apr.apache.org/ -========= =============================================================================================================== -version toolchain -========= =============================================================================================================== -``1.6.1`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``iomkl/2018a`` -========= =============================================================================================================== +========= =================================================================================================================================== +version toolchain +========= =================================================================================================================================== +``1.6.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``iomkl/2018a`` +========= =================================================================================================================================== .. _list_software_ARAGORN_522: @@ -1569,6 +1603,7 @@ version versionsuffix toolchain ``3.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.20.1`` ``-Python-3.8.2`` ``intel/2020a`` ``3.21.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``3.21.1`` ``-Python-3.8.2`` ``foss/2020a`` ============== ================== =================================================== @@ -1752,7 +1787,7 @@ version toolchain ``2.28.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a`` ``2.32.0`` ``GCCcore/8.2.0`` ``2.34.1`` ``GCCcore/8.3.0`` -``2.36.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.36.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ========== =================================================================== @@ -1849,12 +1884,13 @@ Commands for Manipulating Filesystem Extended Attributes *homepage*: https://savannah.nongnu.org/projects/attr -========== ================= -version toolchain -========== ================= -``2.4.47`` ``GCCcore/8.2.0`` -``2.4.48`` ``GCCcore/9.3.0`` -========== ================= +========== ================== +version toolchain +========== ================== +``2.4.47`` ``GCCcore/8.2.0`` +``2.4.48`` ``GCCcore/9.3.0`` +``2.5.1`` ``GCCcore/10.3.0`` +========== ================== .. _list_software_attrdict_863: @@ -1935,7 +1971,7 @@ version toolchain *Autoconf-archive* ++++++++++++++++++ -The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet. Every single one of those macros can be re-used without imposing any restrictions whatsoever on the licensing of the generated configure script. In particular, it is possible to use all those macros in configure scripts that are meant for non-free software. This policy is unusual for a Free Software Foundation project. The FSF firmly believes that software ought to be free, and software licenses like the GPL are specifically designed to ensure that derivative work based on free software must be free as well. In case of Autoconf, however, an exception has been made, because Autoconf is at such a pivotal position in the software development tool chain that the benefits from having this tool available as widely as possible outweigh the disadvantage that some authors may choose to use it, too, for proprietary software. +The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet. Every single one of those macros can be re-used without imposing any restrictions whatsoever on the licensing of the generated configure script. In particular, it is possible to use all those macros in configure scripts that are meant for non-free software. This policy is unusual for a Free Software Foundation project. The FSF firmly believes that software ought to be free, and software licenses like the GPL are specifically designed to ensure that derivative work based on free software must be free as well. In case of Autoconf, however, an exception has been made, because Autoconf is at such a pivotal position in the software development tool chain that the benefits from having this tool available as widely as possible outweigh the disadvantage that some authors may choose to use it, too, for proprietary software. *homepage*: https://www.gnu.org/software/autoconf-archive @@ -1943,6 +1979,7 @@ The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autocon version toolchain ============== ==================== ``2019.01.06`` ``GCC/8.2.0-2.31.1`` +``2021.02.19`` ``GCCcore/10.2.0`` ============== ==================== @@ -2484,6 +2521,7 @@ version versionsuffix toolchain ``38.76`` ``GCC/8.2.0-2.31.1`` ``38.79`` ``GCC/8.3.0`` ``38.87`` ``iccifort/2020.1.217`` +``38.90`` ``GCC/10.2.0``, ``GCC/9.3.0`` ========== =================== =============================== @@ -2585,14 +2623,14 @@ bcl2fastq Conversion Software both demultiplexes data and converts BCL files gen *homepage*: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html -========== ================== ============================================================= -version versionsuffix toolchain -========== ================== ============================================================= -``2.19.1`` ``-Python-2.7.12`` ``foss/2016b`` -``2.20.0`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``intel/2019a`` -``2.20.0`` ``-Python-2.7.12`` ``foss/2016b`` -``2.20.0`` ``-Python-2.7.14`` ``intel/2017b`` -========== ================== ============================================================= +========== ================== ============================================================================= +version versionsuffix toolchain +========== ================== ============================================================================= +``2.19.1`` ``-Python-2.7.12`` ``foss/2016b`` +``2.20.0`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``intel/2019a`` +``2.20.0`` ``-Python-2.7.12`` ``foss/2016b`` +``2.20.0`` ``-Python-2.7.14`` ``intel/2017b`` +========== ================== ============================================================================= .. _list_software_bcolz_538: @@ -2639,15 +2677,15 @@ beagle-lib is a high-performance library that can perform the core calculations *homepage*: https://github.com/beagle-dev/beagle-lib -========= ================ =================================== -version versionsuffix toolchain -========= ================ =================================== -``2.1.2`` ``foss/2016a``, ``foss/2017a`` -``3.0.1`` ``foss/2018a``, ``intel/2018a`` -``3.0.2`` ``foss/2018b`` -``3.0.2`` ``-CUDA-9.2.88`` ``foss/2018b`` -``3.1.2`` ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0`` -========= ================ =================================== +========= ================ ====================================================================== +version versionsuffix toolchain +========= ================ ====================================================================== +``2.1.2`` ``foss/2016a``, ``foss/2017a`` +``3.0.1`` ``foss/2018a``, ``intel/2018a`` +``3.0.2`` ``foss/2018b`` +``3.0.2`` ``-CUDA-9.2.88`` ``foss/2018b`` +``3.1.2`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0``, ``gcccuda/2019b`` +========= ================ ====================================================================== .. _list_software_Beast_495: @@ -2657,20 +2695,22 @@ version versionsuffix toolchain BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. -*homepage*: http://beast2.org/ +*homepage*: http://beast2.org -========== ==================== -version toolchain -========== ==================== -``1.8.4`` ``system`` -``1.10.1`` ``intel/2018a`` -``1.10.4`` ``GCC/8.2.0-2.31.1`` -``2.4.0`` ``foss/2016a`` -``2.4.7`` ``foss/2017a`` -``2.5.0`` ``foss/2018a`` -``2.5.1`` ``foss/2018b`` -``2.5.2`` ``GCC/8.2.0-2.31.1`` -========== ==================== +========== ==================================== +version toolchain +========== ==================================== +``1.8.4`` ``system`` +``1.10.1`` ``intel/2018a`` +``1.10.4`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1`` +``2.4.0`` ``foss/2016a`` +``2.4.7`` ``foss/2017a`` +``2.5.0`` ``foss/2018a`` +``2.5.1`` ``foss/2018b`` +``2.5.2`` ``GCC/8.2.0-2.31.1`` +``2.6.3`` ``gcccuda/2019b`` +``2.6.4`` ``GCC/10.2.0`` +========== ==================================== .. _list_software_BeautifulSoup_1352: @@ -2926,7 +2966,7 @@ version toolchain ``2.32`` ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` ``2.34`` ``GCCcore/10.1.0``, ``GCCcore/9.3.0``, ``system`` ``2.35`` ``GCCcore/10.2.0``, ``system`` -``2.36.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``system`` +``2.36.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/8.4.0``, ``GCCcore/9.4.0``, ``system`` ========== ======================================================================================================================================================================================== @@ -3114,7 +3154,7 @@ version versionsuffix toolchain Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols). -*homepage*: http://bioservices.readthedocs.io/ +*homepage*: https://bioservices.readthedocs.io/ ========= ================= ============== version versionsuffix toolchain @@ -3190,12 +3230,12 @@ version toolchain ``3.0.4`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``GCCcore/system``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``3.0.5`` ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/system``, ``system`` ``3.2.2`` ``GCCcore/7.4.0`` -``3.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` +``3.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` ``3.5.2`` ``system`` ``3.5.3`` ``GCCcore/9.3.0``, ``system`` ``3.6.1`` ``GCCcore/10.1.0`` ``3.7.1`` ``GCCcore/10.2.0``, ``system`` -``3.7.6`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``system`` +``3.7.6`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/9.4.0``, ``system`` ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -3309,7 +3349,7 @@ version versionsuffix toolchain ``2.8.1`` ``foss/2018b`` ``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a``, ``iimpi/2019b`` ``2.10.1`` ``gompi/2020a``, ``iimpi/2020a`` -``2.11.0`` ``gompi/2019b``, ``gompi/2020b`` +``2.11.0`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b`` ========== ================== ================================================================== @@ -3367,6 +3407,7 @@ version versionsuffix toolchain ``0.8.1`` ``GCCcore/10.3.0`` ``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` ``2.2`` ``-amd`` ``GCCcore/9.3.0`` +``3.0`` ``-amd`` ``GCCcore/10.3.0`` ========= ============= ===================================== @@ -3531,6 +3572,7 @@ version versionsuffix toolchain ``0.3.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``0.3.5`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``0.3.8`` ``fosscuda/2020b`` +``0.4.0`` ``fosscuda/2020b`` ========= ================= ================================== @@ -3856,6 +3898,7 @@ version versionsuffix toolchain ========= ================== ================== ``6.2.6`` ``GCCcore/8.2.0`` ``6.2.6`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``6.2.9`` ``GCCcore/10.2.0`` ========= ================== ================== @@ -4173,7 +4216,7 @@ version toolchain --- -:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_C3D_186: @@ -4314,6 +4357,22 @@ version toolchain ========= ============= +.. _list_software_CAMPARI_509: + +*CAMPARI* ++++++++++ + +CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte Carlo and molecular dynamics in seamless fashion. + +*homepage*: http://campari.sourceforge.net/V4/index.html + +======= =============== +version toolchain +======= =============== +``4.0`` ``intel/2020b`` +======= =============== + + .. _list_software_Cantera_702: *Cantera* @@ -4353,6 +4412,7 @@ version versionsuffix toolchain ``1.8`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` ``1.9`` ``-Java-11`` ``GCCcore/8.3.0`` ``2.1.1`` ``GCCcore/10.2.0`` +``2.1.1`` ``-Java-11`` ``GCCcore/9.3.0`` ========= ================ =============================== @@ -4516,7 +4576,7 @@ version toolchain Catalyst Micro-kinetic Analysis Package for automated creation of micro-kinetic models used in catalyst screening. -*homepage*: http://catmap.readthedocs.io/ +*homepage*: https://catmap.readthedocs.io/ ============ ================== =============== version versionsuffix toolchain @@ -4901,6 +4961,7 @@ Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cel version toolchain ========= ========== ``1.0.1`` ``system`` +``2.0.0`` ``system`` ========= ========== @@ -4917,6 +4978,7 @@ Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Ce version toolchain ========= ========== ``1.2.0`` ``system`` +``2.0.0`` ``system`` ========= ========== @@ -5195,11 +5257,11 @@ Check is a unit testing framework for C. It features a simple interface for defi *homepage*: https://libcheck.github.io/check/ -========== ===================================== -version toolchain -========== ===================================== -``0.15.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========== ===================================== +========== ========================================================= +version toolchain +========== ========================================================= +``0.15.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +========== ========================================================= .. _list_software_check_510: @@ -5247,7 +5309,7 @@ version versionsuffix toolchain Cheetah is an open source template engine and code generation tool. -*homepage*: http://cheetahtemplate.org +*homepage*: https://cheetahtemplate.org ========= ================== =============== version versionsuffix toolchain @@ -5414,7 +5476,7 @@ version versionsuffix toolchain CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. -*homepage*: http://circexplorer2.readthedocs.io/ +*homepage*: https://circexplorer2.readthedocs.io/ ========== ================== =============== version versionsuffix toolchain @@ -5726,7 +5788,7 @@ version toolchain ClusterShell is an event-driven open source Python library, designed to run local or distant commands in parallel on server farms or on large Linux clusters. -*homepage*: http://cea-hpc.github.io/clustershell/ +*homepage*: https://cea-hpc.github.io/clustershell/ ========= ========== version toolchain @@ -5781,7 +5843,7 @@ version toolchain ``3.15.1`` ``system`` ``3.15.3`` ``GCCcore/8.3.0`` ``3.16.4`` ``GCCcore/9.3.0`` -``3.18.4`` ``GCCcore/10.2.0`` +``3.18.4`` ``GCCcore/10.2.0``, ``system`` ``3.20.1`` ``GCCcore/10.3.0`` ========== ================================================================================================================================================= @@ -6114,14 +6176,14 @@ The GNU Core Utilities are the basic file, shell and text manipulation utilities *homepage*: https://www.gnu.org/software/coreutils/ -======== ================= -version toolchain -======== ================= -``8.23`` ``GCC/4.9.2`` -``8.27`` ``GCCcore/5.4.0`` -``8.29`` ``GCCcore/6.4.0`` -``8.32`` ``GCCcore/8.3.0`` -======== ================= +======== ==================================== +version toolchain +======== ==================================== +``8.23`` ``GCC/4.9.2`` +``8.27`` ``GCCcore/5.4.0`` +``8.29`` ``GCCcore/6.4.0`` +``8.32`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======== ==================================== .. _list_software_corner_649: @@ -6474,6 +6536,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_CSB_216: + +*CSB* ++++++ + +Computational Structural Biology Toolbox CSB is a python library and application framework, which can be used to solve problems in the field of structural bioinformatics. If you are a bioinformatician, software engineer or a researcher working in this field, chances are you may find something useful here. Our package consists of a few major components: 1. Core class library - object-oriented, granular, with an emphasis on design and clean interfaces. 2. Application framework - console applications ("protocols"), which consume objects from the core library in order to build something executable (and hopefully useful). 3. Test framework - ensures that the library actually works. + +*homepage*: https://github.com/csb-toolbox + +========= ============== +version toolchain +========= ============== +``1.2.5`` ``foss/2020b`` +========= ============== + + .. _list_software_CSBDeep_598: *CSBDeep* @@ -6585,6 +6663,7 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is version toolchain ========= ==================================== ``4.4.4`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +``4.6`` ``GCCcore/10.2.0`` ========= ==================================== @@ -6601,6 +6680,7 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is version toolchain ========= ======================================================= ``4.4.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.6`` ``GCCcore/10.2.0`` ========= ======================================================= @@ -6613,11 +6693,12 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is *homepage*: https://www.scalasca.org/software/cube-4.x/download.html -========= ======================================================= -version toolchain -========= ======================================================= -``4.4.3`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ======================================================= +========= =========================================================================== +version toolchain +========= =========================================================================== +``4.4.3`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.6`` ``GCCcore/10.2.0`` +========= =========================================================================== .. _list_software_CUDA_285: @@ -6709,6 +6790,9 @@ version versionsuffix toolchain ``8.0.4.30`` ``-CUDA-11.0.2`` ``system`` ``8.0.4.30`` ``-CUDA-11.1.1`` ``system`` ``8.0.5.39`` ``-CUDA-11.1.1`` ``system`` +``8.1.0.77`` ``-CUDA-11.2.1`` ``system`` +``8.1.1.33`` ``-CUDA-11.2.1`` ``system`` +``8.2.1.32`` ``-CUDA-11.3.1`` ``system`` ============ ================== =========================================================== @@ -6893,6 +6977,7 @@ version versionsuffix toolchain ``1.2.1`` ``-Python-3.6.4`` ``intel/2018a`` ``1.2.3`` ``foss/2019a`` ``1.2.4`` ``-Python-3.7.4`` ``intel/2019b`` +``1.2.6`` ``foss/2020b`` ========= ================== =============== @@ -7009,7 +7094,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` .. _list_software_dadi_402: @@ -7167,12 +7252,12 @@ GNU datamash performs basic numeric, textual and statistical operations on input *homepage*: https://www.gnu.org/software/datamash/ -======= ==================================== -version toolchain -======= ==================================== -``1.3`` ``foss/2018a`` -``1.5`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` -======= ==================================== +======= ======================================================== +version toolchain +======= ======================================================== +``1.3`` ``foss/2018a`` +``1.5`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +======= ======================================================== .. _list_software_davix_540: @@ -7738,6 +7823,22 @@ version toolchain ======= ============= +.. _list_software_dijitso_758: + +*dijitso* ++++++++++ + +dijitso is a Python module for distributed just-in-time shared library building. + +*homepage*: https://bitbucket.org/fenics-project/dijitso + +============ ================= ============== +version versionsuffix toolchain +============ ================= ============== +``2019.1.0`` ``-Python-3.7.4`` ``foss/2019b`` +============ ================= ============== + + .. _list_software_dill_421: *dill* @@ -7752,6 +7853,7 @@ version toolchain ========= ===================================== ``0.3.0`` ``GCCcore/8.2.0`` ``0.3.3`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +``0.3.4`` ``GCCcore/10.3.0`` ========= ===================================== @@ -7906,6 +8008,7 @@ DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Prob version versionsuffix toolchain ================== ================= ============== ``2018.1.0.post1`` ``-Python-3.6.4`` ``foss/2018a`` +``2019.1.0.post0`` ``-Python-3.7.4`` ``foss/2019b`` ================== ================= ============== @@ -7927,6 +8030,22 @@ version toolchain ============= =============================== +.. _list_software_DosageConvertor_1557: + +*DosageConvertor* ++++++++++++++++++ + +DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK. Please note that this tool CANNOT handle missing values in the input files and may NOT work for non-Minimac3/4 VCF files. + +*homepage*: http://genome.sph.umich.edu/wiki/DosageConvertor + +========= ============== +version toolchain +========= ============== +``1.0.4`` ``GCC/10.2.0`` +========= ============== + + .. _list_software_dotNET-Core-Runtime_1781: *dotNET-Core-Runtime* @@ -8082,6 +8201,22 @@ version versionsuffix toolchain ======= ============= ============== +.. _list_software_dSFMT_414: + +*dSFMT* ++++++++ + +Double precision SIMD-oriented Fast Mersenne Twister. + +*homepage*: https://github.com/MersenneTwister-Lab/dSFMT + +========= ================== +version toolchain +========= ================== +``2.2.5`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_DSRC_300: *DSRC* @@ -8169,7 +8304,7 @@ version versionsuffix toolchain --- -:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExifTool_810` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_E-ANTIC_481: @@ -8314,6 +8449,7 @@ version toolchain ``4.3.2`` ``system`` ``4.3.3`` ``system`` ``4.3.4`` ``system`` +``4.4.0`` ``system`` ========== ========== @@ -8431,14 +8567,15 @@ version toolchain *eggnog-mapper* +++++++++++++++ -eggnog-mapper is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments +EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. -*homepage*: http://eggnog-mapper.embl.de +*homepage*: https://github.com/eggnogdb/eggnog-mapper ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.0.3`` ``-Python-2.7.14`` ``intel/2018a`` +``2.1.4`` ``foss/2020b`` ========= ================== =============== @@ -8515,12 +8652,13 @@ The elfutils project provides libraries and tools for ELF files and DWARF data. *homepage*: https://elfutils.org/ -========= ================== -version toolchain -========= ================== -``0.182`` ``GCCcore/9.3.0`` -``0.183`` ``GCCcore/10.2.0`` -========= ================== +========= ======================================================== +version toolchain +========= ======================================================== +``0.182`` ``GCCcore/9.3.0`` +``0.183`` ``GCCcore/10.2.0`` +``0.185`` ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ======================================================== .. _list_software_Elk_284: @@ -8563,6 +8701,7 @@ version toolchain ``2019.11.001`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a``, ``iomkl/2019b`` ``2020.05.001`` ``intel/2020a`` ``2020.11.001`` ``foss/2020b``, ``intel/2020b`` +``2021.05.001`` ``foss/2021a``, ``intel/2021a`` =================== ================================================================================= @@ -8654,6 +8793,7 @@ version versionsuffix toolchain ========= ================= ================================================================================================================================ ``6.6.0`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` ``6.6.0`` ``-Java-11`` ``GCC/8.3.0`` +``6.6.0`` ``-Java-13`` ``GCC/10.2.0`` ``6.6.0`` ``-X11-20170314`` ``intel/2017a`` ========= ================= ================================================================================================================================ @@ -9010,6 +9150,22 @@ version toolchain ========= ================= +.. _list_software_exiv2_494: + +*exiv2* ++++++++ + +Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata. + +*homepage*: https://exiv2.org + +========== ================== +version toolchain +========== ================== +``0.27.4`` ``GCCcore/10.3.0`` +========== ================== + + .. _list_software_Exonerate_939: *Exonerate* @@ -9019,11 +9175,11 @@ Exonerate is a generic tool for pairwise sequence comparison. It allows you to *homepage*: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate -========= ============================================================================================================================================================================================= -version toolchain -========= ============================================================================================================================================================================================= -``2.4.0`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a`` -========= ============================================================================================================================================================================================= +========= ============================================================================================================================================================================================================= +version toolchain +========= ============================================================================================================================================================================================================= +``2.4.0`` ``GCC/10.2.0``, ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a`` +========= ============================================================================================================================================================================================================= .. _list_software_expat_546: @@ -9105,7 +9261,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -9622,7 +9778,7 @@ version toolchain Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. -*homepage*: https://pages.nist.gov/fds-smv/ +*homepage*: https://pages.nist.gov/fds-smv ========= ============= ================================ version versionsuffix toolchain @@ -9634,6 +9790,7 @@ version versionsuffix toolchain ``6.7.0`` ``intel/2018a`` ``6.7.4`` ``intel/2020a`` ``6.7.5`` ``intel/2020a`` +``6.7.6`` ``intel/2020b`` ========= ============= ================================ @@ -9688,6 +9845,22 @@ version toolchain ======== ================= +.. _list_software_FEniCS_504: + +*FEniCS* +++++++++ + +FEniCS is a computing platform for solving partial differential equations (PDEs). + +*homepage*: https://fenicsproject.org/ + +============ ================= ============== +version versionsuffix toolchain +============ ================= ============== +``2019.1.0`` ``-Python-3.7.4`` ``foss/2019b`` +============ ================= ============== + + .. _list_software_fermi-lite_1006: *fermi-lite* @@ -9762,11 +9935,12 @@ The FEniCS Form Compiler (FFC) is a compiler for finite element variational form *homepage*: https://bitbucket.org/fenics-project/ffc -============ ================= ============== -version versionsuffix toolchain -============ ================= ============== -``2018.1.0`` ``-Python-3.6.4`` ``foss/2018a`` -============ ================= ============== +================== ================= ============== +version versionsuffix toolchain +================== ================= ============== +``2018.1.0`` ``-Python-3.6.4`` ``foss/2018a`` +``2019.1.0.post0`` ``-Python-3.7.4`` ``foss/2019b`` +================== ================= ============== .. _list_software_FFLAS-FFPACK_836: @@ -9816,6 +9990,7 @@ version toolchain ``4.2.1`` ``GCCcore/8.3.0`` ``4.2.2`` ``GCCcore/9.3.0`` ``4.3.1`` ``GCCcore/10.2.0`` +``4.3.2`` ``GCCcore/10.3.0`` =========== =================================================== @@ -9874,7 +10049,7 @@ version toolchain FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. -*homepage*: http://www.fftw.org +*homepage*: https://www.fftw.org ========= ============= ======================================================================================================================================================================================================================================================================================================================= version versionsuffix toolchain @@ -9889,7 +10064,7 @@ version versionsuffix toolchain ``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``iomkl/2018b`` ``3.3.8`` ``-amd`` ``gompi/2020a`` ``3.3.8`` ``-serial`` ``GCC/9.3.0`` -``3.3.9`` ``gompi/2021a`` +``3.3.9`` ``gompi/2021a``, ``intel/2021a`` ========= ============= ======================================================================================================================================================================================================================================================================================================================= @@ -9946,7 +10121,7 @@ version toolchain *FIAT* ++++++ -The FInite element Automatic Tabulator (FIAT) supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes. +The FInite element Automatic Tabulator (FIAT) supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes. *homepage*: https://bitbucket.org/fenics-project/fiat @@ -9955,6 +10130,7 @@ version versionsuffix toolchain ============ ================== =============================== ``1.6.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``2018.1.0`` ``-Python-3.6.4`` ``foss/2018a`` +``2019.1.0`` ``-Python-3.7.4`` ``foss/2019b`` ============ ================== =============================== @@ -10056,11 +10232,11 @@ Filtlong is a tool for filtering long reads by quality. It can take a set of lo *homepage*: https://github.com/rrwick/Filtlong -========= ============== -version toolchain -========= ============== -``0.2.0`` ``foss/2016b`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``0.2.0`` ``GCC/10.2.0``, ``foss/2016b`` +========= ============================== .. _list_software_find_circ_929: @@ -10356,6 +10532,7 @@ FlatBuffers: Memory Efficient Serialization Library version toolchain ========== ======================================================== ``1.12.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.0.0`` ``GCCcore/10.3.0`` ========== ======================================================== @@ -10373,6 +10550,7 @@ version versionsuffix toolchain ======== ================= ================== ``1.12`` ``GCCcore/10.2.0`` ``1.12`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.0`` ``GCCcore/10.3.0`` ======== ================= ================== @@ -10401,17 +10579,17 @@ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, some *homepage*: http://flex.sourceforge.net/ -========== ======================================================================================================================================================================================================================================================================================================================================================================================= -version toolchain -========== ======================================================================================================================================================================================================================================================================================================================================================================================= -``2.5.35`` ``system`` -``2.5.38`` ``GCC/4.8.2`` -``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` -``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.6.2`` ``intel/2016b`` -``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` -``2.6.4`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` -========== ======================================================================================================================================================================================================================================================================================================================================================================================= +========== ======================================================================================================================================================================================================================================================================================================================================================================================================= +version toolchain +========== ======================================================================================================================================================================================================================================================================================================================================================================================================= +``2.5.35`` ``system`` +``2.5.38`` ``GCC/4.8.2`` +``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` +``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +``2.6.2`` ``intel/2016b`` +``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` +``2.6.4`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``system`` +========== ======================================================================================================================================================================================================================================================================================================================================================================================================= .. _list_software_Flexbar_708: @@ -10509,6 +10687,7 @@ version toolchain ``1.3.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.3.4`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b`` ``1.3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.3.6`` ``GCCcore/10.3.0`` ========= =================================================================================================================================================================================================== @@ -10834,6 +11013,22 @@ version toolchain ========= ============== +.. _list_software_FreeFEM_602: + +*FreeFEM* ++++++++++ + +FreeFEM offers a fast interpolation algorithm and a language for the manipulation of data on multiple meshes. + +*homepage*: https://freefem.org + +======= ================= ============== +version versionsuffix toolchain +======= ================= ============== +``4.5`` ``-Python-3.7.4`` ``foss/2019b`` +======= ================= ============== + + .. _list_software_FreeFem++_752: *FreeFem++* @@ -10866,7 +11061,7 @@ version versionsuffix toolchain ========= ================ ====================================================================================================================================================================================== ``3.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` -``3.2.1`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``3.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ================ ====================================================================================================================================================================================== @@ -11002,7 +11197,7 @@ version toolchain ``1.0.2`` ``GCCcore/6.4.0`` ``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``1.0.9`` ``GCCcore/9.3.0`` -``1.0.10`` ``GCCcore/10.2.0`` +``1.0.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========== ======================================================= @@ -11136,7 +11331,7 @@ version toolchain Reverse Monte Carlo (RMC) is probably best known for its applications in condensed matter physics and solid state chemistry. fullrmc which stands for FUndamental Library Language for Reverse Monte Carlo is different than traditional RMC but a stochastic modelling method to solve an inverse problem whereby an atomic/molecular model is adjusted until its atoms position havei the greatest consistency with a set of experimental data. -*homepage*: http://bachiraoun.github.io/fullrmc +*homepage*: https://bachiraoun.github.io/fullrmc ========= ================== =============== version versionsuffix toolchain @@ -11212,6 +11407,38 @@ version versionsuffix toolchain ======== ================== ============== +.. _list_software_futhark_757: + +*futhark* ++++++++++ + +Futhark is a small programming language designed to be compiled to efficient parallel code. It is a statically typed, data-parallel, and purely functional array language in the ML family, and comes with a heavily optimising ahead-of-time compiler that presently generates GPU code via CUDA and OpenCL, although the language itself is hardware-agnostic and can also run on multicore CPUs + +*homepage*: https://futhark-lang.org/ + +========== ========== +version toolchain +========== ========== +``0.19.5`` ``system`` +========== ========== + + +.. _list_software_futile_649: + +*futile* +++++++++ + +The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules and wrapper that encapsulate the most common low-level operations of a Fortran code. + +*homepage*: https://launchpad.net/futile + +========= =============================== +version toolchain +========= =============================== +``1.8.3`` ``foss/2020b``, ``intel/2020b`` +========= =============================== + + .. _list_software_future_667: *future* @@ -11219,7 +11446,7 @@ version versionsuffix toolchain python-future is the missing compatibility layer between Python 2 and Python 3. -*homepage*: http://python-future.org/ +*homepage*: https://python-future.org/ ========== ================== ================================================ version versionsuffix toolchain @@ -11253,7 +11480,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -11390,6 +11617,22 @@ version toolchain ========= =============== +.. _list_software_gappa_521: + +*gappa* ++++++++ + +gappa is a collection of commands for working with phylogenetic data. Its main focus are evolutionary placements of short environmental sequences on a reference phylogenetic tree. Such data is typically produced by tools like EPA-ng, RAxML-EPA or pplacer and usually stored in jplace files. + +*homepage*: https://github.com/lczech/gappa + +========= ============== +version toolchain +========= ============== +``0.7.1`` ``GCC/10.3.0`` +========= ============== + + .. _list_software_GARLI_367: *GARLI* @@ -11610,6 +11853,7 @@ version toolchain ``7.6.4`` ``GCCcore/7.3.0`` ``7.6.10`` ``GCCcore/8.2.0`` ``7.6.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``8.0.4`` ``GCCcore/10.3.0`` ========== ==================================== @@ -11689,10 +11933,12 @@ version versionsuffix toolchain ``8.2.0`` ``-2.31.1`` ``system`` ``8.3.0`` ``system`` ``8.3.0`` ``-2.32`` ``system`` +``8.4.0`` ``system`` ``9.1.0`` ``-2.32`` ``system`` ``9.2.0`` ``system`` ``9.2.0`` ``-2.32`` ``system`` ``9.3.0`` ``system`` +``9.4.0`` ``system`` ``10.1.0`` ``system`` ``10.2.0`` ``system`` ``10.3.0`` ``system`` @@ -11732,9 +11978,11 @@ version toolchain ``8.1.0`` ``system`` ``8.2.0`` ``system`` ``8.3.0`` ``system`` +``8.4.0`` ``system`` ``9.1.0`` ``system`` ``9.2.0`` ``system`` ``9.3.0`` ``system`` +``9.4.0`` ``system`` ``10.1.0`` ``system`` ``10.2.0`` ``system`` ``10.3.0`` ``system`` @@ -11851,7 +12099,8 @@ version versionsuffix toolchain ``3.0.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``3.0.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``3.0.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``3.2.1`` ``foss/2020b``, ``fosscuda/2020b`` +``3.2.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``3.3.0`` ``foss/2021a`` ========= ============================== ================================================================ @@ -11880,6 +12129,7 @@ version versionsuffix toolchain ``9.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``10.1`` ``GCCcore/10.2.0`` ``10.2`` ``GCCcore/10.3.0`` +``10.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========== ================== =============================== @@ -12024,6 +12274,7 @@ version toolchain ``2.38.1`` ``GCCcore/8.2.0`` ``2.38.2`` ``GCCcore/8.3.0`` ``2.40.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.42.6`` ``GCCcore/10.3.0`` =========== ==================================================================================== @@ -12276,14 +12527,30 @@ A comprehensive software library for efficient processing of structured genome a *homepage*: http://genometools.org -========== ================== ============== -version versionsuffix toolchain -========== ================== ============== -``1.5.10`` ``foss/2018b`` -``1.5.10`` ``-Python-2.7.15`` ``foss/2018b`` -``1.6.1`` ``GCC/8.3.0`` -``1.6.1`` ``-Python-2.7.16`` ``GCC/8.3.0`` -========== ================== ============== +========== ================== ============================= +version versionsuffix toolchain +========== ================== ============================= +``1.5.10`` ``foss/2018b`` +``1.5.10`` ``-Python-2.7.15`` ``foss/2018b`` +``1.6.1`` ``GCC/10.2.0``, ``GCC/8.3.0`` +``1.6.1`` ``-Python-2.7.16`` ``GCC/8.3.0`` +========== ================== ============================= + + +.. _list_software_GenomeWorks_1137: + +*GenomeWorks* ++++++++++++++ + +SDK for GPU accelerated genome assembly and analysis + +*homepage*: https://github.com/clara-parabricks/GenomeWorks + +============= ================== +version toolchain +============= ================== +``2021.02.2`` ``fosscuda/2020b`` +============= ================== .. _list_software_GenotypeHarmonizer_1898: @@ -12359,15 +12626,16 @@ version versionsuffix toolchain *geopy* +++++++ -geopy is a Python 2 and 3 client for several popular geocoding web services. +geopy is a Python client for several popular geocoding web services. geopy makes it easy for Python developers to locate the coordinates of addresses, cities, countries, and landmarks across the globe using third-party geocoders and other data sources. -*homepage*: https://github.com/geopy/geopy +*homepage*: https://geopy.readthedocs.io/en/stable/ -========== ================= =============== -version versionsuffix toolchain -========== ================= =============== -``1.11.0`` ``-Python-3.6.1`` ``intel/2017a`` -========== ================= =============== +========== ================= ================== +version versionsuffix toolchain +========== ================= ================== +``1.11.0`` ``-Python-3.6.1`` ``intel/2017a`` +``2.1.0`` ``GCCcore/10.2.0`` +========== ================= ================== .. _list_software_georges_748: @@ -12413,7 +12681,7 @@ version versionsuffix toolchain ``3.7.2`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``3.8.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ``3.8.1`` ``-Python-3.8.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` -``3.9.1`` ``GCC/10.2.0`` +``3.9.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` ========= ================== ================================================================ @@ -12490,6 +12758,22 @@ version versionsuffix toolchain ============ ================== =================================================================================================== +.. _list_software_gexiv2_597: + +*gexiv2* +++++++++ + +gexiv2 is a GObject wrapper around the Exiv2 photo metadata library. + +*homepage*: https://wiki.gnome.org/Projects/gexiv2 + +========== ================== +version toolchain +========== ================== +``0.12.2`` ``GCCcore/10.3.0`` +========== ================== + + .. _list_software_GffCompare_986: *GffCompare* @@ -12616,6 +12900,7 @@ version versionsuffix toolchain ``9.50`` ``GCCcore/8.3.0`` ``9.52`` ``GCCcore/9.3.0`` ``9.53.3`` ``GCCcore/10.2.0`` +``9.54.0`` ``GCCcore/10.3.0`` ========== ================== ================================================== @@ -12799,6 +13084,7 @@ version versionsuffix toolchain ``2.23.0`` ``GCCcore/8.3.0`` ``2.23.0`` ``-nodocs`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.28.0`` ``-nodocs`` ``GCCcore/10.2.0`` +``2.32.0`` ``-nodocs`` ``GCCcore/10.3.0`` =========== ============= ==================================== @@ -12854,6 +13140,7 @@ version versionsuffix toolchain ``3.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``3.1.9`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``3.1.14`` ``GCCcore/10.2.0`` +``3.1.18`` ``GCCcore/10.3.0`` ========== ================= =============================== @@ -12904,7 +13191,7 @@ version versionsuffix toolchain ``1.3.9`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.3.9`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` ``1.4.0`` ``GCCcore/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``1.4.2`` ``GCCcore/9.3.0`` +``1.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ========= ================ ==================================================================================================================================== @@ -12936,14 +13223,14 @@ The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C *homepage*: https://github.com/nigels-com/glew -========= ============= =========================================================================================== -version versionsuffix toolchain -========= ============= =========================================================================================== -``2.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b`` -``2.2.0`` ``-egl`` ``GCCcore/10.2.0`` -``2.2.0`` ``-glx`` ``GCCcore/10.2.0`` -``2.2.0`` ``-osmesa`` ``GCCcore/10.2.0`` -========= ============= =========================================================================================== +========= ============= =============================================================================================================== +version versionsuffix toolchain +========= ============= =============================================================================================================== +``2.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b`` +``2.2.0`` ``-egl`` ``GCCcore/10.2.0`` +``2.2.0`` ``-glx`` ``GCCcore/10.2.0`` +``2.2.0`` ``-osmesa`` ``GCCcore/10.2.0`` +========= ============= =============================================================================================================== .. _list_software_GLFW_304: @@ -12961,6 +13248,7 @@ version toolchain ``3.2.1`` ``intel/2018a`` ``3.3.2`` ``GCCcore/9.3.0`` ``3.3.3`` ``GCCcore/10.2.0`` +``3.3.4`` ``GCCcore/10.3.0`` ========= ================== @@ -13069,14 +13357,14 @@ OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics s *homepage*: https://github.com/g-truc/glm -=========== ===================================== -version toolchain -=========== ===================================== -``0.9.7.6`` ``intel/2016a`` -``0.9.8.3`` ``GCCcore/5.4.0``, ``GCCcore/7.3.0`` -``0.9.9.0`` ``GCCcore/6.4.0`` -``0.9.9.8`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` -=========== ===================================== +=========== ========================================================= +version toolchain +=========== ========================================================= +``0.9.7.6`` ``intel/2016a`` +``0.9.8.3`` ``GCCcore/5.4.0``, ``GCCcore/7.3.0`` +``0.9.9.0`` ``GCCcore/6.4.0`` +``0.9.9.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0`` +=========== ========================================================= .. _list_software_GlobalArrays_1219: @@ -13290,17 +13578,17 @@ GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x *homepage*: https://github.com/aleaxit/gmpy -=========== ================== =============================== -version versionsuffix toolchain -=========== ================== =============================== -``2.0.8`` ``-Python-2.7.13`` ``intel/2017a`` -``2.0.8`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.0.8`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b4`` ``GCC/8.3.0`` -``2.1.0b5`` ``GCC/10.2.0``, ``GCC/9.3.0`` -=========== ================== =============================== +=========== ================== ============================================= +version versionsuffix toolchain +=========== ================== ============================================= +``2.0.8`` ``-Python-2.7.13`` ``intel/2017a`` +``2.0.8`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2.0.8`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b4`` ``GCC/8.3.0`` +``2.1.0b5`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` +=========== ================== ============================================= .. _list_software_gmsh_431: @@ -13321,6 +13609,7 @@ version versionsuffix toolchain ``4.5.6`` ``-Python-2.7.16`` ``intel/2019b`` ``4.5.6`` ``-Python-3.7.4`` ``foss/2019b`` ``4.7.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``4.8.4`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================== =============================== @@ -13415,6 +13704,7 @@ version toolchain ``5.2.6`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b`` ``5.2.8`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``5.4.1`` ``GCCcore/10.2.0`` +``5.4.2`` ``GCCcore/10.3.0`` ========= ================================================================ @@ -13425,7 +13715,7 @@ version toolchain GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability. -*homepage*: http://www.gnutls.org/ +*homepage*: https://www.gnutls.org ========== ================== version toolchain @@ -13433,6 +13723,7 @@ version toolchain ``3.3.21`` ``intel/2016a`` ``3.4.7`` ``GNU/4.9.3-2.25`` ``3.4.11`` ``foss/2016a`` +``3.7.2`` ``GCCcore/10.3.0`` ========== ================== @@ -13459,6 +13750,7 @@ version toolchain ``1.14`` ``system`` ``1.14.1`` ``system`` ``1.16.3`` ``system`` +``1.16.5`` ``system`` ========== ================= @@ -13523,6 +13815,7 @@ version versionsuffix toolchain ``1.63.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``1.64.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``1.66.1`` ``GCCcore/10.2.0`` +``1.68.0`` ``GCCcore/10.3.0`` ========== ================== ================================== @@ -13665,6 +13958,7 @@ version toolchain ``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b`` ``1.8.1`` ``GCCcore/8.2.0`` ``1.10.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.11.0`` ``GCCcore/10.3.0`` ========== ===================================================================== @@ -13767,14 +14061,15 @@ gperftools is a collection of a high-performance multi-threaded malloc() impleme *homepage*: https://github.com/gperftools/gperftools -========== ==================================== -version toolchain -========== ==================================== -``2.5`` ``foss/2016a``, ``intel/2016b`` -``2.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.7.90`` ``GCCcore/8.3.0`` -``2.8`` ``GCCcore/9.3.0`` -========== ==================================== +========== ====================================== +version toolchain +========== ====================================== +``2.5`` ``foss/2016a``, ``intel/2016b`` +``2.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.7.90`` ``GCCcore/8.3.0`` +``2.8`` ``GCCcore/9.3.0`` +``2.9.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========== ====================================== .. _list_software_gpustat_776: @@ -13944,6 +14239,7 @@ version toolchain ``1.3.28`` ``foss/2018a`` ``1.3.31`` ``foss/2018b`` ``1.3.34`` ``foss/2019a``, ``foss/2019b`` +``1.3.36`` ``foss/2020b`` ========== ================================ @@ -14016,6 +14312,7 @@ version versionsuffix toolchain ``2.44.1`` ``-Java-11`` ``GCCcore/9.3.0`` ``2.44.1`` ``-Java-11-Python-3.8.2`` ``GCCcore/9.3.0`` ``2.47.0`` ``-Java-11`` ``GCCcore/10.2.0`` +``2.47.2`` ``GCCcore/10.3.0`` ========== ========================= =============================== @@ -14271,7 +14568,7 @@ version versionsuffix toolchain GroopM is a metagenomic binning toolset. It leverages spatio-temporal dynamics (differential coverage) to accurately (and almost automatically) extract population genomes from multi-sample metagenomic datasets. -*homepage*: http://ecogenomics.github.io/GroopM/ +*homepage*: https://ecogenomics.github.io/GroopM/ ========= ================== ============== version versionsuffix toolchain @@ -14347,6 +14644,7 @@ version toolchain ``2.4`` ``GCCcore/6.4.0`` ``2.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.6`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` +``2.7`` ``GCC/10.3.0`` ========= ============================================================================================================================ @@ -14462,6 +14760,7 @@ version toolchain ``2.24.30`` ``foss/2016a``, ``intel/2016a`` ``2.24.31`` ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``2.24.32`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` +``2.24.33`` ``GCCcore/10.3.0`` ``3.22.30`` ``fosscuda/2018b`` ``3.24.8`` ``GCCcore/8.2.0`` ``3.24.13`` ``GCCcore/8.3.0`` @@ -14512,12 +14811,12 @@ GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free *homepage*: http://gts.sourceforge.net/ -============ =========================================================================================================================================================================================== -version toolchain -============ =========================================================================================================================================================================================== -``0.7.6`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` -``20121130`` ``foss/2017b`` -============ =========================================================================================================================================================================================== +============ =============================================================================================================================================================================================================== +version toolchain +============ =============================================================================================================================================================================================================== +``0.7.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` +``20121130`` ``foss/2017b`` +============ =============================================================================================================================================================================================================== .. _list_software_gubbins_746: @@ -14568,6 +14867,7 @@ version toolchain ``2.0.11`` ``GCC/4.9.3-2.25``, ``foss/2016a`` ``2.2.2`` ``GCCcore/6.4.0`` ``2.2.4`` ``GCCcore/7.3.0``, ``GCCcore/9.3.0`` +``2.2.7`` ``GCCcore/10.3.0`` ========== ====================================================================================================================================================================================================================== @@ -14640,7 +14940,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -14719,6 +15019,7 @@ version versionsuffix toolchain ``2.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` ``2.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``3.1.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +``3.2.1`` ``foss/2021a`` ========== ===================================== ==================================================================================== @@ -14746,6 +15047,22 @@ version versionsuffix toolchain =================== ========================== ================== +.. _list_software_HAL_213: + +*HAL* ++++++ + +HAL is a structure to efficiently store and index multiple genome alignments and ancestral reconstructions. HAL is a graph-based representation which provides several advantages over matrix/block-based formats such as MAF, such as improved scalability and the ability to perform queries with respect to an arbitrary reference or subtree. This package includes the HAL API and several analysis and conversion tools which are described below. HAL files are presently stored in either HDF5 or mmap format, but we note that the tools and most of the API are format-independent, so other databases could be implemented in the future. + +*homepage*: https://github.com/ComparativeGenomicsToolkit/hal + +======= ============== +version toolchain +======= ============== +``2.1`` ``foss/2020b`` +======= ============== + + .. _list_software_hanythingondemand_1808: *hanythingondemand* @@ -14819,6 +15136,7 @@ version toolchain ``2.4.0`` ``GCCcore/8.2.0`` ``2.6.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.6.7`` ``GCCcore/10.2.0`` +``2.8.1`` ``GCCcore/10.3.0`` ========= ================================================ @@ -14906,7 +15224,7 @@ version versionsuffix toolchain ``4.2.13`` ``GCCcore/6.4.0`` ``4.2.13`` ``-no-netcdf`` ``intel/2017a`` ``4.2.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``4.2.15`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``4.2.15`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ========== ============== ========================================================================== @@ -14972,7 +15290,7 @@ version versionsuffix toolchain ``1.10.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompic/2019a``, ``gompic/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpic/2019a``, ``iimpic/2019b``, ``iompi/2019b`` ``1.10.5`` ``-serial`` ``GCCcore/8.3.0`` ``1.10.6`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpic/2020a`` -``1.10.7`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpic/2020b`` +``1.10.7`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpic/2020b`` ``1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` ================= ============= ================================================================================================================================================================================================================== @@ -15090,12 +15408,12 @@ version toolchain ``1.47.5`` ``GCCcore/5.5.0`` ``1.47.6`` ``GCCcore/8.1.0`` ``1.47.7`` ``GCCcore/8.2.0`` -``1.47.8`` ``GCCcore/7.4.0``, ``GCCcore/8.3.0`` +``1.47.8`` ``GCCcore/7.4.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0`` ``1.47.10`` ``GCCcore/9.1.0``, ``GCCcore/9.2.0`` ``1.47.12`` ``GCCcore/9.3.0`` ``1.47.15`` ``GCCcore/10.1.0`` ``1.47.16`` ``GCCcore/10.2.0`` -``1.48.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0`` +``1.48.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/9.4.0`` =========== ================================================================================================================================================================================== @@ -15181,6 +15499,22 @@ version toolchain ========== ================= +.. _list_software_hipify-clang_1211: + +*hipify-clang* +++++++++++++++ + +Hipify-clang is a clang-based tool for translating CUDA sources into HIP sources. It translates CUDA source into an abstract syntax tree, which is traversed by transformation matchers. After applying all the matchers, the output HIP source is produced. + +*homepage*: https://github.com/ROCm-Developer-Tools/HIPIFY + +========= ================= +version toolchain +========= ================= +``4.2.0`` ``gcccuda/2020b`` +========= ================= + + .. _list_software_HIPS_308: *HIPS* @@ -15214,7 +15548,7 @@ version toolchain ``2.0.5`` ``intel/2017a`` ``2.1.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``2.2.0`` ``foss/2018b`` -``2.2.1`` ``foss/2019b``, ``gompi/2020b`` +``2.2.1`` ``foss/2019b``, ``foss/2020a``, ``gompi/2020b`` ============== ================================================================================= @@ -15343,6 +15677,7 @@ version versionsuffix toolchain ``0.21.1`` ``-TensorFlow-2.4.1-Python-3.7.4`` ``fosscuda/2019b`` ``0.21.3`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` ``0.21.3`` ``-TensorFlow-2.3.1-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``0.22.0`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` ========== =================================== ================================== @@ -15453,7 +15788,7 @@ version toolchain A framework to process and analyze data from high-throughput sequencing (HTS) assays -*homepage*: http://www-huber.embl.de/users/anders/HTSeq/ +*homepage*: https://www-huber.embl.de/users/anders/HTSeq/ =========== ================== ================================================ version versionsuffix toolchain @@ -15613,7 +15948,7 @@ version versionsuffix toolchain HyperSpy is an open source Python library which provides tools to facilitate the interactive data analysis of multi-dimensional datasets that can be described as multi-dimensional arrays of a given signal (e.g. a 2D array of spectra a.k.a spectrum image) -*homepage*: http://hyperspy.org/ +*homepage*: https://hyperspy.org/ ========= ================= =============== version versionsuffix toolchain @@ -15671,6 +16006,7 @@ version versionsuffix toolchain ``4.23.4`` ``GCCcore/8.2.0`` ``4.39.3`` ``-Python-3.6.4`` ``intel/2018a`` ``4.44.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``4.53.1`` ``GCCcore/10.2.0`` ``5.6.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``5.41.2`` ``GCCcore/10.2.0`` ``5.41.5`` ``GCCcore/10.2.0`` @@ -15696,6 +16032,7 @@ version toolchain ``2.15.1`` ``foss/2019a``, ``intel/2019a`` ``2.18.2`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` ``2.20.0`` ``foss/2020b`` +``2.21.0`` ``foss/2021a`` ========== ================================================================ @@ -15705,7 +16042,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -15947,6 +16284,7 @@ version toolchain ``65.1`` ``GCCcore/8.3.0`` ``66.1`` ``GCCcore/9.3.0`` ``67.1`` ``GCCcore/10.2.0`` +``69.1`` ``GCCcore/10.3.0`` ======== ==================================== @@ -16348,6 +16686,7 @@ version versionsuffix toolchain ``7.0.9-5`` ``GCCcore/8.3.0`` ``7.0.10-1`` ``GCCcore/9.3.0`` ``7.0.10-35`` ``GCCcore/10.2.0`` +``7.0.11-14`` ``GCCcore/10.3.0`` ============= =================================== =============================== @@ -16648,6 +16987,22 @@ version toolchain ============ ==================== +.. _list_software_inline_639: + +*inline* +++++++++ + +Functionality to dynamically define R functions and S4 methods with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling conventions. + +*homepage*: https://cran.r-project.org/web/packages/inline + +========== ============= ============== +version versionsuffix toolchain +========== ============= ============== +``0.3.19`` ``-R-4.0.4`` ``foss/2020b`` +========== ============= ============== + + .. _list_software_inputproto_1124: *inputproto* @@ -17025,14 +17380,15 @@ version toolchain The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. -*homepage*: https://github.com/IOR-LANL/ior +*homepage*: https://github.com/hpc/ior -========= ============= =============== -version versionsuffix toolchain -========= ============= =============== -``3.0.1`` ``-mpiio`` ``foss/2016a`` -``3.2.1`` ``gompi/2019b`` -========= ============= =============== +========= ============= ================================ +version versionsuffix toolchain +========= ============= ================================ +``3.0.1`` ``-mpiio`` ``foss/2016a`` +``3.2.1`` ``gompi/2019b`` +``3.3.0`` ``gompi/2020b``, ``gompi/2021a`` +========= ============= ================================ .. _list_software_IOzone_596: @@ -17184,6 +17540,7 @@ version versionsuffix toolchain ``7.13.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``7.15.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``7.18.1`` ``GCCcore/10.2.0`` +``7.25.0`` ``GCCcore/10.3.0`` ========== ================== ======================================================================================= @@ -17221,6 +17578,7 @@ version versionsuffix toolchain ``0.8.15`` ``-R-3.4.3-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.1`` ``-R-3.6.2-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``1.1`` ``-R-3.6.3-Python-3.8.2`` ``foss/2020a`` +``1.2`` ``-R-4.0.0-Python-3.8.2`` ``foss/2020a`` ========== ========================== ================================== @@ -17249,15 +17607,15 @@ isl is a library for manipulating sets and relations of integer points bounded b *homepage*: http://isl.gforge.inria.fr/ -======== ====================================================== -version toolchain -======== ====================================================== -``0.14`` ``GCC/4.9.2`` -``0.15`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a`` -``0.16`` ``GCC/4.9.3-2.25`` -``0.17`` ``foss/2016a`` -``0.23`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -======== ====================================================== +======== ========================================================= +version toolchain +======== ========================================================= +``0.14`` ``GCC/4.9.2`` +``0.15`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a`` +``0.16`` ``GCC/4.9.3-2.25`` +``0.17`` ``foss/2016a`` +``0.23`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +======== ========================================================= .. _list_software_ispc_431: @@ -17275,6 +17633,7 @@ version toolchain ``1.6.0`` ``system`` ``1.10.0`` ``system`` ``1.12.0`` ``system`` +``1.16.0`` ``system`` ========== ========== @@ -17513,6 +17872,7 @@ version versionsuffix toolchain ``1.8.0_241`` ``system`` ``1.8.0_271`` ``system`` ``1.8.0_281`` ``system`` +``1.8.0_292`` ``-OpenJDK`` ``system`` ``1.8_191`` ``-b26-OpenJDK`` ``system`` ``1.8_265`` ``-b01-OpenJDK-aarch64`` ``system`` ``1.9.0.4`` ``system`` @@ -17707,13 +18067,13 @@ JsonCpp is a C++ library that allows manipulating JSON values, including serial *homepage*: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html -========== ===================================== -version toolchain -========== ===================================== -``0.10.7`` ``GCCcore/8.2.0`` -``1.9.3`` ``GCCcore/8.3.0`` -``1.9.4`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========== ===================================== +========== ========================================================= +version toolchain +========== ========================================================= +``0.10.7`` ``GCCcore/8.2.0`` +``1.9.3`` ``GCCcore/8.3.0`` +``1.9.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +========== ========================================================= .. _list_software_JUBE_294: @@ -17745,11 +18105,11 @@ A C library that implements a dynamic array. *homepage*: http://judy.sourceforge.net/ -========= ======================================================== -version toolchain -========= ======================================================== -``1.0.5`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= ======================================================== +========= ============================================================================ +version toolchain +========= ============================================================================ +``1.0.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ============================================================================ .. _list_software_Julia_501: @@ -17836,12 +18196,13 @@ JupyterLab is the next-generation user interface for Project Jupyter offering al *homepage*: https://jupyter.org/ -========= ================= ================================== -version versionsuffix toolchain -========= ================= ================================== -``1.2.5`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``2.2.8`` ``GCCcore/10.2.0`` -========= ================= ================================== +========== ================= ================================== +version versionsuffix toolchain +========== ================= ================================== +``1.2.5`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.2.8`` ``GCCcore/10.2.0`` +``3.0.16`` ``GCCcore/10.3.0`` +========== ================= ================================== .. _list_software_JWM_238: @@ -18313,7 +18674,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -18341,12 +18702,12 @@ LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGP *homepage*: http://lame.sourceforge.net/ -========== ================================================================================================================================== -version toolchain -========== ================================================================================================================================== -``3.99.5`` ``foss/2016b``, ``intel/2017a`` -``3.100`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` -========== ================================================================================================================================== +========== ====================================================================================================================================================== +version toolchain +========== ====================================================================================================================================================== +``3.99.5`` ``foss/2016b``, ``intel/2017a`` +``3.100`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` +========== ====================================================================================================================================================== .. _list_software_LAMMPS_458: @@ -18484,6 +18845,7 @@ version versionsuffix toolchain ========== ============= ================== ``0.17.6`` ``-x86_64`` ``system`` ``1.25.1`` ``GCCcore/10.2.0`` +``1.26.0`` ``GCCcore/10.3.0`` ========== ============= ================== @@ -18613,12 +18975,12 @@ Asynchronous input/output library that uses the kernels native interface. *homepage*: https://pagure.io/libaio -=========== ==================================== -version toolchain -=========== ==================================== -``0.3.111`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.3.112`` ``GCCcore/10.2.0`` -=========== ==================================== +=========== ====================================== +version toolchain +=========== ====================================== +``0.3.111`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.3.112`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +=========== ====================================== .. _list_software_libarchive_1049: @@ -18630,14 +18992,14 @@ Multi-format archive and compression library *homepage*: https://www.libarchive.org/ -========= ================== -version toolchain -========= ================== -``3.4.0`` ``GCCcore/8.2.0`` -``3.4.2`` ``GCCcore/9.3.0`` -``3.4.3`` ``GCCcore/10.2.0`` -``3.5.1`` ``GCCcore/10.3.0`` -========= ================== +========= ===================================== +version toolchain +========= ===================================== +``3.4.0`` ``GCCcore/8.2.0`` +``3.4.2`` ``GCCcore/9.3.0`` +``3.4.3`` ``GCCcore/10.2.0`` +``3.5.1`` ``GCCcore/10.3.0``, ``GCCcore/8.3.0`` +========= ===================================== .. _list_software_libav_526: @@ -18722,9 +19084,26 @@ version toolchain ``1.11`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.14`` ``GCCcore/10.2.0`` +``1.17`` ``GCCcore/10.3.0`` ======== ========================================================================================================= +.. _list_software_libcint_741: + +*libcint* ++++++++++ + +libcint is an open source library for analytical Gaussian integrals. + +*homepage*: https://github.com/sunqm/libcint + +========= ============================== +version toolchain +========= ============================== +``4.4.0`` ``foss/2020b``, ``foss/2021a`` +========= ============================== + + .. _list_software_libcircle_937: *libcircle* @@ -18976,6 +19355,7 @@ version toolchain ``1.5.2`` ``foss/2018a`` ``1.5.3`` ``GCCcore/8.2.0``, ``fosscuda/2018b`` ``1.5.4`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.5.8`` ``GCCcore/10.3.0`` ========= ======================================================== @@ -19121,6 +19501,7 @@ version toolchain ``2.2.4`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` ``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b``, ``intel/2018a`` ``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.3.1`` ``GCCcore/10.3.0`` ========= ============================================================================================================ @@ -19154,7 +19535,7 @@ version toolchain ========= ======================================================= ``1.4.2`` ``foss/2018a``, ``foss/2018b``, ``intel/2018b`` ``1.5.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.6.0`` ``GCCcore/10.2.0`` +``1.6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ======================================================= @@ -19310,11 +19691,11 @@ libHaru is a free, cross platform, open source library for generating PDF files. *homepage*: http://libharu.org/ -========= ========================================================================================================================= -version toolchain -========= ========================================================================================================================= -``2.3.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2017a``, ``intel/2018b`` -========= ========================================================================================================================= +========= ============================================================================================================================================= +version toolchain +========= ============================================================================================================================================= +``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2017a``, ``intel/2018b`` +========= ============================================================================================================================================= .. _list_software_libibmad_820: @@ -19539,12 +19920,12 @@ GNU libmicrohttpd is a small C library that is supposed to make it easy to run *homepage*: https://www.gnu.org/software/libmicrohttpd/ -========== ================== -version toolchain -========== ================== -``0.9.71`` ``GCCcore/9.3.0`` -``0.9.73`` ``GCCcore/10.2.0`` -========== ================== +========== ======================================================== +version toolchain +========== ======================================================== +``0.9.71`` ``GCCcore/9.3.0`` +``0.9.73`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========== ======================================================== .. _list_software_libmo_unpack_1268: @@ -19954,18 +20335,18 @@ Sodium is a modern, easy-to-use software library for encryption, decryption, sig *homepage*: https://doc.libsodium.org/ -========== ======================================================== -version toolchain -========== ======================================================== -``1.0.6`` ``intel/2016a`` -``1.0.8`` ``foss/2016a`` -``1.0.11`` ``foss/2016b``, ``intel/2016b`` -``1.0.12`` ``GCCcore/6.4.0``, ``intel/2017a`` -``1.0.13`` ``GCCcore/6.4.0``, ``foss/2017a`` -``1.0.16`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.0.17`` ``GCCcore/8.2.0`` -``1.0.18`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ======================================================== +========== ============================================================================ +version toolchain +========== ============================================================================ +``1.0.6`` ``intel/2016a`` +``1.0.8`` ``foss/2016a`` +``1.0.11`` ``foss/2016b``, ``intel/2016b`` +``1.0.12`` ``GCCcore/6.4.0``, ``intel/2017a`` +``1.0.13`` ``GCCcore/6.4.0``, ``foss/2017a`` +``1.0.16`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.0.17`` ``GCCcore/8.2.0`` +``1.0.18`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ============================================================================ .. _list_software_LibSoup_702: @@ -20045,11 +20426,12 @@ Useful set of classes for creating statistical genetic programs. *homepage*: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen -============ ================= -version toolchain -============ ================= -``20190330`` ``GCCcore/6.4.0`` -============ ================= +============ ================== +version toolchain +============ ================== +``1.0.15`` ``GCCcore/10.2.0`` +``20190330`` ``GCCcore/6.4.0`` +============ ================== .. _list_software_LIBSVM_461: @@ -20102,6 +20484,7 @@ version toolchain ``4.12`` ``GCCcore/5.4.0`` ``4.13`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``4.16.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +``4.17.0`` ``GCCcore/10.3.0`` ========== =================================================== @@ -20142,6 +20525,7 @@ version toolchain ``1.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.2.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.3.1`` ``GCCcore/10.2.0`` +``1.3.2`` ``GCCcore/10.3.0`` ========= ==================================== @@ -20172,14 +20556,14 @@ This library provides functions for manipulating Unicode strings and for manipu *homepage*: http://www.gnu.org/software/libunistring/ -========== ========================================================================== -version toolchain -========== ========================================================================== -``0.9.3`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` -``0.9.6`` ``GCCcore/5.4.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016b`` -``0.9.7`` ``GCCcore/6.4.0`` -``0.9.10`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ========================================================================== +========== ============================================================================================== +version toolchain +========== ============================================================================================== +``0.9.3`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` +``0.9.6`` ``GCCcore/5.4.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016b`` +``0.9.7`` ``GCCcore/6.4.0`` +``0.9.10`` ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ============================================================================================== .. _list_software_libunwind_972: @@ -20343,20 +20727,21 @@ Libxc is a library of exchange-correlation functionals for density-functional th *homepage*: https://www.tddft.org/programs/libxc -========= ======================================================================================================================================================================================= -version toolchain -========= ======================================================================================================================================================================================= -``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` -``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` -``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` -``4.0.1`` ``foss/2017b``, ``intel/2017b`` -``4.0.3`` ``foss/2016b``, ``foss/2017a`` -``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` -``4.3.4`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` -``5.1.2`` ``GCC/10.2.0`` -``5.1.3`` ``GCC/10.2.0`` -========= ======================================================================================================================================================================================= +========= ===================================================================================================================================================================================================================================== +version toolchain +========= ===================================================================================================================================================================================================================================== +``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` +``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` +``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` +``4.0.1`` ``foss/2017b``, ``intel/2017b`` +``4.0.3`` ``foss/2016b``, ``foss/2017a`` +``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` +``4.3.4`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0`` +``5.1.2`` ``GCC/10.2.0`` +``5.1.3`` ``GCC/10.2.0`` +``5.1.5`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` +========= ===================================================================================================================================================================================================================================== .. _list_software_libxcb_628: @@ -20960,6 +21345,7 @@ version toolchain ``2.8`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``2.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` ``2.11`` ``GCCcore/10.2.0`` +``2.12`` ``GCCcore/10.3.0`` ======== ============================================================================================================================================== @@ -21050,6 +21436,7 @@ version versionsuffix toolchain ``0.9.14`` ``-Python-2.7.15`` ``intel/2018b`` ``1.0.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``1.0.1`` ``-Python-3.8.2`` ``foss/2020a`` +``1.0.2`` ``foss/2020b``, ``intel/2020b`` ========== ================== =============================== @@ -21331,6 +21718,22 @@ version toolchain ============ ============== +.. _list_software_LTR_retriever_1321: + +*LTR_retriever* ++++++++++++++++ + +LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package. + +*homepage*: https://github.com/oushujun/LTR_retriever + +========= ============== +version toolchain +========= ============== +``2.9.0`` ``foss/2020b`` +========= ============== + + .. _list_software_LtrDetector_1132: *LtrDetector* @@ -21366,6 +21769,7 @@ version toolchain ``5.3.4`` ``GCCcore/7.2.0``, ``system`` ``5.3.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ``5.4.2`` ``GCCcore/10.2.0`` +``5.4.3`` ``GCCcore/10.3.0`` =========== =================================================================== @@ -21537,7 +21941,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -21547,14 +21951,15 @@ version toolchain GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. -*homepage*: http://www.gnu.org/software/m4/m4.html +*homepage*: https://www.gnu.org/software/m4/m4.html ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.4.16`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.4.18`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` +``1.4.18`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` +``1.4.19`` ``GCCcore/9.4.0``, ``system`` ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -21709,7 +22114,7 @@ version versionsuffix toolchain Mahotas is a computer vision and image processing library for Python -*homepage*: http://mahotas.readthedocs.io/ +*homepage*: https://mahotas.readthedocs.io/ ========= ================== =============== version versionsuffix toolchain @@ -21795,11 +22200,12 @@ makeinfo is part of the Texinfo project, the official documentation format of th *homepage*: https://www.gnu.org/software/texinfo/ -======= =========================================================================================== -version toolchain -======= =========================================================================================== -``6.7`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= =========================================================================================== +======= ============= =========================================================================================== +version versionsuffix toolchain +======= ============= =========================================================================================== +``6.7`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``6.7`` ``-minimal`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +======= ============= =========================================================================================== .. _list_software_Mako_392: @@ -21847,6 +22253,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_mapDamage_893: + +*mapDamage* ++++++++++++ + +mapDamage2 is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms. + +*homepage*: https://ginolhac.github.io/mapDamage/ + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``2.2.1`` ``-R-4.0.4`` ``foss/2020b`` +========= ============= ============== + + .. _list_software_Maple_495: *Maple* @@ -22292,6 +22714,22 @@ version toolchain ============ ============== +.. _list_software_MbedTLS_619: + +*MbedTLS* ++++++++++ + +An open source, portable, easy to use, readable and flexible SSL library. + +*homepage*: https://tls.mbed.org/ + +========== ================== +version toolchain +========== ================== +``2.26.0`` ``GCCcore/10.2.0`` +========== ================== + + .. _list_software_MBROLA_445: *MBROLA* @@ -22386,6 +22824,7 @@ version versionsuffix toolchain ``R2020a`` ``.6`` ``system`` ``R2020b`` ``.5`` ``system`` ``R2021a`` ``.0`` ``system`` +``R2021a`` ``.3`` ``system`` ========== ============= ========== @@ -22526,6 +22965,7 @@ version versionsuffix toolchain ``1.1.1`` ``-Python-3.7.4`` ``foss/2019b`` ``1.1.3`` ``-Python-3.7.4`` ``foss/2019b`` ``1.2.0`` ``-Python-3.7.4`` ``foss/2019b`` +``1.4.3`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================= ============== @@ -22764,6 +23204,7 @@ version versionsuffix toolchain ``3.8.3`` ``-Python-2.7.11`` ``foss/2016a`` ``5.7.1`` ``GCCcore/10.2.0`` ``5.7.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``5.8`` ``GCCcore/10.3.0`` ========= ================== ================== @@ -23113,13 +23554,13 @@ METIS is a set of serial programs for partitioning graphs, partitioning finite e *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview -========= ============= ====================================================================================================================================================================================================================================================== -version versionsuffix toolchain -========= ============= ====================================================================================================================================================================================================================================================== -``5.0.2`` ``gimkl/2.11.5`` -``5.1.0`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``5.1.0`` ``-32bitIDX`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -========= ============= ====================================================================================================================================================================================================================================================== +========= ============= ========================================================================================================================================================================================================================================================================== +version versionsuffix toolchain +========= ============= ========================================================================================================================================================================================================================================================================== +``5.0.2`` ``gimkl/2.11.5`` +``5.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``5.1.0`` ``-32bitIDX`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +========= ============= ========================================================================================================================================================================================================================================================================== .. _list_software_mhcflurry_988: @@ -23154,6 +23595,22 @@ version versionsuffix toolchain ======= ================= ================================== +.. _list_software_microctools_1198: + +*microctools* ++++++++++++++ + +Various worker functions for microclimc package + +*homepage*: https://github.com/ilyamaclean/microctools + +================== ============= ============== +version versionsuffix toolchain +================== ============= ============== +``0.1.0-20201209`` ``-R-4.0.4`` ``foss/2020b`` +================== ============= ============== + + .. _list_software_MiGEC_389: *MiGEC* @@ -23362,6 +23819,7 @@ version toolchain ``2.13`` ``foss/2018b`` ``2.17`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/9.3.0`` ``2.18`` ``GCCcore/10.2.0`` +``2.20`` ``GCCcore/10.2.0`` ========== ====================================================== @@ -23634,6 +24092,7 @@ version toolchain ``8-fac81`` ``intel/2018b`` ``10-6d92c`` ``gompi/2019b``, ``iimpi/2019b`` ``11-e1a1c`` ``iimpi/2019b`` +``13-45111`` ``gompi/2020b`` ============ ================================ @@ -24019,14 +24478,14 @@ Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily h *homepage*: http://www.multiprecision.org/ -========= =============== ====================================== -version versionsuffix toolchain -========= =============== ====================================== -``1.0.3`` ``intel/2017a`` -``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` -``1.1.0`` ``GCC/8.3.0``, ``GCC/9.3.0`` -``1.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========= =============== ====================================== +========= =============== =============================================== +version versionsuffix toolchain +========= =============== =============================================== +``1.0.3`` ``intel/2017a`` +``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` +``1.1.0`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/9.3.0`` +``1.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= =============== =============================================== .. _list_software_MPFR_309: @@ -24183,15 +24642,16 @@ version versionsuffix toolchain *MrBayes* +++++++++ -MrBayes is a program for the Bayesian estimation of phylogeny. +MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. -*homepage*: http://mrbayes.csit.fsu.edu +*homepage*: https://nbisweden.github.io/MrBayes/ -========= ============================== -version toolchain -========= ============================== -``3.2.6`` ``foss/2016a``, ``foss/2017a`` -========= ============================== +========= ================================= +version toolchain +========= ================================= +``3.2.6`` ``foss/2016a``, ``foss/2017a`` +``3.2.7`` ``gompi/2020b``, ``gompic/2019b`` +========= ================================= .. _list_software_mrcfile_738: @@ -24470,6 +24930,7 @@ version versionsuffix toolchain ``5.2.1`` ``-metis`` ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a`` ``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` ``5.3.5`` ``-metis`` ``foss/2020b`` +``5.4.0`` ``-metis`` ``foss/2021a`` ========= ============== ================================================================================================================= @@ -24815,7 +25276,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_NINJA_368` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -25163,17 +25624,18 @@ The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and mul *homepage*: https://developer.nvidia.com/nccl -========== =================== ================== -version versionsuffix toolchain -========== =================== ================== -``2.1.4`` ``-CUDA-9.0.176`` ``system`` -``2.2.13`` ``-CUDA-9.2.148.1`` ``system`` -``2.3.7`` ``fosscuda/2018b`` -``2.4.2`` ``gcccuda/2019a`` -``2.4.8`` ``gcccuda/2019b`` -``2.8.3`` ``-CUDA-11.0.2`` ``system`` -``2.8.3`` ``-CUDA-11.1.1`` ``system`` -========== =================== ================== +========== =================== ============================== +version versionsuffix toolchain +========== =================== ============================== +``2.1.4`` ``-CUDA-9.0.176`` ``system`` +``2.2.13`` ``-CUDA-9.2.148.1`` ``system`` +``2.3.7`` ``fosscuda/2018b`` +``2.4.2`` ``gcccuda/2019a`` +``2.4.8`` ``gcccuda/2019b`` +``2.8.3`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0``, ``system`` +``2.8.3`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0``, ``system`` +``2.9.9`` ``-CUDA-11.3.1`` ``system`` +========== =================== ============================== .. _list_software_NCCL-tests_896: @@ -25368,7 +25830,7 @@ version toolchain nd2reader is a pure-Python package that reads images produced by NIS Elements 4.0+. -*homepage*: http://www.lighthacking.nl/nd2reader/ +*homepage*: https://www.lighthacking.nl/nd2reader/ ========= ================== =============== version versionsuffix toolchain @@ -25425,6 +25887,22 @@ version toolchain ======== =============== +.. _list_software_Nektar++_699: + +*Nektar++* +++++++++++ + +Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers. + +*homepage*: https://www.nektar.info + +========= ============== +version toolchain +========= ============== +``5.0.1`` ``foss/2020b`` +========= ============== + + .. _list_software_neon_432: *neon* @@ -25500,6 +25978,7 @@ version versionsuffix toolchain ``4.6.2`` ``gompi/2019a``, ``iimpi/2019a`` ``4.7.1`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` ``4.7.4`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2020b`` +``4.8.0`` ``gompi/2021a``, ``iimpi/2021a`` =========== ================ ========================================================================================================================== @@ -25558,7 +26037,7 @@ version versionsuffix toolchain ``4.4.4`` ``-HDF5-1.8.19`` ``foss/2017b``, ``intel/2017b`` ``4.4.5`` ``gompi/2019a``, ``iimpi/2019a`` ``4.5.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` -``4.5.3`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b`` +``4.5.3`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a`` ========= ================ ==================================================================================================================================================================================================================================================================================================================================== @@ -25995,22 +26474,22 @@ NiBabel provides read/write access to some common medical and neuroimaging file *homepage*: https://nipy.github.io/nibabel -========= ================================= =============================== -version versionsuffix toolchain -========= ================================= =============================== -``2.0.2`` ``-Python-2.7.11`` ``intel/2016a`` -``2.0.2`` ``-Python-2.7.11-freetype-2.6.3`` ``intel/2016a`` -``2.1.0`` ``-Python-2.7.13`` ``intel/2017a`` -``2.2.1`` ``-Python-3.6.4`` ``intel/2018a`` -``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.3.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.3.0`` ``-Python-3.6.6`` ``foss/2018b`` -``2.4.0`` ``foss/2019a``, ``intel/2019a`` -``2.5.1`` ``-Python-3.6.6`` ``foss/2018b`` -``3.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``3.2.0`` ``-Python-3.8.2`` ``foss/2020a`` -``3.2.1`` ``foss/2020b`` -========= ================================= =============================== +========= ================================= ================================== +version versionsuffix toolchain +========= ================================= ================================== +``2.0.2`` ``-Python-2.7.11`` ``intel/2016a`` +``2.0.2`` ``-Python-2.7.11-freetype-2.6.3`` ``intel/2016a`` +``2.1.0`` ``-Python-2.7.13`` ``intel/2017a`` +``2.2.1`` ``-Python-3.6.4`` ``intel/2018a`` +``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2.3.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.3.0`` ``-Python-3.6.6`` ``foss/2018b`` +``2.4.0`` ``foss/2019a``, ``intel/2019a`` +``2.5.1`` ``-Python-3.6.6`` ``foss/2018b`` +``3.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.2.0`` ``-Python-3.8.2`` ``foss/2020a`` +``3.2.1`` ``foss/2020b``, ``fosscuda/2020b`` +========= ================================= ================================== .. _list_software_NIfTI_410: @@ -26081,6 +26560,7 @@ version toolchain ``0.19.2`` ``GCCcore/7.3.0`` ``1.0.0`` ``GCCcore/8.3.0`` ``1.4.6`` ``GCCcore/10.2.0`` +``1.4.8`` ``GCCcore/10.3.0`` ========== ================== @@ -26100,6 +26580,22 @@ version versionsuffix toolchain ========= ============= ============== +.. _list_software_NINJA_368: + +*NINJA* ++++++++ + +Nearly Infinite Neighbor Joining Application. + +*homepage*: https://github.com/TravisWheelerLab/NINJA + +===================== ============== +version toolchain +===================== ============== +``0.97-cluster_only`` ``GCC/10.2.0`` +===================== ============== + + .. _list_software_Ninja_496: *Ninja* @@ -26227,6 +26723,7 @@ version toolchain ``10.15.3`` ``GCCcore/8.2.0`` ``12.16.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``12.19.0`` ``GCCcore/10.2.0`` +``14.17.0`` ``GCCcore/10.3.0`` =========== ======================================================= @@ -26337,7 +26834,7 @@ version toolchain *Nsight-Compute* ++++++++++++++++ -NVIDIA® Nsight™ Compute is an interactive kernel profiler for CUDA applications. It provides detailed performance metrics and API debugging via a user interface and command line tool. In addition, its baseline feature allows users to compare results within the tool. Nsight Compute provides a customizable and data-driven user interface and metric collection and can be extended with analysis scripts for post-processing results. +NVIDIA® Nsight™ Compute is an interactive kernel profiler for CUDA applications. It provides detailed performance metrics and API debugging via a user interface and a command line tool. In addition, its baseline feature allows users to compare results within the tool. Nsight Compute provides a customizable and data-driven user interface and fast metric collection, which can be extended with rules-based analysis scripts for post-processing results. The rules-based guided analysis helps isolate and fix memory throughput, compute, and occupancy inefficiencies in the target application. *homepage*: https://developer.nvidia.com/nsight-compute @@ -26345,6 +26842,7 @@ NVIDIA® Nsight™ Compute is an interactive kernel profiler for CUDA applicatio version toolchain ============ ========== ``2020.3.0`` ``system`` +``2021.2.0`` ``system`` ============ ========== @@ -26414,11 +26912,11 @@ nsync is a C library that exports various synchronization primitives, such as mu *homepage*: https://github.com/google/nsync -========== ======================================================== -version toolchain -========== ======================================================== -``1.24.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ======================================================== +========== ============================================================================ +version toolchain +========== ============================================================================ +``1.24.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ============================================================================ .. _list_software_ntCard_604: @@ -26531,6 +27029,7 @@ version versionsuffix toolchain ``0.50.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``0.52.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``0.52.0`` ``-Python-3.8.2`` ``foss/2020a`` +``0.53.1`` ``foss/2020b``, ``fosscuda/2020b`` ========== ================== =================================================== @@ -26602,6 +27101,8 @@ version toolchain ``20.9`` ``system`` ``20.11`` ``system`` ``21.2`` ``system`` +``21.3`` ``system`` +``21.5`` ``system`` ========= ========== @@ -26614,12 +27115,13 @@ htop-like GPU usage monitor *homepage*: https://github.com/Syllo/nvtop -========= ================== -version toolchain -========= ================== -``1.0.0`` ``fosscuda/2018b`` -``1.1.0`` ``fosscuda/2019b`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.0.0`` ``fosscuda/2018b`` +``1.1.0`` ``fosscuda/2019b`` +``1.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_NWChem_546: @@ -26664,7 +27166,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -26700,6 +27202,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_OBITools3_798: + +*OBITools3* ++++++++++++ + +A package for the management of analyses and data in DNA metabarcoding. + +*homepage*: https://metabarcoding.org/obitools3 + +=========== ================== +version toolchain +=========== ================== +``3.0.1b8`` ``GCCcore/10.2.0`` +=========== ================== + + .. _list_software_OCaml_460: *OCaml* @@ -26768,6 +27286,7 @@ version versionsuffix toolchain ``4.2.2`` ``foss/2018a`` ``4.4.1`` ``foss/2018b`` ``5.1.0`` ``foss/2019a``, ``foss/2019b`` +``6.2.0`` ``foss/2020b`` ========= ============= ================================================ @@ -26820,6 +27339,23 @@ version toolchain ========== ================== +.. _list_software_ont-fast5-api_1224: + +*ont-fast5-api* ++++++++++++++++ + +ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format. + +*homepage*: https://github.com/nanoporetech/ont_fast5_api + +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``3.3.0`` ``foss/2020b``, ``fosscuda/2020b`` +``3.3.0`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ================================== + + .. _list_software_OOMPA_380: *OOMPA* @@ -26850,6 +27386,7 @@ version toolchain ========= ======================================================= ``2.0`` ``foss/2016a`` ``2.0.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.0.6`` ``GCCcore/10.2.0`` ========= ======================================================= @@ -27194,6 +27731,7 @@ Open Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of version toolchain ============ ==================================================================================== ``20190725`` ``GCCcore/10.2.0``, ``foss/2019a``, ``foss/2019b``, ``intel/2019a``, ``intel/2019b`` +``20210128`` ``GCCcore/10.2.0`` ============ ==================================================================================== @@ -27204,17 +27742,33 @@ version toolchain OpenMM is a toolkit for molecular simulation. -*homepage*: http://openmm.org +*homepage*: https://openmm.org -========= ================= =================================== -version versionsuffix toolchain -========= ================= =================================== -``7.1.1`` ``-Python-3.6.3`` ``intel/2017b`` -``7.4.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``7.4.2`` ``-Python-3.8.2`` ``intel/2020a`` -``7.5.0`` ``foss/2020b``, ``intel/2020b`` -``7.5.0`` ``-Python-3.8.2`` ``fosscuda/2020a``, ``intel/2020a`` -========= ================= =================================== +========= ================= =================================================== +version versionsuffix toolchain +========= ================= =================================================== +``7.1.1`` ``-Python-3.6.3`` ``intel/2017b`` +``7.4.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``7.4.2`` ``-Python-3.8.2`` ``intel/2020a`` +``7.5.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``7.5.0`` ``-Python-3.8.2`` ``fosscuda/2020a``, ``intel/2020a`` +========= ================= =================================================== + + +.. _list_software_OpenMM-PLUMED_1056: + +*OpenMM-PLUMED* ++++++++++++++++ + +This project provides a connection between OpenMM and PLUMED. It allows you to bias or analyze an OpenMM simulation based on collective variables. + +*homepage*: https://github.com/openmm/openmm-plumed/ + +======= ================= =============== +version versionsuffix toolchain +======= ================= =============== +``1.0`` ``-Python-3.8.2`` ``intel/2020a`` +======= ================= =============== .. _list_software_OpenMMTools_1085: @@ -27296,6 +27850,7 @@ version versionsuffix toolchain ``4.0.2`` ``GCC/9.2.0-2.32`` ``4.0.3`` ``GCC/9.3.0``, ``gcccuda/2020a``, ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` ``4.0.5`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` +``4.0.6`` ``GCC/10.3.0`` ``4.1.0`` ``GCC/10.2.0`` ``4.1.1`` ``GCC/10.3.0`` ``system`` ``GCC/system-2.29`` @@ -27343,11 +27898,11 @@ OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM *homepage*: http://code.google.com/p/openpgm/ -=========== ==================================================================================================================================================================================================================== -version toolchain -=========== ==================================================================================================================================================================================================================== -``5.2.122`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -=========== ==================================================================================================================================================================================================================== +=========== ======================================================================================================================================================================================================================================== +version toolchain +=========== ======================================================================================================================================================================================================================================== +``5.2.122`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +=========== ======================================================================================================================================================================================================================================== .. _list_software_OpenPIV_641: @@ -27678,7 +28233,7 @@ version toolchain OSU Micro-Benchmarks -*homepage*: http://mvapich.cse.ohio-state.edu/benchmarks/ +*homepage*: https://mvapich.cse.ohio-state.edu/benchmarks/ ========= ============================================================================================================================================================================================= version toolchain @@ -27687,7 +28242,7 @@ version toolchain ``5.6.2`` ``gompi/2019a`` ``5.6.3`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2019b``, ``iimpic/2020a`` ``5.7`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b`` -``5.7.1`` ``ffmpi/4.5.0``, ``gompi/2021a`` +``5.7.1`` ``ffmpi/4.5.0``, ``gompi/2021a``, ``iimpi/2021a`` ========= ============================================================================================================================================================================================= @@ -27705,6 +28260,7 @@ version toolchain ======= ======================================================= ``2.0`` ``foss/2016a``, ``foss/2017a`` ``2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.3`` ``GCCcore/10.2.0`` ======= ======================================================= @@ -27747,7 +28303,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -27757,12 +28313,13 @@ version versionsuffix toolchain Provides a way to load and enumerate PKCS#11 modules. Provides a standard configuration setup for installing PKCS#11 modules in such a way that they're discoverable. Also solves problems with coordinating the use of PKCS#11 by different components or libraries living in the same process. -*homepage*: http://p11-glue.freedesktop.org/p11-kit.html +*homepage*: https://p11-glue.freedesktop.org/p11-kit.html ========== ====================================================================== version toolchain ========== ====================================================================== ``0.23.2`` ``GCCcore/5.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` +``0.24.0`` ``GCCcore/10.3.0`` ========== ====================================================================== @@ -27990,6 +28547,7 @@ version toolchain ``1.43.0`` ``GCCcore/8.2.0`` ``1.44.7`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.47.0`` ``GCCcore/10.2.0`` +``1.48.5`` ``GCCcore/10.3.0`` =========== ==================================== @@ -28002,15 +28560,16 @@ PAPI provides the tool designer and application engineer with a consistent inte *homepage*: https://icl.cs.utk.edu/projects/papi/ -========= ======================================================== -version toolchain -========= ======================================================== -``5.4.3`` ``foss/2016a`` -``5.5.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``5.6.0`` ``GCCcore/6.4.0`` -``5.7.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``6.0.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ======================================================== +=========== ======================================================== +version toolchain +=========== ======================================================== +``5.4.3`` ``foss/2016a`` +``5.5.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``5.6.0`` ``GCCcore/6.4.0`` +``5.7.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``6.0.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``6.0.0.1`` ``GCCcore/10.3.0`` +=========== ======================================================== .. _list_software_parallel_845: @@ -28041,6 +28600,7 @@ version toolchain ``20200422`` ``GCCcore/9.3.0`` ``20200522`` ``GCCcore/9.3.0`` ``20210322`` ``GCCcore/10.2.0`` +``20210622`` ``GCCcore/10.3.0`` ============ =============================== @@ -28180,11 +28740,11 @@ ParMETIS is an MPI-based parallel library that implements a variety of algorithm *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview -========= ============================================================================================================================================================================================================================================================================================================================ -version toolchain -========= ============================================================================================================================================================================================================================================================================================================================ -``4.0.3`` ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -========= ============================================================================================================================================================================================================================================================================================================================ +========= ============================================================================================================================================================================================================================================================================================================================================= +version toolchain +========= ============================================================================================================================================================================================================================================================================================================================================= +``4.0.3`` ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +========= ============================================================================================================================================================================================================================================================================================================================================= .. _list_software_ParMGridGen_1040: @@ -28260,14 +28820,14 @@ PatchELF is a small utility to modify the dynamic linker and RPATH of ELF execut *homepage*: http://nixos.org/patchelf.html -======== ==================================== -version toolchain -======== ==================================== -``0.8`` ``GNU/4.9.3-2.25`` -``0.9`` ``GCCcore/6.4.0``, ``foss/2016a`` -``0.10`` ``GCCcore/7.2.0``, ``GCCcore/8.3.0`` -``0.12`` ``GCCcore/9.3.0`` -======== ==================================== +======== ===================================== +version toolchain +======== ===================================== +``0.8`` ``GNU/4.9.3-2.25`` +``0.9`` ``GCCcore/6.4.0``, ``foss/2016a`` +``0.10`` ``GCCcore/7.2.0``, ``GCCcore/8.3.0`` +``0.12`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +======== ===================================== .. _list_software_path.py_708: @@ -28561,13 +29121,13 @@ Program Database Toolkit (PDT) is a framework for analyzing source code written *homepage*: https://www.cs.uoregon.edu/research/pdt/ -========== ==================================== -version toolchain -========== ==================================== -``3.22`` ``foss/2016a`` -``3.25`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.25.1`` ``GCCcore/9.3.0`` -========== ==================================== +========== ======================================================== +version toolchain +========== ======================================================== +``3.22`` ``foss/2016a`` +``3.25`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.25.1`` ``GCCcore/9.3.0`` +========== ======================================================== .. _list_software_PEAR_296: @@ -28649,8 +29209,11 @@ version versionsuffix toolchain ``5.28.1`` ``GCCcore/8.2.0`` ``5.30.0`` ``GCCcore/8.3.0`` ``5.30.2`` ``GCCcore/9.3.0`` +``5.30.2`` ``-minimal`` ``GCCcore/9.3.0`` ``5.32.0`` ``GCCcore/10.2.0`` +``5.32.0`` ``-minimal`` ``GCCcore/10.2.0`` ``5.32.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` +``5.32.1`` ``-minimal`` ``GCCcore/10.3.0`` ========== ============= ========================================================================================= @@ -28738,11 +29301,12 @@ petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for S *homepage*: https://bitbucket.org/petsc/petsc4py -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``3.9.1`` ``-Python-3.6.4`` ``foss/2018a`` -========= ================= ============== +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``3.9.1`` ``-Python-3.6.4`` ``foss/2018a`` +``3.12.0`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== .. _list_software_pftoolsV3_912: @@ -28950,7 +29514,7 @@ version versionsuffix toolchain phono3py calculates phonon-phonon interaction and related properties using the supercell approach. -*homepage*: http://atztogo.github.io/phono3py/ +*homepage*: https://atztogo.github.io/phono3py/ ============= ================== =============================== version versionsuffix toolchain @@ -28984,6 +29548,22 @@ version versionsuffix toolchain ============= ================== =============================== +.. _list_software_phototonic_1095: + +*phototonic* +++++++++++++ + +Phototonic is an image viewer and organizer + +*homepage*: https://github.com/oferkv/phototonic + +======= ================== +version toolchain +======= ================== +``2.1`` ``GCCcore/10.3.0`` +======= ================== + + .. _list_software_PHYLIP_470: *PHYLIP* @@ -29119,6 +29699,7 @@ version versionsuffix toolchain ``2.22.1`` ``-Java-11`` ``system`` ``2.25.0`` ``-Java-11`` ``system`` ``2.25.1`` ``-Java-11`` ``system`` +``2.25.5`` ``-Java-13`` ``system`` =========== =================== ========== @@ -29209,6 +29790,7 @@ version versionsuffix toolchain ``6.2.1`` ``GCCcore/8.3.0`` ``7.0.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``8.0.1`` ``GCCcore/10.2.0`` +``8.2.0`` ``GCCcore/10.3.0`` ========= ================================= =================================================== @@ -29258,7 +29840,7 @@ version versionsuffix toolchain PIMS is a lazy-loading interface to sequential data with numpy-like slicing. -*homepage*: http://soft-matter.github.io/pims +*homepage*: https://soft-matter.github.io/pims ========= ================== =============== version versionsuffix toolchain @@ -29495,6 +30077,7 @@ version versionsuffix toolchain ``1.5.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``1.5.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``1.5.1`` ``-python`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0`` +``1.5.4`` ``-python`` ``GCCcore/10.3.0`` ========= ================== =================================================== @@ -29608,6 +30191,7 @@ plc is the public Planck Likelihood Code. It provides C and Fortran libraries t version versionsuffix toolchain ========= ================== =============================== ``3.0.1`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2018b`` +``3.0.1`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== =============================== @@ -29796,11 +30380,12 @@ PLY is yet another implementation of lex and yacc for Python. *homepage*: http://www.dabeaz.com/ply/ -======== ================= ============== -version versionsuffix toolchain -======== ================= ============== -``3.11`` ``-Python-3.6.4`` ``foss/2018a`` -======== ================= ============== +======== ================= ================= +version versionsuffix toolchain +======== ================= ================= +``3.11`` ``-Python-3.6.4`` ``foss/2018a`` +``3.11`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +======== ================= ================= .. _list_software_PMIx_350: @@ -29837,14 +30422,15 @@ Parallel netCDF: A Parallel I/O Library for NetCDF File Access *homepage*: https://trac.mcs.anl.gov/projects/parallel-netcdf -========== ================================================== -version toolchain -========== ================================================== -``1.8.1`` ``intel/2017a`` -``1.9.0`` ``intel/2018a`` -``1.10.0`` ``foss/2018b``, ``intel/2018b`` -``1.12.1`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a`` -========== ================================================== +========== ===================================================================================== +version toolchain +========== ===================================================================================== +``1.8.1`` ``intel/2017a`` +``1.9.0`` ``intel/2018a`` +``1.10.0`` ``foss/2018b``, ``intel/2018b`` +``1.12.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2020a`` +``1.12.2`` ``gompi/2020b``, ``gompic/2020b`` +========== ===================================================================================== .. _list_software_pocl_430: @@ -30010,7 +30596,7 @@ version versionsuffix toolchain A toolkit for working with nanopore sequencing data from Oxford Nanopore. -*homepage*: http://poretools.readthedocs.io/en/latest/ +*homepage*: https://poretools.readthedocs.io/en/latest/ ========= ================== =============== version versionsuffix toolchain @@ -30377,6 +30963,7 @@ version toolchain ``6.2.1`` ``GCCcore/8.3.0`` ``7.0.0`` ``GCCcore/9.3.0`` ``7.2.1`` ``GCCcore/10.2.0`` +``8.0.1`` ``GCCcore/10.3.0`` ========= ================================================================================= @@ -30527,6 +31114,7 @@ version toolchain ``3.10.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``3.13.0`` ``GCCcore/9.3.0`` ``3.14.0`` ``GCCcore/10.2.0`` +``3.17.3`` ``GCCcore/10.3.0`` =========== ==================================================================== @@ -30558,6 +31146,7 @@ version versionsuffix toolchain ``3.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``3.13.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` ``3.14.0`` ``GCCcore/10.2.0`` +``3.17.3`` ``GCCcore/10.3.0`` ========== ================== ================================== @@ -30707,14 +31296,15 @@ version versionsuffix toolchain *PSolver* +++++++++ -Poisson Solver from the BigDFT code compiled as a standalone library. +Interpolating scaling function Poisson Solver Library -*homepage*: http://bigdft.org/Wiki/index.php?title=BigDFT_website +*homepage*: http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html ========= ================================================================================================= version toolchain ========= ================================================================================================= ``1.7.6`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``1.8.3`` ``foss/2020b``, ``intel/2020b`` ========= ================================================================================================= @@ -30880,7 +31470,7 @@ version toolchain library with cross-python path, ini-parsing, io, code, log facilities -*homepage*: http://pylib.readthedocs.org/ +*homepage*: https://pylib.readthedocs.org/ ========== ================== ============== version versionsuffix toolchain @@ -31388,11 +31978,12 @@ pyfaidx: efficient pythonic random access to fasta subsequences *homepage*: https://pypi.python.org/pypi/pyfaidx -=========== ================== -version toolchain -=========== ================== -``0.5.9.5`` ``GCCcore/10.2.0`` -=========== ================== +=========== ================= ================== +version versionsuffix toolchain +=========== ================= ================== +``0.5.9.5`` ``GCCcore/10.2.0`` +``0.5.9.5`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +=========== ================= ================== .. _list_software_pyfasta_760: @@ -31477,6 +32068,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_PyFoam_588: + +*PyFoam* +++++++++ + +A Python library to control OpenFOAM-runs and manipulate OpenFOAM-data. + +*homepage*: http://openfoamwiki.net/index.php/Contrib/PyFoam + +========== ============== +version toolchain +========== ============== +``2020.5`` ``foss/2020b`` +========== ============== + + .. _list_software_PyFR_353: *PyFR* @@ -31552,7 +32159,7 @@ version versionsuffix toolchain Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code. -*homepage*: http://pygments.org/ +*homepage*: https://pygments.org/ ========= ================== ============== version versionsuffix toolchain @@ -31934,7 +32541,7 @@ version toolchain Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models. -*homepage*: http://www.pyomo.org/ +*homepage*: https://www.pyomo.org/ ========= ================== ============== version versionsuffix toolchain @@ -32307,11 +32914,12 @@ PySCF is an open-source collection of electronic structure modules powered by Py *homepage*: http://www.pyscf.org -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``1.6.3`` ``-Python-3.7.2`` ``foss/2019a`` -========= ================= ============== +========= ================= ============================== +version versionsuffix toolchain +========= ================= ============================== +``1.6.3`` ``-Python-3.7.2`` ``foss/2019a`` +``1.7.6`` ``foss/2020b``, ``foss/2021a`` +========= ================= ============================== .. _list_software_pysheds_768: @@ -32369,7 +32977,7 @@ version versionsuffix toolchain Pysolar is a collection of Python libraries for simulating the irradiation of any point on earth by the sun. -*homepage*: http://pysolar.org/ +*homepage*: https://pysolar.org/ ======= ================= ================= version versionsuffix toolchain @@ -32390,11 +32998,12 @@ Python bindings to spoa. *homepage*: https://github.com/nanoporetech/pyspoa -========= ================= ============= -version versionsuffix toolchain -========= ================= ============= -``0.0.4`` ``-Python-3.7.4`` ``GCC/8.3.0`` -========= ================= ============= +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.0.4`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``0.0.8`` ``GCC/10.2.0`` +========= ================= ============== .. _list_software_pysqlite_891: @@ -32437,7 +33046,7 @@ version versionsuffix toolchain Toolset of dynamical model STRucture ANalysis algorithms -*homepage*: http://stijnvanhoey.github.io/pystran/ +*homepage*: https://stijnvanhoey.github.io/pystran/ ============== ================== =============== version versionsuffix toolchain @@ -32517,6 +33126,7 @@ xdist: pytest distributed testing plugin The pytest-xdist plugin extends pytest version toolchain ========= ================== ``2.1.0`` ``GCCcore/10.2.0`` +``2.3.0`` ``GCCcore/10.3.0`` ========= ================== @@ -32579,6 +33189,7 @@ version versionsuffix toolchain ``3.8.2`` ``GCCcore/9.3.0`` ``3.8.6`` ``GCCcore/10.2.0`` ``3.9.5`` ``GCCcore/10.3.0`` +``3.9.5`` ``-bare`` ``GCCcore/10.3.0`` ========== ================= ================================================================================================================================================================= @@ -32706,13 +33317,16 @@ version versionsuffix toolchain ``1.0.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``1.1.0`` ``-Python-3.7.2`` ``foss/2019a`` ``1.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` +``1.3.1`` ``fosscuda/2020b`` ``1.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``1.6.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``1.6.0`` ``-Python-3.7.4-imkl`` ``fosscuda/2019b`` ``1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` ``1.7.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``1.8.1`` ``foss/2020b`` +``1.7.1`` ``-Python-3.8.2`` ``fosscuda/2020a`` +``1.8.1`` ``foss/2020b``, ``fosscuda/2020b`` +``1.9.0`` ``foss/2020b``, ``fosscuda/2020b`` ========= ============================= ================================== @@ -32794,6 +33408,7 @@ version versionsuffix toolchain ``5.1.2`` ``GCCcore/8.3.0`` ``5.3`` ``GCCcore/9.3.0`` ``5.3.1`` ``GCCcore/10.2.0`` +``5.4.1`` ``GCCcore/10.3.0`` ========= ================== ==================================================================================== @@ -32964,6 +33579,7 @@ version toolchain ========== ============================================================================================================================================================================= ``2015.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``2019.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2020.2`` ``GCCcore/10.2.0`` ========== ============================================================================================================================================================================= @@ -33044,7 +33660,7 @@ version toolchain QML is a Python2/3-compatible toolkit for representation learning of properties of molecules and solids. -*homepage*: http://www.qmlcode.org +*homepage*: https://www.qmlcode.org ========== ================== =============== version versionsuffix toolchain @@ -33078,11 +33694,11 @@ qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions *homepage*: https://sourceforge.net/projects/qrupdate/ -========= ================================================================================================================================================================================= -version toolchain -========= ================================================================================================================================================================================= -``1.1.2`` ``GCC/5.4.0-2.26``, ``GCC/8.2.0-2.31.1``, ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -========= ================================================================================================================================================================================= +========= ===================================================================================================================================================================================================== +version toolchain +========= ===================================================================================================================================================================================================== +``1.1.2`` ``GCC/5.4.0-2.26``, ``GCC/8.2.0-2.31.1``, ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +========= ===================================================================================================================================================================================================== .. _list_software_QScintilla_1012: @@ -33278,6 +33894,7 @@ version versionsuffix toolchain ========= ================= =============== ``3.4.2`` ``-Python-3.6.4`` ``intel/2018a`` ``3.4.8`` ``foss/2019a`` +``3.6.1`` ``foss/2020b`` ========= ================= =============== @@ -33290,22 +33907,22 @@ Quantum ESPRESSO is an integrated suite of computer codes for electronic-struc *homepage*: https://www.quantum-espresso.org -========= ============= =============================================================== -version versionsuffix toolchain -========= ============= =============================================================== -``5.3.0`` ``intel/2016.02-GCC-4.9`` -``5.4.0`` ``intel/2016.02-GCC-4.9`` -``5.4.0`` ``-hybrid`` ``foss/2016b`` -``6.0`` ``intel/2016b`` -``6.1`` ``intel/2017a`` -``6.2`` ``intel/2017b`` -``6.2.1`` ``iomkl/2017b`` -``6.3`` ``foss/2018b``, ``intel/2018b`` -``6.4.1`` ``intel/2019a`` -``6.5`` ``intel/2019a``, ``intel/2019b`` -``6.6`` ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2019b`` -``6.7`` ``foss/2019b``, ``intel/2019b``, ``iomkl/2019b`` -========= ============= =============================================================== +========= ============= ================================================================================================= +version versionsuffix toolchain +========= ============= ================================================================================================= +``5.3.0`` ``intel/2016.02-GCC-4.9`` +``5.4.0`` ``intel/2016.02-GCC-4.9`` +``5.4.0`` ``-hybrid`` ``foss/2016b`` +``6.0`` ``intel/2016b`` +``6.1`` ``intel/2017a`` +``6.2`` ``intel/2017b`` +``6.2.1`` ``iomkl/2017b`` +``6.3`` ``foss/2018b``, ``intel/2018b`` +``6.4.1`` ``intel/2019a`` +``6.5`` ``intel/2019a``, ``intel/2019b`` +``6.6`` ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2019b`` +``6.7`` ``foss/2019b``, ``foss/2020b``, ``foss/2021a``, ``intel/2019b``, ``intel/2021a``, ``iomkl/2019b`` +========= ============= ================================================================================================= .. _list_software_QUAST_398: @@ -33455,7 +34072,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -33491,6 +34108,8 @@ version versionsuffix toolchain ``4.0.0`` ``foss/2020a``, ``fosscuda/2020a`` ``4.0.3`` ``foss/2020b``, ``fosscuda/2020b`` ``4.0.4`` ``foss/2020b``, ``fosscuda/2020b`` +``4.0.5`` ``foss/2020b``, ``fosscuda/2020b`` +``4.1.0`` ``foss/2021a`` ========= ============================= =================================================== @@ -33612,17 +34231,34 @@ version toolchain *Ragout* ++++++++ -Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome assembly using multiple references. Given a set of assembly fragments (contigs/scaffolds) and one or multiple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds). +Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome-level scaffolding using multiple references. Given initial assembly fragments (contigs/scaffolds) and one or multiple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds). -*homepage*: http://fenderglass.github.io/Ragout/ +*homepage*: https://github.com/fenderglass/Ragout ======= ================== ============== version versionsuffix toolchain ======= ================== ============== ``2.0`` ``-Python-2.7.12`` ``foss/2016b`` +``2.3`` ``foss/2020b`` ======= ================== ============== +.. _list_software_RagTag_566: + +*RagTag* +++++++++ + +RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: homology-based misassembly correction, homology-based assembly scaffolding and patching, and scaffold merging. RagTag also provides command line utilities for working with common genome assembly file formats. + +*homepage*: https://github.com/malonge/RagTag + +========= ============== +version toolchain +========= ============== +``2.0.1`` ``foss/2020b`` +========= ============== + + .. _list_software_rampart_759: *rampart* @@ -33794,17 +34430,18 @@ RAxML search algorithm for maximum likelihood based inference of phylogenetic tr *homepage*: https://github.com/stamatak/standard-RAxML -========== ================ ================================================================== -version versionsuffix toolchain -========== ================ ================================================================== -``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` -``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` -``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` -``8.2.12`` ``-hybrid-avx2`` ``gompi/2020a``, ``iimpi/2019b``, ``intel/2018b``, ``intel/2019a`` -========== ================ ================================================================== +========== ================== ================================================================== +version versionsuffix toolchain +========== ================== ================================================================== +``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` +``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` +``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` +``8.2.12`` ``-hybrid-avx2`` ``gompi/2020a``, ``iimpi/2019b``, ``intel/2018b``, ``intel/2019a`` +``8.2.12`` ``-pthreads-avx2`` ``GCC/10.2.0`` +========== ================== ================================================================== .. _list_software_RAxML-NG_614: @@ -33924,6 +34561,22 @@ version toolchain ========= =============== +.. _list_software_RcppGSL_635: + +*RcppGSL* ++++++++++ + +The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data structures and R using concepts from 'Rcpp' which is itself a package that eases the interfaces between R and C++. + +*homepage*: https://cran.r-project.org/web/packages/RcppGSL + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``0.3.8`` ``-R-4.0.4`` ``foss/2020b`` +========= ============= ============== + + .. _list_software_rCUDA_399: *rCUDA* @@ -34004,11 +34657,12 @@ RE2 is a fast, safe, thread-friendly alternative to backtracking regular express *homepage*: https://github.com/google/re2 -============== ================= -version toolchain -============== ================= -``2020-07-01`` ``GCCcore/8.3.0`` -============== ================= +============== ================== +version toolchain +============== ================== +``2020-07-01`` ``GCCcore/8.3.0`` +``2021-06-01`` ``GCCcore/10.2.0`` +============== ================== .. _list_software_re2c_364: @@ -34063,6 +34717,22 @@ version toolchain ========== ============== +.. _list_software_RECON_375: + +*RECON* ++++++++ + +Patched version of RECON to be used with RepeatModeler. + +*homepage*: https://www.repeatmasker.org/RepeatModeler/ + +======== ============== +version toolchain +======== ============== +``1.08`` ``GCC/10.2.0`` +======== ============== + + .. _list_software_Red_283: *Red* @@ -34118,6 +34788,7 @@ version toolchain ``3.5.0`` ``system`` ``3.5.1`` ``system`` ``3.5.2`` ``system`` +``3.6.2`` ``system`` ========= ========== @@ -34133,6 +34804,7 @@ RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help inter ========= ============== version toolchain ========= ============== +``0.4.2`` ``foss/2020b`` ``0.5.2`` ``foss/2020b`` ========= ============== @@ -34231,7 +34903,7 @@ version toolchain RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. -*homepage*: http://www.repeatmasker.org/ +*homepage*: https://www.repeatmasker.org/ ============ ====================== ========================================================== version versionsuffix toolchain @@ -34239,9 +34911,26 @@ version versionsuffix toolchain ``4.0.8`` ``-Perl-5.26.0-HMMER`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ``4.0.8`` ``-Perl-5.28.0-HMMER`` ``intel/2018b`` ``4.0.9-p2`` ``-HMMER`` ``gompi/2019b`` +``4.1.2-p1`` ``foss/2020b`` ============ ====================== ========================================================== +.. _list_software_RepeatScout_1135: + +*RepeatScout* ++++++++++++++ + +De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and tested with our multiple sequence version of RepeatScout ( 1.0.6 ) + +*homepage*: https://www.repeatmasker.org/ + +========= ============== +version toolchain +========= ============== +``1.0.6`` ``GCC/10.2.0`` +========= ============== + + .. _list_software_request_777: *request* @@ -34294,6 +34983,22 @@ version versionsuffix toolchain ========= ============= =============================== +.. _list_software_retworkx_902: + +*retworkx* +++++++++++ + +retworkx is a general purpose graph library for python3 written in Rust to take advantage of the performance and safety that Rust provides. It was built as a replacement for qiskit's previous (and current) networkx usage (hence the name) but is designed to provide a high performance general purpose graph library for any python application. The project was originally started to build a faster directed graph to use as the underlying data structure for the DAG at the center of qiskit-terra's transpiler, but it has since grown to cover all the graph usage in Qiskit and other applications. + +*homepage*: https://github.com/Qiskit/retworkx + +========= ============== +version toolchain +========= ============== +``0.9.0`` ``foss/2021a`` +========= ============== + + .. _list_software_RevBayes_801: *RevBayes* @@ -34326,6 +35031,7 @@ version versionsuffix toolchain ``1.4-8`` ``-R-3.6.2`` ``foss/2019b`` ``1.4-8`` ``-R-4.0.0`` ``foss/2020a`` ``1.5-16`` ``-R-4.0.0`` ``foss/2020a`` +``1.5-23`` ``-R-4.0.4`` ``foss/2020b`` ========== ============= ============== @@ -34469,6 +35175,7 @@ version versionsuffix toolchain ``2.2.28`` ``-Python-2.7.11`` ``foss/2016a`` ``2.9.0`` ``gompi/2019b`` ``2.10.0`` ``gompi/2019b`` +``2.11.0`` ``gompi/2020b`` ========== ================== =============== @@ -34911,7 +35618,7 @@ version versionsuffix toolchain Rtree is a ctypes Python wrapper of libspatialindex that provides a number of advanced spatial indexing features for the spatially curious Python user. -*homepage*: http://toblerity.org/rtree/ +*homepage*: https://toblerity.org/rtree/ ========= ================== =============== version versionsuffix toolchain @@ -34943,6 +35650,7 @@ version toolchain ``2.6.3`` ``GCCcore/8.2.0`` ``2.7.1`` ``GCCcore/8.3.0`` ``2.7.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.0.1`` ``GCCcore/10.3.0`` ========= ================================================ @@ -35071,7 +35779,7 @@ version versionsuffix toolchain Sensitivity Analysis Library in Python (Numpy). Contains Sobol, Morris, Fractional Factorial and FAST methods. -*homepage*: http://SALib.github.io/SALib/ +*homepage*: https://SALib.github.io/SALib/ ========= ================== =============== version versionsuffix toolchain @@ -35493,13 +36201,13 @@ Scikit-Build, or skbuild, is an improved build system generator for CPython C/C+ *homepage*: https://scikit-build.readthedocs.io/en/latest -========== ================= ======================================================================== -version versionsuffix toolchain -========== ================= ======================================================================== -``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` -``0.11.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -========== ================= ======================================================================== +========== ================= ============================================================================================ +version versionsuffix toolchain +========== ================= ============================================================================================ +``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``0.11.1`` ``GCCcore/10.3.0``, ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +========== ================= ============================================================================================ .. _list_software_scikit-cuda_1105: @@ -35587,6 +36295,7 @@ version versionsuffix toolchain ``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``0.23.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``0.23.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +``0.24.2`` ``foss/2021a`` ========== ================================= ======================================================================== @@ -35760,7 +36469,7 @@ version versionsuffix toolchain ``3.1.1`` ``GCCcore/8.3.0`` ``3.1.2`` ``GCCcore/9.3.0`` ``4.0.1`` ``GCCcore/10.2.0`` -``4.1.0.post1`` ``GCCcore/10.2.0`` +``4.1.0.post1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` =============== ======================= ================================================================================= @@ -35798,6 +36507,7 @@ version toolchain ========= ================================================== ``2.0.1`` ``foss/2016a`` ``6.0`` ``gompi/2019a``, ``gompi/2020a``, ``gompic/2019b`` +``7.0`` ``gompic/2020b`` ========= ================================================== @@ -35818,7 +36528,7 @@ version versionsuffix toolchain ``6.0.4`` ``-64bitint`` ``foss/2017b`` ``6.0.6`` ``foss/2018a``, ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2018a`` ``6.0.9`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` -``6.1.0`` ``gompi/2020b``, ``iimpi/2020b`` +``6.1.0`` ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2020b`` =================== ============= ===================================================================================================================================================== @@ -36140,12 +36850,13 @@ Unsupervised text tokenizer for Neural Network-based text generation. *homepage*: https://github.com/google/sentencepiece -========== ================= ============= -version versionsuffix toolchain -========== ================= ============= -``0.1.85`` ``-Python-3.7.4`` ``GCC/8.3.0`` -``0.1.94`` ``-Python-3.8.2`` ``GCC/9.3.0`` -========== ================= ============= +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.1.85`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``0.1.94`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``0.1.96`` ``GCC/10.2.0`` +========== ================= ============== .. _list_software_sep_328: @@ -36323,12 +37034,12 @@ Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FA *homepage*: https://github.com/lh3/seqtk/ -======= ================================================================================== -version toolchain -======= ================================================================================== -``1.2`` ``foss/2016b``, ``intel/2017a`` -``1.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` -======= ================================================================================== +======= ================================================================================================== +version toolchain +======= ================================================================================================== +``1.2`` ``foss/2016b``, ``intel/2017a`` +``1.3`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` +======= ================================================================================================== .. _list_software_Serf_400: @@ -36340,11 +37051,11 @@ The serf library is a high performance C-based HTTP client library built upon t *homepage*: http://serf.apache.org/ -========= ============================================================================================================================= -version toolchain -========= ============================================================================================================================= -``1.3.9`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``intel/2017b``, ``iomkl/2018a`` -========= ============================================================================================================================= +========= ================================================================================================================================================= +version toolchain +========= ================================================================================================================================================= +``1.3.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``intel/2017b``, ``iomkl/2018a`` +========= ================================================================================================================================================= .. _list_software_setuptools_1122: @@ -36382,6 +37093,7 @@ version versionsuffix toolchain ``3.1.2`` ``-R-3.6.0`` ``foss/2019a`` ``3.1.5`` ``-R-4.0.0`` ``foss/2020a`` ``4.0.1`` ``-R-4.0.3`` ``foss/2020b`` +``4.0.3`` ``-R-4.0.3`` ``foss/2020b`` ============ ============= =============== @@ -36639,12 +37351,12 @@ Sibelia: A comparative genomics tool: It assists biologists in analysing the g *homepage*: http://bioinf.spbau.ru/en/sibelia -========= ============== -version toolchain -========= ============== -``3.0.6`` ``foss/2016b`` -``3.0.7`` ``foss/2018b`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``3.0.6`` ``foss/2016b`` +``3.0.7`` ``foss/2018b``, ``foss/2020b`` +========= ============================== .. _list_software_SICER2_424: @@ -36741,7 +37453,7 @@ version versionsuffix toolchain Simulation and Parameter Estimation in Geophysics: a python package for simulation and gradient based parameter estimation in the context of geophysical applications. -*homepage*: http://simpeg.xyz +*homepage*: https://simpeg.xyz ========== ================== =============== version versionsuffix toolchain @@ -36895,16 +37607,16 @@ SIONlib is a scalable I/O library for parallel access to task-local files. The *homepage*: https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html -========= ============= ==================================== -version versionsuffix toolchain -========= ============= ==================================== -``1.6.1`` ``foss/2016a`` -``1.6.1`` ``-tools`` ``foss/2016a`` -``1.7.1`` ``foss/2017a`` -``1.7.1`` ``-tools`` ``foss/2017a`` -``1.7.4`` ``-tools`` ``GCCcore/8.2.0`` -``1.7.6`` ``-tools`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ============= ==================================== +========= ============= ======================================================== +version versionsuffix toolchain +========= ============= ======================================================== +``1.6.1`` ``foss/2016a`` +``1.6.1`` ``-tools`` ``foss/2016a`` +``1.7.1`` ``foss/2017a`` +``1.7.1`` ``-tools`` ``foss/2017a`` +``1.7.4`` ``-tools`` ``GCCcore/8.2.0`` +``1.7.6`` ``-tools`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ============= ======================================================== .. _list_software_SIP_236: @@ -37025,11 +37737,12 @@ Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computati *homepage*: https://bitbucket.org/slepc/slepc4py -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``3.9.0`` ``-Python-3.6.4`` ``foss/2018a`` -========= ================= ============== +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``3.9.0`` ``-Python-3.6.4`` ``foss/2018a`` +``3.12.0`` ``-Python-3.7.4`` ``foss/2019b`` +========== ================= ============== .. _list_software_sleuth_661: @@ -37325,14 +38038,15 @@ SnpEff is a variant annotation and effect prediction tool. It annotates and pr *homepage*: https://pcingola.github.io/SnpEff/ -======== ================== ========== -version versionsuffix toolchain -======== ================== ========== -``3.6`` ``-Java-1.7.0_80`` ``system`` -``4.1d`` ``-Java-1.7.0_80`` ``system`` -``4.3t`` ``-Java-1.8`` ``system`` -``5.0`` ``-Java-13`` ``system`` -======== ================== ========== +======== ========================= ================= +version versionsuffix toolchain +======== ========================= ================= +``3.6`` ``-Java-1.7.0_80`` ``system`` +``4.1d`` ``-Java-1.7.0_80`` ``system`` +``4.3t`` ``-Java-1.8`` ``system`` +``5.0`` ``-Java-13`` ``system`` +``5.0`` ``-Java-13-Python-3.8.2`` ``GCCcore/9.3.0`` +======== ========================= ================= .. _list_software_SNPhylo_685: @@ -37747,7 +38461,7 @@ version versionsuffix toolchain ``1.14.1.post0`` ``-Python-3.7.2`` ``intel/2019a`` ``1.16.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.16.0`` ``-Python-3.7.4`` ``intel/2019b`` -``1.16.0`` ``-Python-3.8.2`` ``intel/2020a`` +``1.16.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ================ ================== =================================================== @@ -37904,6 +38618,7 @@ version toolchain ========= ================== ``3.0.1`` ``GCC/7.3.0-2.30`` ``4.0.0`` ``GCC/8.3.0`` +``4.0.7`` ``GCC/10.2.0`` ========= ================== @@ -38483,6 +39198,7 @@ version toolchain ``1.6.3`` ``foss/2018b`` ``1.6.4`` ``foss/2018b`` ``2.0.0`` ``GCC/7.3.0-2.30``, ``GCC/8.3.0`` +``2.0.2`` ``GCC/10.2.0`` ============ ================================= @@ -38503,6 +39219,7 @@ version toolchain ``1.10.0`` ``foss/2017b``, ``intel/2017b`` ``1.12.0`` ``GCCcore/8.2.0`` ``1.14.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.14.1`` ``GCCcore/10.3.0`` ========== ===================================== @@ -38531,23 +39248,24 @@ SuiteSparse is a collection of libraries manipulate sparse matrices. *homepage*: https://faculty.cse.tamu.edu/davis/suitesparse.html -========= =================== ================================================================================================= -version versionsuffix toolchain -========= =================== ================================================================================================= -``4.5.1`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` -``4.5.2`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` -``4.5.3`` ``-METIS-5.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``4.5.3`` ``-ParMETIS-4.0.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``4.5.5`` ``-METIS-5.1.0`` ``foss/2017a``, ``intel/2017a`` -``4.5.5`` ``-ParMETIS-4.0.3`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``4.5.6`` ``-METIS-5.1.0`` ``foss/2017b`` -``5.1.2`` ``-METIS-5.1.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``5.1.2`` ``-ParMETIS-4.0.3`` ``foss/2017b``, ``intel/2017b`` -``5.4.0`` ``-METIS-5.1.0`` ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` -``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b``, ``intel/2019b`` -``5.7.1`` ``-METIS-5.1.0`` ``foss/2020a``, ``intel/2020a`` -``5.8.1`` ``-METIS-5.1.0`` ``foss/2020b`` -========= =================== ================================================================================================= +========== =================== ================================================================================================= +version versionsuffix toolchain +========== =================== ================================================================================================= +``4.5.1`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` +``4.5.2`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` +``4.5.3`` ``-METIS-5.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` +``4.5.3`` ``-ParMETIS-4.0.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``4.5.5`` ``-METIS-5.1.0`` ``foss/2017a``, ``intel/2017a`` +``4.5.5`` ``-ParMETIS-4.0.3`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``4.5.6`` ``-METIS-5.1.0`` ``foss/2017b`` +``5.1.2`` ``-METIS-5.1.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``5.1.2`` ``-ParMETIS-4.0.3`` ``foss/2017b``, ``intel/2017b`` +``5.4.0`` ``-METIS-5.1.0`` ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` +``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b``, ``intel/2019b`` +``5.7.1`` ``-METIS-5.1.0`` ``foss/2020a``, ``intel/2020a`` +``5.8.1`` ``-METIS-5.1.0`` ``foss/2020b`` +``5.10.1`` ``-METIS-5.1.0`` ``foss/2021a`` +========== =================== ================================================================================================= .. _list_software_SUMACLUST_705: @@ -38829,7 +39547,7 @@ version versionsuffix toolchain ``3.0.12`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.0.12`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``4.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.0.2`` ``GCCcore/10.2.0`` +``4.0.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========== ============================ ================================================================ @@ -38903,6 +39621,7 @@ version versionsuffix toolchain ``1.5.1`` ``-Python-3.7.4`` ``foss/2019b`` ``1.6.2`` ``-Python-3.8.2`` ``foss/2020a`` ``1.7.1`` ``foss/2020b`` +``1.8`` ``foss/2021a`` ========= ================== =============================== @@ -38957,11 +39676,11 @@ C++ wrapper to tabix indexer *homepage*: https://github.com/ekg/tabixpp -========= ============= -version toolchain -========= ============= -``1.1.0`` ``GCC/9.3.0`` -========= ============= +========= ============================= +version toolchain +========= ============================= +``1.1.0`` ``GCC/10.2.0``, ``GCC/9.3.0`` +========= ============================= .. _list_software_taco_423: @@ -39264,12 +39983,13 @@ Tensorboard for PyTorch. *homepage*: https://github.com/lanpa/tensorboardX -======= ================== ================== -version versionsuffix toolchain -======= ================== ================== -``2.0`` ``-Python-3.7.4`` ``foss/2019b`` -``2.1`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` -======= ================== ================== +======= ================== ================================== +version versionsuffix toolchain +======= ================== ================================== +``2.0`` ``-Python-3.7.4`` ``foss/2019b`` +``2.1`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` +``2.2`` ``-PyTorch-1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` +======= ================== ================================== .. _list_software_TensorFlow_1043: @@ -39330,6 +40050,7 @@ version versionsuffix toolchain ``2.3.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` ``2.4.1`` ``foss/2020b``, ``fosscuda/2020b`` ``2.4.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2.5.0`` ``foss/2020b``, ``fosscuda/2020b`` ========== ============================= =================================================== @@ -39756,6 +40477,7 @@ version versionsuffix toolchain ``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2018a``, ``iomkl/2018a`` ``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``8.6.10`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``8.6.11`` ``GCCcore/10.3.0`` ========== ================= ================================================================================================================================================ @@ -39838,6 +40560,7 @@ version toolchain ``2.3`` ``GCC/5.4.0-2.26``, ``system`` ``3.1c`` ``GCCcore/8.3.0`` ``3.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.2a`` ``GCCcore/10.3.0`` ======== ===================================== @@ -39942,6 +40665,7 @@ version versionsuffix toolchain ========= =============================== ================================== ``0.5.0`` ``-PyTorch-1.4.0-Python-3.7.4`` ``fosscuda/2019b`` ``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` +``0.8.1`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` ========= =============================== ================================== @@ -39961,12 +40685,14 @@ version versionsuffix toolchain ``0.2.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` ``0.2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` +``0.4.2`` ``-PyTorch-1.3.1`` ``fosscuda/2020b`` ``0.4.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``0.5.0`` ``-Python-3.7.4-PyTorch-1.4.0`` ``fosscuda/2019b`` ``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` ``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0-imkl`` ``fosscuda/2019b`` -``0.8.2`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` +``0.8.2`` ``-PyTorch-1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` ``0.8.2`` ``-Python-3.7.4-PyTorch-1.7.1`` ``fosscuda/2019b`` +``0.9.1`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` ========= ==================================== ================================== @@ -40474,7 +41200,7 @@ version versionsuffix toolchain Bundle of dependency Python packages for TVB (The Virtual Brain) -*homepage*: http://thevirtualbrain.org +*homepage*: https://thevirtualbrain.org ============ ================== =============== version versionsuffix toolchain @@ -40526,12 +41252,14 @@ Typing Extensions – Backported and Experimental Type Hints for Python *homepage*: https://github.com/python/typing/blob/master/typing_extensions/README.rst -=========== ================= ================== -version versionsuffix toolchain -=========== ================= ================== -``3.7.4.3`` ``GCCcore/10.2.0`` -``3.7.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -=========== ================= ================== +============ ================= ================== +version versionsuffix toolchain +============ ================= ================== +``3.7.4.3`` ``GCCcore/10.2.0`` +``3.7.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``3.7.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``3.10.0.0`` ``GCCcore/10.3.0`` +============ ================= ================== .. _list_software_letter_u: @@ -40540,7 +41268,7 @@ version versionsuffix toolchain --- -:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` +:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_UCX-CUDA_570` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_unimap_650` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` .. _list_software_UCLUST_480: @@ -40584,6 +41312,22 @@ version versionsuffix toolchain ============ ================ ======================================================= +.. _list_software_UCX-CUDA_570: + +*UCX-CUDA* +++++++++++ + +Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support. + +*homepage*: http://www.openucx.org/ + +========== ================ ================== +version versionsuffix toolchain +========== ================ ================== +``1.10.0`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` +========== ================ ================== + + .. _list_software_udocker_749: *udocker* @@ -40617,6 +41361,7 @@ version toolchain ``2.2.24`` ``intel/2017a`` ``2.2.25`` ``foss/2017b``, ``intel/2017b`` ``2.2.26`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +``2.2.28`` ``GCCcore/10.3.0`` ========== =============================================================================================================================================================================================== @@ -40633,6 +41378,7 @@ The Unified Form Language (UFL) is a domain specific language for declaration version versionsuffix toolchain ============ ================= ============== ``2018.1.0`` ``-Python-3.6.4`` ``foss/2018a`` +``2019.1.0`` ``-Python-3.7.4`` ``foss/2019b`` ============ ================= ============== @@ -40751,6 +41497,22 @@ version versionsuffix toolchain ========= ================= ================= +.. _list_software_unimap_650: + +*unimap* +++++++++ + +Unimap is a fork of minimap2 optimized for assembly-to-reference alignment. It integrates the minigraph chaining algorithm and can align through long INDELs (up to 100kb by default) much faster than minimap2. Unimap is a better fit for resolving segmental duplications and is recommended over minimap2 for alignment between high-quality assemblies. Unimap does not replace minimap2 for other types of alignment. It drops the support of multi-part index and short-read mapping. Its long-read alignment is different from minimap2 but is not necessarily better. Unimap is more of a specialized minimap2 at the moment. + +*homepage*: https://github.com/lh3/unimap + +======= ================== +version toolchain +======= ================== +``0.1`` ``GCCcore/10.2.0`` +======= ================== + + .. _list_software_units_563: *units* @@ -40882,6 +41644,7 @@ version toolchain ``2.2.0`` ``GCCcore/6.4.0`` ``2.3.0`` ``GCCcore/8.2.0`` ``2.5.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.6.1`` ``GCCcore/10.3.0`` ========= ======================================================== @@ -40921,7 +41684,7 @@ version toolchain --- -:ref:`list_software_V8_142` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcflib_630` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VMD_231` - :ref:`list_software_voltools_898` - :ref:`list_software_vorbis-tools_1267` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` +:ref:`list_software_V8_142` - :ref:`list_software_Vala_388` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcflib_630` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VMD_231` - :ref:`list_software_voltools_898` - :ref:`list_software_vorbis-tools_1267` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` .. _list_software_V8_142: @@ -40943,6 +41706,22 @@ version versionsuffix toolchain ========= ============= =============================== +.. _list_software_Vala_388: + +*Vala* +++++++ + +Vala is a programming language using modern high level abstractions without imposing additional runtime requirements and without using a different ABI compared to applications and libraries written in C. + +*homepage*: https://wiki.gnome.org/Projects/Vala + +========== ================== +version toolchain +========== ================== +``0.52.4`` ``GCCcore/10.3.0`` +========== ================== + + .. _list_software_Valgrind_823: *Valgrind* @@ -41221,15 +42000,16 @@ Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, in *homepage*: https://www.ensembl.org/info/docs/tools/vep -======== ================ =============================== -version versionsuffix toolchain -======== ================ =============================== -``93.4`` ``-Perl-5.26.1`` ``intel/2018a`` -``94.0`` ``-Perl-5.28.0`` ``foss/2018b`` -``94.5`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``95.0`` ``-Perl-5.28.0`` ``foss/2018b`` -``96.0`` ``-Perl-5.28.1`` ``foss/2019a`` -======== ================ =============================== +========= ================ =============================== +version versionsuffix toolchain +========= ================ =============================== +``93.4`` ``-Perl-5.26.1`` ``intel/2018a`` +``94.0`` ``-Perl-5.28.0`` ``foss/2018b`` +``94.5`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``95.0`` ``-Perl-5.28.0`` ``foss/2018b`` +``96.0`` ``-Perl-5.28.1`` ``foss/2019a`` +``103.1`` ``GCC/10.2.0`` +========= ================ =============================== .. _list_software_verifyBamID_1074: @@ -41345,14 +42125,15 @@ VMD is a molecular visualization program for displaying, animating, and analyzin *homepage*: https://www.ks.uiuc.edu/Research/vmd -============ ================== =============================== -version versionsuffix toolchain -============ ================== =============================== -``1.9.3`` ``-Python-2.7.12`` ``intel/2016b`` -``1.9.3`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2018a`` -``1.9.3`` ``-Python-2.7.15`` ``intel/2018b`` -``1.9.4a43`` ``-Python-3.7.4`` ``fosscuda/2019b`` -============ ================== =============================== +============ ================== ================================== +version versionsuffix toolchain +============ ================== ================================== +``1.9.3`` ``-Python-2.7.12`` ``intel/2016b`` +``1.9.3`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2018a`` +``1.9.3`` ``-Python-2.7.15`` ``intel/2018b`` +``1.9.4a43`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.9.4a51`` ``foss/2020b``, ``fosscuda/2020b`` +============ ================== ================================== .. _list_software_voltools_898: @@ -41489,6 +42270,7 @@ version versionsuffix toolchain ``5.2.3`` ``system`` ``5.2.4`` ``system`` ``5.2.5`` ``system`` +``5.2.6`` ``system`` =========== ================================== =============== @@ -41586,7 +42368,7 @@ version versionsuffix toolchain ``8.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``8.2.0`` ``-Python-3.7.4`` ``foss/2019b`` ``8.2.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` -``9.0.1`` ``foss/2020b`` +``9.0.1`` ``foss/2020b``, ``foss/2021a`` ========= ================== =================================================== @@ -41661,7 +42443,7 @@ version toolchain --- -:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_WCT_238` - :ref:`list_software_wcwidth_762` - :ref:`list_software_webin-cli_890` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_WHAM_301` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` +:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_WCT_238` - :ref:`list_software_wcwidth_762` - :ref:`list_software_webin-cli_890` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_WHAM_301` - :ref:`list_software_WhatsHap_800` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` .. _list_software_wandb_524: @@ -41689,16 +42471,16 @@ A tool for obtaining maximally-localised Wannier functions *homepage*: http://www.wannier.org -=========== ============= ================================================ -version versionsuffix toolchain -=========== ============= ================================================ -``1.2`` ``intel/2016.02-GCC-4.9`` -``2.0.1`` ``intel/2016.02-GCC-4.9``, ``intel/2016a`` -``2.0.1.1`` ``-abinit`` ``intel/2018b`` -``2.1.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``3.0.0`` ``intel/2018b`` -``3.1.0`` ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` -=========== ============= ================================================ +=========== ============= ================================================================================= +version versionsuffix toolchain +=========== ============= ================================================================================= +``1.2`` ``intel/2016.02-GCC-4.9`` +``2.0.1`` ``intel/2016.02-GCC-4.9``, ``intel/2016a`` +``2.0.1.1`` ``-abinit`` ``intel/2018b`` +``2.1.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``3.0.0`` ``intel/2018b`` +``3.1.0`` ``foss/2020b``, ``foss/2021a``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a`` +=========== ============= ================================================================================= .. _list_software_WannierTools_1253: @@ -41858,6 +42640,22 @@ version versionsuffix toolchain ============ ============= =============== +.. _list_software_WhatsHap_800: + +*WhatsHap* +++++++++++ + +WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. + +*homepage*: https://whatshap.readthedocs.io + +======= ============== +version toolchain +======= ============== +``1.1`` ``foss/2020b`` +======= ============== + + .. _list_software_wheel_533: *wheel* @@ -42425,13 +43223,14 @@ XCFun is a library of DFT exchange-correlation (XC) functionals. It is based on *homepage*: http://dftlibs.org/xcfun/ -============ ================== ================= -version versionsuffix toolchain -============ ================== ================= -``2.1.0`` ``GCCcore/9.3.0`` -``20180122`` ``-Python-2.7.14`` ``intel/2017b`` -``20190127`` ``-Python-3.7.2`` ``foss/2019a`` -============ ================== ================= +============ ================== ====================================== +version versionsuffix toolchain +============ ================== ====================================== +``2.1.0`` ``GCCcore/9.3.0`` +``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``20180122`` ``-Python-2.7.14`` ``intel/2017b`` +``20190127`` ``-Python-3.7.2`` ``foss/2019a`` +============ ================== ====================================== .. _list_software_XCrySDen_752: @@ -42722,7 +43521,7 @@ version toolchain Xonsh is a Python-ish, BASHwards-looking shell language and command prompt. -*homepage*: http://xon.sh/ +*homepage*: https://xon.sh/ ========= =============== version toolchain @@ -42766,7 +43565,7 @@ version versionsuffix toolchain ``1.2.2`` ``-X11-20180131`` ``GCCcore/6.4.0`` ``1.2.3`` ``GCCcore/7.3.0`` ``1.2.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.2.5`` ``GCCcore/10.2.0`` +``1.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ================= ======================================================================================================================= @@ -42862,12 +43661,13 @@ Xvfb is an X server that can run on machines with no display hardware and no phy *homepage*: https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml -========== ===================================== -version toolchain -========== ===================================== -``1.20.8`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``1.20.9`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========== ===================================== +=========== ===================================== +version toolchain +=========== ===================================== +``1.20.8`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.20.9`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.20.11`` ``GCCcore/10.3.0`` +=========== ===================================== .. _list_software_XZ_178: @@ -43069,6 +43869,7 @@ version toolchain ========== ==================================== ``4.8.9`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.8.10`` ``GCCcore/10.2.0`` +``4.8.11`` ``GCCcore/10.3.0`` ========== ==================================== @@ -43109,6 +43910,7 @@ version toolchain ``4.2.5`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` ``4.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.3.3`` ``GCCcore/10.2.0`` +``4.3.4`` ``GCCcore/10.3.0`` ========= ========================================================================================================= @@ -43159,7 +43961,7 @@ version toolchain ``1.2.7`` ``GCC/4.8.1``, ``GCC/4.8.2`` ``1.2.8`` ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.2.10`` ``system`` -``1.2.11`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` +``1.2.11`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index 59509f14..ddc2880d 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -8,6 +8,7 @@ * EB_ABAQUS * EB_Allinea * EB_Anaconda + * EB_AOMP * EB_CPLEX * EB_CUDA * EB_EPD @@ -66,6 +67,7 @@ * EB_pybind11 * EB_UFC + * EB_Amber * EB_Armadillo * EB_BamTools * EB_Blender @@ -90,7 +92,6 @@ * EB_Trilinos * ConfigureMakePythonPackage - * EB_Amber * EB_ARB * EB_ATLAS * EB_BerkeleyGW @@ -115,6 +116,7 @@ * EB_Ferret * EB_FFTW * EB_flex + * EB_FreeFEM * EB_freetype * EB_g2clib * EB_g2lib @@ -149,6 +151,7 @@ * EB_MUMmer * EB_MUMPS * EB_MyMediaLite + * EB_NCCL * EB_ncurses * EB_netCDF_minus_Fortran * EB_NEURON @@ -186,6 +189,7 @@ * EB_TAU * EB_tbb * EB_tbb + * EB_UCX_Plugins * EB_Velvet * EB_VMD * EB_XALT @@ -223,6 +227,7 @@ * EB_Gctf * EB_libsmm * EB_Modeller + * EB_MOOSE * EB_MotionCor2 * EB_MRtrix * EB_NCL @@ -273,6 +278,7 @@ * EB_SEPP * EB_TensorFlow * EB_TensorRT + * EB_torchvision * EB_VSC_minus_tools * EB_wxPython * FortranPythonPackage @@ -406,6 +412,7 @@ * EB_SEPP * EB_TensorFlow * EB_TensorRT + * EB_torchvision * EB_VSC_minus_tools * EB_wxPython * FortranPythonPackage diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index 45addaba..911e781f 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -183,6 +183,7 @@ easyconfig parameter description ``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` ``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` ``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` ``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` ``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``configure_cmd`` Configure command to use ``"cmake"`` @@ -258,6 +259,7 @@ easyconfig parameter description ``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` ``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` ``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` ``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` ``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``configure_cmd`` Configure command to use ``"cmake"`` @@ -296,6 +298,7 @@ easyconfig parameter description ``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` ``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` ``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` ``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` ``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``configure_cmd`` Configure command to use ``"cmake"`` @@ -341,6 +344,7 @@ easyconfig parameter description ``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` ``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` ``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` ``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` ``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` ``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` @@ -399,6 +403,7 @@ Extra easyconfig parameters specific to ``CmdCp`` easyblock easyconfig parameter description default value ======================== =================================================================================================================================================================================================== ==================================================== ``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` ``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``cmds_map`` List of regex/template command (with 'source'/'target' fields) tuples ``[('.*', '$CC $CFLAGS %(source)s -o %(target)s')]`` ``configure_cmd`` Configure command to use ``"./configure"`` @@ -462,6 +467,7 @@ Extra easyconfig parameters specific to ``ConfigureMake`` easyblock easyconfig parameter description default value ======================== =================================================================================================================================================================================================== ================== ``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` ``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``configure_cmd`` Configure command to use ``"./configure"`` ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` @@ -539,6 +545,7 @@ Extra easyconfig parameters specific to ``ConfigureMakePythonPackage`` easyblock easyconfig parameter description default value ======================== =================================================================================================================================================================================================== ======================================================================= ``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` ``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` ``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` @@ -772,6 +779,7 @@ Extra easyconfig parameters specific to ``MakeCp`` easyblock easyconfig parameter description default value ======================== =================================================================================================================================================================================================== ================== ``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` ``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``configure_cmd`` Configure command to use ``"./configure"`` ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` @@ -1143,6 +1151,7 @@ easyconfig parameter description ``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` ``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` ``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` ``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``clooguseisl`` Use ISL with CLooG or not ``False`` ``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` @@ -1198,6 +1207,7 @@ easyconfig parameter description ``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` ``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` ``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` ``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` ``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` ``configure_cmd`` Configure command to use ``"./configure"`` diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index 97f0b758..1c74dd02 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -293,6 +293,7 @@ Option flag Opt ``--http-header-fields-urlpat=[URLPAT::][HEADER:]FILE|FIELD`` Set extra HTTP header FIELDs when downloading files from URL PATterns. To not log sensitive values, specify a file containing newline separated FIELDs. e.g. "^https://www.example.com::/path/to/headers.txt" or "client[A-z0-9]*.example.com': ['Authorization: Basic token']". ``--ignore-checksums`` Ignore failing checksum verification (default: False) ``--ignore-osdeps`` Ignore any listed OS dependencies (default: False) +``--ignore-test-failure`` Ignore a failing test step (default: False) ``--install-latest-eb-release`` Install latest known version of easybuild (default: False) ``--lib-lib64-symlink`` Automatically create symlinks for lib/ pointing to lib64/ if the former is missing (default: True; disable with --disable-lib-lib64-symlink) ``--lib64-fallback-sanity-check`` Fallback in sanity check to lib64/ equivalent for missing libraries (default: True; disable with --disable-lib64-fallback-sanity-check) diff --git a/docs/version-specific/toolchain_opts.rst b/docs/version-specific/toolchain_opts.rst index cc8159a6..e0b40376 100644 --- a/docs/version-specific/toolchain_opts.rst +++ b/docs/version-specific/toolchain_opts.rst @@ -5,7 +5,7 @@ Available toolchain options (by toolchain) *(see also* ``eb --avail-toolchain-opts `` *)* -ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iiblf_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ +ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iiblf_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - nvompic_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ .. _ClangGCC: @@ -3414,6 +3414,49 @@ option description ========================= ======================================================================= ========= +.. _nvompic: + +Available options for nvompic toolchain +--------------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + .. _pmkl: Available options for pmkl toolchain diff --git a/docs/version-specific/toolchains.rst b/docs/version-specific/toolchains.rst index 4a4780c5..b6beba4a 100644 --- a/docs/version-specific/toolchains.rst +++ b/docs/version-specific/toolchains.rst @@ -21,7 +21,7 @@ Name Compiler(s) MPI Linear algebra **ffmpi** FCC *(none)* *(none)* *(none)* **foss** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW **fosscuda** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW -**Fujitsu** *(none)* *(none)* *(none)* FFTW +**Fujitsu** FCC *(none)* *(none)* FFTW **GCC** GCC *(none)* *(none)* *(none)* **GCCcore** GCCcore *(none)* *(none)* *(none)* **gcccuda** GCC, CUDA *(none)* *(none)* *(none)* @@ -80,6 +80,7 @@ Name Compiler(s) MPI Linear algebra **iqacml** icc, ifort QLogicMPI ACML, ScaLAPACK FFTW **ismkl** icc, ifort MPICH2 imkl imkl **NVHPC** NVHPC *(none)* *(none)* *(none)* +**nvompic** NVHPC OpenMPI *(none)* *(none)* **PGI** PGI *(none)* *(none)* *(none)* **pmkl** PGI *(none)* imkl imkl **pomkl** PGI OpenMPI imkl imkl From 84d15ee63fe7d96cb49d17ddcca71e799b6ec37e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jul 2021 08:24:46 +0200 Subject: [PATCH 159/286] fix list of easyblocks for EasyBuild v4.4.1 --- docs/version-specific/easyblocks.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index ddc2880d..c7328338 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -227,7 +227,6 @@ * EB_Gctf * EB_libsmm * EB_Modeller - * EB_MOOSE * EB_MotionCor2 * EB_MRtrix * EB_NCL From e8dbcc3789bf41d2b4b20ee1f76493eb988fbaa5 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 6 Jul 2021 09:31:26 +0800 Subject: [PATCH 160/286] update release notes and changelog for EasyBuild v4.4.1 + bump version to 4.4.1 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 174 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 174 insertions(+), 5 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 8f7d9101..2ce0810e 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20210706.01** (`Jul 6th 2021`): update release notes for EasyBuild v4.4.1 (see :ref:`release_notes_eb441`) * **release 20210602.01** (`Jun 2nd 2021`): update release notes for EasyBuild v4.4.0 (see :ref:`release_notes_eb440`) * **release 20210409.01** (`Apr 9th 2021`): update release notes for EasyBuild v4.3.4 (see :ref:`release_notes_eb434`) * **release 20210223.01** (`Feb 23rd 2021`): update release notes for EasyBuild v4.3.3 (see :ref:`release_notes_eb433`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 04b02342..1cc08a9b 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,180 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,349** different software packages, -including 36 different (compiler) toolchains. It contains 232 software-specific easyblocks and 37 generic easyblocks, -alongside 12,266 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,388** different software packages, +including 36 different (compiler) toolchains. It contains 237 software-specific easyblocks and 37 generic easyblocks, +alongside 12,607 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb441: + +EasyBuild v4.4.1 (July 6th 2021) +-------------------------------- + +bugfix/update release + +**framework** + +* various enhancements, including: + + * enhance detection of patch files supplied to ``eb`` command with better error messages (`#3709 `_) + * add per-step timing information (`#3716 `_) + * add ``module-write hook`` (`#3728 `_) + * add ``ignore-test-failure`` configuration option to ignore failing test step (`#3732 `_) + * add toolchain definition for nvompic (NVHPC + OpenMPI) (`#3735 `_) + * warn about generic milestone in ``--review-pr`` and ``--merge-pr`` (`#3751 `_) + +* various bug fixes, including: + + * don't override ``COMPILER_MODULE_NAME``, inherited from ``Ffmpi``, in Fujitsu toolchain definition (`#3721 `_) + * avoid overwriting ``pr_nr`` in ``post_pr_test_report`` for reports with ``--include-easyblocks-from-pr`` (`#3724 `_, `#3726 `_) + * fix crash in ``get_config_dict`` when copying modules that were imported in easyconfig file (like ``import os``) (`#3729 `_) + * parse C standard flags in ``CFLAGS`` for Fujitsu compiler (`#3731 `_) + * fix error message for ``--use-ccache`` (`#3733 `_) + * error out when passing a list to ``run_cmd*`` to avoid running wrong command unintended, unless ``shell=True`` is used (`#3737 `_) + * minor fixes to output of test reports when using multiple PRs (`#3741 `_) + * fix location for modules installed with intel-compilers toolchain in HierarchicalMNS by always checking toolchain compiler name against template map (`#3745 `_) + * avoid checking ``msg`` attribute of ``GitCommandError`` (`#3756 `_) + * consider sources provided as dict in ``EasyBlock.check_checksums_for`` (`#3758 `_) + * don't make changes to software installation directory when using ``--sanity-check-only`` (`#3761 `_) + * honor specified easyblock for extensions (`#3762 `_) + +* other changes: + + * make sure that tests requiring a github token have ``github`` in the test name so that they can be easily filtered (`#3730 `_) + * deprecate EasyBuild bootstrap script (`#3742 `_) + * use temporary download folder in ``test_http_header_fields_urlpat`` (`#3755 `_) + +**easyblocks** + +* 5 new software-specific easyblocks: + + * AOMP (`#2435 `_, `#2462 `_, `#2464 `_), FreeFEM (`#1969 `_), NCCL (built from source) (`#2337 `_, `#2460 `_), torchvision (`#2467 `_), UCX plugins (`#2491 `_) + +* minor enhancements, including: + + * enhance Amber easyblock to support installing Amber via CMake (`#2445 `_) + * enhance ConfigureMake generic easyblock to add support for building multiple build targets (`#2449 `_, `#2479 `_, `#2480 `_) + * enhance sanity check for Clang to verify if CUDA offload library was produced (`#2454 `_) + * update custom easyblock for Boost to always build single and multi threaded versions (`#2456 `_) + * enhance ``sitecustomize.py`` in Python easyblock to support overriding core Python packages, and allowing overriding in virtualenv (`#2458 `_, `#2483 `_) + * update CMakeMake to handle old and new Boost/Boost.Python builds using custom easyblock for Boost (`#2461 `_) + * add file prefix option to XALT easyblock (`#2463 `_) + * enhance Java easyblock to define ``%(jdkarch)s`` template (`#2472 `_) + * adjust Perl easyblock to only check for a ``man`` subdirectory if groff is a dependency (`#2474 `_) + * support arbitrary version strings in OpenSSL wrapper and add ``minimum_openssl_version`` option (`#2475 `_) + * enhance Python easyblock to explicitly disable installing core-pip when ``install_pip`` is not ``True`` (`#2476 `_) + * enhance intel-compiler easyblock to include multipath include dir in ``$CPATH`` (`#2477 `_) + * enhance Hypre easyblock to enable CUDA support (`#2482 `_) + * update Xmipp easyblock for new version (v3.20.07) (`#2486 `_) + * enhance FFTW easyblock to skip tests if ``--mpi-tests`` EasyBuild configuration option is disabled (`#2490 `_) + * use ``PYPI_SOURCE`` as the default for ``source_urls`` of extensions of Python easyconfigs (`#2493 `_) + +* various bug fixes, including: + + * only use siterc fix for NVHPC < 21.3 (`#2453 `_) + * fix CPU-only runtime for dpcpp-generated executables in custom easyblock for intel-compilers (`#2457 `_) + * always add ``distinct_host_configuration=false`` to build command for TensorFlow (`#2459 `_) + * disable installation of bundled BioPerl and HTSLib if they are dependencies of VEP (`#2468 `_) + * don't use list value for command to detect installed Python packages in TensorFlow easyblock (`#2469 `_) + * change Bundle easyblock to also collect ``altroot`` and ``altversion`` in the module step so they are set when running ``--module-only`` (`#2485 `_) + * always strip output from ``gcc -print-multiarch`` in intel-compilers easyblock (`#2489 `_) + * don't overwrite all of ``exts_default_options`` in TensorFlow easyblock (`#2494 `_) + * enhance GCC easyblock to make sure that system GCC provides LTO support, and disable LTO when building MPFR if not (`#2498 `_) + * rework the dependency handling of OpenMPI to use explicit configure options to disable features if required dependency is not provided (`#2500 `_, `#2501 `_) + +**easyconfigs** + +* added example easyconfig files for 39 new software packages: + + * AMPHORA2 (`#13003 `_), AOMP (`#12909 `_), CAMPARI (`#13152 `_), CSB (`#12877 `_), dijitso (`#10719 `_), DosageConvertor (`#13278 `_), + dSFMT (`#12971 `_), exiv2 (`#13204 `_), FEniCS (`#10719 `_), FreeFEM (`#9902 `_), futhark (`#12921 `_), futile (`#12864 `_), + gappa (`#13186 `_), GenomeWorks (`#13083 `_, `#13092 `_), gexiv2 (`#13204 `_), HAL (`#13267 `_), hipify-clang (`#12961 `_), inline (`#12029 `_), + libcint (`#13214 `_), LTR_retriever (`#13125 `_), mapDamage (`#13172 `_), MbedTLS (`#13061 `_), microctools (`#13010 `_), + Nektar++ (`#12664 `_), NINJA (`#13125 `_), OBITools3 (`#12969 `_), ont-fast5-api (`#13033 `_), OpenMM-PLUMED (`#13268 `_), + phototonic (`#13241 `_), PyFoam (`#12675 `_), RagTag (`#13247 `_), RcppGSL (`#13172 `_), RECON (`#13123 `_), RepeatScout (`#13124 `_), + retworkx (`#13228 `_), UCX-CUDA (`#13260 `_), unimap (`#13247 `_), Vala (`#13204 `_), WhatsHap (`#12989 `_) + +* added additional easyconfigs for various supported software packages, including: + + * Amber 20.11, BBMap 38.90, Beast 2.6.4, BLIS 3.0 (AMDo fork), Bonito 0.4.0, CellRanger-ARC 2.0.0, + CellRanger-ATAC 2.0.0, Check 0.15.2, CubeGUI 4.6, CubeLib 4.6, CubeWriter 4.6, cuDNN 8.2.1.32, CVXOPT 1.2.6, + DOLFIN 2019.1.0.post0, eggnog-mapper 2.1.4, ELPA 2021.05.001, FDS 6.7.6, FFC 2019.1.0.post0, FFmpeg 4.3.2, + FIAT 2019.1.0, flatbuffers 2.0.0, flatbuffers-python 2.0, FLTK 1.3.6, gc 8.0.4, GCC 8.4.0 + 9.4.0, GDAL 3.3.0, + Gdk-Pixbuf 2.42.6, geopy 2.1.0, Ghostscript 9.54.0, git 2.32.0, GitPython 3.1.18, GLFW 3.3.4, gmsh 4.8.4, + gnuplot 5.4.2, GnuTLS 3.7.2, Go 1.16.5, GObject-Introspection 1.68.0, gperftools 2.9.1, GraphicsMagick 1.3.36, + Graphviz 2.47.2, GSL 2.7, GTK+ 2.24.33, Guile 2.2.7, h5py 3.2.1, HarfBuzz 2.8.1, Horovod 0.22.0, Hypre 2.21.0, + ICU 69.1, ImageMagick 7.0.11-14, IOR 3.3.0, IPython 7.25.0, IRkernel 1.2, ispc 1.16.0, JupyterLab 3.0.16, + LDC 1.26.0, libcerf 1.17, libepoxy 1.5.8, libgd 2.3.1, libStatGen 1.0.15, libxc 5.1.5, LittleCMS 2.12, + LMfit 1.0.2, Lua 5.4.3, M4 1.4.19, MCR R2021a.3, medaka 1.4.3, Mercurial 5.8, minimap2 2.20, MMseqs2 13, + MrBayes 3.2.7, MUMPS 5.4.0, NCCL 2.9.9, netCDF 4.8.0, Nim 1.4.8, nodejs 14.17.0, Nsight-Compute 2021.2.0, + numba 0.53.1, NVHPC 21.5.eb, nvtop 1.2.1, Octave 6.2.0, OPARI2 2.0.6, openkim-models 20210128, OpenMPI 4.0.6, + OTF2 2.3, p11-kit 0.24.0, Pango 1.48.5, parallel 20210622, petsc4py 3.12.0, picard 2.25.5, Pillow 8.2.0, + PROJ 8.0.1, protobuf 3.17.3, protobuf-python 3.17.3, PSolver 1.8.3, PySCF 1.7.6, pyspoa 0.0.8, pytest-xdist 2.3.0, + PyTorch 1.9.0, PyYAML 5.4.1, Qhull 2020.2, Quandl 3.6.1, R 4.0.5 + R 4.1.0, Ragout 2.3, RE2 2021-06-01, + ReFrame 3.6.2, RepeatMasker 4.1.2, rgdal 1.5-23, RMBlast 2.11.0, Ruby 3.0.1, scikit-learn 0.24.2, + Score-P 7.0, Seurat 4.0.3, slepc4py 3.12.0, spoa 4.0.7, Subread 2.0.2, Subversion 1.14.1, SuiteSparse 5.10.1, + sympy 1.8, tensorboardX 2.2, TensorFlow 2.5.0, Tk 8.6.11, tmux 3.2a, torchtext 0.8.1, torchvision 0.9.1, + UDUNITS 2.2.28, UFL 2019.1.0, utf8proc 2.6.1, VEP 103.1, VMD 1.9.4a51, vsc-mympirun 5.2.6, XCFun 2.1.1, + Xvfb 1.20.11, Z3 4.8.11, ZeroMQ 4.3.4 + +* minor enhancements, including: + + * update cuDNN 8.0.x easyconfigs with a download location (`#12368 `_) + * add extensions to recent R easyconfigs: GxEScanR (`#13039 `_), cSEM (`#13208 `_), cubelyr + broom.mixed (`#13252 `_), + grf (`#13261 `_), twang + xgboost (`#13284 `_), neuralnet (`#13330 `_) + * add check to easyconfigs test suite to ensure OpenSSL wrapper is used in easyconfigs using a recent toolchain (`#13079 `_) + * add gipaw to QuantumESPRESSO/6.7 (`#13087 `_) + * add checksum for aarch64 installation file for CUDAcore easyconfigs (`#13014 `_, `#13097 `_) + * add Perl dependency to makeinfo easyconfigs (`#13166 `_) + * set minimal OpenSSL version to 1.1.1 for OpenSSL v1.1 wrapper (`#13188 `_) + * add JIT support for CUDA 11 to PyTorch 1.7.1 (`#13207 `_) + * add ``ninja --version`` as sanity check command in Ninja easyconfigs (`#13222 `_) + * code cleanup + improvements for easyconfigs test suite (`#13257 `_) + +* various bug fixes, including: + + * download sources via git for XGBoost 20171120 easyconfig due to use of submodules (`#6880 `_) + * add elfutils as build dependency for Clang 8.0.x and 9.0.1 (`#13015 `_) and Clang 11.0.1 (`#13008 `_) easyconfigs that have a CUDA dependency + * add missing CMake option to Geant4 v10.7.1 in order to actually use external CLHEP (`#13019 `_) + * add new checksum for mvabund extension to R v4.0.4 eaysconfigs (`#13020 `_, `#13021 `_) + * add patch to fix numpy ``test_ccompiler_opt`` in SciPy-bundle v2021.05 (`#13042 `_) + * add patch to fix installation of HDF 4.2.15 on aarch64 (`#13059 `_) + * make sure that MbedTLS' Makefile uses ``python`` rather than ``python2`` (`#13061 `_) + * fix checksum for snpEff 5.0 (`#13062 `_) + * fix source URL for LIBSVM 3.24 by downloading from GitHub (`#13076 `_) + * add ``preinstallopts`` for minimap2 to fix installation on aarch64 (`#13080 `_) + * add patch for GCC 10.2.0 to fix internal compiler error on aarch64 (`#13086 `_) + * switch to NCCL 2.8.3 built from source for CuPy, Horovod, libgpuarray, PyTorch and TensorFlow using fosscuda/2020b (`#13103 `_) + * add astor to dependencies of TensorFlow with 2019b (`#13111 `_) and 2020b (`#13103 `_, `#13112 `_) toolchains + * break cyclic dependency between groff, makeinfo and Perl by adding Perl-minimal and makeinfo-minimal easyconfigs (`#13163 `_ - `#13165 `_) + * add missing rgdal dep to R-INLA (`#13179 `_) + * add patch to fix ``uniq`` operation in TensorFlow 2.4.1 (`#13181 `_) + * add Perl build dependency for PnetCDF 1.12.1 (`#13183 `_) + * disable own avx detection of libfabric v1.12.1 (`#13215 `_) + * add GCCcore-[1-9][0-9].x to ``test_dep_versions_per_toolchain_generation`` (`#13243 `_, `#13249 `_, `#13251 `_) + * add patch to fix installation of TensorFlow 2.0.x (`#13248 `_) + * add patch for recent GCCcore versions to fix compatibility with CUDA 11 (`#13290 `_) + * fix install step for glew (`#13297 `_) + * update Boost 1.74.0 easyconfigs to use ``tagged_layout`` rather than ``boost_multi_thread`` (`#13300 `_) + * avoid using PMIx from system instead of PMIx dependency specified via ``--with-pmix`` for OpenMPI 4.x (`#13307 `_) + * add patch for GCCcore 10.3.0 to prevent issues when compiling with nvcc (`#13310 `_) + * add patch for OpenMPI 4.0.x to fix building against (system) UCX version > 1.7 (`#13329 `_) + * fix build of manta 1.6.0 on top of Boost 1.74.0 (`#13338 `_) + * fix recent taxator-tk easyconfigs by adding (back) ``-DBoost_NO_BOOST_CMAKE=ON`` configure option (`#13342 `_) + +* other changes: + + * disable ``debuginfod`` for elfutils to minimize required dependencies (`#13034 `_) + * add bare Python 3.9.5 easyconfig and use that as builddep for LLVM 11.1.0 (`#13035 `_) + * remove misleading comment from Python >= 3.7 easyconfigs, libffi is now also required for Python itself (no longer bundled) (`#13041 `_) + * use new custom easyblock in torchvision easyconfigs (`#13102 `_) + * remove superfluous TensorFlow patch (`#13223 `_) + * cleanup of easyconfigs for (bundles) of Python packages: remove default ``PYPI_SOURCE`` source URLs + use ``PythonBundle`` rather than ``Bundle`` easyblock (`#13253 `_, `#13295 `_, `#13336 `_) + * update ``README`` with instructions for MATLAB easyconfigs (`#12597 `_) + + .. _release_notes_eb440: EasyBuild v4.4.0 (June 2nd 2021) diff --git a/docs/conf.py b/docs/conf.py index ce6781aa..12f4879b 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.4.0' # this is meant to reference the version of EasyBuild +version = '4.4.1' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20210602.0' # this is meant to reference the version of the documentation itself +release = '20210706.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 8262dba63075b344f32d8535284609becbcc9303 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 6 Jul 2021 16:45:44 +0800 Subject: [PATCH 161/286] bump version to 4.4.1 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 13545939..343778a0 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.4.0' +VERSION = '4.4.1' # Utility function to read README file From ff295a3c0c93ff240ba7ea94f713c4e2b7155cb1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Jul 2021 12:34:24 +0200 Subject: [PATCH 162/286] remove Python 2.6 from list of supported Python versions in setup.py --- setup.py | 1 - 1 file changed, 1 deletion(-) diff --git a/setup.py b/setup.py index 13545939..d0212e2d 100644 --- a/setup.py +++ b/setup.py @@ -69,7 +69,6 @@ def read(fname): "Intended Audience :: System Administrators", "License :: OSI Approved :: GNU General Public License v2 (GPLv2)", "Operating System :: POSIX :: Linux", - "Programming Language :: Python :: 2.6", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", From 9caa7844ee93696a0ff6a338e2bd49c2765e7004 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Aug 2021 10:10:42 +0200 Subject: [PATCH 163/286] remove mentions of --experimental in docs for RPATH support --- docs/RPATH-support.rst | 5 ----- 1 file changed, 5 deletions(-) diff --git a/docs/RPATH-support.rst b/docs/RPATH-support.rst index ede648b0..6709dcca 100644 --- a/docs/RPATH-support.rst +++ b/docs/RPATH-support.rst @@ -5,9 +5,6 @@ Support for RPATH Since EasyBuild v3.5.2, (stable) support is available for using RPATH. -.. note:: RPATH support has been available since EasyBuild v3.0.0, but was considered experimental - until EasyBuild v3.5.2 (cfr. :ref:`experimental_features` for more information on experimental features). - .. contents:: :depth: 3 :backlinks: none @@ -54,8 +51,6 @@ Enabling RPATH linking To instruct EasyBuild to enable RPATH linking, use the ``--rpath`` configuration option. -.. note:: For now, ``--experimental`` is also required, since the implementation of RPATH support is not considered fully stable yet. - .. _rpath_support_implementation: From d1e42c9388c3a9fdfc34bcb114c46e9e2ac95b3f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 Sep 2021 22:06:41 +0200 Subject: [PATCH 164/286] auto-update documentation for EasyBuild v4.4.2 --- docs/version-specific/Supported_software.rst | 4638 +++++++++++------ docs/version-specific/easyblocks.rst | 7 + .../easyconfig_parameters.rst | 1 + docs/version-specific/generic_easyblocks.rst | 424 +- docs/version-specific/help.rst | 1 + docs/version-specific/toolchain_opts.rst | 45 +- docs/version-specific/toolchains.rst | 1 + 7 files changed, 3372 insertions(+), 1745 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 411772aa..23b3cd33 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2388 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2469 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -85,6 +85,7 @@ version versionsuffix toolchain ``6.14.1`` ``-linux-x86_64`` ``system`` ``2017`` ``-hotfix-1721`` ``system`` ``2018`` ``-hotfix-1806`` ``system`` +``2020`` ``system`` ========== ================= ========== @@ -93,7 +94,7 @@ version versionsuffix toolchain *ABINIT* ++++++++ -ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. +ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. *homepage*: https://www.abinit.org/ @@ -114,6 +115,7 @@ version versionsuffix toolchain ``8.10.3`` ``intel/2018b`` ``9.2.1`` ``intel/2020a`` ``9.4.1`` ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` +``9.4.2`` ``intel/2021a`` ========== ======================== ================================================ @@ -126,12 +128,12 @@ Assembly Based ReAligner *homepage*: https://github.com/mozack/abra2 -======== ======================= -version toolchain -======== ======================= -``2.22`` ``iccifort/2019.5.281`` -``2.23`` ``GCC/9.3.0`` -======== ======================= +======== ============================= +version toolchain +======== ============================= +``2.22`` ``iccifort/2019.5.281`` +``2.23`` ``GCC/10.2.0``, ``GCC/9.3.0`` +======== ============================= .. _list_software_ABRicate_731: @@ -185,6 +187,7 @@ version toolchain ========= ================== ``2.14`` ``system`` ``3.4.0`` ``GCCcore/10.2.0`` +``3.5.0`` ``GCCcore/10.3.0`` ========= ================== @@ -244,7 +247,7 @@ version versionsuffix toolchain AdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. -*homepage*: https://github.com/%/(github_account)s/%(namelower)s +*homepage*: https://github.com/MikkelSchubert/adapterremoval ========= ============== version toolchain @@ -252,6 +255,7 @@ version toolchain ``2.2.0`` ``foss/2016b`` ``2.2.2`` ``foss/2018b`` ``2.3.1`` ``foss/2018b`` +``2.3.2`` ``GCC/10.3.0`` ========= ============== @@ -376,6 +380,7 @@ version toolchain ``2019_update2`` ``system`` ``2019_update3`` ``system`` ``2019_update5`` ``system`` +``2021.2.0`` ``system`` ================ ========== @@ -537,12 +542,13 @@ Progress indicator C library. ATHR is a simple yet powerful progress indicator l *homepage*: https://github.com/horta/almosthere -========== ================= -version toolchain -========== ================= -``1.0.1`` ``GCCcore/7.3.0`` -``1.0.10`` ``GCCcore/9.3.0`` -========== ================= +========== ================== +version toolchain +========== ================== +``1.0.1`` ``GCCcore/7.3.0`` +``1.0.10`` ``GCCcore/9.3.0`` +``2.0.2`` ``GCCcore/10.2.0`` +========== ================== .. _list_software_Alpha_486: @@ -561,6 +567,22 @@ version versionsuffix toolchain ============ ================== ============== +.. _list_software_AlphaFold_875: + +*AlphaFold* ++++++++++++ + +AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known + +*homepage*: https://deepmind.com/research/case-studies/alphafold + +========= ================================== +version toolchain +========= ================================== +``2.0.0`` ``foss/2020b``, ``fosscuda/2020b`` +========= ================================== + + .. _list_software_ALPS_304: *ALPS* @@ -869,6 +891,7 @@ version toolchain ``2020.02`` ``system`` ``2020.07`` ``system`` ``2020.11`` ``system`` +``2021.05`` ``system`` =========== ========== @@ -888,6 +911,22 @@ version toolchain ======= ======================= +.. _list_software_andi_412: + +*andi* +++++++ + +This is the andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes. + +*homepage*: https://github.com/evolbioinf/andi/ + +======== ============== +version toolchain +======== ============== +``0.13`` ``foss/2018b`` +======== ============== + + .. _list_software_angsd_525: *angsd* @@ -983,34 +1022,36 @@ Apache Ant is a Java library and command-line tool whose mission is to drive pro *homepage*: http://ant.apache.org/ -========== =================== ========== -version versionsuffix toolchain -========== =================== ========== -``1.8.4`` ``-Java-1.7.0_10`` ``system`` -``1.8.4`` ``-Java-1.7.0_21`` ``system`` -``1.9.0`` ``-Java-1.7.0_15`` ``system`` -``1.9.0`` ``-Java-1.7.0_21`` ``system`` -``1.9.3`` ``-Java-1.7.0_60`` ``system`` -``1.9.3`` ``-Java-1.7.0_79`` ``system`` -``1.9.6`` ``-Java-1.7.0_75`` ``system`` -``1.9.6`` ``-Java-1.7.0_79`` ``system`` -``1.9.6`` ``-Java-1.7.0_80`` ``system`` -``1.9.6`` ``-Java-1.8.0_66`` ``system`` -``1.9.6`` ``-Java-1.8.0_72`` ``system`` -``1.9.6`` ``-Java-1.8.0_77`` ``system`` -``1.9.7`` ``-Java-1.8.0_92`` ``system`` -``1.10.0`` ``-Java-1.8.0_112`` ``system`` -``1.10.1`` ``-Java-1.8`` ``system`` -``1.10.1`` ``-Java-1.8.0_121`` ``system`` -``1.10.1`` ``-Java-1.8.0_144`` ``system`` -``1.10.1`` ``-Java-1.8.0_152`` ``system`` -``1.10.1`` ``-Java-1.8.0_162`` ``system`` -``1.10.5`` ``-Java-1.8`` ``system`` -``1.10.6`` ``-Java-1.8`` ``system`` -``1.10.7`` ``-Java-11`` ``system`` -``1.10.8`` ``-Java-11`` ``system`` -``1.10.9`` ``-Java-11`` ``system`` -========== =================== ========== +=========== =================== ========== +version versionsuffix toolchain +=========== =================== ========== +``1.8.4`` ``-Java-1.7.0_10`` ``system`` +``1.8.4`` ``-Java-1.7.0_21`` ``system`` +``1.9.0`` ``-Java-1.7.0_15`` ``system`` +``1.9.0`` ``-Java-1.7.0_21`` ``system`` +``1.9.3`` ``-Java-1.7.0_60`` ``system`` +``1.9.3`` ``-Java-1.7.0_79`` ``system`` +``1.9.6`` ``-Java-1.7.0_75`` ``system`` +``1.9.6`` ``-Java-1.7.0_79`` ``system`` +``1.9.6`` ``-Java-1.7.0_80`` ``system`` +``1.9.6`` ``-Java-1.8.0_66`` ``system`` +``1.9.6`` ``-Java-1.8.0_72`` ``system`` +``1.9.6`` ``-Java-1.8.0_77`` ``system`` +``1.9.7`` ``-Java-1.8.0_92`` ``system`` +``1.10.0`` ``-Java-1.8.0_112`` ``system`` +``1.10.1`` ``-Java-1.8`` ``system`` +``1.10.1`` ``-Java-1.8.0_121`` ``system`` +``1.10.1`` ``-Java-1.8.0_144`` ``system`` +``1.10.1`` ``-Java-1.8.0_152`` ``system`` +``1.10.1`` ``-Java-1.8.0_162`` ``system`` +``1.10.5`` ``-Java-1.8`` ``system`` +``1.10.6`` ``-Java-1.8`` ``system`` +``1.10.7`` ``-Java-11`` ``system`` +``1.10.8`` ``-Java-11`` ``system`` +``1.10.9`` ``-Java-11`` ``system`` +``1.10.11`` ``-Java-11`` ``system`` +``1.10.11`` ``-Java-13`` ``system`` +=========== =================== ========== .. _list_software_antiSMASH_808: @@ -1042,7 +1083,7 @@ ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language to version versionsuffix toolchain ========= ================== ===================================================================================================== ``2.7.7`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b`` -``2.7.7`` ``-Java-11`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.7.7`` ``-Java-11`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.7.7`` ``-Python-2.7.11`` ``foss/2016a`` ``2.7.7`` ``-Python-2.7.13`` ``intel/2017a`` ``2.7.7`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` @@ -1066,6 +1107,7 @@ version versionsuffix toolchain ``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2.3.1`` ``-Python-3.6.6`` ``foss/2018b`` ``2.3.2`` ``-Python-3.7.4`` ``foss/2019b`` +``2.3.5`` ``foss/2021a`` ========= ================== =============================== @@ -1094,12 +1136,12 @@ Convert various sequence formats to FASTA *homepage*: https://github.com/tseemann/any2fasta -========= ================ ==================================== -version versionsuffix toolchain -========= ================ ==================================== -``0.4.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.4.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -========= ================ ==================================== +========= ================ ======================================================== +version versionsuffix toolchain +========= ================ ======================================================== +``0.4.2`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.4.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +========= ================ ======================================================== .. _list_software_AOCC_278: @@ -1116,6 +1158,7 @@ version toolchain ========= ====================================== ``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``3.0.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``3.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ====================================== @@ -1177,12 +1220,12 @@ Apache Portable Runtime (APR) libraries. *homepage*: https://apr.apache.org/ -========= ============================================================================ -version toolchain -========= ============================================================================ -``1.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``iomkl/2018a`` -``1.7.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` -========= ============================================================================ +========= ================================================================================================ +version toolchain +========= ================================================================================================ +``1.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``iomkl/2018a`` +``1.7.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +========= ================================================================================================ .. _list_software_APR-util_718: @@ -1194,11 +1237,11 @@ Apache Portable Runtime (APR) util libraries. *homepage*: http://apr.apache.org/ -========= =================================================================================================================================== -version toolchain -========= =================================================================================================================================== -``1.6.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``iomkl/2018a`` -========= =================================================================================================================================== +========= ======================================================================================================================================================= +version toolchain +========= ======================================================================================================================================================= +``1.6.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``iomkl/2018a`` +========= ======================================================================================================================================================= .. _list_software_ARAGORN_522: @@ -1231,6 +1274,7 @@ version toolchain ========== ================================================================================ ``2.16.0`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` ``2.17.0`` ``GCC/8.3.0`` +``2.19.0`` ``GCC/10.3.0`` ========== ================================================================================ @@ -1275,11 +1319,11 @@ Provide an interface to ZIP archive files. *homepage*: https://metacpan.org/pod/Archive::Zip -======== ================== -version toolchain -======== ================== -``1.68`` ``GCCcore/10.2.0`` -======== ================== +======== ========================================================== +version toolchain +======== ========================================================== +``1.68`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +======== ========================================================== .. _list_software_archspec_841: @@ -1291,12 +1335,13 @@ A library for detecting, labeling, and reasoning about microarchitectures *homepage*: https://github.com/archspec/archspec -========= ================= ================= -version versionsuffix toolchain -========= ================= ================= -``0.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``0.1.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -========= ================= ================= +========= ================= ====================================== +version versionsuffix toolchain +========= ================= ====================================== +``0.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.1.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``0.1.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ================= ====================================== .. _list_software_ARGoS_412: @@ -1324,11 +1369,27 @@ Argtable is an ANSI C library for parsing GNU style command line options with a *homepage*: http://argtable.sourceforge.net/ -======== ====================================================================================================== -version toolchain -======== ====================================================================================================== -``2.13`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -======== ====================================================================================================== +======== ========================================================================================================================== +version toolchain +======== ========================================================================================================================== +``2.13`` ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +======== ========================================================================================================================== + + +.. _list_software_aria2_463: + +*aria2* ++++++++ + +aria2 is a lightweight multi-protocol & multi-source command-line download utility. + +*homepage*: https://aria2.github.io + +========== ================== +version toolchain +========== ================== +``1.35.0`` ``GCCcore/10.3.0`` +========== ================== .. _list_software_Arlequin_833: @@ -1368,6 +1429,7 @@ version versionsuffix toolchain ``9.700.2`` ``foss/2019a`` ``9.880.1`` ``foss/2020a`` ``9.900.1`` ``foss/2019b``, ``foss/2020a`` +``10.5.3`` ``foss/2020b`` =========== ================== =============================== @@ -1404,7 +1466,7 @@ version toolchain ``3.5.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b`` ``3.6.2`` ``intel/2018a`` ``3.7.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` -``3.8.0`` ``foss/2020b`` +``3.8.0`` ``foss/2020b``, ``foss/2021a`` ========= ================================================================================ @@ -1434,12 +1496,12 @@ Arriba is a command-line tool for the detection of gene fusions from RNA-Seq dat *homepage*: https://github.com/suhrig/arriba -========= ============== -version toolchain -========= ============== -``1.1.0`` ``foss/2018b`` -``2.1.0`` ``GCC/10.2.0`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``1.1.0`` ``foss/2018b`` +``2.1.0`` ``GCC/10.2.0``, ``GCC/10.3.0`` +========= ============================== .. _list_software_Arrow_523: @@ -1604,6 +1666,7 @@ version versionsuffix toolchain ``3.20.1`` ``-Python-3.8.2`` ``intel/2020a`` ``3.21.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``3.21.1`` ``-Python-3.8.2`` ``foss/2020a`` +``3.22.0`` ``foss/2021a`` ============== ================== =================================================== @@ -1735,15 +1798,15 @@ AT-SPI 2 toolkit bridge *homepage*: https://wiki.gnome.org/Accessibility -========== ================== -version toolchain -========== ================== -``2.26.3`` ``fosscuda/2018b`` -``2.32.0`` ``GCCcore/8.2.0`` -``2.34.1`` ``GCCcore/8.3.0`` -``2.34.2`` ``GCCcore/9.3.0`` -``2.38.0`` ``GCCcore/10.2.0`` -========== ================== +========== ========================================================== +version toolchain +========== ========================================================== +``2.26.3`` ``fosscuda/2018b`` +``2.32.0`` ``GCCcore/8.2.0`` +``2.34.1`` ``GCCcore/8.3.0`` +``2.34.2`` ``GCCcore/9.3.0`` +``2.38.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ========================================================== .. _list_software_at-spi2-core_1110: @@ -1763,6 +1826,8 @@ version toolchain ``2.34.0`` ``GCCcore/8.3.0`` ``2.36.0`` ``GCCcore/9.3.0`` ``2.38.0`` ``GCCcore/10.2.0`` +``2.40.2`` ``GCCcore/10.3.0`` +``2.40.3`` ``GCCcore/11.2.0`` ========== ================== @@ -1775,20 +1840,20 @@ ATK provides the set of accessibility interfaces that are implemented by other *homepage*: https://developer.gnome.org/atk/ -========== =================================================================== -version toolchain -========== =================================================================== -``2.18.0`` ``intel/2016a`` -``2.20.0`` ``foss/2016a``, ``intel/2016a`` -``2.22.0`` ``foss/2016b``, ``intel/2016b`` -``2.26.0`` ``intel/2017a`` -``2.26.1`` ``foss/2018b``, ``intel/2017b`` -``2.27.1`` ``foss/2017b``, ``intel/2017b`` -``2.28.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a`` -``2.32.0`` ``GCCcore/8.2.0`` -``2.34.1`` ``GCCcore/8.3.0`` -``2.36.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -========== =================================================================== +========== ============================================================================= +version toolchain +========== ============================================================================= +``2.18.0`` ``intel/2016a`` +``2.20.0`` ``foss/2016a``, ``intel/2016a`` +``2.22.0`` ``foss/2016b``, ``intel/2016b`` +``2.26.0`` ``intel/2017a`` +``2.26.1`` ``foss/2018b``, ``intel/2017b`` +``2.27.1`` ``foss/2017b``, ``intel/2017b`` +``2.28.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a`` +``2.32.0`` ``GCCcore/8.2.0`` +``2.34.1`` ``GCCcore/8.3.0`` +``2.36.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========== ============================================================================= .. _list_software_ATLAS_373: @@ -1948,6 +2013,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_AUTO-07p_573: + +*AUTO-07p* +++++++++++ + +AUTO is a publicly available software for continuation and bifurcation problems in ordinary differential equations originally written in 1980 and widely used in the dynamical systems community. + +*homepage*: https://github.com/auto-07p + +========= ============== +version toolchain +========= ============== +``0.9.3`` ``foss/2021a`` +========= ============== + + .. _list_software_Autoconf_831: *Autoconf* @@ -1962,7 +2043,7 @@ version toolchain ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= ``2.68`` ``foss/2016b`` ``2.69`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.71`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``system`` +``2.71`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``system`` ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= @@ -2051,6 +2132,7 @@ version toolchain ``1.16.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ``1.16.2`` ``GCCcore/10.2.0`` ``1.16.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` +``1.16.4`` ``GCCcore/11.2.0`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -2104,6 +2186,7 @@ version toolchain ``20180311`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ``20200321`` ``GCCcore/10.2.0`` ``20210128`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` +``20210726`` ``GCCcore/11.2.0`` ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -2134,7 +2217,23 @@ version versionsuffix toolchain --- -:ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` +:ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` + + +.. _list_software_babl_401: + +*babl* +++++++ + +babl is pixel encoding and color space conversion engine in C + +*homepage*: https://www.gegl.org/babl + +========== ================== +version toolchain +========== ================== +``0.1.86`` ``GCCcore/10.3.0`` +========== ================== .. _list_software_Bader_478: @@ -2170,6 +2269,22 @@ version toolchain ========= =============== +.. _list_software_BAli-Phy_694: + +*BAli-Phy* +++++++++++ + +BAli-Phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. + +*homepage*: http://www.bali-phy.org/ + +========= ========== +version toolchain +========= ========== +``3.6.0`` ``system`` +========= ========== + + .. _list_software_bam-readcount_1314: *bam-readcount* @@ -2251,6 +2366,7 @@ version toolchain ``2.4.1`` ``intel/2017a`` ``2.5.0`` ``foss/2016b``, ``intel/2017b`` ``2.5.1`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018b`` +``2.5.2`` ``GCC/10.3.0`` ========= ================================================================================================================================================================================================================================================ @@ -2297,11 +2413,11 @@ Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal *homepage*: https://github.com/tseemann/barrnap -======= ==================================== -version toolchain -======= ==================================== -``0.9`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` -======= ==================================== +======= ===================================================== +version toolchain +======= ===================================================== +``0.9`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2020b`` +======= ===================================================== .. _list_software_basemap_729: @@ -2446,28 +2562,29 @@ Bazel is a build tool that builds code quickly and reliably. It is used to build *homepage*: https://bazel.io/ -========== ==================================== -version toolchain -========== ==================================== -``0.4.4`` ``system`` -``0.7.0`` ``GCCcore/6.4.0`` -``0.10.0`` ``GCCcore/6.4.0`` -``0.11.0`` ``GCCcore/6.4.0`` -``0.11.1`` ``GCCcore/6.4.0`` -``0.12.0`` ``GCCcore/6.4.0`` -``0.16.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``0.18.0`` ``GCCcore/7.3.0`` -``0.20.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``0.25.2`` ``GCCcore/8.2.0`` -``0.26.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.29.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``1.1.0`` ``GCCcore/8.3.0`` -``2.0.0`` ``GCCcore/8.3.0`` -``3.4.1`` ``GCCcore/8.3.0`` -``3.6.0`` ``GCCcore/9.3.0`` -``3.7.1`` ``GCCcore/8.3.0`` -``3.7.2`` ``GCCcore/10.2.0`` -========== ==================================== +========== ============= ====================================== +version versionsuffix toolchain +========== ============= ====================================== +``0.4.4`` ``system`` +``0.7.0`` ``GCCcore/6.4.0`` +``0.10.0`` ``GCCcore/6.4.0`` +``0.11.0`` ``GCCcore/6.4.0`` +``0.11.1`` ``GCCcore/6.4.0`` +``0.12.0`` ``GCCcore/6.4.0`` +``0.16.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``0.18.0`` ``GCCcore/7.3.0`` +``0.20.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``0.25.2`` ``GCCcore/8.2.0`` +``0.26.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.29.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.29.1`` ``-Java-1.8`` ``GCCcore/9.3.0`` +``1.1.0`` ``GCCcore/8.3.0`` +``2.0.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +``3.4.1`` ``GCCcore/8.3.0`` +``3.6.0`` ``GCCcore/9.3.0`` +``3.7.1`` ``GCCcore/8.3.0`` +``3.7.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========== ============= ====================================== .. _list_software_bbcp_407: @@ -2593,7 +2710,7 @@ version toolchain ``1.9`` ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ``1.11`` ``GCC/10.2.0`` -``1.12`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` ========== ========================================================================================= @@ -2623,14 +2740,14 @@ bcl2fastq Conversion Software both demultiplexes data and converts BCL files gen *homepage*: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html -========== ================== ============================================================================= -version versionsuffix toolchain -========== ================== ============================================================================= -``2.19.1`` ``-Python-2.7.12`` ``foss/2016b`` -``2.20.0`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``intel/2019a`` -``2.20.0`` ``-Python-2.7.12`` ``foss/2016b`` -``2.20.0`` ``-Python-2.7.14`` ``intel/2017b`` -========== ================== ============================================================================= +========== ================== ============================================================================================= +version versionsuffix toolchain +========== ================== ============================================================================================= +``2.19.1`` ``-Python-2.7.12`` ``foss/2016b`` +``2.20.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``intel/2019a`` +``2.20.0`` ``-Python-2.7.12`` ``foss/2016b`` +``2.20.0`` ``-Python-2.7.14`` ``intel/2017b`` +========== ================== ============================================================================================= .. _list_software_bcolz_538: @@ -2773,7 +2890,7 @@ version toolchain ``2.27.1`` ``GCCcore/6.4.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` ``2.28.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.29.2`` ``GCC/8.3.0``, ``GCC/9.3.0`` -``2.30.0`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``2.30.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` ========== ==================================================================================== @@ -2871,12 +2988,13 @@ A BGEN file format reader. It fully supports the BGEN format specifications 1.2 *homepage*: https://github.com/limix/bgen -========= ================= -version toolchain -========= ================= -``3.0.2`` ``GCCcore/7.3.0`` -``3.0.3`` ``GCCcore/9.3.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``3.0.2`` ``GCCcore/7.3.0`` +``3.0.3`` ``GCCcore/9.3.0`` +``4.1.3`` ``GCCcore/10.2.0`` +========= ================== .. _list_software_bgen-reader_1084: @@ -2967,6 +3085,7 @@ version toolchain ``2.34`` ``GCCcore/10.1.0``, ``GCCcore/9.3.0``, ``system`` ``2.35`` ``GCCcore/10.2.0``, ``system`` ``2.36.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/8.4.0``, ``GCCcore/9.4.0``, ``system`` +``2.37`` ``GCCcore/11.2.0``, ``system`` ========== ======================================================================================================================================================================================== @@ -3022,6 +3141,22 @@ version versionsuffix toolchain ======== ================ =============== +.. _list_software_Bio-SearchIO-hmmer_1659: + +*Bio-SearchIO-hmmer* +++++++++++++++++++++ + +Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with both version 2 and version 3 of the HMMER package from http://hmmer.org. + +*homepage*: https://metacpan.org/pod/Bio::SearchIO::hmmer3 + +========= ============== +version toolchain +========= ============== +``1.7.3`` ``GCC/10.2.0`` +========= ============== + + .. _list_software_bioawk_637: *bioawk* @@ -3031,11 +3166,11 @@ Bioawk is an extension to Brian Kernighan's awk, adding the support of several *homepage*: https://github.com/lh3/bioawk -======= ============== -version toolchain -======= ============== -``1.0`` ``foss/2018b`` -======= ============== +======= ============================== +version toolchain +======= ============================== +``1.0`` ``GCC/10.3.0``, ``foss/2018b`` +======= ============================== .. _list_software_biobambam2_972: @@ -3054,6 +3189,23 @@ version toolchain ========== =============== +.. _list_software_biogeme_728: + +*biogeme* ++++++++++ + +Biogeme is a open source Python package designed for the maximum likelihood estimation of parametric models in general, with a special emphasis on discrete choice models. + +*homepage*: https://pypi.python.org/pypi/biogeme + +========= ============== +version toolchain +========= ============== +``3.1.2`` ``foss/2021a`` +``3.2.8`` ``foss/2021a`` +========= ============== + + .. _list_software_biomart-perl_1230: *biomart-perl* @@ -3144,6 +3296,7 @@ version versionsuffix toolchain ``1.76`` ``-Python-2.7.18`` ``foss/2020b`` ``1.78`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.78`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.79`` ``foss/2021a`` ======== ================== =================================================== @@ -3235,7 +3388,7 @@ version toolchain ``3.5.3`` ``GCCcore/9.3.0``, ``system`` ``3.6.1`` ``GCCcore/10.1.0`` ``3.7.1`` ``GCCcore/10.2.0``, ``system`` -``3.7.6`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/9.4.0``, ``system`` +``3.7.6`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0``, ``system`` ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -3254,6 +3407,7 @@ version versionsuffix toolchain ``0.8.3`` ``-Python-2.7.15`` ``intel/2018b`` ``0.8.3`` ``-Python-3.6.6`` ``intel/2018b`` ``1.2.1`` ``-Python-3.7.4`` ``foss/2019b`` +``1.5.3`` ``-Python-2.7.16`` ``GCC/8.3.0`` ========= ================== =============== @@ -3398,17 +3552,18 @@ AMD's fork of BLIS. BLIS is a portable software framework for instantiating high *homepage*: https://developer.amd.com/amd-cpu-libraries/blas-library/ -========= ============= ===================================== -version versionsuffix toolchain -========= ============= ===================================== -``0.3.2`` ``GCC/7.3.0-2.30`` -``0.6.0`` ``GCC/8.3.0-2.32`` -``0.8.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``0.8.1`` ``GCCcore/10.3.0`` -``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` -``2.2`` ``-amd`` ``GCCcore/9.3.0`` -``3.0`` ``-amd`` ``GCCcore/10.3.0`` -========= ============= ===================================== +========= ============= ====================================== +version versionsuffix toolchain +========= ============= ====================================== +``0.3.2`` ``GCC/7.3.0-2.30`` +``0.6.0`` ``GCC/8.3.0-2.32`` +``0.8.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``0.8.1`` ``GCCcore/10.3.0`` +``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` +``2.2`` ``-amd`` ``GCCcore/9.3.0`` +``3.0`` ``-amd`` ``GCCcore/10.3.0`` +``3.0.1`` ``-amd`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ============= ====================================== .. _list_software_Blitz++_603: @@ -3462,7 +3617,7 @@ version toolchain ``1.14.4`` ``GCCcore/7.3.0`` ``1.17.0`` ``GCCcore/8.2.0`` ``1.17.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.21.0`` ``GCCcore/10.2.0`` +``1.21.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========== ================================================================== @@ -3663,6 +3818,7 @@ version versionsuffix toolchain ``1.72.0`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a`` ``1.72.0`` ``-no_mpi`` ``GCCcore/9.3.0`` ``1.74.0`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``1.76.0`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` ========== ================== ==================================================================== @@ -3751,6 +3907,7 @@ version toolchain ``2.3.5.1`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` ``2.4.1`` ``GCC/9.3.0`` ``2.4.2`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``2.4.4`` ``GCC/10.3.0`` =========== ====================================================================================================== @@ -3799,6 +3956,7 @@ Resource monitor that shows usage and stats for processor, memory, disks, networ version toolchain ========== ================== ``1.0.60`` ``GCCcore/10.2.0`` +``1.0.67`` ``GCCcore/10.3.0`` ========== ================== @@ -3877,11 +4035,11 @@ Brotli is a generic-purpose lossless compression algorithm that compresses data *homepage*: https://github.com/google/brotli -========= ================= -version toolchain -========= ================= -``1.0.9`` ``GCCcore/8.3.0`` -========= ================= +========= ===================================== +version toolchain +========= ===================================== +``1.0.9`` ``GCCcore/10.3.0``, ``GCCcore/8.3.0`` +========= ===================================== .. _list_software_bsddb3_562: @@ -3951,6 +4109,22 @@ version versionsuffix toolchain ========= ================== ====================================== +.. _list_software_BuDDy_440: + +*BuDDy* ++++++++ + +A Binary Decision Diagram library, with many highly efficient vectorized BDD operations, dynamic variable reordering, automated garbage collection, a C++ interface with automatic reference counting, and much more. + +*homepage*: http://buddy.sourceforge.net/ + +======= ================== +version toolchain +======= ================== +``2.4`` ``GCCcore/10.2.0`` +======= ================== + + .. _list_software_BUFRLIB_518: *BUFRLIB* @@ -4130,17 +4304,18 @@ The bx-python project is a Python library and associated set of scripts to allow *homepage*: https://github.com/bxlab/bx-python -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``0.7.4`` ``-Python-2.7.12`` ``foss/2016b`` -``0.7.4`` ``-Python-2.7.13`` ``intel/2017a`` -``0.8.1`` ``-Python-2.7.14`` ``intel/2018a`` -``0.8.2`` ``-Python-3.6.6`` ``foss/2018b`` -``0.8.4`` ``foss/2019a`` -``0.8.8`` ``-Python-3.7.4`` ``foss/2019b`` -``0.8.9`` ``-Python-3.8.2`` ``foss/2020a`` -========= ================== =============== +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``0.7.4`` ``-Python-2.7.12`` ``foss/2016b`` +``0.7.4`` ``-Python-2.7.13`` ``intel/2017a`` +``0.8.1`` ``-Python-2.7.14`` ``intel/2018a`` +``0.8.2`` ``-Python-3.6.6`` ``foss/2018b`` +``0.8.4`` ``foss/2019a`` +``0.8.8`` ``-Python-3.7.4`` ``foss/2019b`` +``0.8.9`` ``-Python-3.8.2`` ``foss/2020a`` +``0.8.11`` ``foss/2021a`` +========== ================== =============== .. _list_software_BXH_XCEDE_TOOLS_1178: @@ -4206,7 +4381,7 @@ bzip2 is a freely available, patent free, high-quality data compressor. It typi version toolchain ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.0.6`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -4216,7 +4391,23 @@ version toolchain --- -:ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` + + +.. _list_software_c-ares_571: + +*c-ares* +++++++++ + +c-ares is a C library for asynchronous DNS requests (including name resolves) + +*homepage*: https://c-ares.haxx.se + +========== ================== +version toolchain +========== ================== +``1.17.2`` ``GCCcore/10.3.0`` +========== ================== .. _list_software_C3D_186: @@ -4295,16 +4486,16 @@ Cairo is a 2D graphics library with support for multiple output devices. Curren *homepage*: https://cairographics.org -=========== ================ =============================================================================================== -version versionsuffix toolchain -=========== ================ =============================================================================================== -``1.14.6`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``1.14.6`` ``-GLib-2.48.0`` ``foss/2016a``, ``intel/2016a`` -``1.14.8`` ``intel/2017a`` -``1.14.10`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017b`` -``1.14.12`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.16.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -=========== ================ =============================================================================================== +=========== ================ =================================================================================================================== +version versionsuffix toolchain +=========== ================ =================================================================================================================== +``1.14.6`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``1.14.6`` ``-GLib-2.48.0`` ``foss/2016a``, ``intel/2016a`` +``1.14.8`` ``intel/2017a`` +``1.14.10`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017b`` +``1.14.12`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.16.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +=========== ================ =================================================================================================================== .. _list_software_cairomm_744: @@ -4509,12 +4700,13 @@ Cartopy is a Python package designed to make drawing maps for data analysis and *homepage*: https://scitools.org.uk/cartopy/docs/latest/ -========== ================= ============== -version versionsuffix toolchain -========== ================= ============== -``0.18.0`` ``-Python-3.7.4`` ``foss/2019b`` -``0.18.0`` ``-Python-3.8.2`` ``foss/2020a`` -========== ================= ============== +================ ================= =============================== +version versionsuffix toolchain +================ ================= =============================== +``0.18.0`` ``-Python-3.7.4`` ``foss/2019b`` +``0.18.0`` ``-Python-3.8.2`` ``foss/2020a`` +``0.19.0.post1`` ``foss/2020b``, ``intel/2020b`` +================ ================= =============================== .. _list_software_CaSpER_510: @@ -4663,6 +4855,7 @@ Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming version toolchain ========== ============== ``2.10.3`` ``foss/2018b`` +``2.10.5`` ``foss/2020b`` ========== ============== @@ -4871,7 +5064,7 @@ version toolchain ``1.9.2`` ``intel/2017b`` ``1.9.5`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``1.9.8`` ``intel/2019b`` -``1.9.10`` ``gompi/2020b`` +``1.9.10`` ``gompi/2020b``, ``gompi/2021a`` ========== ================================================= @@ -4982,6 +5175,22 @@ version toolchain ========= ========== +.. _list_software_CellRank_780: + +*CellRank* +++++++++++ + +CellRank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data. It contains two main modules: kernels compute cell-cell transition probabilities and estimators generate hypothesis based on these. + +*homepage*: https://cellrank.readthedocs.io/en/stable/ + +========= ============== +version toolchain +========= ============== +``1.4.0`` ``foss/2021a`` +========= ============== + + .. _list_software_Centrifuge_1036: *Centrifuge* @@ -4995,6 +5204,7 @@ Classifier for metagenomic sequences version toolchain ============== =============================== ``1.0.3`` ``foss/2018b`` +``1.0.4`` ``gompi/2020b`` ``1.0.4-beta`` ``foss/2018b``, ``gompi/2020a`` ============== =============================== @@ -5113,6 +5323,7 @@ version versionsuffix toolchain ``4.11.1`` ``-Python-3.6.6`` ``foss/2018b`` ``4.14`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``4.14.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``4.14.3`` ``gompi/2021a`` ``4.14.3`` ``-Python-3.8.2`` ``gompi/2020a``, ``iimpi/2020a`` ``5.2`` ``gompi/2020b`` ========== ================== ================================ @@ -5147,6 +5358,7 @@ The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that version toolchain ========== ============== ``0.60.2`` ``foss/2018b`` +``0.60.3`` ``foss/2020b`` ========== ============== @@ -5197,6 +5409,7 @@ version toolchain ========= ==================================== ``2.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.1.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.2.0`` ``GCCcore/10.2.0`` ========= ==================================== @@ -5608,6 +5821,7 @@ version versionsuffix toolchain ``10.0.1`` ``GCCcore/9.3.0`` ``11.0.0`` ``GCCcore/9.3.0`` ``11.0.1`` ``GCCcore/10.2.0``, ``gcccuda/2020b`` +``12.0.1`` ``GCCcore/10.3.0`` ========== ================== ====================================== @@ -5729,6 +5943,7 @@ Clp (Coin-or linear programming) is an open-source linear programming solver. It version toolchain ========== ============== ``1.17.3`` ``foss/2018b`` +``1.17.6`` ``foss/2020b`` ========== ============== @@ -5741,12 +5956,12 @@ Clustal Omega is a multiple sequence alignment program for proteins. It produce *homepage*: http://www.clustal.org/omega/ -========= =============================================================== -version toolchain -========= =============================================================== -``1.2.0`` ``foss/2016b`` -``1.2.4`` ``GCC/8.3.0``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -========= =============================================================== +========= ============================================================================================================= +version toolchain +========= ============================================================================================================= +``1.2.0`` ``foss/2016b`` +``1.2.4`` ``GCC/10.3.0``, ``GCC/8.3.0``, ``foss/2018b``, ``intel-compilers/2021.2.0``, ``intel/2018a``, ``intel/2018b`` +========= ============================================================================================================= .. _list_software_ClustalW2_865: @@ -5758,11 +5973,11 @@ ClustalW2 is a general purpose multiple sequence alignment program for DNA or pr *homepage*: https://www.ebi.ac.uk/Tools/msa/clustalw2/ -======= =========================================================================================================================== -version toolchain -======= =========================================================================================================================== -``2.1`` ``foss/2016b``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b``, ``intel/2020a`` -======= =========================================================================================================================== +======= =========================================================================================================================================== +version toolchain +======= =========================================================================================================================================== +``2.1`` ``GCC/10.3.0``, ``foss/2016b``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b``, ``intel/2020a`` +======= =========================================================================================================================================== .. _list_software_Cluster-Buster_1412: @@ -5845,6 +6060,7 @@ version toolchain ``3.16.4`` ``GCCcore/9.3.0`` ``3.18.4`` ``GCCcore/10.2.0``, ``system`` ``3.20.1`` ``GCCcore/10.3.0`` +``3.21.1`` ``GCCcore/11.2.0`` ========== ================================================================================================================================================= @@ -5899,6 +6115,22 @@ version toolchain ========= ============== +.. _list_software_Co-phylog_882: + +*Co-phylog* ++++++++++++ + +Co-phylog: an assembly-free phylogenomic approach for closely related organisms H Yi, L Jin Nucleic acids research 41 (7), e75-e75 + +*homepage*: https://github.com/yhg926/co-phylog + +============ ================== +version toolchain +============ ================== +``20201012`` ``GCC/7.3.0-2.30`` +============ ================== + + .. _list_software_CoCoALib_700: *CoCoALib* @@ -5948,6 +6180,22 @@ version versionsuffix toolchain ============ ============= =============== +.. _list_software_Coin_393: + +*Coin* +++++++ + +Coin is an OpenGL-based, 3D graphics library that has its roots in the Open Inventor 2.1 API, which Coin still is compatible with. + +*homepage*: https://coin3d.github.io + +========= ============== +version toolchain +========= ============== +``4.0.0`` ``GCC/10.3.0`` +========= ============== + + .. _list_software_CoinUtils_922: *CoinUtils* @@ -5961,6 +6209,7 @@ CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functi version toolchain ========== ================================= ``2.11.3`` ``GCCcore/7.3.0``, ``foss/2018b`` +``2.11.4`` ``GCCcore/10.2.0`` ========== ================================= @@ -6082,6 +6331,7 @@ version versionsuffix toolchain ``1.3.0`` ``-nodejs-4.4.7`` ``foss/2016a`` ``3.1.1`` ``-nodejs-8.9.4`` ``foss/2017a`` ``4.2.1`` ``GCCcore/10.2.0`` +``4.4.0`` ``GCCcore/10.3.0`` ========= ================= ================== @@ -6116,6 +6366,7 @@ Copy number and genotype annotation from whole genome and whole exome sequencin version toolchain ======== ======================================== ``11.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1`` +``11.6`` ``GCC/10.2.0`` ======== ======================================== @@ -6212,11 +6463,12 @@ Coverage.py is a tool for measuring code coverage of Python programs. It monito *homepage*: https://coverage.readthedocs.io -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``4.5.1`` ``-Python-2.7.14`` ``intel/2017b`` -========= ================== =============== +========= ================== ================== +version versionsuffix toolchain +========= ================== ================== +``4.5.1`` ``-Python-2.7.14`` ``intel/2017b`` +``5.5`` ``GCCcore/10.2.0`` +========= ================== ================== .. _list_software_cowsay_662: @@ -6244,19 +6496,19 @@ CP2K is a freely available (GPL) program, written in Fortran 95, to perform atom *homepage*: https://www.cp2k.org/ -======= ============= ================================================================== -version versionsuffix toolchain -======= ============= ================================================================== -``3.0`` ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` -``3.0`` ``-psmp`` ``intel/2016b`` -``4.1`` ``intel/2016b`` -``4.1`` ``-psmp`` ``foss/2016b`` -``5.1`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a``, ``intel/2020a`` -``6.1`` ``foss/2019a``, ``intel/2018a``, ``intel/2020a`` -``7.1`` ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` -``7.1`` ``-psmp`` ``foss/2020b`` -``8.1`` ``foss/2020b`` -======= ============= ================================================================== +======= ============= ================================================================================= +version versionsuffix toolchain +======= ============= ================================================================================= +``3.0`` ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` +``3.0`` ``-psmp`` ``intel/2016b`` +``4.1`` ``intel/2016b`` +``4.1`` ``-psmp`` ``foss/2016b`` +``5.1`` ``foss/2018a``, ``foss/2020a``, ``intel/2017b``, ``intel/2018a``, ``intel/2020a`` +``6.1`` ``foss/2019a``, ``intel/2018a``, ``intel/2020a`` +``7.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` +``7.1`` ``-psmp`` ``foss/2020b`` +``8.1`` ``foss/2020b`` +======= ============= ================================================================================= .. _list_software_CPB_213: @@ -6301,12 +6553,28 @@ CppUnit is the C++ port of the famous JUnit framework for unit testing. *homepage*: https://freedesktop.org/wiki/Software/cppunit/ -========== ==================================================== -version toolchain -========== ==================================================== -``1.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a`` -``1.15.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ==================================================== +========== ======================================================== +version toolchain +========== ======================================================== +``1.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a`` +``1.15.1`` ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ======================================================== + + +.. _list_software_cppy_444: + +*cppy* +++++++ + +A small C++ header library which makes it easier to write Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations. + +*homepage*: https://github.com/nucleic/cppy + +========= ================== +version toolchain +========= ================== +``1.1.0`` ``GCCcore/10.3.0`` +========= ================== .. _list_software_cram_419: @@ -6423,6 +6691,22 @@ version versionsuffix toolchain ========= =============== =============== +.. _list_software_CREST_385: + +*CREST* ++++++++ + +CREST is an utility/driver program for the xtb program. Originally it was designed as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb program) and tool for the creation and analysation of structure ensembles. + +*homepage*: https://xtb-docs.readthedocs.io/en/latest/crest.html + +======== =============== +version toolchain +======== =============== +``2.11`` ``intel/2021a`` +======== =============== + + .. _list_software_CRF++_305: *CRF++* @@ -6439,19 +6723,37 @@ version toolchain ======== ========================================================= +.. _list_software_CRISPR-DAV_731: + +*CRISPR-DAV* +++++++++++++ + +CRISPR-DAV is a pipeline to analyze amplicon-based NGS data of CRISPR clones in a high throughput manner. + +*homepage*: https://github.com/pinetree1/crispr-dav/ + +========= ============== +version toolchain +========= ============== +``2.3.4`` ``foss/2020b`` +========= ============== + + .. _list_software_CRISPResso2_959: *CRISPResso2* +++++++++++++ -CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. +CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. -*homepage*: https://github.com/pinellolab/CRISPResso2 +*homepage*: https://github.com/pinellolab/CRISPResso2/ ========== ================== ============== version versionsuffix toolchain ========== ================== ============== ``2.0.44`` ``-Python-2.7.16`` ``foss/2019b`` +``2.1.2`` ``-Python-2.7.18`` ``foss/2020b`` +``2.2.1`` ``foss/2020b`` ========== ================== ============== @@ -6568,6 +6870,22 @@ version versionsuffix toolchain ========= ================= ================================== +.. _list_software_CSBLAST_524: + +*CSBLAST* ++++++++++ + +Context-specific extension of BLAST that significantly improves sensitivity and alignment quality. + +*homepage*: https://github.com/soedinglab/csblast/ + +========= ================= +version toolchain +========= ================= +``2.2.3`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_cscope_637: *cscope* @@ -6626,12 +6944,13 @@ Program for finding CTFs of electron micrographs. *homepage*: https://grigoriefflab.umassmed.edu/ctffind4 -========== ====================================================== -version toolchain -========== ====================================================== -``4.1.13`` ``foss/2019a``, ``fosscuda/2019a``, ``fosscuda/2019b`` -``4.1.14`` ``foss/2019b``, ``fosscuda/2019b``, ``fosscuda/2020b`` -========== ====================================================== +========== ================ ====================================================== +version versionsuffix toolchain +========== ================ ====================================================== +``4.1.13`` ``foss/2019a``, ``fosscuda/2019a``, ``fosscuda/2019b`` +``4.1.14`` ``foss/2019b``, ``fosscuda/2019b``, ``fosscuda/2020b`` +``4.1.14`` ``-CUDA-11.3.1`` ``foss/2021a`` +========== ================ ====================================================== .. _list_software_Cube_383: @@ -6659,12 +6978,12 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is *homepage*: https://www.scalasca.org/software/cube-4.x/download.html -========= ==================================== -version toolchain -========= ==================================== -``4.4.4`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` -``4.6`` ``GCCcore/10.2.0`` -========= ==================================== +========= ====================================== +version toolchain +========= ====================================== +``4.4.4`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +``4.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_CubeLib_662: @@ -6680,7 +6999,7 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is version toolchain ========= ======================================================= ``4.4.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.6`` ``GCCcore/10.2.0`` +``4.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ======================================================= @@ -6697,7 +7016,7 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is version toolchain ========= =========================================================================== ``4.4.3`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.6`` ``GCCcore/10.2.0`` +``4.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= =========================================================================== @@ -6732,6 +7051,8 @@ version toolchain ``10.2.89`` ``GCC/8.3.0`` ``11.0.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` ``11.1.1`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``11.3.1`` ``system`` +``11.4.1`` ``system`` ================= ========================================================================== @@ -6752,7 +7073,6 @@ version toolchain ``11.2.1`` ``system`` ``11.2.2`` ``system`` ``11.3.0`` ``system`` -``11.3.1`` ``system`` ========== ========== @@ -6793,6 +7113,7 @@ version versionsuffix toolchain ``8.1.0.77`` ``-CUDA-11.2.1`` ``system`` ``8.1.1.33`` ``-CUDA-11.2.1`` ``system`` ``8.2.1.32`` ``-CUDA-11.3.1`` ``system`` +``8.2.2.26`` ``-CUDA-11.4.1`` ``system`` ============ ================== =========================================================== @@ -6878,6 +7199,7 @@ version toolchain ``7.69.1`` ``GCCcore/9.3.0`` ``7.72.0`` ``GCCcore/10.2.0`` ``7.76.0`` ``GCCcore/10.3.0`` +``7.78.0`` ``GCCcore/11.2.0`` ========== =================================================================================== @@ -6925,6 +7247,7 @@ version versionsuffix toolchain ``2.8`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``2.10`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``2.10`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``3.4`` ``GCCcore/10.3.0`` ========= ================== ================================================ @@ -6970,15 +7293,15 @@ CVXOPT is a free software package for convex optimization based on the Python pr *homepage*: https://cvxopt.org -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``1.1.9`` ``-Python-2.7.13`` ``intel/2017a`` -``1.2.1`` ``-Python-3.6.4`` ``intel/2018a`` -``1.2.3`` ``foss/2019a`` -``1.2.4`` ``-Python-3.7.4`` ``intel/2019b`` -``1.2.6`` ``foss/2020b`` -========= ================== =============== +========= ================== ============================== +version versionsuffix toolchain +========= ================== ============================== +``1.1.9`` ``-Python-2.7.13`` ``intel/2017a`` +``1.2.1`` ``-Python-3.6.4`` ``intel/2018a`` +``1.2.3`` ``foss/2019a`` +``1.2.4`` ``-Python-3.7.4`` ``intel/2019b`` +``1.2.6`` ``foss/2020b``, ``foss/2021a`` +========= ================== ============================== .. _list_software_CVXPY_410: @@ -7094,7 +7417,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` .. _list_software_dadi_402: @@ -7286,16 +7609,16 @@ Berkeley DB enables the development of custom data management solutions, withou *homepage*: http://www.oracle.com/technetwork/products/berkeleydb -=========== ======================================================= -version toolchain -=========== ======================================================= -``4.8.30`` ``intel/2016a`` -``6.2.23`` ``foss/2016a`` -``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` -``18.1.25`` ``GCCcore/7.3.0`` -``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``18.1.40`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -=========== ======================================================= +=========== ========================================================================= +version toolchain +=========== ========================================================================= +``4.8.30`` ``intel/2016a`` +``6.2.23`` ``foss/2016a`` +``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` +``18.1.25`` ``GCCcore/7.3.0`` +``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``18.1.40`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +=========== ========================================================================= .. _list_software_DB_File_613: @@ -7366,19 +7689,19 @@ D-Bus is a message bus system, a simple way for applications to talk to one ano *homepage*: http://dbus.freedesktop.org/ -=========== ====================================== -version toolchain -=========== ====================================== -``1.10.8`` ``foss/2016a``, ``intel/2016a`` -``1.10.12`` ``intel/2016b`` -``1.10.20`` ``GCCcore/6.4.0`` -``1.11.20`` ``intel/2017a`` -``1.13.0`` ``intel/2017b`` -``1.13.6`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.13.8`` ``GCCcore/8.2.0`` -``1.13.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.13.18`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -=========== ====================================== +=========== ========================================================== +version toolchain +=========== ========================================================== +``1.10.8`` ``foss/2016a``, ``intel/2016a`` +``1.10.12`` ``intel/2016b`` +``1.10.20`` ``GCCcore/6.4.0`` +``1.11.20`` ``intel/2017a`` +``1.13.0`` ``intel/2017b`` +``1.13.6`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.13.8`` ``GCCcore/8.2.0`` +``1.13.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.13.18`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +=========== ========================================================== .. _list_software_dbus-glib_889: @@ -7695,11 +8018,11 @@ DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock *homepage*: http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english -========= ============================== -version toolchain -========= ============================== -``3.2.0`` ``GCC/8.3.0``, ``intel/2019a`` -========= ============================== +========= ===================================================================================== +version toolchain +========= ===================================================================================== +``3.2.0`` ``GCC/8.3.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel/2019a`` +========= ===================================================================================== .. _list_software_DFTB+_331: @@ -7737,6 +8060,22 @@ version toolchain ======= ============= +.. _list_software_DGL_215: + +*DGL* ++++++ + +DGL is an easy-to-use, high performance and scalable Python package for deep learning on graphs. DGL is framework agnostic, meaning if a deep graph model is a component of an end-to-end application, the rest of the logics can be implemented in any major frameworks, such as PyTorch, Apache MXNet or TensorFlow. + +*homepage*: https://www.dgl.ai + +========= =============================== ================== +version versionsuffix toolchain +========= =============================== ================== +``0.6.1`` ``-Python-3.7.4-PyTorch-1.8.1`` ``fosscuda/2019b`` +========= =============================== ================== + + .. _list_software_DIAL_282: *DIAL* @@ -7772,6 +8111,7 @@ version toolchain ``2.0.4`` ``GCC/9.3.0`` ``2.0.6`` ``GCC/7.3.0-2.30`` ``2.0.7`` ``GCC/10.2.0`` +``2.0.11`` ``GCC/10.3.0`` ========== ================================================================ @@ -7892,6 +8232,22 @@ version versionsuffix toolchain ========== ================== =============== +.. _list_software_DistributedStream_1775: + +*DistributedStream* ++++++++++++++++++++ + +A MPI distributed stream benchmark, useful to identifying nodes with poor memory performance and characterising memory bandwidth variation over systems. + +*homepage*: https://github.com/adrianjhpc/DistributedStream + +======= =============== +version toolchain +======= =============== +``1.0`` ``gompi/2021a`` +======= =============== + + .. _list_software_DL_POLY_4_710: *DL_POLY_4* @@ -8087,13 +8443,13 @@ Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles *homepage*: https://github.com/google/double-conversion -========= ========================================================= -version toolchain -========= ========================================================= -``3.0.3`` ``foss/2018a`` -``3.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -========= ========================================================= +========= ============================================================================= +version toolchain +========= ============================================================================= +``3.0.3`` ``foss/2018a`` +``3.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========= ============================================================================= .. _list_software_DoubletFinder_1319: @@ -8133,7 +8489,7 @@ version toolchain ``1.8.16`` ``GCCcore/8.3.0`` ``1.8.17`` ``GCCcore/9.3.0`` ``1.8.20`` ``GCCcore/10.2.0`` -``1.9.1`` ``GCCcore/10.3.0`` +``1.9.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` =========== ======================================================================================================================================================= @@ -8166,6 +8522,7 @@ Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare d version versionsuffix toolchain ========= ============= ============== ``1.0.3`` ``-R-4.0.3`` ``foss/2020b`` +``1.1.0`` ``-R-4.0.3`` ``foss/2020b`` ========= ============= ============== @@ -8242,11 +8599,12 @@ Fast calculation of the ABBA-BABA statistics across many populations/species *homepage*: https://github.com/millanek/Dsuite -============ ======================================== -version toolchain -============ ======================================== -``20190713`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -============ ======================================== +============ ============================================ +version toolchain +============ ============================================ +``20190713`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``20210718`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` +============ ============================================ .. _list_software_dtcmp_536: @@ -8254,14 +8612,15 @@ version toolchain *dtcmp* +++++++ -Datatype Compare (DTCMP) Library for sorting and ranking distributed data using MPI. +The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined comparison operations to compare the values of two items which can be arbitrary MPI datatypes. Using these comparison operations, the library provides various routines for manipulating data, which may be distributed over the processes of an MPI communicator. -*homepage*: https://github.com/llnl/dtcmp +*homepage*: https://github.com/LLNL/dtcmp ========= ================================================================== version toolchain ========= ================================================================== ``1.1.0`` ``gompi/2019a``, ``gompi/2020a``, ``iimpi/2019a``, ``iimpi/2020a`` +``1.1.2`` ``gompi/2020b`` ========= ================================================================== @@ -8304,7 +8663,7 @@ version versionsuffix toolchain --- -:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Excel-Writer-XLSX_1559` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_E-ANTIC_481: @@ -8450,6 +8809,7 @@ version toolchain ``4.3.3`` ``system`` ``4.3.4`` ``system`` ``4.4.0`` ``system`` +``4.4.1`` ``system`` ========== ========== @@ -8490,6 +8850,7 @@ version versionsuffix toolchain ``2.17.0`` ``foss/2018b``, ``gompi/2019b`` ``2.18.0`` ``gompi/2020a`` ``2.20.0`` ``gompi/2020b`` +``2.22.1`` ``gompi/2021a`` ========== ================== ================================ @@ -8604,7 +8965,7 @@ version toolchain ``3.3.5`` ``system`` ``3.3.7`` ``GCCcore/9.3.0``, ``system`` ``3.3.8`` ``GCCcore/10.2.0`` -``3.3.9`` ``GCCcore/10.3.0`` +``3.3.9`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== =========================================== @@ -8652,13 +9013,13 @@ The elfutils project provides libraries and tools for ELF files and DWARF data. *homepage*: https://elfutils.org/ -========= ======================================================== -version toolchain -========= ======================================================== -``0.182`` ``GCCcore/9.3.0`` -``0.183`` ``GCCcore/10.2.0`` -``0.185`` ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= ======================================================== +========= ============================================================================ +version toolchain +========= ============================================================================ +``0.182`` ``GCCcore/9.3.0`` +``0.183`` ``GCCcore/10.2.0`` +``0.185`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ============================================================================ .. _list_software_Elk_284: @@ -8677,6 +9038,7 @@ version toolchain ``4.3.6`` ``intel/2017a`` ``6.3.2`` ``intel/2019b`` ``7.0.12`` ``foss/2020b`` +``7.2.42`` ``foss/2021a`` ========== =============== @@ -8966,6 +9328,7 @@ version versionsuffix toolchain ``7.1.0r`` ``foss/2018b``, ``foss/2019a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``8.0.0`` ``foss/2019b``, ``intel/2019b`` ``8.0.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` +``8.1.1`` ``foss/2021a``, ``intel/2021a`` ============ ================ ================================================================================= @@ -9134,6 +9497,22 @@ version toolchain ======= ============== +.. _list_software_Excel-Writer-XLSX_1559: + +*Excel-Writer-XLSX* ++++++++++++++++++++ + +The Excel::Writer::XLSX module can be used to create an Excel file in the 2007+ XLSX format. Multiple worksheets can be added to a workbook and formatting can be applied to cells. Text, numbers, and formulas can be written to the cells. + +*homepage*: https://metacpan.org/pod/Excel::Writer::XLSX + +======== ============== +version toolchain +======== ============== +``1.09`` ``foss/2020b`` +======== ============== + + .. _list_software_ExifTool_810: *ExifTool* @@ -9202,6 +9581,7 @@ version toolchain ``2.2.6`` ``GCCcore/8.2.0`` ``2.2.7`` ``GCCcore/8.3.0`` ``2.2.9`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``2.4.1`` ``GCCcore/11.2.0`` ========= ========================================================================================================================= @@ -9261,7 +9641,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -9403,11 +9783,11 @@ Utilities for indexing and sequence extraction from FASTA files. *homepage*: https://github.com/ekg/fastahack -========= ================= -version toolchain -========= ================= -``1.0.0`` ``GCCcore/9.3.0`` -========= ================= +========= ===================================== +version toolchain +========= ===================================== +``1.0.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========= ===================================== .. _list_software_FastaIndex_999: @@ -9521,11 +9901,12 @@ This package provides a number of small and efficient programs to perform commo *homepage*: https://homes.cs.washington.edu/~dcjones/fastq-tools/ -======= ============================== -version toolchain -======= ============================== -``0.8`` ``foss/2016b``, ``foss/2018b`` -======= ============================== +========= ============================== +version toolchain +========= ============================== +``0.8`` ``foss/2016b``, ``foss/2018b`` +``0.8.3`` ``GCC/10.3.0`` +========= ============================== .. _list_software_FastQ_Screen_1182: @@ -9700,11 +10081,11 @@ The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/ *homepage*: http://hannonlab.cshl.edu/fastx_toolkit/ -========== ================================================================================= -version toolchain -========== ================================================================================= -``0.0.14`` ``GCC/9.3.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2018a`` -========== ================================================================================= +========== ================================================================================================= +version toolchain +========== ================================================================================================= +``0.0.14`` ``GCC/10.3.0``, ``GCC/9.3.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2018a`` +========== ================================================================================================= .. _list_software_fatslim_752: @@ -9739,6 +10120,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_FBPIC_356: + +*FBPIC* ++++++++ + +FBPIC (Fourier-Bessel Particle-In-Cell) is a Particle-In-Cell (PIC) code for relativistic plasma physics. It is especially well-suited for physical simulations of laser-wakefield acceleration and plasma-wakefield acceleration. + +*homepage*: https://fbpic.github.io/ + +========== ================== +version toolchain +========== ================== +``0.20.3`` ``fosscuda/2020b`` +========== ================== + + .. _list_software_FCC_204: *FCC* @@ -9870,11 +10267,11 @@ Standalone C library for assembling Illumina short reads in small regions. *homepage*: https://github.com/lh3/fermi-lite -============ ================= -version toolchain -============ ================= -``20190320`` ``GCCcore/9.3.0`` -============ ================= +============ ===================================== +version toolchain +============ ===================================== +``20190320`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +============ ===================================== .. _list_software_Ferret_616: @@ -9990,7 +10387,7 @@ version toolchain ``4.2.1`` ``GCCcore/8.3.0`` ``4.2.2`` ``GCCcore/9.3.0`` ``4.3.1`` ``GCCcore/10.2.0`` -``4.3.2`` ``GCCcore/10.3.0`` +``4.3.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` =========== =================================================== @@ -10064,7 +10461,7 @@ version versionsuffix toolchain ``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``iomkl/2018b`` ``3.3.8`` ``-amd`` ``gompi/2020a`` ``3.3.8`` ``-serial`` ``GCC/9.3.0`` -``3.3.9`` ``gompi/2021a``, ``intel/2021a`` +``3.3.9`` ``gompi/2021.07``, ``gompi/2021a``, ``intel/2021a`` ========= ============= ======================================================================================================================================================================================================================================================================================================================= @@ -10204,6 +10601,7 @@ version toolchain ``5.35`` ``GCCcore/7.3.0`` ``5.38`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``5.39`` ``GCCcore/10.2.0`` +``5.40`` ``GCCcore/10.3.0`` ======== ==================================== @@ -10216,11 +10614,12 @@ filevercmp function as in sort --version-sort. *homepage*: https://github.com/ekg/filevercmp -============ ================= -version toolchain -============ ================= -``20141119`` ``GCCcore/9.3.0`` -============ ================= +============ ================== +version toolchain +============ ================== +``20141119`` ``GCCcore/9.3.0`` +``20191210`` ``GCCcore/10.2.0`` +============ ================== .. _list_software_Filtlong_831: @@ -10334,6 +10733,7 @@ version versionsuffix toolchain ``1.8.13`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``1.8.13.post1`` ``-Python-3.7.2`` ``foss/2019a`` ``1.8.16`` ``-Python-3.8.2`` ``foss/2020a`` +``1.8.20`` ``foss/2020b``, ``intel/2020b`` ================ ================= =================================================== @@ -10442,11 +10842,11 @@ FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but l *homepage*: https://xiph.org/flac/ -========= ====================================== -version toolchain -========= ====================================== -``1.3.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========= ====================================== +========= ========================================================== +version toolchain +========= ========================================================== +``1.3.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ========================================================== .. _list_software_FLAIR_366: @@ -10496,7 +10896,7 @@ FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate softwa version toolchain ========== ============================================================= ``1.2.11`` ``GCC/8.3.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b`` -``2.2.00`` ``foss/2018b`` +``2.2.00`` ``foss/2018b``, ``foss/2020b`` ========== ============================================================= @@ -10516,6 +10916,7 @@ version versionsuffix toolchain ``1.1.2`` ``GCCcore/10.2.0`` ``1.1.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``1.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``1.1.4`` ``GCCcore/10.3.0`` ========= ================= ================== @@ -10579,17 +10980,17 @@ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, some *homepage*: http://flex.sourceforge.net/ -========== ======================================================================================================================================================================================================================================================================================================================================================================================================= -version toolchain -========== ======================================================================================================================================================================================================================================================================================================================================================================================================= -``2.5.35`` ``system`` -``2.5.38`` ``GCC/4.8.2`` -``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` -``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.6.2`` ``intel/2016b`` -``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` -``2.6.4`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``system`` -========== ======================================================================================================================================================================================================================================================================================================================================================================================================= +========== =========================================================================================================================================================================================================================================================================================================================================================================================================================== +version toolchain +========== =========================================================================================================================================================================================================================================================================================================================================================================================================================== +``2.5.35`` ``system`` +``2.5.38`` ``GCC/4.8.2`` +``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` +``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +``2.6.2`` ``intel/2016b`` +``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` +``2.6.4`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``system`` +========== =========================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_Flexbar_708: @@ -10617,11 +11018,11 @@ FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK *homepage*: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release -========= ============== -version toolchain -========= ============== -``3.0.4`` ``GCC/10.3.0`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``3.0.4`` ``GCC/10.3.0``, ``GCC/11.2.0`` +========= ============================== .. _list_software_FlexiDot_799: @@ -10663,12 +11064,13 @@ version versionsuffix toolchain FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested. -*homepage*: http://www.flintlib.org +*homepage*: https://www.flintlib.org/ ========= =============================================================================================== version toolchain ========= =============================================================================================== ``2.5.2`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` +``2.7.1`` ``GCC/10.3.0`` ========= =============================================================================================== @@ -10688,6 +11090,7 @@ version toolchain ``1.3.4`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b`` ``1.3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``1.3.6`` ``GCCcore/10.3.0`` +``1.3.7`` ``GCCcore/11.2.0`` ========= =================================================================================================================================================================================================== @@ -10828,6 +11231,7 @@ version versionsuffix toolchain ``2.13.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.13.92`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``2.13.93`` ``GCCcore/10.3.0`` +``2.13.94`` ``GCCcore/11.2.0`` =========== ================== ====================================================================================== @@ -10874,6 +11278,7 @@ version toolchain ``2019b`` ``system`` ``2020a`` ``system`` ``2020b`` ``system`` +``2021.07`` ``system`` ``2021a`` ``system`` =========== ========== @@ -11013,6 +11418,23 @@ version toolchain ========= ============== +.. _list_software_freebayes_950: + +*freebayes* ++++++++++++ + +FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. + +*homepage*: https://github.com/ekg/freebayes + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.3.5`` ``GCC/10.2.0`` +``1.3.5`` ``-Python-3.8.2`` ``GCC/9.3.0`` +========= ================= ============== + + .. _list_software_FreeFEM_602: *FreeFEM* @@ -11074,11 +11496,11 @@ FreeImage is an Open Source library project for developers who would like to sup *homepage*: http://freeimage.sourceforge.net -========== ======================================================= -version toolchain -========== ======================================================= -``3.18.0`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ======================================================= +========== =========================================================================== +version toolchain +========== =========================================================================== +``3.18.0`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== =========================================================================== .. _list_software_FreeSASA_682: @@ -11144,6 +11566,7 @@ version versionsuffix toolchain ``2.10.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.10.3`` ``GCCcore/10.2.0`` ``2.10.4`` ``GCCcore/10.3.0`` +``2.11.0`` ``GCCcore/11.2.0`` ========== ================== ====================================================================== @@ -11181,6 +11604,22 @@ version toolchain ========= ======================================================= +.. _list_software_freud-analysis_1447: + +*freud-analysis* +++++++++++++++++ + +The freud Python library provides a simple, flexible, powerful set of tools for analyzing trajectories obtained from molecular dynamics or Monte Carlo simulations. High performance, parallelized C++ is used to compute standard tools such as radial distribution functions, correlation functions, order parameters, and clusters, as well as original analysis methods including potentials of mean force and torque (PMFTs) and local environment matching. The freud library supports many input formats and outputs NumPy arrays, enabling integration with the scientific Python ecosystem for many typical materials science workflows. + +*homepage*: https://github.com/glotzerlab/freud + +========= ============== +version toolchain +========= ============== +``2.6.2`` ``foss/2020b`` +========= ============== + + .. _list_software_FriBidi_665: *FriBidi* @@ -11190,15 +11629,15 @@ The Free Implementation of the Unicode Bidirectional Algorithm. *homepage*: https://github.com/fribidi/fribidi -========== ======================================================= -version toolchain -========== ======================================================= -``1.0.1`` ``foss/2018a``, ``intel/2018a`` -``1.0.2`` ``GCCcore/6.4.0`` -``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``1.0.9`` ``GCCcore/9.3.0`` -``1.0.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========== ======================================================= +========== ========================================================== +version toolchain +========== ========================================================== +``1.0.1`` ``foss/2018a``, ``intel/2018a`` +``1.0.2`` ``GCCcore/6.4.0`` +``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.0.9`` ``GCCcore/9.3.0`` +``1.0.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ========================================================== .. _list_software_FRUIT_394: @@ -11285,11 +11724,11 @@ A tiny C library for managing SOM (Self-Organizing Maps) neural networks. *homepage*: https://github.com/ekg/fsom -============ ================= -version toolchain -============ ================= -``20141119`` ``GCCcore/9.3.0`` -============ ================= +============ ===================================== +version toolchain +============ ===================================== +``20141119`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +============ ===================================== .. _list_software_FTGL_301: @@ -11340,6 +11779,23 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_fumi_tools_1089: + +*fumi_tools* +++++++++++++ + +This tool is intended to deduplicate UMIs from single-end and paired-end sequencing data. Reads are considered identical when their UMIs have the same sequence, they have the same length and map at the same position. + +*homepage*: https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.18.2`` ``GCC/10.3.0`` +``0.18.2`` ``-Python-3.6.6`` ``foss/2018b`` +========== ================= ============== + + .. _list_software_FUNWAVE-TVD_823: *FUNWAVE-TVD* @@ -11480,7 +11936,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -11496,6 +11952,7 @@ Library contains GRIB2 encoder/decoder ('C' version). version toolchain ========= ======================================================================================================================== ``1.6.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``1.6.3`` ``GCCcore/10.3.0`` ========= ======================================================================================================================== @@ -11506,13 +11963,14 @@ version toolchain Library contains GRIB2 encoder/decoder and search/indexing routines. -*homepage*: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ +*homepage*: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ ========= ===================================================================== version toolchain ========= ===================================================================== ``1.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.1.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2018b`` +``3.2.0`` ``GCCcore/10.3.0`` ========= ===================================================================== @@ -11943,6 +12401,7 @@ version versionsuffix toolchain ``10.2.0`` ``system`` ``10.3.0`` ``system`` ``11.1.0`` ``system`` +``11.2.0`` ``system`` ``system`` ``system`` ``system`` ``-2.29`` ``system`` ========== =================== ========== @@ -11987,6 +12446,7 @@ version toolchain ``10.2.0`` ``system`` ``10.3.0`` ``system`` ``11.1.0`` ``system`` +``11.2.0`` ``system`` ``system`` ``system`` ========== ========== @@ -12209,14 +12669,15 @@ Grassroots DICOM: Cross-platform DICOM implementation *homepage*: https://sourceforge.net/projects/gdcm -========= ================= -version toolchain -========= ================= -``2.8.8`` ``GCCcore/6.4.0`` -``2.8.9`` ``GCCcore/7.3.0`` -``3.0.4`` ``GCCcore/8.2.0`` -``3.0.5`` ``GCCcore/8.3.0`` -========= ================= +========= ===================================== +version toolchain +========= ===================================== +``2.8.8`` ``GCCcore/6.4.0`` +``2.8.9`` ``GCCcore/7.3.0`` +``3.0.4`` ``GCCcore/8.2.0`` +``3.0.5`` ``GCCcore/8.3.0`` +``3.0.8`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========= ===================================== .. _list_software_GDGraph_637: @@ -12274,7 +12735,7 @@ version toolchain ``2.38.1`` ``GCCcore/8.2.0`` ``2.38.2`` ``GCCcore/8.3.0`` ``2.40.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``2.42.6`` ``GCCcore/10.3.0`` +``2.42.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` =========== ==================================================================================== @@ -12293,6 +12754,7 @@ version versionsuffix toolchain ``2.1`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` ``2.1`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` ``2.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.3`` ``GCCcore/11.2.0`` ======= ================ ====================================== @@ -12354,6 +12816,22 @@ version toolchain ========= ============== +.. _list_software_GEGL_287: + +*GEGL* +++++++ + +GEGL (Generic Graphics Library) is a data flow based image processing framework, providing floating point processing and non-destructive image processing capabilities to GNU Image Manipulation Program (GIMP) and other projects. + +*homepage*: https://www.gegl.org + +========== ================== +version toolchain +========== ================== +``0.4.30`` ``GCCcore/10.3.0`` +========== ================== + + .. _list_software_GEM-library_1019: *GEM-library* @@ -12527,14 +13005,15 @@ A comprehensive software library for efficient processing of structured genome a *homepage*: http://genometools.org -========== ================== ============================= -version versionsuffix toolchain -========== ================== ============================= -``1.5.10`` ``foss/2018b`` -``1.5.10`` ``-Python-2.7.15`` ``foss/2018b`` -``1.6.1`` ``GCC/10.2.0``, ``GCC/8.3.0`` -``1.6.1`` ``-Python-2.7.16`` ``GCC/8.3.0`` -========== ================== ============================= +========== ================== ============================================ +version versionsuffix toolchain +========== ================== ============================================ +``1.5.10`` ``foss/2018b`` +``1.5.10`` ``-Python-2.7.15`` ``foss/2018b`` +``1.6.1`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0`` +``1.6.1`` ``-Python-2.7.16`` ``GCC/8.3.0`` +``1.6.2`` ``GCC/10.3.0`` +========== ================== ============================================ .. _list_software_GenomeWorks_1137: @@ -12663,26 +13142,26 @@ GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (J *homepage*: https://trac.osgeo.org/geos -========= ================== ================================================================ -version versionsuffix toolchain -========= ================== ================================================================ -``3.5.0`` ``-Python-2.7.11`` ``intel/2016a`` -``3.5.0`` ``-Python-2.7.12`` ``intel/2016b`` -``3.6.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.6.1`` ``-Python-2.7.13`` ``intel/2017a`` -``3.6.1`` ``-Python-3.6.1`` ``intel/2017a`` -``3.6.2`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``3.6.2`` ``-Python-2.7.15`` ``foss/2018b`` -``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` -``3.6.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.01`` -``3.6.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` -``3.6.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.7.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` -``3.7.2`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.8.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``3.8.1`` ``-Python-3.8.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` -``3.9.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` -========= ================== ================================================================ +========= ================== ======================================================================= +version versionsuffix toolchain +========= ================== ======================================================================= +``3.5.0`` ``-Python-2.7.11`` ``intel/2016a`` +``3.5.0`` ``-Python-2.7.12`` ``intel/2016b`` +``3.6.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.6.1`` ``-Python-2.7.13`` ``intel/2017a`` +``3.6.1`` ``-Python-3.6.1`` ``intel/2017a`` +``3.6.2`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``3.6.2`` ``-Python-2.7.15`` ``foss/2018b`` +``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` +``3.6.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.01`` +``3.6.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` +``3.6.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.7.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` +``3.7.2`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.8.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``3.8.1`` ``-Python-3.8.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` +``3.9.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304`` +========= ================== ======================================================================= .. _list_software_Gerris_620: @@ -12754,7 +13233,7 @@ version versionsuffix toolchain ``0.19.8.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` ``0.19.8.1`` ``-libxml2-2.9.7`` ``GCCcore/6.4.0`` ``0.20.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` -``0.21`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``system`` +``0.21`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``system`` ============ ================== =================================================================================================== @@ -12789,6 +13268,7 @@ version toolchain ``0.10.1`` ``foss/2016b`` ``0.10.6`` ``GCCcore/7.3.0`` ``0.11.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.12.2`` ``GCC/10.3.0`` ========== ==================================== @@ -12807,6 +13287,7 @@ version toolchain ``0.9.12`` ``foss/2016b`` ``0.10.6`` ``GCCcore/7.3.0`` ``0.11.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.12.7`` ``GCC/10.3.0`` ========== ==================================== @@ -12819,13 +13300,13 @@ The gflags package contains a C++ library that implements commandline flags proc *homepage*: https://github.com/gflags/gflags -========= ======================================================= -version toolchain -========= ======================================================= -``2.1.2`` ``foss/2016a`` -``2.2.1`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` -``2.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ======================================================= +========= =========================================================================== +version toolchain +========= =========================================================================== +``2.1.2`` ``foss/2016a`` +``2.2.1`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` +``2.2.2`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= =========================================================================== .. _list_software_GFOLD_364: @@ -12900,7 +13381,7 @@ version versionsuffix toolchain ``9.50`` ``GCCcore/8.3.0`` ``9.52`` ``GCCcore/9.3.0`` ``9.53.3`` ``GCCcore/10.2.0`` -``9.54.0`` ``GCCcore/10.3.0`` +``9.54.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ================== ================================================== @@ -12913,12 +13394,12 @@ giflib is a library for reading and writing gif images. It is API and ABI compat *homepage*: http://giflib.sourceforge.net/ -========= ============================================================================ -version toolchain -========= ============================================================================ -``5.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``5.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ============================================================================ +========= ================================================================================================ +version toolchain +========= ================================================================================================ +``5.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``5.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ================================================================================================ .. _list_software_gifsicle_838: @@ -12971,6 +13452,22 @@ version toolchain ========== ========== +.. _list_software_GIMP_301: + +*GIMP* +++++++ + +GIMP is a cross-platform image editor available for GNU/Linux, OS X, Windows and more operating systems. + +*homepage*: https://www.gimp.org + +=========== ============== +version toolchain +=========== ============== +``2.10.24`` ``GCC/10.3.0`` +=========== ============== + + .. _list_software_gimpi_534: *gimpi* @@ -13278,9 +13775,26 @@ version toolchain ``2.64.1`` ``GCCcore/9.3.0`` ``2.66.1`` ``GCCcore/10.2.0`` ``2.68.2`` ``GCCcore/10.3.0`` +``2.69.1`` ``GCCcore/11.2.0`` ========== ================================================= +.. _list_software_glib-networking_1555: + +*glib-networking* ++++++++++++++++++ + +Network extensions for GLib + +*homepage*: https://gitlab.gnome.org/GNOME/glib-networking + +========== ================== +version toolchain +========== ================== +``2.68.1`` ``GCCcore/10.3.0`` +========== ================== + + .. _list_software_glibc_513: *glibc* @@ -13376,15 +13890,15 @@ Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming mode *homepage*: https://hpc.pnl.gov/globalarrays -========= ============= =============== -version versionsuffix toolchain -========= ============= =============== -``5.7`` ``intel/2018b`` -``5.7`` ``-peigs`` ``intel/2019a`` -``5.7.2`` ``intel/2019b`` -``5.7.2`` ``-peigs`` ``intel/2019b`` -``5.8`` ``intel/2020a`` -========= ============= =============== +========= ============= ================================ +version versionsuffix toolchain +========= ============= ================================ +``5.7`` ``intel/2018b`` +``5.7`` ``-peigs`` ``intel/2019a`` +``5.7.2`` ``intel/2019b`` +``5.7.2`` ``-peigs`` ``intel/2019b`` +``5.8`` ``intel/2020a``, ``intel/2021a`` +========= ============= ================================ .. _list_software_Globus-CLI_881: @@ -13434,6 +13948,7 @@ version toolchain ``0.3.4`` ``foss/2016a`` ``0.3.5`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` ``0.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.5.0`` ``GCCcore/10.2.0`` ========= ======================================================= @@ -13453,7 +13968,7 @@ version toolchain ``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` ``4.61`` ``intel/2017a`` ``4.65`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``5.0`` ``GCCcore/10.3.0`` +``5.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ======== ================================================================================================================= @@ -13531,7 +14046,7 @@ version toolchain ``6.1.1`` ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``6.1.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b`` ``6.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``6.2.1`` ``GCCcore/10.3.0`` +``6.2.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ===================================================================================================================================================== @@ -13578,17 +14093,17 @@ GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x *homepage*: https://github.com/aleaxit/gmpy -=========== ================== ============================================= -version versionsuffix toolchain -=========== ================== ============================================= -``2.0.8`` ``-Python-2.7.13`` ``intel/2017a`` -``2.0.8`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.0.8`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b4`` ``GCC/8.3.0`` -``2.1.0b5`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` -=========== ================== ============================================= +=========== ================== ====================================================================== +version versionsuffix toolchain +=========== ================== ====================================================================== +``2.0.8`` ``-Python-2.7.13`` ``intel/2017a`` +``2.0.8`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2.0.8`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b4`` ``GCC/8.3.0`` +``2.1.0b5`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` +=========== ================== ====================================================================== .. _list_software_gmsh_431: @@ -13620,7 +14135,7 @@ version versionsuffix toolchain GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools. -*homepage*: https://gmt.soest.hawaii.edu/ +*homepage*: https://www.generic-mapping-tools.org/ ========== =============================== version toolchain @@ -13629,6 +14144,7 @@ version toolchain ``5.4.1`` ``intel/2017a`` ``5.4.3`` ``foss/2018a``, ``intel/2017b`` ``5.4.5`` ``foss/2019a`` +``6.2.0`` ``foss/2019b``, ``foss/2020b`` ========== =============================== @@ -13751,6 +14267,7 @@ version toolchain ``1.14.1`` ``system`` ``1.16.3`` ``system`` ``1.16.5`` ``system`` +``1.16.6`` ``system`` ========== ================= @@ -13770,6 +14287,22 @@ version toolchain ========= ========== +.. _list_software_GOATOOLS_616: + +*GOATOOLS* +++++++++++ + +A Python library for Gene Ontology analyses + +*homepage*: https://github.com/tanghaibao/goatools + +========= ============== +version toolchain +========= ============== +``1.1.6`` ``foss/2020b`` +========= ============== + + .. _list_software_gobff_516: *gobff* @@ -13797,26 +14330,26 @@ GObject introspection is a middleware layer between C libraries (using GObject) *homepage*: https://gi.readthedocs.io/en/latest/ -========== ================== ================================== -version versionsuffix toolchain -========== ================== ================================== -``1.47.1`` ``foss/2016a``, ``intel/2016a`` -``1.48.0`` ``foss/2016a``, ``intel/2016a`` -``1.49.1`` ``foss/2016b``, ``intel/2016b`` -``1.52.0`` ``intel/2017a`` -``1.53.5`` ``-Python-2.7.13`` ``intel/2017a`` -``1.53.5`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``1.53.5`` ``-Python-3.6.1`` ``intel/2017a`` -``1.54.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``1.54.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` -``1.54.1`` ``-Python-3.6.6`` ``fosscuda/2018b`` -``1.58.3`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` -``1.60.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``1.63.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``1.64.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``1.66.1`` ``GCCcore/10.2.0`` -``1.68.0`` ``GCCcore/10.3.0`` -========== ================== ================================== +========== ================== ====================================== +version versionsuffix toolchain +========== ================== ====================================== +``1.47.1`` ``foss/2016a``, ``intel/2016a`` +``1.48.0`` ``foss/2016a``, ``intel/2016a`` +``1.49.1`` ``foss/2016b``, ``intel/2016b`` +``1.52.0`` ``intel/2017a`` +``1.53.5`` ``-Python-2.7.13`` ``intel/2017a`` +``1.53.5`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``1.53.5`` ``-Python-3.6.1`` ``intel/2017a`` +``1.54.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``1.54.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` +``1.54.1`` ``-Python-3.6.6`` ``fosscuda/2018b`` +``1.58.3`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +``1.60.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``1.63.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``1.64.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``1.66.1`` ``GCCcore/10.2.0`` +``1.68.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ================== ====================================== .. _list_software_goblf_522: @@ -13836,6 +14369,22 @@ version toolchain ========= ========== +.. _list_software_gofasta_741: + +*gofasta* ++++++++++ + +Some functions for dealing with alignments, developed to handle SARS-CoV-2 data as part of the COG-UK project. + +*homepage*: https://github.com/cov-ert/gofasta + +========= ========== +version toolchain +========= ========== +``0.0.5`` ``system`` +========= ========== + + .. _list_software_golf_424: *golf* @@ -13900,6 +14449,7 @@ version versionsuffix toolchain ``2019b`` ``system`` ``2020a`` ``system`` ``2020b`` ``system`` +``2021.07`` ``system`` ``2021a`` ``system`` ``system`` ``-2.29`` ``system`` =========== ============= ========== @@ -13958,7 +14508,7 @@ version toolchain ``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b`` ``1.8.1`` ``GCCcore/8.2.0`` ``1.10.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.11.0`` ``GCCcore/10.3.0`` +``1.11.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ===================================================================== @@ -14013,6 +14563,7 @@ version versionsuffix toolchain ``20.10.0`` ``foss/2020b``, ``intel/2020b`` ``20.10.0`` ``-ASE-3.20.1-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``21.1.0`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` +``21.6.0`` ``foss/2021a`` =========== ============================ =============================== @@ -14044,12 +14595,12 @@ GNU gperf is a perfect hash function generator. For a given list of strings, it *homepage*: https://www.gnu.org/software/gperf/ -========= ===================================================================================================================================== -version toolchain -========= ===================================================================================================================================== -``3.0.4`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``3.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ===================================================================================================================================== +========= ========================================================================================================================================================= +version toolchain +========= ========================================================================================================================================================= +``3.0.4`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``3.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ========================================================================================================================================================= .. _list_software_gperftools_1093: @@ -14061,15 +14612,15 @@ gperftools is a collection of a high-performance multi-threaded malloc() impleme *homepage*: https://github.com/gperftools/gperftools -========== ====================================== -version toolchain -========== ====================================== -``2.5`` ``foss/2016a``, ``intel/2016b`` -``2.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.7.90`` ``GCCcore/8.3.0`` -``2.8`` ``GCCcore/9.3.0`` -``2.9.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========== ====================================== +========== ========================================================== +version toolchain +========== ========================================================== +``2.5`` ``foss/2016a``, ``intel/2016b`` +``2.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.7.90`` ``GCCcore/8.3.0`` +``2.8`` ``GCCcore/9.3.0`` +``2.9.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ========================================================== .. _list_software_gpustat_776: @@ -14081,13 +14632,13 @@ dstat-like utilization monitor for NVIDIA GPUs *homepage*: https://github.com/wookayin/gpustat -========= ================== ================== -version versionsuffix toolchain -========= ================== ================== -``0.5.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``0.6.0`` ``gcccuda/2020b`` -``0.6.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` -========= ================== ================== +========= ================== ===================================== +version versionsuffix toolchain +========= ================== ===================================== +``0.5.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``0.6.0`` ``GCCcore/10.3.0``, ``gcccuda/2020b`` +``0.6.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +========= ================== ===================================== .. _list_software_GPyOpt_579: @@ -14159,7 +14710,7 @@ version toolchain *Gradle* ++++++++ -Complete Gradle install. From mobile apps to microservices, from small startups to big enterprises, Gradle helps teams build, automate and deliver better software, faster. +Complete Gradle install. From mobile apps to microservices, from small startups to big enterprises, Gradle helps teams build, automate and deliver better software, faster. *homepage*: https://gradle.org @@ -14168,6 +14719,7 @@ version toolchain ========= ========== ``4.5.1`` ``system`` ``6.1.1`` ``system`` +``6.9.1`` ``system`` ========= ========== @@ -14477,11 +15029,11 @@ Groff (GNU troff) is a typesetting system that reads plain text mixed with forma *homepage*: https://www.gnu.org/software/groff -========== =========================================================================================== -version toolchain -========== =========================================================================================== -``1.22.4`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== =========================================================================================== +========== =============================================================================================================== +version toolchain +========== =============================================================================================================== +``1.22.4`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== =============================================================================================================== .. _list_software_GroIMP_526: @@ -14542,6 +15094,7 @@ version versionsuffix toolchain ``2020.5`` ``-Python-3.8.2`` ``fosscuda/2020a`` ``2021`` ``foss/2020b``, ``fosscuda/2020b`` ``2021.2`` ``fosscuda/2020b`` +``2021.3`` ``foss/2021a`` ========== ================= ============================================================================================================ @@ -14644,7 +15197,7 @@ version toolchain ``2.4`` ``GCCcore/6.4.0`` ``2.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.6`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` -``2.7`` ``GCC/10.3.0`` +``2.7`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========= ============================================================================================================================ @@ -14698,7 +15251,7 @@ version toolchain ``1.8.3`` ``foss/2016a`` ``1.16.0`` ``GCC/8.2.0-2.31.1`` ``1.16.2`` ``GCC/8.3.0`` -``1.18.4`` ``GCC/10.2.0`` +``1.18.4`` ``GCC/10.2.0``, ``GCC/10.3.0`` =========== ================================================================================================================== @@ -14720,7 +15273,7 @@ version toolchain ``1.15.1`` ``fosscuda/2018b`` ``1.16.0`` ``GCC/8.2.0-2.31.1`` ``1.16.2`` ``GCC/8.3.0`` -``1.18.4`` ``GCC/10.2.0`` +``1.18.4`` ``GCC/10.2.0``, ``GCC/10.3.0`` =========== ================================================================================================================== @@ -14769,6 +15322,38 @@ version toolchain =========== ================================================================================ +.. _list_software_GTK2_280: + +*GTK2* +++++++ + +The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. + +*homepage*: https://developer.gnome.org/gtk+/stable/ + +=========== ================== +version toolchain +=========== ================== +``2.24.33`` ``GCCcore/10.3.0`` +=========== ================== + + +.. _list_software_GTK3_281: + +*GTK3* +++++++ + +GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. + +*homepage*: https://developer.gnome.org/gtk3/stable/ + +=========== ================== +version toolchain +=========== ================== +``3.24.29`` ``GCCcore/10.3.0`` +=========== ================== + + .. _list_software_GtkSourceView_1330: *GtkSourceView* @@ -14778,12 +15363,12 @@ GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK+ wi *homepage*: https://wiki.gnome.org/Projects/GtkSourceView -=========== ================= -version toolchain -=========== ================= -``3.24.11`` ``GCCcore/8.2.0`` -``4.4.0`` ``GCCcore/8.2.0`` -=========== ================= +=========== ===================================== +version toolchain +=========== ===================================== +``3.24.11`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0`` +``4.4.0`` ``GCCcore/8.2.0`` +=========== ===================================== .. _list_software_GTOOL_389: @@ -14925,13 +15510,13 @@ gzip (GNU zip) is a popular data compression program as a replacement for compre *homepage*: http://www.gnu.org/software/gzip/ -======== =============================================================================================== -version toolchain -======== =============================================================================================== -``1.8`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``1.9`` ``GCCcore/7.3.0`` -``1.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======== =============================================================================================== +======== =================================================================================================================== +version toolchain +======== =================================================================================================================== +``1.8`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``1.9`` ``GCCcore/7.3.0`` +``1.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======== =================================================================================================================== .. _list_software_letter_h: @@ -14940,7 +15525,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -14952,12 +15537,12 @@ The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, a *homepage*: http://www.hdfgroup.org/h4toh5/ -========= ======================== =============================== -version versionsuffix toolchain -========= ======================== =============================== -``2.2.2`` ``-linux-x86_64-static`` ``system`` -``2.2.3`` ``foss/2018b``, ``gompi/2019b`` -========= ======================== =============================== +========= ======================== ================================================ +version versionsuffix toolchain +========= ======================== ================================================ +``2.2.2`` ``-linux-x86_64-static`` ``system`` +``2.2.3`` ``foss/2018b``, ``gompi/2019b``, ``gompi/2020b`` +========= ======================== ================================================ .. _list_software_H5hut_462: @@ -15016,8 +15601,10 @@ version versionsuffix toolchain ``2.8.0`` ``-Python-2.7.15-serial`` ``intel/2018b`` ``2.8.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.9.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` +``2.10.0`` ``-Python-2.7.18`` ``intel/2020a`` ``2.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` ``2.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` +``2.10.0`` ``-serial-Python-3.7.4`` ``foss/2019b`` ``3.1.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``3.2.1`` ``foss/2021a`` ========== ===================================== ==================================================================================== @@ -15137,6 +15724,7 @@ version toolchain ``2.6.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.6.7`` ``GCCcore/10.2.0`` ``2.8.1`` ``GCCcore/10.3.0`` +``2.8.2`` ``GCCcore/11.2.0`` ========= ================================================ @@ -15216,16 +15804,16 @@ HDF (also known as HDF4) is a library and multi-object file format for storing *homepage*: https://www.hdfgroup.org/products/hdf4/ -========== ============== ========================================================================== -version versionsuffix toolchain -========== ============== ========================================================================== -``4.2.11`` ``intel/2016a`` -``4.2.12`` ``intel/2017a`` -``4.2.13`` ``GCCcore/6.4.0`` -``4.2.13`` ``-no-netcdf`` ``intel/2017a`` -``4.2.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``4.2.15`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -========== ============== ========================================================================== +========== ============== ============================================================================= +version versionsuffix toolchain +========== ============== ============================================================================= +``4.2.11`` ``intel/2016a`` +``4.2.12`` ``intel/2017a`` +``4.2.13`` ``GCCcore/6.4.0`` +``4.2.13`` ``-no-netcdf`` ``intel/2017a`` +``4.2.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``4.2.15`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========== ============== ============================================================================= .. _list_software_HDF-EOS_486: @@ -15237,11 +15825,11 @@ HDF-EOS libraries are software libraries built on HDF libraries. It supports th *homepage*: https://hdfeos.org/ -======== ==================================== -version toolchain -======== ==================================== -``2.20`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` -======== ==================================== +======== ======================================================== +version toolchain +======== ======================================================== +``2.20`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +======== ======================================================== .. _list_software_HDF-EOS5_539: @@ -15253,11 +15841,11 @@ HDF-EOS libraries are software libraries built on HDF libraries. It supports th *homepage*: https://hdfeos.org/ -======== =============================== -version toolchain -======== =============================== -``1.16`` ``foss/2018b``, ``gompi/2019b`` -======== =============================== +======== ================================================ +version toolchain +======== ================================================ +``1.16`` ``foss/2018b``, ``gompi/2019b``, ``gompi/2020b`` +======== ================================================ .. _list_software_HDF5_263: @@ -15292,6 +15880,7 @@ version versionsuffix toolchain ``1.10.6`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpic/2020a`` ``1.10.7`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpic/2020b`` ``1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` +``1.12.1`` ``gompi/2021a`` ================= ============= ================================================================================================================================================================================================================== @@ -15413,7 +16002,7 @@ version toolchain ``1.47.12`` ``GCCcore/9.3.0`` ``1.47.15`` ``GCCcore/10.1.0`` ``1.47.16`` ``GCCcore/10.2.0`` -``1.48.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/9.4.0`` +``1.48.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0`` =========== ================================================================================================================================================================================== @@ -15422,17 +16011,17 @@ version toolchain *HH-suite* ++++++++++ -HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases. +The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). *homepage*: https://github.com/soedinglab/hh-suite -============== =============== -version toolchain -============== =============== -``3.0-beta.3`` ``intel/2018a`` -``3.2.0`` ``foss/2019b`` -``3.3.0`` ``foss/2020a`` -============== =============== +============== ================================================= +version toolchain +============== ================================================= +``3.0-beta.3`` ``intel/2018a`` +``3.2.0`` ``foss/2019b``, ``fosscuda/2019b`` +``3.3.0`` ``foss/2020a``, ``gompi/2020b``, ``gompic/2020b`` +============== ================================================= .. _list_software_HiC-Pro_594: @@ -15499,6 +16088,22 @@ version toolchain ========== ================= +.. _list_software_Highway_721: + +*Highway* ++++++++++ + +Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same operation to 'lanes'. + +*homepage*: https://github.com/google/highway + +========== ================== +version toolchain +========== ================== +``0.12.2`` ``GCCcore/10.3.0`` +========== ================== + + .. _list_software_hipify-clang_1211: *hipify-clang* @@ -15531,6 +16136,22 @@ version toolchain ============ ============== +.. _list_software_hipSYCL_636: + +*hipSYCL* ++++++++++ + +hipSYCL is a modern SYCL implementation targeting CPUs and GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP + +*homepage*: https://github.com/illuhad/hipSYCL + +========= ================================= +version toolchain +========= ================================= +``0.9.1`` ``GCC/10.2.0``, ``gcccuda/2020b`` +========= ================================= + + .. _list_software_HISAT2_427: *HISAT2* @@ -15599,7 +16220,7 @@ version toolchain ``3.1b2`` ``GCC/6.4.0-2.28``, ``foss/2016a``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a``, ``intel/2018a`` ``3.2.1`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iimpi/2019b``, ``intel/2018b`` ``3.3.1`` ``gompi/2020a``, ``iimpi/2020a`` -``3.3.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020b`` +``3.3.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2020b`` ========= ============================================================================================================================================ @@ -15678,6 +16299,7 @@ version versionsuffix toolchain ``0.21.3`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` ``0.21.3`` ``-TensorFlow-2.3.1-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` ``0.22.0`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` +``0.22.1`` ``-CUDA-11.3.1-TensorFlow-2.6.0`` ``foss/2021a`` ========== =================================== ================================== @@ -15694,6 +16316,7 @@ HORTON is a Helpful Open-source Research TOol for N-fermion systems, written pr version versionsuffix toolchain ========= ================== =============================== ``2.1.1`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``2.1.1`` ``-Python-2.7.18`` ``intel/2020a`` ========= ================== =============================== @@ -15706,12 +16329,12 @@ The HPCG Benchmark project is an effort to create a more relevant metric for ran *homepage*: https://software.sandia.gov/hpcg -======= =============================================== -version toolchain -======= =============================================== -``3.0`` ``foss/2016b``, ``foss/2018b``, ``intel/2018b`` -``3.1`` ``foss/2018b``, ``intel/2018b`` -======= =============================================== +======= ================================================================================== +version toolchain +======= ================================================================================== +``3.0`` ``foss/2016b``, ``foss/2018b``, ``intel/2018b`` +``3.1`` ``foss/2018b``, ``foss/2021.07``, ``foss/2021a``, ``intel/2018b``, ``intel/2021a`` +======= ================================================================================== .. _list_software_HPCX_307: @@ -15753,14 +16376,14 @@ version toolchain HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. -*homepage*: http://www.netlib.org/benchmark/hpl/ +*homepage*: https://www.netlib.org/benchmark/hpl/ ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021.07``, ``foss/2021a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -15832,7 +16455,7 @@ version versionsuffix toolchain ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ``1.11`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -``1.12`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` ``20160107`` ``-PacBio`` ``intel/2017a`` ============ ============= =========================================================================================================================================================== @@ -15904,6 +16527,7 @@ version toolchain ``2.1.0`` ``GCCcore/9.2.0`` ``2.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``2.4.1`` ``GCCcore/10.3.0`` +``2.5.0`` ``GCCcore/11.2.0`` =========== ===================================================================================================================================================================================================================================================== @@ -16012,6 +16636,7 @@ version versionsuffix toolchain ``5.41.5`` ``GCCcore/10.2.0`` ``6.7.0`` ``GCCcore/10.2.0`` ``6.13.1`` ``GCCcore/10.3.0`` +``6.14.6`` ``GCCcore/11.2.0`` ========== ================= ================================== @@ -16031,8 +16656,8 @@ version toolchain ``2.14.0`` ``foss/2018a``, ``intel/2018a`` ``2.15.1`` ``foss/2019a``, ``intel/2019a`` ``2.18.2`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` -``2.20.0`` ``foss/2020b`` -``2.21.0`` ``foss/2021a`` +``2.20.0`` ``foss/2020b``, ``intel/2020b`` +``2.21.0`` ``foss/2021a``, ``fosscuda/2020b`` ========== ================================================================ @@ -16042,7 +16667,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -16276,16 +16901,16 @@ ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode a *homepage*: https://icu-project.org/ -======== ==================================== -version toolchain -======== ==================================== -``61.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``64.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``65.1`` ``GCCcore/8.3.0`` -``66.1`` ``GCCcore/9.3.0`` -``67.1`` ``GCCcore/10.2.0`` -``69.1`` ``GCCcore/10.3.0`` -======== ==================================== +======== ====================================== +version toolchain +======== ====================================== +``61.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``64.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``65.1`` ``GCCcore/8.3.0`` +``66.1`` ``GCCcore/9.3.0`` +``67.1`` ``GCCcore/10.2.0`` +``69.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +======== ====================================== .. _list_software_IDBA-UD_470: @@ -16398,7 +17023,7 @@ version toolchain *igraph* ++++++++ -igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. +igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. *homepage*: https://igraph.org @@ -16410,6 +17035,7 @@ version toolchain ``0.8.2`` ``foss/2020a`` ``0.8.5`` ``foss/2020b`` ``0.9.1`` ``foss/2020b``, ``fosscuda/2020b`` +``0.9.4`` ``foss/2021a`` ========= ================================================ @@ -16687,6 +17313,7 @@ version versionsuffix toolchain ``7.0.10-1`` ``GCCcore/9.3.0`` ``7.0.10-35`` ``GCCcore/10.2.0`` ``7.0.11-14`` ``GCCcore/10.3.0`` +``7.1.0-4`` ``GCCcore/11.2.0`` ============= =================================== =============================== @@ -16699,12 +17326,12 @@ imake is a Makefile-generator that is intended to make it easier to develop soft *homepage*: https://www.x.org/ -========= ====================================== -version toolchain -========= ====================================== -``1.0.7`` ``intel/2016a`` -``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========= ====================================== +========= ========================================================== +version toolchain +========= ========================================================== +``1.0.7`` ``intel/2016a`` +``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ========================================================== .. _list_software_IMB_216: @@ -16797,9 +17424,9 @@ version versionsuffix toolchain ``2019.5.281`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b``, ``iompi/2019b`` ``2020.0.166`` ``iimpi/2020.00`` ``2020.1.217`` ``gompi/2020a``, ``iimpi/2020.06-impi-18.5``, ``iimpi/2020a``, ``iimpic/2020a``, ``iompi/2020a`` -``2020.4.304`` ``gompi/2020b``, ``iimpi/2020b``, ``iimpic/2020b``, ``iompi/2020b`` +``2020.4.304`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpic/2020b``, ``iompi/2020b`` ``2021.1.1`` ``iimpi/2020.12`` -``2021.2.0`` ``gompi/2021a``, ``iimpi/2021a`` +``2021.2.0`` ``gompi/2021a``, ``iimpi/2021a``, ``iompi/2021a`` ============== ============= ====================================================================================================================================================================================================================================================================== @@ -16844,11 +17471,12 @@ IMOD is a set of image processing, modeling and display programs used for tomogr *homepage*: http://bio3d.colorado.edu/imod/ -========== ===================== ========== -version versionsuffix toolchain -========== ===================== ========== -``4.7.15`` ``_RHEL6-64_CUDA6.0`` ``system`` -========== ===================== ========== +========== ===================== ================================== +version versionsuffix toolchain +========== ===================== ================================== +``4.7.15`` ``_RHEL6-64_CUDA6.0`` ``system`` +``4.11.5`` ``foss/2020b``, ``fosscuda/2020b`` +========== ===================== ================================== .. _list_software_impi_431: @@ -16946,13 +17574,14 @@ InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence *homepage*: https://github.com/broadinstitute/inferCNV/wiki -========= ========================= ============== -version versionsuffix toolchain -========= ========================= ============== -``1.0.4`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` -``1.2.1`` ``-Python-3.7.4`` ``foss/2019b`` -``1.3.3`` ``-Python-3.8.2`` ``foss/2020a`` -========= ========================= ============== +========= ========================= ============================== +version versionsuffix toolchain +========= ========================= ============================== +``1.0.4`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` +``1.2.1`` ``-Python-3.7.4`` ``foss/2019b`` +``1.3.3`` ``foss/2020b``, ``foss/2021a`` +``1.3.3`` ``-Python-3.8.2`` ``foss/2020a`` +========= ========================= ============================== .. _list_software_Infernal_815: @@ -17155,6 +17784,7 @@ version toolchain ============ ========== ``2021.1.2`` ``system`` ``2021.2.0`` ``system`` +``2021.3.0`` ``system`` ============ ========== @@ -17255,11 +17885,11 @@ An interval tree can be used to efficiently find a set of numeric intervals ove *homepage*: https://github.com/ekg/intervaltree -======= ================= -version toolchain -======= ================= -``0.1`` ``GCCcore/9.3.0`` -======= ================= +======= ===================================== +version toolchain +======= ===================================== +``0.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +======= ===================================== .. _list_software_intltool_885: @@ -17271,18 +17901,18 @@ intltool is a set of tools to centralize translation of many different file for *homepage*: http://freedesktop.org/wiki/Software/intltool/ -========== ================ =============================================================================================== -version versionsuffix toolchain -========== ================ =============================================================================================== -``0.51.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.51.0`` ``-Perl-5.20.3`` ``intel/2016a`` -``0.51.0`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` -``0.51.0`` ``-Perl-5.24.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` -``0.51.0`` ``-Perl-5.24.1`` ``GCCcore/6.3.0``, ``intel/2017a`` -``0.51.0`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` -``0.51.0`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``0.51.0`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -========== ================ =============================================================================================== +========== ================ =================================================================================================================== +version versionsuffix toolchain +========== ================ =================================================================================================================== +``0.51.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.51.0`` ``-Perl-5.20.3`` ``intel/2016a`` +``0.51.0`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` +``0.51.0`` ``-Perl-5.24.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` +``0.51.0`` ``-Perl-5.24.1`` ``GCCcore/6.3.0``, ``intel/2017a`` +``0.51.0`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` +``0.51.0`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``0.51.0`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +========== ================ =================================================================================================================== .. _list_software_io_lib_622: @@ -17322,9 +17952,9 @@ version versionsuffix toolchain *iomkl* +++++++ -Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI. +Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL). -*homepage*: https://software.intel.com/en-us/intel-cluster-toolkit-compiler/ +*homepage*: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html ========================== ========== version toolchain @@ -17342,6 +17972,7 @@ version toolchain ``2019b`` ``system`` ``2020a`` ``system`` ``2020b`` ``system`` +``2021a`` ``system`` ========================== ========== @@ -17352,7 +17983,7 @@ version toolchain Intel C/C++ and Fortran compilers, alongside Open MPI. -*homepage*: https://software.intel.com/en-us/intel-cluster-toolkit-compiler/ +*homepage*: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html ========================== ========== version toolchain @@ -17370,6 +18001,7 @@ version toolchain ``2019b`` ``system`` ``2020a`` ``system`` ``2020b`` ``system`` +``2021a`` ``system`` ========================== ========== @@ -17541,6 +18173,7 @@ version versionsuffix toolchain ``7.15.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``7.18.1`` ``GCCcore/10.2.0`` ``7.25.0`` ``GCCcore/10.3.0`` +``7.26.0`` ``GCCcore/11.2.0`` ========== ================== ======================================================================================= @@ -17579,6 +18212,7 @@ version versionsuffix toolchain ``1.1`` ``-R-3.6.2-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``1.1`` ``-R-3.6.3-Python-3.8.2`` ``foss/2020a`` ``1.2`` ``-R-4.0.0-Python-3.8.2`` ``foss/2020a`` +``1.2`` ``-R-4.1.0`` ``foss/2021a`` ========== ========================== ================================== @@ -17598,6 +18232,22 @@ version toolchain ======= =============== +.. _list_software_ISA-L_342: + +*ISA-L* ++++++++ + +Intelligent Storage Acceleration Library + +*homepage*: https://github.com/intel/isa-l + +========== ================== +version toolchain +========== ================== +``2.30.0`` ``GCCcore/10.3.0`` +========== ================== + + .. _list_software_ISL_232: *ISL* @@ -17615,6 +18265,7 @@ version toolchain ``0.16`` ``GCC/4.9.3-2.25`` ``0.17`` ``foss/2016a`` ``0.23`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``0.24`` ``GCCcore/11.2.0`` ======== ========================================================= @@ -17760,7 +18411,7 @@ version toolchain --- -:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` +:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_jax_323` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_JSON-GLib_709` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` .. _list_software_JAGS_293: @@ -17772,12 +18423,12 @@ JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian *homepage*: http://mcmc-jags.sourceforge.net/ -========= =============================================================================================================== -version toolchain -========= =============================================================================================================== -``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` -``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2017b`` -========= =============================================================================================================== +========= =================================================================================================================================================== +version toolchain +========= =================================================================================================================================================== +``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` +``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b``, ``intel/2017b`` +========= =================================================================================================================================================== .. _list_software_Jansson_732: @@ -17816,6 +18467,7 @@ version toolchain ``2.0.16`` ``GCCcore/9.3.0`` ``2.0.24`` ``GCCcore/10.2.0`` ``2.0.28`` ``GCCcore/10.3.0`` +``2.0.33`` ``GCCcore/11.2.0`` =========== ========================================================================================================================================================== @@ -17882,9 +18534,27 @@ version versionsuffix toolchain ``11.0.8`` ``-aarch64`` ``system`` ``13`` ``system`` ``13.0.2`` ``system`` +``16`` ``system`` +``16.0.1`` ``system`` ============= ======================== ========== +.. _list_software_jax_323: + +*jax* ++++++ + +Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more + +*homepage*: https://pypi.python.org/pypi/jax + +========== ================================== +version toolchain +========== ================================== +``0.2.19`` ``foss/2020b``, ``fosscuda/2020b`` +========== ================================== + + .. _list_software_JAXFrontCE_884: *JAXFrontCE* @@ -17910,11 +18580,11 @@ JBIG-KIT is a software implementation of the JBIG1 data compression standard (I *homepage*: https://www.cl.cam.ac.uk/~mgk25/jbigkit/ -======= ============================================================================================== -version toolchain -======= ============================================================================================== -``2.1`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ============================================================================================== +======= ================================================================================================================== +version toolchain +======= ================================================================================================================== +``2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ================================================================================================================== .. _list_software_Jellyfish_938: @@ -17926,15 +18596,15 @@ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. *homepage*: http://www.genome.umd.edu/jellyfish.html -========== =================================== -version toolchain -========== =================================== -``1.1.11`` ``foss/2016a``, ``foss/2016b`` -``1.1.12`` ``foss/2018b``, ``intel/2018a`` -``2.2.6`` ``foss/2016b``, ``intel/2017a`` -``2.2.10`` ``foss/2018b``, ``intel/2018a`` -``2.3.0`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` -========== =================================== +========== =================================================== +version toolchain +========== =================================================== +``1.1.11`` ``foss/2016a``, ``foss/2016b`` +``1.1.12`` ``foss/2018b``, ``intel/2018a`` +``2.2.6`` ``foss/2016b``, ``intel/2017a`` +``2.2.10`` ``foss/2018b``, ``intel/2018a`` +``2.3.0`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` +========== =================================================== .. _list_software_jemalloc_839: @@ -17946,18 +18616,18 @@ jemalloc is a general purpose malloc(3) implementation that emphasizes fragmenta *homepage*: http://jemalloc.net -========= ======================================================== -version toolchain -========= ======================================================== -``4.1.0`` ``intel/2016a`` -``4.2.0`` ``foss/2016a``, ``intel/2016a`` -``4.2.1`` ``intel/2016b`` -``4.5.0`` ``intel/2017a`` -``5.0.1`` ``GCCcore/6.4.0`` -``5.1.0`` ``GCCcore/7.3.0`` -``5.2.0`` ``GCCcore/8.2.0`` -``5.2.1`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ======================================================== +========= ================================================================================================ +version toolchain +========= ================================================================================================ +``4.1.0`` ``intel/2016a`` +``4.2.0`` ``foss/2016a``, ``intel/2016a`` +``4.2.1`` ``intel/2016b`` +``4.5.0`` ``intel/2017a`` +``5.0.1`` ``GCCcore/6.4.0`` +``5.1.0`` ``GCCcore/7.3.0`` +``5.2.0`` ``GCCcore/8.2.0`` +``5.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ================================================================================================ .. _list_software_jhbuild_738: @@ -18051,11 +18721,27 @@ JSON-C implements a reference counting object model that allows you to easily co *homepage*: https://github.com/json-c/json-c -======== ================== -version toolchain -======== ================== -``0.15`` ``GCCcore/10.2.0`` -======== ================== +======== ========================================================== +version toolchain +======== ========================================================== +``0.15`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +======== ========================================================== + + +.. _list_software_JSON-GLib_709: + +*JSON-GLib* ++++++++++++ + +JSON-GLib implements a full JSON parser and generator using GLib and GObject, and integrates JSON with GLib data types. + +*homepage*: https://wiki.gnome.org/Projects/JsonGlib + +========= ================== +version toolchain +========= ================== +``1.6.2`` ``GCCcore/10.3.0`` +========= ================== .. _list_software_JsonCpp_701: @@ -18067,13 +18753,13 @@ JsonCpp is a C++ library that allows manipulating JSON values, including serial *homepage*: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html -========== ========================================================= -version toolchain -========== ========================================================= -``0.10.7`` ``GCCcore/8.2.0`` -``1.9.3`` ``GCCcore/8.3.0`` -``1.9.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -========== ========================================================= +========== ============================================================================= +version toolchain +========== ============================================================================= +``0.10.7`` ``GCCcore/8.2.0`` +``1.9.3`` ``GCCcore/8.3.0`` +``1.9.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========== ============================================================================= .. _list_software_JUBE_294: @@ -18133,6 +18819,7 @@ version versionsuffix toolchain ``1.5.1`` ``-linux-x86_64`` ``system`` ``1.5.3`` ``-linux-x86_64`` ``system`` ``1.6.1`` ``-linux-x86_64`` ``system`` +``1.6.2`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -18184,6 +18871,7 @@ version versionsuffix toolchain ``0.6.1`` ``-Python-3.5.1`` ``foss/2016a`` ``0.8.1`` ``-Python-3.6.4`` ``foss/2017a`` ``1.1.0`` ``GCCcore/10.2.0`` +``1.4.1`` ``GCCcore/10.3.0`` ========= ================= ================== @@ -18202,6 +18890,7 @@ version versionsuffix toolchain ``1.2.5`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.2.8`` ``GCCcore/10.2.0`` ``3.0.16`` ``GCCcore/10.3.0`` +``3.1.6`` ``GCCcore/11.2.0`` ========== ================= ================================== @@ -18227,7 +18916,7 @@ version toolchain --- -:ref:`list_software_Kaiju_500` - :ref:`list_software_Kaleido_697` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_kedro_533` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_king_425` - :ref:`list_software_kma_313` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` +:ref:`list_software_Kaiju_500` - :ref:`list_software_Kaleido_697` - :ref:`list_software_Kalign_598` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_kedro_533` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_king_425` - :ref:`list_software_kma_313` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` .. _list_software_Kaiju_500: @@ -18264,6 +18953,23 @@ version toolchain ========= ================== +.. _list_software_Kalign_598: + +*Kalign* +++++++++ + +Kalign is a fast multiple sequence alignment program for biological sequences. + +*homepage*: https://github.com/TimoLassmann/kalign + +========= ================== +version toolchain +========= ================== +``2.0.4`` ``GCCcore/10.2.0`` +``3.3.1`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_kallisto_867: *kallisto* @@ -18351,6 +19057,7 @@ version versionsuffix toolchain ============ ================= =============== ``401`` ``gompi/2019b`` ``411`` ``GCC/10.2.0`` +``418`` ``GCC/10.3.0`` ``20130806`` ``-linux.x86_64`` ``system`` ``20171107`` ``-linux.x86_64`` ``system`` ``20180716`` ``-linux.x86_64`` ``system`` @@ -18425,7 +19132,7 @@ version toolchain ========= ================================================================ ``2.1.2`` ``foss/2019a``, ``intel/2019a`` ``2.1.3`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` -``2.2.1`` ``GCCcore/10.2.0`` +``2.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ================================================================ @@ -18595,13 +19302,13 @@ Krona Tools is a set of scripts to create Krona charts from several Bioinformat *homepage*: https://github.com/marbl/Krona/wiki/KronaTools -========= ================== -version toolchain -========= ================== -``2.7`` ``GCCcore/7.3.0`` -``2.7.1`` ``GCCcore/8.2.0`` -``2.8`` ``GCCcore/10.2.0`` -========= ================== +========= ================================== +version toolchain +========= ================================== +``2.7`` ``GCCcore/7.3.0`` +``2.7.1`` ``GCCcore/8.2.0`` +``2.8`` ``GCC/10.3.0``, ``GCCcore/10.2.0`` +========= ================================== .. _list_software_kwant_549: @@ -18674,7 +19381,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -18693,6 +19400,22 @@ version versionsuffix toolchain ============ ================ =============== +.. _list_software_LADR_291: + +*LADR* +++++++ + +Prover9, Mace4, and several related programs come packaged in a system called LADR (Library for Automated Deduction Research). + +*homepage*: https://www.cs.unm.edu/~mccune/mace4/download + +============ ================== +version toolchain +============ ================== +``2009-11A`` ``GCCcore/10.2.0`` +============ ================== + + .. _list_software_LAME_287: *LAME* @@ -18702,12 +19425,12 @@ LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGP *homepage*: http://lame.sourceforge.net/ -========== ====================================================================================================================================================== -version toolchain -========== ====================================================================================================================================================== -``3.99.5`` ``foss/2016b``, ``intel/2017a`` -``3.100`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` -========== ====================================================================================================================================================== +========== ========================================================================================================================================================================== +version toolchain +========== ========================================================================================================================================================================== +``3.99.5`` ``foss/2016b``, ``intel/2017a`` +``3.100`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` +========== ========================================================================================================================================================================== .. _list_software_LAMMPS_458: @@ -18803,15 +19526,16 @@ version toolchain *lavaan* ++++++++ -lavaan is a free, open source R package for latent variable analysis +Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models. -*homepage*: http://lavaan.org +*homepage*: https://cran.r-project.org/web/packages/lavaan ============== ============= =============== version versionsuffix toolchain ============== ============= =============== ``0.6-2`` ``-R-3.4.4`` ``intel/2018a`` ``0.6-4.1433`` ``-R-3.6.0`` ``foss/2019a`` +``0.6-9`` ``-R-4.1.0`` ``foss/2021a`` ============== ============= =============== @@ -18849,6 +19573,22 @@ version versionsuffix toolchain ========== ============= ================== +.. _list_software_lDDT_328: + +*lDDT* +++++++ + +The local Distance Difference Test (lDDT) is a superposition-free score which evaluates local distance differences in a model compared to a reference structure. + +*homepage*: https://openstructure.org + +======= ========== +version toolchain +======= ========== +``1.2`` ``system`` +======= ========== + + .. _list_software_LeadIT_531: *LeadIT* @@ -18992,14 +19732,14 @@ Multi-format archive and compression library *homepage*: https://www.libarchive.org/ -========= ===================================== -version toolchain -========= ===================================== -``3.4.0`` ``GCCcore/8.2.0`` -``3.4.2`` ``GCCcore/9.3.0`` -``3.4.3`` ``GCCcore/10.2.0`` -``3.5.1`` ``GCCcore/10.3.0``, ``GCCcore/8.3.0`` -========= ===================================== +========= ========================================================= +version toolchain +========= ========================================================= +``3.4.0`` ``GCCcore/8.2.0`` +``3.4.2`` ``GCCcore/9.3.0`` +``3.4.3`` ``GCCcore/10.2.0`` +``3.5.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` +========= ========================================================= .. _list_software_libav_526: @@ -19084,6 +19824,7 @@ version toolchain ``1.11`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.14`` ``GCCcore/10.2.0`` +``1.15`` ``GCCcore/10.3.0`` ``1.17`` ``GCCcore/10.3.0`` ======== ========================================================================================================= @@ -19113,12 +19854,12 @@ An API to provide an efficient distributed queue on a cluster. libcircle is an *homepage*: https://github.com/hpc/libcircle/ -============== ================================ -version toolchain -============== ================================ -``0.2.1-rc.1`` ``gompi/2019a``, ``iimpi/2019a`` -``0.3`` ``gompi/2020a``, ``iimpi/2020a`` -============== ================================ +============== ================================================= +version toolchain +============== ================================================= +``0.2.1-rc.1`` ``gompi/2019a``, ``iimpi/2019a`` +``0.3`` ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020a`` +============== ================================================= .. _list_software_libcmaes_832: @@ -19214,17 +19955,17 @@ A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes *homepage*: https://www.opendap.org/software/libdap -========== ================== ================================================== -version versionsuffix toolchain -========== ================== ================================================== -``3.18.1`` ``intel/2017a`` -``3.18.1`` ``-Python-2.7.11`` ``foss/2016a`` -``3.19.1`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` -``3.20.3`` ``GCCcore/7.3.0`` -``3.20.4`` ``GCCcore/8.2.0`` -``3.20.6`` ``GCCcore/8.3.0`` -``3.20.7`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========== ================== ================================================== +========== ================== ========================================================= +version versionsuffix toolchain +========== ================== ========================================================= +``3.18.1`` ``intel/2017a`` +``3.18.1`` ``-Python-2.7.11`` ``foss/2016a`` +``3.19.1`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` +``3.20.3`` ``GCCcore/7.3.0`` +``3.20.4`` ``GCCcore/8.2.0`` +``3.20.6`` ``GCCcore/8.3.0`` +``3.20.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +========== ================== ========================================================= .. _list_software_libdeflate_1036: @@ -19236,12 +19977,28 @@ Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. *homepage*: https://github.com/ebiggers/libdeflate -======= ================= -version toolchain -======= ================= -``1.5`` ``GCCcore/7.3.0`` -``1.7`` ``GCCcore/9.3.0`` -======= ================= +======= ===================================== +version toolchain +======= ===================================== +``1.5`` ``GCCcore/7.3.0`` +``1.7`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +======= ===================================== + + +.. _list_software_libdivsufsort_1424: + +*libdivsufsort* ++++++++++++++++ + +libdivsufsort is a software library that implements a lightweight suffix array construction algorithm. + +*homepage*: https://github.com/y-256/libdivsufsort + +========= ============== +version toolchain +========= ============== +``2.0.1`` ``foss/2018b`` +========= ============== .. _list_software_libdrm_634: @@ -19268,6 +20025,7 @@ version toolchain ``2.4.100`` ``GCCcore/9.3.0`` ``2.4.102`` ``GCCcore/10.2.0`` ``2.4.106`` ``GCCcore/10.3.0`` +``2.4.107`` ``GCCcore/11.2.0`` =========== ================================================== @@ -19355,7 +20113,7 @@ version toolchain ``1.5.2`` ``foss/2018a`` ``1.5.3`` ``GCCcore/8.2.0``, ``fosscuda/2018b`` ``1.5.4`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.5.8`` ``GCCcore/10.3.0`` +``1.5.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ======================================================== @@ -19374,7 +20132,7 @@ version toolchain ``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` ``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` ``2.1.11`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.1.12`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.1.12`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ====================================================================================== @@ -19394,6 +20152,7 @@ version toolchain ``1.10.1`` ``GCCcore/9.3.0`` ``1.11.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``1.12.1`` ``GCCcore/10.3.0`` +``1.13.0`` ``GCCcore/11.2.0`` ========== ===================================== @@ -19411,6 +20170,7 @@ version toolchain ======== ==================================== ``1.13`` ``GCCcore/6.4.0`` ``2.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.4`` ``GCCcore/10.2.0`` ======== ==================================== @@ -19428,6 +20188,7 @@ version toolchain ========= ============================================================================================================================================================================================================================================================================================================= ``3.2.1`` ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``system`` ``3.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``3.4.2`` ``GCCcore/11.2.0`` ========= ============================================================================================================================================================================================================================================================================================================= @@ -19481,6 +20242,7 @@ version toolchain ``1.8.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.8.5`` ``GCCcore/8.3.0`` ``1.9.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.9.3`` ``GCCcore/11.2.0`` ========= ====================================== @@ -19536,6 +20298,7 @@ version toolchain ``1.4.2`` ``foss/2018a``, ``foss/2018b``, ``intel/2018b`` ``1.5.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.7.0`` ``GCCcore/11.2.0`` ========= ======================================================= @@ -19553,6 +20316,7 @@ version toolchain ========= ========================================================= ``1.0.0`` ``GCCcore/8.3.0`` ``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``1.1.1`` ``GCCcore/11.2.0`` ========= ========================================================= @@ -19587,6 +20351,7 @@ version versionsuffix toolchain ``9.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b``, ``iomkl/2018a`` ``9.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` ``9.0.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``9.0.2`` ``GCCcore/11.2.0`` ========= ================ =========================================================================================================================================================================================================================================================================================================================================== @@ -19604,7 +20369,7 @@ version toolchain ========= ======================================================= ``1.2.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.3.2`` ``GCCcore/10.2.0`` -``1.3.3`` ``GCCcore/10.3.0`` +``1.3.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ======================================================= @@ -19617,16 +20382,16 @@ Libgpg-error is a small library that defines common error values for all GnuPG c *homepage*: https://gnupg.org/related_software/libgpg-error/index.html -======== ================== -version toolchain -======== ================== -``1.21`` ``intel/2016a`` -``1.35`` ``GCCcore/7.3.0`` -``1.36`` ``GCCcore/8.2.0`` -``1.38`` ``GCCcore/8.3.0`` -``1.41`` ``GCCcore/10.2.0`` -``1.42`` ``GCCcore/10.3.0`` -======== ================== +======== ====================================== +version toolchain +======== ====================================== +``1.21`` ``intel/2016a`` +``1.35`` ``GCCcore/7.3.0`` +``1.36`` ``GCCcore/8.2.0`` +``1.38`` ``GCCcore/8.3.0`` +``1.41`` ``GCCcore/10.2.0`` +``1.42`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +======== ====================================== .. _list_software_libgpuarray_1186: @@ -19755,12 +20520,12 @@ Libiconv converts from one character encoding to another through Unicode convers *homepage*: https://www.gnu.org/software/libiconv -======== =============================================================================================== -version toolchain -======== =============================================================================================== -``1.15`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``1.16`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======== =============================================================================================== +======== =================================================================================================================== +version toolchain +======== =================================================================================================================== +``1.15`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``1.16`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======== =================================================================================================================== .. _list_software_libidn_626: @@ -19779,6 +20544,7 @@ version toolchain ``1.34`` ``GCCcore/6.4.0`` ``1.35`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.36`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.38`` ``GCCcore/11.2.0`` ======== ====================================================================================== @@ -19787,14 +20553,15 @@ version toolchain *libidn2* +++++++++ -GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn's purpose is to encode and decode internationalized domain names. +Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46. -*homepage*: https://www.gnu.org/software/libidn +*homepage*: http://www.gnu.org/software/libidn2 ========= ===================================================================================================================================== version toolchain ========= ===================================================================================================================================== ``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.3.2`` ``GCCcore/11.2.0`` ========= ===================================================================================================================================== @@ -19807,17 +20574,17 @@ Libint library is used to evaluate the traditional (electron repulsion) and cert *homepage*: https://github.com/evaleev/libint -========= ================ =================================================================================================================================================================================== -version versionsuffix toolchain -========= ================ =================================================================================================================================================================================== -``1.1.4`` ``intel/2016a`` -``1.1.6`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` -``2.0.3`` ``foss/2018b``, ``gompi/2019a``, ``intel/2018b`` -``2.1.0`` ``intel/2016b`` -``2.4.2`` ``intel/2018a`` -``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` -``2.6.0`` ``-lmax-6-cp2k`` ``GCC/10.2.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a`` -========= ================ =================================================================================================================================================================================== +========= ================ =================================================================================================================================================================================================== +version versionsuffix toolchain +========= ================ =================================================================================================================================================================================================== +``1.1.4`` ``intel/2016a`` +``1.1.6`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018a``, ``foss/2020a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` +``2.0.3`` ``foss/2018b``, ``gompi/2019a``, ``intel/2018b`` +``2.1.0`` ``intel/2016b`` +``2.4.2`` ``intel/2018a`` +``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` +``2.6.0`` ``-lmax-6-cp2k`` ``GCC/10.2.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a`` +========= ================ =================================================================================================================================================================================================== .. _list_software_LiBis_467: @@ -19859,10 +20626,26 @@ version versionsuffix toolchain ``2.0.3`` ``GCCcore/8.3.0`` ``2.0.4`` ``GCCcore/9.3.0`` ``2.0.5`` ``GCCcore/10.2.0`` -``2.0.6`` ``GCCcore/10.3.0`` +``2.0.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ================= ================================================================== +.. _list_software_libjxl_645: + +*libjxl* +++++++++ + +JPEG XL image format reference implementation + +*homepage*: https://github.com/libjxl/libjxl + +======= ================== +version toolchain +======= ================== +``0.5`` ``GCCcore/10.3.0`` +======= ================== + + .. _list_software_libmatheval_1161: *libmatheval* @@ -19944,6 +20727,22 @@ version toolchain ========= ================= +.. _list_software_libmypaint_1081: + +*libmypaint* +++++++++++++ + +libmypaint, a.k.a. "brushlib", is a library for making brushstrokes which is used by MyPaint and other projects + +*homepage*: https://github.com/mypaint/libmypaint + +========= ================== +version toolchain +========= ================== +``1.6.1`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_libobjcryst_1191: *libobjcryst* @@ -19973,6 +20772,7 @@ Ogg is a multimedia container format, and the native file and stream format for version toolchain ========= ====================================== ``1.3.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.3.5`` ``GCCcore/11.2.0`` ========= ====================================== @@ -20002,11 +20802,11 @@ Library for portable access to PCI bus configuration registers from PCI Utils. *homepage*: https://github.com/pciutils/pciutils -========= ========================================================= -version toolchain -========= ========================================================= -``3.7.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0`` -========= ========================================================= +========= ============================================================================= +version toolchain +========= ============================================================================= +``3.7.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0`` +========= ============================================================================= .. _list_software_libpciaccess_1253: @@ -20018,13 +20818,13 @@ Generic PCI access library. *homepage*: https://cgit.freedesktop.org/xorg/lib/libpciaccess/ -========== ============================================================================================= -version toolchain -========== ============================================================================================= -``0.13.4`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` -``0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.16`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -========== ============================================================================================= +========== ================================================================================================ +version toolchain +========== ================================================================================================ +``0.13.4`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` +``0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.16`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +========== ================================================================================================ .. _list_software_libpng_636: @@ -20036,23 +20836,23 @@ libpng is the official PNG reference library *homepage*: http://www.libpng.org/pub/png/libpng.html -========== ============================================================================ -version toolchain -========== ============================================================================ -``1.2.58`` ``system`` -``1.2.59`` ``system`` -``1.6.21`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``1.6.23`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``1.6.24`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` -``1.6.26`` ``foss/2016b``, ``intel/2016b`` -``1.6.27`` ``intel/2016b`` -``1.6.28`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``gimkl/2017a`` -``1.6.29`` ``GCCcore/6.3.0`` -``1.6.32`` ``GCCcore/6.4.0`` -``1.6.34`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.6.36`` ``GCCcore/8.2.0`` -``1.6.37`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ============================================================================ +========== ================================================================================================ +version toolchain +========== ================================================================================================ +``1.2.58`` ``system`` +``1.2.59`` ``system`` +``1.6.21`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``1.6.23`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` +``1.6.24`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` +``1.6.26`` ``foss/2016b``, ``intel/2016b`` +``1.6.27`` ``intel/2016b`` +``1.6.28`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``gimkl/2017a`` +``1.6.29`` ``GCCcore/6.3.0`` +``1.6.32`` ``GCCcore/6.4.0`` +``1.6.34`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.6.36`` ``GCCcore/8.2.0`` +``1.6.37`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ================================================================================================ .. _list_software_libpsl_646: @@ -20064,13 +20864,13 @@ C library for the Public Suffix List *homepage*: https://rockdaboot.github.io/libpsl -========== ==================================== -version toolchain -========== ==================================== -``0.20.2`` ``GCCcore/7.3.0`` -``0.21.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.21.1`` ``GCCcore/10.2.0`` -========== ==================================== +========== ====================================== +version toolchain +========== ====================================== +``0.20.2`` ``GCCcore/7.3.0`` +``0.21.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.21.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========== ====================================== .. _list_software_libPSML_627: @@ -20172,7 +20972,7 @@ version toolchain ``6.3`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``7.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``8.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` -``8.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` +``8.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ======= =================================================================================================================================================================================================================================================================================================================================================================================== @@ -20185,12 +20985,13 @@ The routines supporting the distribution and special functions in R and a few ot *homepage*: https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library -========= ================= -version toolchain -========= ================= -``3.6.0`` ``foss/2018b`` -``4.0.0`` ``GCCcore/9.3.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``3.6.0`` ``foss/2018b`` +``4.0.0`` ``GCCcore/9.3.0`` +``4.1.0`` ``GCCcore/10.2.0`` +========= ================== .. _list_software_librosa_748: @@ -20230,16 +21031,17 @@ version toolchain *librsvg* +++++++++ -librsvg is a library to render SVG files using cairo. +Librsvg is a library to render SVG files using cairo. -*homepage*: https://wiki.gnome.org/action/show/Projects/LibRsvg +*homepage*: https://wiki.gnome.org/Projects/LibRsvg -=========== =============== -version toolchain -=========== =============== -``2.40.15`` ``intel/2016a`` -``2.48.4`` ``foss/2019a`` -=========== =============== +=========== ================== +version toolchain +=========== ================== +``2.40.15`` ``intel/2016a`` +``2.48.4`` ``foss/2019a`` +``2.51.2`` ``GCCcore/10.3.0`` +=========== ================== .. _list_software_libsamplerate_1381: @@ -20285,12 +21087,13 @@ GNU libsigsegv is a library for handling page faults in user mode. *homepage*: https://www.gnu.org/software/libsigsegv/ -======== ================= -version toolchain -======== ================= -``2.11`` ``GCCcore/6.4.0`` -``2.12`` ``GCCcore/9.3.0`` -======== ================= +======== ================== +version toolchain +======== ================== +``2.11`` ``GCCcore/6.4.0`` +``2.12`` ``GCCcore/9.3.0`` +``2.13`` ``GCCcore/10.2.0`` +======== ================== .. _list_software_libSM_471: @@ -20322,7 +21125,7 @@ Libsndfile is a C library for reading and writing files containing sampled sound version toolchain ========== ================================================================================================================================== ``1.0.28`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a`` -``1.0.31`` ``GCCcore/10.3.0`` +``1.0.31`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ================================================================================================================================== @@ -20335,18 +21138,18 @@ Sodium is a modern, easy-to-use software library for encryption, decryption, sig *homepage*: https://doc.libsodium.org/ -========== ============================================================================ -version toolchain -========== ============================================================================ -``1.0.6`` ``intel/2016a`` -``1.0.8`` ``foss/2016a`` -``1.0.11`` ``foss/2016b``, ``intel/2016b`` -``1.0.12`` ``GCCcore/6.4.0``, ``intel/2017a`` -``1.0.13`` ``GCCcore/6.4.0``, ``foss/2017a`` -``1.0.16`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.0.17`` ``GCCcore/8.2.0`` -``1.0.18`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ============================================================================ +========== ================================================================================================ +version toolchain +========== ================================================================================================ +``1.0.6`` ``intel/2016a`` +``1.0.8`` ``foss/2016a`` +``1.0.11`` ``foss/2016b``, ``intel/2016b`` +``1.0.12`` ``GCCcore/6.4.0``, ``intel/2017a`` +``1.0.13`` ``GCCcore/6.4.0``, ``foss/2017a`` +``1.0.16`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.0.17`` ``GCCcore/8.2.0`` +``1.0.18`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ================================================================================================ .. _list_software_LibSoup_702: @@ -20449,6 +21252,7 @@ version toolchain ``3.22`` ``intel/2016b``, ``intel/2017b`` ``3.23`` ``foss/2018b``, ``intel/2018b`` ``3.24`` ``GCCcore/9.3.0`` +``3.25`` ``GCCcore/10.2.0`` ======== ================================ @@ -20488,6 +21292,22 @@ version toolchain ========== =================================================== +.. _list_software_libtecla_832: + +*libtecla* +++++++++++ + +The tecla library provides UNIX and LINUX programs with interactive command line editing facilities, similar to those of the UNIX tcsh shell. In addition to simple command-line editing, it supports recall of previously entered command lines, TAB completion of file names or other tokens, and in-line wild-card expansion of filenames. The internal functions which perform file-name completion and wild-card expansion are also available externally for optional use by programs. + +*homepage*: https://sites.astro.caltech.edu/~mcs/tecla/ + +========= ================== +version toolchain +========= ================== +``1.6.3`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_LibTIFF_576: *LibTIFF* @@ -20507,6 +21327,7 @@ version toolchain ``4.0.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``4.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.2.0`` ``GCCcore/10.3.0`` +``4.3.0`` ``GCCcore/11.2.0`` ========== ========================================================================================================= @@ -20519,14 +21340,14 @@ Libtirpc is a port of Suns Transport-Independent RPC library to Linux. *homepage*: https://sourceforge.net/projects/libtirpc/ -========= ==================================== -version toolchain -========= ==================================== -``1.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.2.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.3.1`` ``GCCcore/10.2.0`` -``1.3.2`` ``GCCcore/10.3.0`` -========= ==================================== +========= ====================================== +version toolchain +========= ====================================== +``1.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.2.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.3.1`` ``GCCcore/10.2.0`` +``1.3.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== .. _list_software_libtool_757: @@ -20538,13 +21359,13 @@ GNU libtool is a generic library support script. Libtool hides the complexity of *homepage*: http://www.gnu.org/software/libtool -========= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= -version toolchain -========= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= -``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` -``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` -``2.4.6`` ``FCC/4.5.0``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -========= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= +========= ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +version toolchain +========= ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` +``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``2.4.6`` ``FCC/4.5.0``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +========= ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_libunistring_1306: @@ -20582,7 +21403,7 @@ version toolchain ``1.2.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016b`` ``1.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.4.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``1.5.0`` ``GCCcore/10.3.0`` +``1.5.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ======================================================================= @@ -20643,12 +21464,12 @@ libvdwxc is a general library for evaluating energy and potential for exchange-c *homepage*: https://libvdwxc.org -========= ============================================================== -version toolchain -========= ============================================================== -``0.3.2`` ``foss/2018b`` -``0.4.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b`` -========= ============================================================== +========= ============================================================================== +version toolchain +========= ============================================================================== +``0.3.2`` ``foss/2018b`` +``0.4.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a`` +========= ============================================================================== .. _list_software_libvorbis_972: @@ -20660,11 +21481,11 @@ Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-pu *homepage*: https://xiph.org/vorbis/ -========= ====================================== -version toolchain -========= ====================================== -``1.3.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========= ====================================== +========= ========================================================== +version toolchain +========= ========================================================== +``1.3.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ========================================================== .. _list_software_libwebp_741: @@ -20682,7 +21503,7 @@ version toolchain ``1.0.0`` ``foss/2018b`` ``1.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.2.0`` ``GCCcore/10.3.0`` +``1.2.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ======================================================== @@ -20733,7 +21554,7 @@ version toolchain ``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` ``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` ``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` +``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` ``4.0.1`` ``foss/2017b``, ``intel/2017b`` ``4.0.3`` ``foss/2016b``, ``foss/2017a`` ``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` @@ -20964,7 +21785,7 @@ version versionsuffix toolchain ``2.9.7`` ``GCCcore/6.4.0`` ``2.9.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.9.9`` ``GCCcore/8.3.0`` -``2.9.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``2.9.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ========== ================== ================================================================================================================================================================================== @@ -21075,17 +21896,17 @@ Libxslt is the XSLT C library developed for the GNOME project (but usable outsi *homepage*: http://xmlsoft.org/ -========== ================== ================================================================= -version versionsuffix toolchain -========== ================== ================================================================= -``1.1.28`` ``foss/2016a``, ``intel/2016a`` -``1.1.28`` ``-Python-2.7.11`` ``intel/2016a`` -``1.1.29`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``1.1.30`` ``GCCcore/6.3.0`` -``1.1.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.1.33`` ``GCCcore/8.2.0`` -``1.1.34`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ================== ================================================================= +========== ================== ================================================================================================ +version versionsuffix toolchain +========== ================== ================================================================================================ +``1.1.28`` ``foss/2016a``, ``intel/2016a`` +``1.1.28`` ``-Python-2.7.11`` ``intel/2016a`` +``1.1.29`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``1.1.30`` ``GCCcore/6.3.0`` +``1.1.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.1.33`` ``GCCcore/8.2.0`` +``1.1.34`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ================== ================================================================================================ .. _list_software_libxsmm_764: @@ -21158,7 +21979,7 @@ version toolchain ``0.1.7`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``system`` ``0.2.1`` ``GCCcore/7.3.0``, ``system`` ``0.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``0.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= =================================================================== @@ -21187,12 +22008,28 @@ libzip is a C library for reading, creating, and modifying zip archives. *homepage*: https://libzip.org/ -========= ====================================== -version toolchain -========= ====================================== -``1.5.2`` ``GCCcore/8.2.0`` -``1.7.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========= ====================================== +========= ========================================================== +version toolchain +========= ========================================================== +``1.5.2`` ``GCCcore/8.2.0`` +``1.7.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ========================================================== + + +.. _list_software_lie_learn_939: + +*lie_learn* ++++++++++++ + +lie_learn is a python package that knows how to do various tricky computations related to Lie groups and manifolds (mainly the sphere S2 and rotation group SO3). + +*homepage*: https://github.com/AMLab-Amsterdam/lie_learn + +=============== ================= ================== +version versionsuffix toolchain +=============== ================= ================== +``0.0.1.post1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +=============== ================= ================== .. _list_software_lifelines_955: @@ -21262,6 +22099,7 @@ version toolchain ``4.3.2`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``5.0.1`` ``GCCcore/8.3.0`` ``5.1.0`` ``GCCcore/9.3.0`` +``5.2.0`` ``GCCcore/10.2.0`` ========= ===================================================================== @@ -21345,7 +22183,7 @@ version toolchain ``2.8`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``2.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` ``2.11`` ``GCCcore/10.2.0`` -``2.12`` ``GCCcore/10.3.0`` +``2.12`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ======== ============================================================================================================================================== @@ -21396,6 +22234,7 @@ version toolchain ``10.0.1`` ``GCCcore/10.2.0`` ``11.0.0`` ``GCCcore/10.2.0`` ``11.1.0`` ``GCCcore/10.3.0`` +``12.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ======================================================================== @@ -21417,6 +22256,7 @@ version toolchain ``0.9.23`` ``GCCcore/8.2.0`` ``0.9.24`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.9.28`` ``GCCcore/10.3.0`` +``0.9.29`` ``GCCcore/11.2.0`` ========== ======================================================== @@ -21583,6 +22423,22 @@ version toolchain ========= ================================================================================= +.. _list_software_longestrunsubsequence_2292: + +*longestrunsubsequence* ++++++++++++++++++++++++ + +Implementation of a solver for the Longest Run Subsequence Problem. Given a sequence as input, compute a longest subsequence such that there is at most one run for every character. + +*homepage*: https://pypi.org/project/longestrunsubsequence/ + +========= ================== +version toolchain +========= ================== +``1.0.1`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_Longshot_846: *Longshot* @@ -21843,14 +22699,15 @@ version toolchain *lwgrp* +++++++ -The Light-weight Group Library provides methods for MPI codes to quickly create and destroy process groups +The light-weight group library defines data structures and collective operations to group MPI processes as an ordered set. Such groups are useful as substitutes for MPI communicators when the overhead of communicator creation is too costly. For example, certain sorting algorithms recursively divide processes into subgroups as the sort algorithm progresses. These groups may be different with each invocation, so that it is inefficient to create and destroy communicators during the sort routine. -*homepage*: https://github.com/llnl/lwgrp +*homepage*: https://github.com/LLNL/lwgrp ========= ================================================================== version toolchain ========= ================================================================== ``1.0.2`` ``gompi/2019a``, ``gompi/2020a``, ``iimpi/2019a``, ``iimpi/2020a`` +``1.0.3`` ``gompi/2020b`` ========= ================================================================== @@ -21863,23 +22720,24 @@ The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxs *homepage*: https://lxml.de/ -========= ================== =============================== -version versionsuffix toolchain -========= ================== =============================== -``3.5.0`` ``-Python-2.7.11`` ``intel/2016a`` -``3.6.0`` ``-Python-2.7.11`` ``intel/2016a`` -``3.6.4`` ``-Python-2.7.12`` ``intel/2016b`` -``4.0.0`` ``-Python-2.7.13`` ``intel/2017a`` -``4.1.1`` ``-Python-2.7.14`` ``intel/2017b`` -``4.2.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``4.2.0`` ``-Python-3.6.4`` ``intel/2018a`` -``4.2.5`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``4.2.5`` ``-Python-3.6.6`` ``foss/2018b`` -``4.3.3`` ``GCCcore/8.2.0`` -``4.4.2`` ``GCCcore/8.3.0`` -``4.5.2`` ``GCCcore/9.3.0`` -``4.6.2`` ``GCCcore/10.2.0`` -========= ================== =============================== +========= ================== ====================================== +version versionsuffix toolchain +========= ================== ====================================== +``3.5.0`` ``-Python-2.7.11`` ``intel/2016a`` +``3.6.0`` ``-Python-2.7.11`` ``intel/2016a`` +``3.6.4`` ``-Python-2.7.12`` ``intel/2016b`` +``4.0.0`` ``-Python-2.7.13`` ``intel/2017a`` +``4.1.1`` ``-Python-2.7.14`` ``intel/2017b`` +``4.2.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``4.2.0`` ``-Python-3.6.4`` ``intel/2018a`` +``4.2.5`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``4.2.5`` ``-Python-3.6.6`` ``foss/2018b`` +``4.3.3`` ``GCCcore/8.2.0`` +``4.4.2`` ``GCCcore/8.3.0`` +``4.5.2`` ``GCCcore/9.3.0`` +``4.6.2`` ``GCCcore/10.2.0`` +``4.6.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ================== ====================================== .. _list_software_lynx_459: @@ -21914,7 +22772,7 @@ version toolchain ``1.9.0`` ``GCCcore/7.3.0`` ``1.9.1`` ``GCCcore/8.2.0`` ``1.9.2`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.9.3`` ``GCCcore/10.3.0`` +``1.9.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ======================================================== @@ -21927,12 +22785,12 @@ Portable lossless data compression library *homepage*: http://www.oberhumer.com/opensource/lzo/ -======== ========================================================================================================================================================================================================================================================== -version toolchain -======== ========================================================================================================================================================================================================================================================== -``2.09`` ``intel/2016b``, ``intel/2017b`` -``2.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` -======== ========================================================================================================================================================================================================================================================== +======== ============================================================================================================================================================================================================================================================================== +version toolchain +======== ============================================================================================================================================================================================================================================================================== +``2.09`` ``intel/2016b``, ``intel/2017b`` +``2.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` +======== ============================================================================================================================================================================================================================================================================== .. _list_software_letter_m: @@ -21941,7 +22799,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -21959,7 +22817,7 @@ version toolchain ``1.4.16`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.4.18`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` -``1.4.19`` ``GCCcore/9.4.0``, ``system`` +``1.4.19`` ``GCCcore/11.2.0``, ``GCCcore/9.4.0``, ``system`` ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -22088,6 +22946,7 @@ version versionsuffix toolchain ``2.5.0`` ``fosscuda/2018b`` ``2.5.1`` ``fosscuda/2019a``, ``fosscuda/2019b`` ``2.5.4`` ``fosscuda/2019a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intelcuda/2019b``, ``intelcuda/2020b`` +``2.6.1`` ``-CUDA-11.3.1`` ``foss/2021a`` ========= ================ ======================================================================================================================== @@ -22148,14 +23007,14 @@ GNU version of make utility *homepage*: https://www.gnu.org/software/make/make.html -========= ========================================================= -version toolchain -========= ========================================================= -``3.82`` ``GCC/4.8.2`` -``4.1`` ``GCC/4.9.2`` -``4.2.1`` ``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` -``4.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -========= ========================================================= +========= ============================================================================= +version toolchain +========= ============================================================================= +``3.82`` ``GCC/4.8.2`` +``4.1`` ``GCC/4.9.2`` +``4.2.1`` ``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` +``4.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========= ============================================================================= .. _list_software_makedepend_1038: @@ -22171,7 +23030,7 @@ The makedepend package contains a C-preprocessor like utility to determine build version toolchain ========= ======================================================================================= ``1.0.5`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``1.0.6`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.0.6`` ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ======================================================================================= @@ -22230,7 +23089,7 @@ version versionsuffix toolchain ``1.1.0`` ``GCCcore/8.3.0`` ``1.1.2`` ``GCCcore/9.3.0`` ``1.1.3`` ``GCCcore/10.2.0`` -``1.1.4`` ``GCCcore/10.3.0`` +``1.1.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ================== ================================================================================================================================================================= @@ -22342,6 +23201,7 @@ version toolchain ``10.3.14`` ``foss/2019a`` ``10.4.13`` ``gompi/2019b`` ``10.5.8`` ``GCC/10.2.0`` +``10.6.4`` ``GCC/10.3.0`` =========== =============================== @@ -22362,6 +23222,7 @@ version toolchain ``2.3.7`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` ``3.1.7`` ``GCCcore/9.3.0`` ``3.1.11`` ``GCCcore/10.2.0`` +``3.2.2`` ``GCCcore/10.3.0`` ========== ==================================================== @@ -22468,15 +23329,16 @@ matio is an C library for reading and writing Matlab MAT files. *homepage*: http://sourceforge.net/projects/matio/ -========== ================= -version toolchain -========== ================= -``1.5.9`` ``GCCcore/5.4.0`` -``1.5.11`` ``foss/2017b`` -``1.5.12`` ``GCCcore/6.4.0`` -``1.5.17`` ``GCCcore/8.3.0`` -``1.5.19`` ``GCCcore/9.3.0`` -========== ================= +========== ================== +version toolchain +========== ================== +``1.5.9`` ``GCCcore/5.4.0`` +``1.5.11`` ``foss/2017b`` +``1.5.12`` ``GCCcore/6.4.0`` +``1.5.17`` ``GCCcore/8.3.0`` +``1.5.19`` ``GCCcore/9.3.0`` +``1.5.21`` ``GCCcore/10.2.0`` +========== ================== .. _list_software_MATLAB_433: @@ -22568,9 +23430,10 @@ version versionsuffix toolchain ``3.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` ``3.0.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` ``3.2.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``3.3.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +``3.4.2`` ``foss/2021a`` ========= ================================= ======================================================================== @@ -22590,6 +23453,22 @@ version versionsuffix toolchain ========= =================== =============== +.. _list_software_Maude_492: + +*Maude* ++++++++ + +Maude is a high-performance reflective language and system supporting both equational and rewriting logic specification and programming for a wide range of applications. Maude has been influenced in important ways by the OBJ3 language, which can be regarded as an equational logic sublanguage. Besides supporting equational specification and programming, Maude also supports rewriting logic computation. + +*homepage*: https://maude.cs.illinois.edu/w/index.php/The_Maude_System + +======= ================== +version toolchain +======= ================== +``3.1`` ``GCCcore/10.2.0`` +======= ================== + + .. _list_software_mauveAligner_1248: *mauveAligner* @@ -23031,6 +23910,7 @@ MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an inte version toolchain ============ ========== ``7.0.20-1`` ``system`` +``10.0.5`` ``system`` ============ ========== @@ -23234,6 +24114,7 @@ version toolchain ``20.0.2`` ``GCCcore/9.3.0`` ``20.2.1`` ``GCCcore/10.2.0`` ``21.1.1`` ``GCCcore/10.3.0`` +``21.1.7`` ``GCCcore/11.2.0`` ========== ==================================================================== @@ -23311,6 +24192,8 @@ version versionsuffix toolchain ``0.55.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``0.55.3`` ``GCCcore/10.2.0`` ``0.58.0`` ``GCCcore/10.3.0`` +``0.58.2`` ``GCCcore/11.2.0`` +``0.59.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========== ================= ================================== @@ -23457,6 +24340,7 @@ Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta- version toolchain ============== ============== ``2011-03-25`` ``foss/2016a`` +``2020-05-05`` ``GCC/10.2.0`` ============== ============== @@ -23591,6 +24475,7 @@ MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II. ======= ================= ================================== version versionsuffix toolchain ======= ================= ================================== +``2.3`` ``foss/2020b``, ``fosscuda/2020b`` ``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ======= ================= ================================== @@ -23645,6 +24530,22 @@ version toolchain ========== ============== +.. _list_software_mimalloc_846: + +*mimalloc* +++++++++++ + +mimalloc is a general purpose allocator with excellent performance characteristics. + +*homepage*: https://microsoft.github.io/mimalloc/ + +========= ====================================== +version toolchain +========= ====================================== +``1.7.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== + + .. _list_software_MINC_295: *MINC* @@ -23682,15 +24583,16 @@ version versionsuffix toolchain *Mini-XML* ++++++++++ -Mini-XML is a tiny XML library that you can use to read and write XML and XML-like data files in your application without requiring large non-standard libraries. +Mini-XML is a small XML parsing library that you can use to read XML data files or strings in your application without requiring large non-standard libraries -*homepage*: https://www.msweet.org/mxml/ +*homepage*: https://www.msweet.org/mxml -======= ================= -version toolchain -======= ================= -``2.9`` ``GCCcore/8.2.0`` -======= ================= +======= ================== +version toolchain +======= ================== +``2.9`` ``GCCcore/8.2.0`` +``3.2`` ``GCCcore/10.3.0`` +======= ================== .. _list_software_minibar_738: @@ -23819,7 +24721,7 @@ version toolchain ``2.13`` ``foss/2018b`` ``2.17`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/9.3.0`` ``2.18`` ``GCCcore/10.2.0`` -``2.20`` ``GCCcore/10.2.0`` +``2.20`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========== ====================================================== @@ -23840,6 +24742,22 @@ version toolchain ============ ============= +.. _list_software_MINPACK_515: + +*MINPACK* ++++++++++ + +Minpack includes software for solving nonlinear equations and nonlinear least squares problems. Five algorithmic paths each include a core subroutine and an easy-to-use driver. The algorithms proceed either from an analytic specification of the Jacobian matrix or directly from the problem functions. The paths include facilities for systems of equations with a banded Jacobian matrix, for least squares problems with a large amount of data, and for checking the consistency of the Jacobian matrix with the functions. + +*homepage*: https://www.netlib.org/minpack/ + +============ ============== +version toolchain +============ ============== +``19961126`` ``GCC/10.3.0`` +============ ============== + + .. _list_software_MinPath_689: *MinPath* @@ -23892,6 +24810,22 @@ version versionsuffix toolchain =========== ================= =============== +.. _list_software_Mish-Cuda_827: + +*Mish-Cuda* ++++++++++++ + +Mish-Cuda: Self Regularized Non-Monotonic Activation Function + +*homepage*: https://github.com/JunnYu/mish-cuda + +============ ================== ================== +version versionsuffix toolchain +============ ================== ================== +``20210309`` ``-PyTorch-1.9.0`` ``fosscuda/2020b`` +============ ================== ================== + + .. _list_software_misha_530: *misha* @@ -23955,6 +24889,7 @@ version versionsuffix toolchain ``2.1.9`` ``-Java-1.8.0_162`` ``system`` ``3.0.3`` ``-Java-1.8`` ``system`` ``3.0.13`` ``-Java-1.8`` ``system`` +``3.0.13`` ``-Java-11`` ``system`` ========== =================== ========== @@ -24220,6 +25155,7 @@ version versionsuffix toolchain ``1.4.4`` ``-Python-3.7.2`` ``intel/2019a`` ``1.4.5`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``1.4.5`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.4.8`` ``foss/2021a`` ========= ================== =============================== @@ -24478,14 +25414,14 @@ Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily h *homepage*: http://www.multiprecision.org/ -========= =============== =============================================== -version versionsuffix toolchain -========= =============== =============================================== -``1.0.3`` ``intel/2017a`` -``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` -``1.1.0`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/9.3.0`` -``1.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========= =============== =============================================== +========= =============== ========================================================== +version versionsuffix toolchain +========= =============== ========================================================== +``1.0.3`` ``intel/2017a`` +``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` +``1.1.0`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/9.3.0`` +``1.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= =============== ========================================================== .. _list_software_MPFR_309: @@ -24506,7 +25442,7 @@ version toolchain ``3.1.6`` ``GCCcore/6.4.0`` ``4.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``4.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``4.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ================================================================ @@ -24549,6 +25485,7 @@ version toolchain ``3.2`` ``GCC/4.9.3-2.25``, ``GCC/7.2.0-2.29`` ``3.2.1`` ``GCC/7.2.0-2.29`` ``3.3.2`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``3.4.2`` ``GCC/10.3.0`` ========= ====================================== @@ -24831,11 +25768,11 @@ generate multiset combinations (n multichoose k). *homepage*: https://github.com/ekg/multichoose -========= ================= -version toolchain -========= ================= -``1.0.3`` ``GCCcore/9.3.0`` -========= ================= +========= ===================================== +version toolchain +========= ===================================== +``1.0.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========= ===================================== .. _list_software_MultiNest_933: @@ -24929,7 +25866,7 @@ version versionsuffix toolchain ``5.1.2`` ``-metis`` ``foss/2017b`` ``5.2.1`` ``-metis`` ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a`` ``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` -``5.3.5`` ``-metis`` ``foss/2020b`` +``5.3.5`` ``-metis`` ``foss/2020b``, ``intel/2020b`` ``5.4.0`` ``-metis`` ``foss/2021a`` ========= ============== ================================================================================================================= @@ -24951,6 +25888,22 @@ version toolchain ========= ===================================== +.. _list_software_muparserx_999: + +*muparserx* ++++++++++++ + +A C++ Library for Parsing Expressions with Strings, Complex Numbers, Vectors, Matrices and more. + +*homepage*: https://beltoforion.de/en/muparserx/ + +========= ================== +version toolchain +========= ================== +``4.0.8`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_MuPeXI_536: *MuPeXI* @@ -25276,7 +26229,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_NINJA_368` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -25500,6 +26453,7 @@ version versionsuffix toolchain ``0.10.2`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.13.1`` ``-Python-3.6.6`` ``foss/2018b`` ``0.13.2`` ``-Python-3.8.2`` ``foss/2020a`` +``0.13.3`` ``foss/2020b`` ========== ================== =============================== @@ -25537,7 +26491,7 @@ version toolchain ``2.13.01`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``2.13.03`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.14.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.15.05`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.15.05`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` =========== ==================================================================================== @@ -25635,6 +26589,8 @@ version versionsuffix toolchain ``2.8.3`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0``, ``system`` ``2.8.3`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0``, ``system`` ``2.9.9`` ``-CUDA-11.3.1`` ``system`` +``2.10.3`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` +``2.10.3`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` ========== =================== ============================== @@ -25674,6 +26630,7 @@ version versionsuffix toolchain ``1.17`` ``foss/2019b`` ``1.17`` ``-R-4.0.0`` ``foss/2020a`` ``1.17`` ``-R-4.0.3`` ``foss/2020b`` +``1.17`` ``-R-4.1.0`` ``foss/2021a`` ========== ============= =============================== @@ -25692,6 +26649,7 @@ version toolchain ``1.13`` ``GCCcore/7.3.0`` ``1.14`` ``GCCcore/7.3.0`` ``1.15.1`` ``GCCcore/9.3.0`` +``1.16`` ``GCC/10.3.0`` ========== ================= @@ -25721,13 +26679,13 @@ NCL is an interpreted language designed specifically for scientific data analysi *homepage*: https://www.ncl.ucar.edu -========= ================================================================================= -version toolchain -========= ================================================================================= -``6.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``6.5.0`` ``intel/2018a`` -``6.6.2`` ``foss/2018b``, ``foss/2020a``, ``intel/2018b``, ``intel/2019b``, ``intel/2020a`` -========= ================================================================================= +========= ================================================================================================= +version toolchain +========= ================================================================================================= +``6.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +``6.5.0`` ``intel/2018a`` +``6.6.2`` ``foss/2018b``, ``foss/2020a``, ``foss/2021a``, ``intel/2018b``, ``intel/2019b``, ``intel/2020a`` +========= ================================================================================================= .. _list_software_ncl_317: @@ -25751,9 +26709,9 @@ version toolchain *NCO* +++++ -manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 +The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. -*homepage*: https://nco.sourceforge.net +*homepage*: https://github.com/nco/nco ========= =============================== version toolchain @@ -25768,6 +26726,7 @@ version toolchain ``4.8.1`` ``foss/2019a`` ``4.9.3`` ``foss/2019b`` ``4.9.7`` ``foss/2020a``, ``foss/2020b`` +``5.0.1`` ``foss/2021a`` ========= =============================== @@ -25802,7 +26761,7 @@ version toolchain ``5.9`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25``, ``gimkl/2.11.5``, ``system`` ``6.0`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``6.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` -``6.2`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``system`` +``6.2`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``system`` ======= ============================================================================================================================================================================================================================================================================================================================================================================= @@ -25932,6 +26891,7 @@ Neptune is an experiment tracking hub that brings organization and collaboration version versionsuffix toolchain =========== ================= ============== ``0.4.129`` ``-Python-3.8.2`` ``foss/2020a`` +``0.10.5`` ``foss/2020b`` =========== ================= ============== @@ -26013,7 +26973,7 @@ version versionsuffix toolchain ``4.3.0`` ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``4.3.0`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.3.0`` ``-HDF5-1.8.19`` ``intel/2017b`` -``4.3.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b`` +``4.3.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a`` ========= ================ ====================================================================================================================================================== @@ -26050,24 +27010,25 @@ Python/numpy interface to netCDF. *homepage*: https://unidata.github.io/netcdf4-python/ -=========== ============================= =================================== -version versionsuffix toolchain -=========== ============================= =================================== -``1.2.9`` ``-Python-2.7.13`` ``intel/2017a`` -``1.3.1`` ``-Python-3.6.3`` ``intel/2017b`` -``1.3.1`` ``-Python-3.6.3-HDF5-1.8.19`` ``intel/2017b`` -``1.4.0`` ``-Python-3.6.2-HDF5-1.8.19`` ``foss/2017b`` -``1.4.0`` ``-Python-3.6.4`` ``intel/2018a`` -``1.4.1`` ``-Python-2.7.15`` ``intel/2018b`` -``1.4.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.4.2`` ``-Python-3.6.4`` ``foss/2018a`` -``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` -``1.5.2`` ``intel/2019a`` -``1.5.3`` ``-Python-2.7.16`` ``foss/2019b`` -``1.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.5.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.5.5.1`` ``fosscuda/2020b``, ``intel/2020b`` -=========== ============================= =================================== +=========== ============================= =================================================== +version versionsuffix toolchain +=========== ============================= =================================================== +``1.2.9`` ``-Python-2.7.13`` ``intel/2017a`` +``1.3.1`` ``-Python-3.6.3`` ``intel/2017b`` +``1.3.1`` ``-Python-3.6.3-HDF5-1.8.19`` ``intel/2017b`` +``1.4.0`` ``-Python-3.6.2-HDF5-1.8.19`` ``foss/2017b`` +``1.4.0`` ``-Python-3.6.4`` ``intel/2018a`` +``1.4.1`` ``-Python-2.7.15`` ``intel/2018b`` +``1.4.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.4.2`` ``-Python-3.6.4`` ``foss/2018a`` +``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` +``1.5.2`` ``intel/2019a`` +``1.5.3`` ``-Python-2.7.16`` ``foss/2019b`` +``1.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.5.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.5.5.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``1.5.7`` ``foss/2021a`` +=========== ============================= =================================================== .. _list_software_netloc_645: @@ -26189,6 +27150,7 @@ version toolchain ``3.5.1`` ``GCCcore/8.3.0`` ``3.6`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``3.7.2`` ``GCCcore/10.3.0`` +``3.7.3`` ``GCCcore/11.2.0`` ========= =========================================================================================================================================== @@ -26217,24 +27179,25 @@ NetworkX is a Python package for the creation, manipulation, and study of the st *homepage*: https://pypi.python.org/pypi/networkx -======== ================== =================================================== -version versionsuffix toolchain -======== ================== =================================================== -``1.1`` ``-Python-2.7.12`` ``intel/2016b`` -``1.11`` ``-Python-2.7.11`` ``foss/2016a`` -``1.11`` ``-Python-2.7.14`` ``intel/2017b`` -``1.11`` ``-Python-3.5.1`` ``foss/2016a`` -``2.0`` ``-Python-2.7.14`` ``intel/2017b`` -``2.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b`` -``2.2`` ``-Python-2.7.16`` ``foss/2019b`` -``2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``2.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``2.4`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` -``2.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -======== ================== =================================================== +========= ================== ======================================================================== +version versionsuffix toolchain +========= ================== ======================================================================== +``1.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.11`` ``-Python-2.7.11`` ``foss/2016a`` +``1.11`` ``-Python-2.7.14`` ``intel/2017b`` +``1.11`` ``-Python-3.5.1`` ``foss/2016a`` +``2.0`` ``-Python-2.7.14`` ``intel/2017b`` +``2.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b`` +``2.2`` ``-Python-2.7.16`` ``foss/2019b`` +``2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``2.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` +``2.4`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` +``2.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``2.5.1`` ``foss/2021a`` +========= ================== ======================================================================== .. _list_software_NeuroKit_817: @@ -26580,22 +27543,6 @@ version versionsuffix toolchain ========= ============= ============== -.. _list_software_NINJA_368: - -*NINJA* -+++++++ - -Nearly Infinite Neighbor Joining Application. - -*homepage*: https://github.com/TravisWheelerLab/NINJA - -===================== ============== -version toolchain -===================== ============== -``0.97-cluster_only`` ``GCC/10.2.0`` -===================== ============== - - .. _list_software_Ninja_496: *Ninja* @@ -26612,7 +27559,7 @@ version toolchain ``1.9.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` ``1.10.0`` ``GCCcore/9.3.0`` ``1.10.1`` ``GCCcore/10.2.0`` -``1.10.2`` ``GCCcore/10.3.0`` +``1.10.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ==================================================================================== @@ -26650,6 +27597,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_nlohmann_json_1396: + +*nlohmann_json* ++++++++++++++++ + +JSON for Modern C++ + +*homepage*: https://github.com/nlohmann/json + +========== ================== +version toolchain +========== ================== +``3.10.0`` ``GCCcore/10.3.0`` +========== ================== + + .. _list_software_NLopt_493: *NLopt* @@ -26665,7 +27628,7 @@ version toolchain ``2.4.2`` ``GCC/5.4.0-2.26``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``iomkl/2018a`` ``2.6.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.6.2`` ``GCCcore/10.2.0`` -``2.7.0`` ``GCCcore/10.3.0`` +``2.7.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= =================================================================================================================================================================================================================================================== @@ -26724,6 +27687,8 @@ version toolchain ``12.16.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``12.19.0`` ``GCCcore/10.2.0`` ``14.17.0`` ``GCCcore/10.3.0`` +``14.17.2`` ``GCCcore/10.3.0`` +``14.17.6`` ``GCCcore/11.2.0`` =========== ======================================================= @@ -26879,6 +27844,7 @@ version toolchain ``4.25`` ``GCCcore/9.3.0`` ``4.29`` ``GCCcore/10.2.0`` ``4.30`` ``GCCcore/10.3.0`` +``4.32`` ``GCCcore/11.2.0`` ======== ==================================== @@ -26900,6 +27866,7 @@ version toolchain ``3.51`` ``GCCcore/9.3.0`` ``3.57`` ``GCCcore/10.2.0`` ``3.65`` ``GCCcore/10.3.0`` +``3.69`` ``GCCcore/11.2.0`` ========== ==================================== @@ -26912,11 +27879,11 @@ nsync is a C library that exports various synchronization primitives, such as mu *homepage*: https://github.com/google/nsync -========== ============================================================================ -version toolchain -========== ============================================================================ -``1.24.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ============================================================================ +========== ================================================================================================ +version toolchain +========== ================================================================================================ +``1.24.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ================================================================================================ .. _list_software_ntCard_604: @@ -27000,7 +27967,7 @@ version toolchain ``2.0.11`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.3.0-2.26``, ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``GCC/6.2.0-2.27``, ``GCC/6.3.0-2.27``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` ``2.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.0.13`` ``GCCcore/10.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -``2.0.14`` ``GCCcore/10.3.0`` +``2.0.14`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ============================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -27029,7 +27996,7 @@ version versionsuffix toolchain ``0.50.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``0.52.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``0.52.0`` ``-Python-3.8.2`` ``foss/2020a`` -``0.53.1`` ``foss/2020b``, ``fosscuda/2020b`` +``0.53.1`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` ========== ================== =================================================== @@ -27103,6 +28070,7 @@ version toolchain ``21.2`` ``system`` ``21.3`` ``system`` ``21.5`` ``system`` +``21.7`` ``system`` ========= ========== @@ -27166,7 +28134,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -27386,7 +28354,7 @@ version toolchain ========= ======================================================= ``2.0`` ``foss/2016a`` ``2.0.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.0.6`` ``GCCcore/10.2.0`` +``2.0.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ======================================================= @@ -27477,6 +28445,7 @@ version versionsuffix toolchain ``0.3.9`` ``GCC/9.3.0`` ``0.3.12`` ``GCC/10.2.0`` ``0.3.15`` ``GCC/10.3.0`` +``0.3.17`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========== ================= ========================================================== @@ -27583,6 +28552,7 @@ version toolchain ``2.4.1`` ``GCCcore/9.3.0`` ``2.5.5`` ``GCCcore/10.2.0`` ``3.0.1`` ``GCCcore/10.3.0`` +``3.1.1`` ``GCCcore/11.2.0`` ========= ================================ @@ -27613,6 +28583,7 @@ version versionsuffix toolchain ``7`` ``foss/2019b`` ``7`` ``-20200508`` ``foss/2019b`` ``8`` ``foss/2020a``, ``foss/2020b`` +``9`` ``foss/2021a`` ``v1606+`` ``foss/2018b`` ``v1612+`` ``foss/2018b`` ``v1712`` ``foss/2017b``, ``intel/2017b`` @@ -27620,8 +28591,9 @@ version versionsuffix toolchain ``v1812`` ``foss/2018b`` ``v1906`` ``foss/2019b`` ``v1912`` ``foss/2019b``, ``intel/2019b`` -``v2006`` ``foss/2020a`` +``v2006`` ``foss/2020a``, ``intel/2020a`` ``v2012`` ``foss/2020a`` +``v2106`` ``foss/2021a`` ================ ============= ================================================= @@ -27691,14 +28663,14 @@ OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been d *homepage*: https://www.openjpeg.org/ -========= ========================================================= -version toolchain -========= ========================================================= -``2.1`` ``GCCcore/6.4.0`` -``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2.4.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -========= ========================================================= +========= ============================================================================= +version toolchain +========= ============================================================================= +``2.1`` ``GCCcore/6.4.0`` +``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.4.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========= ============================================================================= .. _list_software_OpenKIM-API_890: @@ -27752,6 +28724,7 @@ version versionsuffix toolchain ``7.4.2`` ``-Python-3.8.2`` ``intel/2020a`` ``7.5.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``7.5.0`` ``-Python-3.8.2`` ``fosscuda/2020a``, ``intel/2020a`` +``7.5.1`` ``foss/2020b``, ``fosscuda/2020b`` ========= ================= =================================================== @@ -27802,6 +28775,7 @@ version versionsuffix toolchain ``18.09`` ``-Python-3.6.6`` ``intel/2018b`` ``20.10`` ``-Python-3.8.2`` ``intel/2020a`` ``20.10`` ``-Python-3.8.2-noGA`` ``intel/2020a`` +``21.06`` ``intel/2021a`` ========= ====================== =============== @@ -27852,7 +28826,7 @@ version versionsuffix toolchain ``4.0.5`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` ``4.0.6`` ``GCC/10.3.0`` ``4.1.0`` ``GCC/10.2.0`` -``4.1.1`` ``GCC/10.3.0`` +``4.1.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0`` ``system`` ``GCC/system-2.29`` ========== ============= ==================================================================================================================== @@ -27898,11 +28872,11 @@ OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM *homepage*: http://code.google.com/p/openpgm/ -=========== ======================================================================================================================================================================================================================================== -version toolchain -=========== ======================================================================================================================================================================================================================================== -``5.2.122`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -=========== ======================================================================================================================================================================================================================================== +=========== ============================================================================================================================================================================================================================================================ +version toolchain +=========== ============================================================================================================================================================================================================================================================ +``5.2.122`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +=========== ============================================================================================================================================================================================================================================================ .. _list_software_OpenPIV_641: @@ -27930,13 +28904,14 @@ A Python library to read/write Excel 2010 xlsx/xlsm files *homepage*: https://openpyxl.readthedocs.io -========= ================== ================= -version versionsuffix toolchain -========= ================== ================= -``2.6.2`` ``GCCcore/8.2.0`` -``2.6.4`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` -``3.0.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -========= ================== ================= +========= ================== ====================================== +version versionsuffix toolchain +========= ================== ====================================== +``2.6.2`` ``GCCcore/8.2.0`` +``2.6.4`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +``3.0.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``3.0.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ================== ====================================== .. _list_software_OpenRefine_1003: @@ -28036,6 +29011,22 @@ version toolchain ========== ===================================================================== +.. _list_software_OpenStackClient_1511: + +*OpenStackClient* ++++++++++++++++++ + +OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the command set for Compute, Identity, Image, Network, Object Store and Block Storage APIs together in a single shell with a uniform command structure. + +*homepage*: https://docs.openstack.org/python-openstackclient/latest/ + +========= ================== +version toolchain +========= ================== +``5.5.0`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_OPERA_375: *OPERA* @@ -28125,7 +29116,7 @@ version versionsuffix toolchain *ORCA* ++++++ -ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. *homepage*: https://orcaforum.kofo.mpg.de @@ -28138,6 +29129,10 @@ version versionsuffix toolchain ``4.1.0`` ``-OpenMPI-3.1.3`` ``system`` ``4.2.0`` ``gompi/2019b`` ``4.2.1`` ``gompi/2019b`` +``5.0.0`` ``gompi/2021a`` +``5.0.0`` ``-static`` ``gompi/2021a`` +``5.0.1`` ``gompi/2021a`` +``5.0.1`` ``-static`` ``gompi/2021a`` ====================== ================== =============== @@ -28223,9 +29218,26 @@ Osi (Open Solver Interface) provides an abstract base class to a generic linear version toolchain =========== ================================= ``0.108.5`` ``GCCcore/7.3.0``, ``foss/2018b`` +``0.108.6`` ``GCCcore/10.2.0`` =========== ================================= +.. _list_software_OSPRay_542: + +*OSPRay* +++++++++ + +Open, Scalable, and Portable Ray Tracing Engine + +*homepage*: https://www.ospray.org + +========= ========== +version toolchain +========= ========== +``2.5.0`` ``system`` +========= ========== + + .. _list_software_OSU-Micro-Benchmarks_1865: *OSU-Micro-Benchmarks* @@ -28235,15 +29247,16 @@ OSU Micro-Benchmarks *homepage*: https://mvapich.cse.ohio-state.edu/benchmarks/ -========= ============================================================================================================================================================================================= -version toolchain -========= ============================================================================================================================================================================================= -``5.3.2`` ``foss/2016a``, ``foss/2017a`` -``5.6.2`` ``gompi/2019a`` -``5.6.3`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2019b``, ``iimpic/2020a`` -``5.7`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b`` -``5.7.1`` ``ffmpi/4.5.0``, ``gompi/2021a``, ``iimpi/2021a`` -========= ============================================================================================================================================================================================= +========= ================ ============================================================================================================================================================================================= +version versionsuffix toolchain +========= ================ ============================================================================================================================================================================================= +``5.3.2`` ``foss/2016a``, ``foss/2017a`` +``5.6.2`` ``gompi/2019a`` +``5.6.3`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2019b``, ``iimpic/2020a`` +``5.7`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b`` +``5.7.1`` ``ffmpi/4.5.0``, ``gompi/2021.07``, ``gompi/2021a``, ``iimpi/2021a``, ``iompi/2021a`` +``5.7.1`` ``-CUDA-11.3.1`` ``gompi/2021a`` +========= ================ ============================================================================================================================================================================================= .. _list_software_OTF2_283: @@ -28260,7 +29273,7 @@ version toolchain ======= ======================================================= ``2.0`` ``foss/2016a``, ``foss/2017a`` ``2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.3`` ``GCCcore/10.2.0`` +``2.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ======= ======================================================= @@ -28303,7 +29316,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAML_298` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -28388,7 +29401,7 @@ version toolchain ``9.38.1`` ``GCC/4.9.2``, ``system`` ``16.02`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2018a`` ``17.03`` ``GCCcore/10.2.0`` -``17.04`` ``GCCcore/10.3.0`` +``17.04`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== =========================================================================== @@ -28444,6 +29457,22 @@ version toolchain ======== ========================================================== +.. _list_software_pandapower_1073: + +*pandapower* +++++++++++++ + +An easy to use open source tool for power system modeling, analysis and optimization with a high degree of automation + +*homepage*: http://www.pandapower.org/ + +========= ============== +version toolchain +========= ============== +``2.7.0`` ``foss/2020b`` +========= ============== + + .. _list_software_pandas_631: *pandas* @@ -28548,9 +29577,26 @@ version toolchain ``1.44.7`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.47.0`` ``GCCcore/10.2.0`` ``1.48.5`` ``GCCcore/10.3.0`` +``1.48.8`` ``GCCcore/11.2.0`` =========== ==================================== +.. _list_software_pangolin_856: + +*pangolin* +++++++++++ + +Software package for assigning SARS-CoV-2 genome sequences to global lineages. This module also contains the faToVcf tool + +*homepage*: https://cov-lineages.org/pangolin.html + +========== ============== +version toolchain +========== ============== +``3.1.11`` ``foss/2020b`` +========== ============== + + .. _list_software_PAPI_298: *PAPI* @@ -28601,6 +29647,7 @@ version toolchain ``20200522`` ``GCCcore/9.3.0`` ``20210322`` ``GCCcore/10.2.0`` ``20210622`` ``GCCcore/10.3.0`` +``20210722`` ``GCCcore/11.2.0`` ============ =============================== @@ -28669,6 +29716,7 @@ A very powerful performance visualization and analysis tool based on traces tha version toolchain ========= ============== ``4.8.1`` ``foss/2019a`` +``4.9.2`` ``foss/2021a`` ========= ============== @@ -28694,6 +29742,7 @@ version versionsuffix toolchain ``5.6.2`` ``-Python-3.7.4-mpi`` ``foss/2019b``, ``intel/2019b`` ``5.8.0`` ``-Python-3.8.2-mpi`` ``foss/2020a``, ``intel/2020a`` ``5.8.1`` ``-mpi`` ``foss/2020b`` +``5.9.1`` ``-mpi`` ``foss/2021a`` ========= ====================== ================================================================================================= @@ -28820,14 +29869,15 @@ PatchELF is a small utility to modify the dynamic linker and RPATH of ELF execut *homepage*: http://nixos.org/patchelf.html -======== ===================================== -version toolchain -======== ===================================== -``0.8`` ``GNU/4.9.3-2.25`` -``0.9`` ``GCCcore/6.4.0``, ``foss/2016a`` -``0.10`` ``GCCcore/7.2.0``, ``GCCcore/8.3.0`` -``0.12`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -======== ===================================== +======== ========================================================= +version toolchain +======== ========================================================= +``0.8`` ``GNU/4.9.3-2.25`` +``0.9`` ``GCCcore/6.4.0``, ``foss/2016a`` +``0.10`` ``GCCcore/7.2.0``, ``GCCcore/8.3.0`` +``0.12`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``0.13`` ``GCCcore/11.2.0`` +======== ========================================================= .. _list_software_path.py_708: @@ -29088,6 +30138,7 @@ version toolchain ``8.42`` ``GCCcore/6.4.0`` ``8.43`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``8.44`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``8.45`` ``GCCcore/11.2.0`` ======== ================================================================================== @@ -29109,6 +30160,7 @@ version toolchain ``10.34`` ``GCCcore/9.3.0`` ``10.35`` ``GCCcore/10.2.0`` ``10.36`` ``GCCcore/10.3.0`` +``10.37`` ``GCCcore/11.2.0`` ========= ==================================== @@ -29126,7 +30178,7 @@ version toolchain ========== ======================================================== ``3.22`` ``foss/2016a`` ``3.25`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.25.1`` ``GCCcore/9.3.0`` +``3.25.1`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ========== ======================================================== @@ -29139,13 +30191,13 @@ PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. *homepage*: http://sco.h-its.org/exelixis/web/software/pear/ -========== ========================================================== -version toolchain -========== ========================================================== -``0.9.8`` ``foss/2016b``, ``intel/2016b`` -``0.9.10`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` -``0.9.11`` ``GCCcore/7.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` -========== ========================================================== +========== ==================================================================== +version toolchain +========== ==================================================================== +``0.9.8`` ``foss/2016b``, ``intel/2016b`` +``0.9.10`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +``0.9.11`` ``GCC/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` +========== ==================================================================== .. _list_software_PennCNV_632: @@ -29214,6 +30266,7 @@ version versionsuffix toolchain ``5.32.0`` ``-minimal`` ``GCCcore/10.2.0`` ``5.32.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` ``5.32.1`` ``-minimal`` ``GCCcore/10.3.0`` +``5.34.0`` ``GCCcore/11.2.0`` ========== ============= ========================================================================================= @@ -29288,7 +30341,8 @@ version versionsuffix toolchain ``3.12.4`` ``-Python-2.7.16`` ``intel/2019b`` ``3.12.4`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.12.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``3.14.4`` ``foss/2020b`` +``3.14.4`` ``foss/2020b``, ``intel/2020b`` +``3.15.1`` ``foss/2021a`` ========== ==================== =============================== @@ -29306,6 +30360,7 @@ version versionsuffix toolchain ========== ================= ============== ``3.9.1`` ``-Python-3.6.4`` ``foss/2018a`` ``3.12.0`` ``-Python-3.7.4`` ``foss/2019b`` +``3.15.0`` ``foss/2021a`` ========== ================= ============== @@ -29718,7 +30773,7 @@ version toolchain ``2.3.3`` ``foss/2016b`` ``2.3.4`` ``GCCcore/6.4.0`` ``2.4`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` -``2.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ================================================================================================================================= @@ -29791,6 +30846,7 @@ version versionsuffix toolchain ``7.0.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``8.0.1`` ``GCCcore/10.2.0`` ``8.2.0`` ``GCCcore/10.3.0`` +``8.3.1`` ``GCCcore/11.2.0`` ========= ================================= =================================================== @@ -29811,6 +30867,8 @@ version versionsuffix toolchain ``6.0.x.post0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``7.1.2`` ``GCCcore/10.2.0`` ``7.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``8.2.0`` ``GCCcore/10.3.0`` +``8.3.1`` ``GCCcore/11.2.0`` =============== ================= =================================================== @@ -30011,7 +31069,7 @@ version toolchain ``0.34.0`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``0.38.0`` ``GCCcore/8.2.0`` ``0.38.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.40.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``0.40.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ============================================================================================================================================ @@ -30040,14 +31098,14 @@ pkg-config is a helper tool used when compiling applications and libraries. It *homepage*: http://www.freedesktop.org/wiki/Software/pkg-config/ -========== ======================================================================================================================================================================================================== -version toolchain -========== ======================================================================================================================================================================================================== -``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` -``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``0.29.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a``, ``system`` -========== ======================================================================================================================================================================================================== +========== ============================================================================================================================================================================================================================ +version toolchain +========== ============================================================================================================================================================================================================================ +``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` +``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``0.29.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a``, ``system`` +========== ============================================================================================================================================================================================================================ .. _list_software_pkgconfig_952: @@ -30318,6 +31376,7 @@ version toolchain ``4.4.1`` ``intel/2019b`` ``4.8.1`` ``GCCcore/9.3.0`` ``4.14.3`` ``GCCcore/10.2.0`` +``5.1.0`` ``GCCcore/10.3.0`` ========== ================== @@ -30368,6 +31427,7 @@ version versionsuffix toolchain ``2.6.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``2.6.2`` ``foss/2020b``, ``intel/2020b`` ``2.7.0`` ``foss/2020b`` +``2.7.2`` ``foss/2021a`` ========= ================== ================================================ @@ -30410,6 +31470,7 @@ version toolchain ``3.1.4`` ``GCCcore/8.3.0`` ``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``3.2.3`` ``GCCcore/10.3.0`` +``4.1.0`` ``GCCcore/11.2.0`` ========= ======================================================= @@ -30429,7 +31490,7 @@ version toolchain ``1.9.0`` ``intel/2018a`` ``1.10.0`` ``foss/2018b``, ``intel/2018b`` ``1.12.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2020a`` -``1.12.2`` ``gompi/2020b``, ``gompic/2020b`` +``1.12.2`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2021a`` ========== ===================================================================================== @@ -30526,16 +31587,17 @@ version toolchain *poppler* +++++++++ -Poppler is a PDF rendering library based on the xpdf-3.0 code base. +Poppler is a PDF rendering library -*homepage*: https://poppler.freedesktop.org/ +*homepage*: https://poppler.freedesktop.org -========== ================= -version toolchain -========== ================= -``0.70.1`` ``foss/2018b`` -``0.90.1`` ``GCCcore/8.3.0`` -========== ================= +=========== ================= +version toolchain +=========== ================= +``0.70.1`` ``foss/2018b`` +``0.90.1`` ``GCCcore/8.3.0`` +``21.06.1`` ``GCC/10.3.0`` +=========== ================= .. _list_software_popscle_758: @@ -30660,6 +31722,7 @@ version versionsuffix toolchain ``11.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``12.4`` ``GCCcore/9.3.0`` ``13.2`` ``GCCcore/10.2.0`` +``13.3`` ``GCCcore/10.3.0`` ========= ================== ================================================================ @@ -30818,13 +31881,14 @@ version versionsuffix toolchain Software for predicting library complexity and genome coverage in high-throughput sequencing. -*homepage*: http://smithlabresearch.org/software/preseq +*homepage*: https://smithlabresearch.org/software/preseq ========= =============================== version toolchain ========= =============================== ``2.0.2`` ``foss/2016b`` ``2.0.3`` ``foss/2018b``, ``intel/2018a`` +``3.1.2`` ``GCC/10.3.0`` ========= =============================== @@ -30876,6 +31940,7 @@ A bioinformatics tool to PRe-process and show INformation of SEQuence data. version versionsuffix toolchain ========== ================ ============== ``0.20.4`` ``-Perl-5.28.0`` ``foss/2018b`` +``0.20.4`` ``-Perl-5.32.0`` ``foss/2020b`` ========== ================ ============== @@ -30964,6 +32029,7 @@ version toolchain ``7.0.0`` ``GCCcore/9.3.0`` ``7.2.1`` ``GCCcore/10.2.0`` ``8.0.1`` ``GCCcore/10.3.0`` +``8.1.0`` ``GCCcore/11.2.0`` ========= ================================================================================= @@ -31114,7 +32180,7 @@ version toolchain ``3.10.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``3.13.0`` ``GCCcore/9.3.0`` ``3.14.0`` ``GCCcore/10.2.0`` -``3.17.3`` ``GCCcore/10.3.0`` +``3.17.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` =========== ==================================================================== @@ -31127,27 +32193,27 @@ Python Protocol Buffers runtime library. *homepage*: https://github.com/google/protobuf/ -========== ================== ================================== -version versionsuffix toolchain -========== ================== ================================== -``3.0.2`` ``-Python-2.7.11`` ``foss/2016a`` -``3.0.2`` ``-Python-3.5.1`` ``foss/2016a`` -``3.2.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.2.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``3.3.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.3.0`` ``-Python-3.5.2`` ``foss/2016b`` -``3.3.0`` ``-Python-3.6.1`` ``intel/2017a`` -``3.4.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.4.0`` ``-Python-2.7.14`` ``intel/2017b`` -``3.4.0`` ``-Python-3.6.1`` ``intel/2017a`` -``3.4.0`` ``-Python-3.6.3`` ``intel/2017b`` -``3.6.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``3.6.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``3.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``3.13.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` -``3.14.0`` ``GCCcore/10.2.0`` -``3.17.3`` ``GCCcore/10.3.0`` -========== ================== ================================== +========== ================== ====================================== +version versionsuffix toolchain +========== ================== ====================================== +``3.0.2`` ``-Python-2.7.11`` ``foss/2016a`` +``3.0.2`` ``-Python-3.5.1`` ``foss/2016a`` +``3.2.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.2.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``3.3.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.3.0`` ``-Python-3.5.2`` ``foss/2016b`` +``3.3.0`` ``-Python-3.6.1`` ``intel/2017a`` +``3.4.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.4.0`` ``-Python-2.7.14`` ``intel/2017b`` +``3.4.0`` ``-Python-3.6.1`` ``intel/2017a`` +``3.4.0`` ``-Python-3.6.3`` ``intel/2017b`` +``3.6.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``3.6.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``3.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``3.13.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``3.14.0`` ``GCCcore/10.2.0`` +``3.17.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ================== ====================================== .. _list_software_protozero_1012: @@ -31176,13 +32242,13 @@ PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculatin *homepage*: https://www.prsice.info/ -========== ================= -version toolchain -========== ================= -``2.2.12`` ``GCCcore/8.3.0`` -``2.3.1`` ``GCCcore/9.3.0`` -``2.3.3`` ``GCCcore/9.3.0`` -========== ================= +========== ===================================== +version toolchain +========== ===================================== +``2.2.12`` ``GCCcore/8.3.0`` +``2.3.1`` ``GCCcore/9.3.0`` +``2.3.3`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +========== ===================================== .. _list_software_pscom_546: @@ -31240,6 +32306,22 @@ version versionsuffix toolchain ========= ========================= =============== +.. _list_software_PSIPRED_535: + +*PSIPRED* ++++++++++ + +Accurate protein secondary structure prediction + +*homepage*: http://bioinf.cs.ucl.ac.uk + +======== ============= +version toolchain +======== ============= +``4.02`` ``GCC/8.3.0`` +======== ============= + + .. _list_software_psmc_435: *psmc* @@ -31629,7 +32711,7 @@ version versionsuffix toolchain ========== ================= ==================================== ``0.3.13`` ``-Python-3.6.6`` ``foss/2018b`` ``0.3.17`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` -``0.3.18`` ``GCCcore/10.2.0`` +``0.3.18`` ``GCCcore/10.2.0``, ``foss/2021a`` ========== ================= ==================================== @@ -31651,6 +32733,7 @@ version versionsuffix toolchain ``2.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``2.6.0`` ``GCCcore/10.2.0`` ``2.6.2`` ``GCCcore/10.3.0`` +``2.7.1`` ``GCCcore/11.2.0`` ========= ================= ================== @@ -31675,6 +32758,7 @@ version versionsuffix toolchain ``1.18.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``1.18.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.20.0`` ``GCCcore/10.2.0`` +``1.20.1`` ``GCCcore/10.3.0`` ========== ================== ==================================== @@ -32028,12 +33112,13 @@ A pythonic wrapper around FFTW, the FFT library, presenting a unified interface *homepage*: https://github.com/pyFFTW/pyFFTW -========== ================= =============== -version versionsuffix toolchain -========== ================= =============== -``0.11.1`` ``intel/2019a`` -``0.11.1`` ``-Python-3.6.6`` ``foss/2018b`` -========== ================= =============== +========== ================= ================== +version versionsuffix toolchain +========== ================= ================== +``0.11.1`` ``intel/2019a`` +``0.11.1`` ``-Python-3.6.6`` ``foss/2018b`` +``0.12.0`` ``fosscuda/2020b`` +========== ================= ================== .. _list_software_pyfits_671: @@ -32127,12 +33212,13 @@ PyGEOS is a C/Python library with vectorized geometry functions. The geometry op *homepage*: https://pygeos.readthedocs.io -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``0.7.1`` ``-Python-3.7.4`` ``foss/2019b`` -``0.8`` ``-Python-3.8.2`` ``foss/2020a`` -========= ================= ============== +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``0.7.1`` ``-Python-3.7.4`` ``foss/2019b`` +``0.8`` ``-Python-3.8.2`` ``foss/2020a`` +``0.10.2`` ``intel/2020b`` +========== ================= =============== .. _list_software_pyGIMLi_635: @@ -32543,12 +33629,13 @@ Pyomo is a Python-based open-source software package that supports a diverse set *homepage*: https://www.pyomo.org/ -========= ================== ============== -version versionsuffix toolchain -========= ================== ============== -``5.5.0`` ``-Python-2.7.15`` ``foss/2018b`` -``5.5.0`` ``-Python-3.6.6`` ``foss/2018b`` -========= ================== ============== +========= ================== ============================== +version versionsuffix toolchain +========= ================== ============================== +``5.5.0`` ``-Python-2.7.15`` ``foss/2018b`` +``5.5.0`` ``-Python-3.6.6`` ``foss/2018b`` +``6.0.1`` ``foss/2020b``, ``foss/2021a`` +========= ================== ============================== .. _list_software_PyOpenCL_746: @@ -32623,6 +33710,22 @@ version versionsuffix toolchain ============ ================== ============== +.. _list_software_PYPOWER_566: + +*PYPOWER* ++++++++++ + +PYPOWER is a power flow and Optimal Power Flow (OPF) solver. It is a port of MATPOWER to the Python programming language. + +*homepage*: https://github.com/rwl/PYPOWER + +========== ============== +version toolchain +========== ============== +``5.1.15`` ``foss/2020b`` +========== ============== + + .. _list_software_pyproj_676: *pyproj* @@ -32642,6 +33745,22 @@ version versionsuffix toolchain =============== ================= ================== +.. _list_software_PyPSA_429: + +*PyPSA* ++++++++ + +PyPSA is an open source toolbox for simulating and optimising modern power systems that include features such as conventional generators with unit commitment, variable wind and solar generation, storage units, coupling to other energy sectors, and mixed alternating and direct current networks. PyPSA is designed to scale well with large networks and long time series. + +*homepage*: https://pypsa.readthedocs.io/ + +========== ============== +version toolchain +========== ============== +``0.17.1`` ``foss/2020b`` +========== ============== + + .. _list_software_pyqstem_787: *pyqstem* @@ -32702,6 +33821,7 @@ version versionsuffix toolchain ``5.13.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``5.15.1`` ``GCCcore/10.2.0`` ``5.15.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``5.15.4`` ``GCCcore/10.3.0`` ========== ================== =============================== @@ -32754,6 +33874,7 @@ PyRETIS is a Python library for rare event molecular simulations with emphasis o version versionsuffix toolchain ========= ================= =============================== ``2.1.0`` ``-Python-3.6.6`` ``intel/2018b`` +``2.5.0`` ``foss/2020b``, ``intel/2020b`` ``2.5.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========= ================= =============================== @@ -32822,6 +33943,22 @@ version versionsuffix toolchain ======== ================== ============== +.. _list_software_PyRosetta_939: + +*PyRosetta* ++++++++++++ + +PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions. + +*homepage*: https://www.pyrosetta.org/ + +================= ================= ================= +version versionsuffix toolchain +================= ================= ================= +``4.release-292`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +================= ================= ================= + + .. _list_software_Pysam_522: *Pysam* @@ -32831,29 +33968,45 @@ Pysam is a python module for reading and manipulating Samfiles. It's a lightwe *homepage*: https://github.com/pysam-developers/pysam -============ ================== ============================================================================================== -version versionsuffix toolchain -============ ================== ============================================================================================== -``0.8.4`` ``-Python-2.7.12`` ``intel/2016b`` -``0.9.1.4`` ``-Python-2.7.12`` ``foss/2016b`` -``0.10.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``0.12.0.1`` ``-Python-2.7.13`` ``intel/2017a`` -``0.12.0.1`` ``-Python-2.7.14`` ``intel/2017b`` -``0.12.0.1`` ``-Python-3.6.3`` ``intel/2017b`` -``0.13`` ``-Python-2.7.14`` ``intel/2017b`` -``0.13.0`` ``-Python-3.6.3`` ``intel/2017b`` -``0.14`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``0.14`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``0.14`` ``-Python-3.6.4`` ``intel/2018a`` -``0.14.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``0.14.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``0.15.1`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``0.15.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.15.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``0.15.3`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``0.16.0.1`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` -``0.16.0.1`` ``-Python-2.7.18`` ``GCC/10.2.0`` -============ ================== ============================================================================================== +============ ================== ============================================================================================================== +version versionsuffix toolchain +============ ================== ============================================================================================================== +``0.8.4`` ``-Python-2.7.12`` ``intel/2016b`` +``0.9.1.4`` ``-Python-2.7.12`` ``foss/2016b`` +``0.10.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``0.12.0.1`` ``-Python-2.7.13`` ``intel/2017a`` +``0.12.0.1`` ``-Python-2.7.14`` ``intel/2017b`` +``0.12.0.1`` ``-Python-3.6.3`` ``intel/2017b`` +``0.13`` ``-Python-2.7.14`` ``intel/2017b`` +``0.13.0`` ``-Python-3.6.3`` ``intel/2017b`` +``0.14`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``0.14`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``0.14`` ``-Python-3.6.4`` ``intel/2018a`` +``0.14.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``0.14.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.15.1`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.15.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.15.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``0.15.3`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``0.16.0.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` +``0.16.0.1`` ``-Python-2.7.18`` ``GCC/10.2.0`` +============ ================== ============================================================================================================== + + +.. _list_software_pysamstats_1113: + +*pysamstats* +++++++++++++ + +A Python utility for calculating statistics against genome positions based on sequence alignments from a SAM or BAM file. + +*homepage*: https://github.com/alimanfoo/pysamstats + +========= ============== +version toolchain +========= ============== +``1.1.2`` ``foss/2020b`` +========= ============== .. _list_software_PySAT_433: @@ -32947,11 +34100,12 @@ Pure Python read/write support for ESRI Shapefile format *homepage*: https://github.com/GeospatialPython/pyshp -========== ================= ============== -version versionsuffix toolchain -========== ================= ============== -``1.2.12`` ``-Python-3.6.2`` ``foss/2017b`` -========== ================= ============== +========== ================= ================== +version versionsuffix toolchain +========== ================= ================== +``1.2.12`` ``-Python-3.6.2`` ``foss/2017b`` +``2.1.3`` ``GCCcore/10.2.0`` +========== ================= ================== .. _list_software_pysndfx_780: @@ -33064,27 +34218,27 @@ PyTables is a package for managing hierarchical datasets and designed to efficie *homepage*: https://www.pytables.org -=========== ================== =================================================== -version versionsuffix toolchain -=========== ================== =================================================== -``3.2.2`` ``-Python-2.7.12`` ``foss/2016b`` -``3.2.3.1`` ``-Python-2.7.12`` ``intel/2016b`` -``3.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.3.0`` ``-Python-3.5.2`` ``intel/2016b`` -``3.4.2`` ``-Python-2.7.13`` ``foss/2017a`` -``3.4.2`` ``-Python-3.6.1`` ``intel/2017a`` -``3.4.2`` ``-Python-3.6.3`` ``intel/2017b`` -``3.4.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``3.4.4`` ``-Python-2.7.15`` ``foss/2018b`` -``3.4.4`` ``-Python-3.5.1`` ``foss/2016a`` -``3.4.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``3.5.2`` ``intel/2019a`` -``3.5.2`` ``-Python-2.7.14`` ``intel/2018a`` -``3.5.2`` ``-Python-2.7.16`` ``intel/2019b`` -``3.6.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``3.6.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``3.6.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -=========== ================== =================================================== +=========== ================== =================================================================== +version versionsuffix toolchain +=========== ================== =================================================================== +``3.2.2`` ``-Python-2.7.12`` ``foss/2016b`` +``3.2.3.1`` ``-Python-2.7.12`` ``intel/2016b`` +``3.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.3.0`` ``-Python-3.5.2`` ``intel/2016b`` +``3.4.2`` ``-Python-2.7.13`` ``foss/2017a`` +``3.4.2`` ``-Python-3.6.1`` ``intel/2017a`` +``3.4.2`` ``-Python-3.6.3`` ``intel/2017b`` +``3.4.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``3.4.4`` ``-Python-2.7.15`` ``foss/2018b`` +``3.4.4`` ``-Python-3.5.1`` ``foss/2016a`` +``3.4.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``3.5.2`` ``intel/2019a`` +``3.5.2`` ``-Python-2.7.14`` ``intel/2018a`` +``3.5.2`` ``-Python-2.7.16`` ``intel/2019b`` +``3.6.1`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b``, ``intel/2020b`` +``3.6.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``3.6.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +=========== ================== =================================================================== .. _list_software_pytest_681: @@ -33113,6 +34267,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_pytest-benchmark_1665: + +*pytest-benchmark* +++++++++++++++++++ + +A pytest fixture for benchmarking code. + +*homepage*: https://github.com/ionelmc/pytest-benchmark + +========= ================== +version toolchain +========= ================== +``3.4.1`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_pytest-xdist_1282: *pytest-xdist* @@ -33122,12 +34292,12 @@ xdist: pytest distributed testing plugin The pytest-xdist plugin extends pytest *homepage*: https://github.com/pytest-dev/pytest-xdist -========= ================== -version toolchain -========= ================== -``2.1.0`` ``GCCcore/10.2.0`` -``2.3.0`` ``GCCcore/10.3.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``2.1.0`` ``GCCcore/10.2.0`` +``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_PYTHIA_463: @@ -33190,6 +34360,8 @@ version versionsuffix toolchain ``3.8.6`` ``GCCcore/10.2.0`` ``3.9.5`` ``GCCcore/10.3.0`` ``3.9.5`` ``-bare`` ``GCCcore/10.3.0`` +``3.9.6`` ``GCCcore/11.2.0`` +``3.9.6`` ``-bare`` ``GCCcore/11.2.0`` ========== ================= ================================================================================================================================================================= @@ -33225,9 +34397,26 @@ version versionsuffix toolchain ``0.7.1.post6`` ``-Python-3.6.6`` ``foss/2018b`` ``0.8.0`` ``foss/2019b``, ``foss/2020a`` ``0.9.0`` ``foss/2020b``, ``fosscuda/2020b`` +``0.9.6`` ``foss/2021a`` =============== ================== ================================== +.. _list_software_python-isal_1144: + +*python-isal* ++++++++++++++ + +Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library. + +*homepage*: https://github.com/pycompression/python-isal + +========== ================== +version toolchain +========== ================== +``0.11.0`` ``GCCcore/10.3.0`` +========== ================== + + .. _list_software_python-Levenshtein_1876: *python-Levenshtein* @@ -33326,7 +34515,9 @@ version versionsuffix toolchain ``1.7.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``1.7.1`` ``-Python-3.8.2`` ``fosscuda/2020a`` ``1.8.1`` ``foss/2020b``, ``fosscuda/2020b`` +``1.8.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``1.9.0`` ``foss/2020b``, ``fosscuda/2020b`` +``1.9.0`` ``-imkl`` ``fosscuda/2020b`` ========= ============================= ================================== @@ -33345,6 +34536,7 @@ version versionsuffix toolchain ``1.3.2`` ``-Python-3.7.4`` ``foss/2019b`` ``1.4.2`` ``-Python-3.7.4-PyTorch-1.4.0`` ``foss/2019b`` ``1.6.3`` ``foss/2020b``, ``fosscuda/2020b`` +``1.6.3`` ``-Python-3.7.4-PyTorch-1.8.1`` ``fosscuda/2019b`` ========= =============================== ================================== @@ -33408,7 +34600,7 @@ version versionsuffix toolchain ``5.1.2`` ``GCCcore/8.3.0`` ``5.3`` ``GCCcore/9.3.0`` ``5.3.1`` ``GCCcore/10.2.0`` -``5.4.1`` ``GCCcore/10.3.0`` +``5.4.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ================== ==================================================================================== @@ -33446,7 +34638,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcat_425` - :ref:`list_software_qcint_543` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_Qtconsole_952` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_QtPy_398` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` +:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcat_425` - :ref:`list_software_qcint_543` - :ref:`list_software_QCxMS_428` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_Qtconsole_952` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_QtPy_398` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` .. _list_software_Q6_135: @@ -33515,6 +34707,22 @@ version toolchain ========== ============== +.. _list_software_QCxMS_428: + +*QCxMS* ++++++++ + +QCxMS is a quantum chemical based program to calculate electron ionization (EI) and collision induced dissociation (CID) mass spectra using Born-Oppenheimer Molecular Dynamics (BO-MD). It is the successor of the QCEIMS program, in which the EI part is exchanged to x to account for the greater general applicibility of the program. + +*homepage*: https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms.html + +========= ========== +version toolchain +========= ========== +``5.0.3`` ``system`` +========= ========== + + .. _list_software_QDD_217: *QDD* @@ -33579,7 +34787,7 @@ version toolchain ========== ============================================================================================================================================================================= ``2015.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``2019.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2020.2`` ``GCCcore/10.2.0`` +``2020.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ============================================================================================================================================================================= @@ -33646,11 +34854,11 @@ QJson is a Qt-based library that maps JSON data to QVariant objects and vice ver *homepage*: http://qjson.sourceforge.net/ -========= ================================================== -version toolchain -========= ================================================== -``0.9.0`` ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b`` -========= ================================================== +========= ====================================================================== +version toolchain +========= ====================================================================== +``0.9.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b`` +========= ====================================================================== .. _list_software_QML_234: @@ -33775,11 +34983,12 @@ Qt Port of WebKit. WebKit is an open source web browser engine. *homepage*: https://github.com/qt/qtwebkit -================== ================= -version toolchain -================== ================= -``5.212.0-alpha3`` ``GCCcore/8.2.0`` -================== ================= +================== ================== +version toolchain +================== ================== +``5.212.0-alpha3`` ``GCCcore/8.2.0`` +``5.212.0-alpha4`` ``GCCcore/10.2.0`` +================== ================== .. _list_software_Qtconsole_952: @@ -33824,11 +35033,12 @@ QTLtools is a tool set for molecular QTL discovery and analysis. It allows to go *homepage*: https://qtltools.github.io/qtltools/ -======= =============== -version toolchain -======= =============== -``1.1`` ``intel/2016b`` -======= =============== +========= =============== +version toolchain +========= =============== +``1.1`` ``intel/2016b`` +``1.3.1`` ``foss/2020b`` +========= =============== .. _list_software_qtop_452: @@ -33877,6 +35087,7 @@ Qualimap 2 is a platform-independent application written in Java and R that prov version versionsuffix toolchain ========= ============= ============== ``2.2.1`` ``-R-3.6.0`` ``foss/2019a`` +``2.2.1`` ``-R-4.0.3`` ``foss/2020b`` ========= ============= ============== @@ -33889,13 +35100,13 @@ A Python library for Quandl’s RESTful API. *homepage*: https://pypi.python.org/pypi/Quandl -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``3.4.2`` ``-Python-3.6.4`` ``intel/2018a`` -``3.4.8`` ``foss/2019a`` -``3.6.1`` ``foss/2020b`` -========= ================= =============== +========= ================= ============================== +version versionsuffix toolchain +========= ================= ============================== +``3.4.2`` ``-Python-3.6.4`` ``intel/2018a`` +``3.4.8`` ``foss/2019a`` +``3.6.1`` ``foss/2020b``, ``foss/2021a`` +========= ================= ============================== .. _list_software_QuantumESPRESSO_1375: @@ -34046,7 +35257,7 @@ version toolchain ``6.1.2`` ``intel/2016a`` ``6.1.3`` ``foss/2016b``, ``intel/2016b`` ``6.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` -``6.1.5`` ``GCCcore/9.3.0`` +``6.1.5`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= ==================================================== @@ -34059,11 +35270,11 @@ The QwtPolar library contains classes for displaying values on a polar coordinat *homepage*: http://qwtpolar.sourceforge.net/ -========= ================================================== -version toolchain -========= ================================================== -``1.1.1`` ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b`` -========= ================================================== +========= ====================================================================== +version toolchain +========= ====================================================================== +``1.1.1`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b`` +========= ====================================================================== .. _list_software_letter_r: @@ -34072,7 +35283,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -34137,6 +35348,7 @@ version versionsuffix toolchain ``3.10`` ``foss/2019b`` ``3.11`` ``-R-4.0.0`` ``foss/2020a`` ``3.12`` ``-R-4.0.3`` ``foss/2020b`` +``3.13`` ``-R-4.1.0`` ``foss/2021a`` ======== ============= =============================== @@ -34430,18 +35642,18 @@ RAxML search algorithm for maximum likelihood based inference of phylogenetic tr *homepage*: https://github.com/stamatak/standard-RAxML -========== ================== ================================================================== -version versionsuffix toolchain -========== ================== ================================================================== -``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` -``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` -``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` -``8.2.12`` ``-hybrid-avx2`` ``gompi/2020a``, ``iimpi/2019b``, ``intel/2018b``, ``intel/2019a`` -``8.2.12`` ``-pthreads-avx2`` ``GCC/10.2.0`` -========== ================== ================================================================== +========== ================== =================================================================================== +version versionsuffix toolchain +========== ================== =================================================================================== +``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` +``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` +``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` +``8.2.12`` ``-hybrid-avx2`` ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2019b``, ``intel/2018b``, ``intel/2019a`` +``8.2.12`` ``-pthreads-avx2`` ``GCC/10.2.0`` +========== ================== =================================================================================== .. _list_software_RAxML-NG_614: @@ -34449,7 +35661,7 @@ version versionsuffix toolchain *RAxML-NG* ++++++++++ -RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. +RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. *homepage*: https://github.com/amkozlov/raxml-ng @@ -34459,6 +35671,7 @@ version toolchain ``0.9.0`` ``GCC/8.3.0``, ``gompi/2019b`` ``1.0.1`` ``gompi/2019b`` ``1.0.2`` ``gompi/2020b`` +``1.0.3`` ``GCC/10.2.0`` ========= ============================== @@ -34682,6 +35895,7 @@ version toolchain ``1.3`` ``GCCcore/9.3.0`` ``2.0.3`` ``GCCcore/10.2.0`` ``2.1.1`` ``GCCcore/10.3.0`` +``2.2`` ``GCCcore/11.2.0`` ========= ================== @@ -34789,6 +36003,9 @@ version toolchain ``3.5.1`` ``system`` ``3.5.2`` ``system`` ``3.6.2`` ``system`` +``3.6.3`` ``system`` +``3.7.3`` ``system`` +``3.8.0`` ``system`` ========= ========== @@ -34915,6 +36132,22 @@ version versionsuffix toolchain ============ ====================== ========================================================== +.. _list_software_RepeatModeler_1321: + +*RepeatModeler* ++++++++++++++++ + +RepeatModeler is a de novo transposable element (TE) family identification and modeling package. + +*homepage*: https://www.repeatmasker.org/ + +========== ============== +version toolchain +========== ============== +``2.0.2a`` ``foss/2020b`` +========== ============== + + .. _list_software_RepeatScout_1135: *RepeatScout* @@ -35032,6 +36265,7 @@ version versionsuffix toolchain ``1.4-8`` ``-R-4.0.0`` ``foss/2020a`` ``1.5-16`` ``-R-4.0.0`` ``foss/2020a`` ``1.5-23`` ``-R-4.0.4`` ``foss/2020b`` +``1.5-23`` ``-R-4.1.0`` ``foss/2021a`` ========== ============= ============== @@ -35051,6 +36285,7 @@ version versionsuffix toolchain ``0.5-1`` ``-R-3.6.0`` ``foss/2019a`` ``0.5-2`` ``-R-3.6.2`` ``foss/2019b`` ``0.5-5`` ``-R-4.0.0`` ``foss/2020a`` +``0.5-5`` ``-R-4.1.0`` ``foss/2021a`` ========== ============= =============== @@ -35115,16 +36350,20 @@ The rjags package is an interface to the JAGS library. *homepage*: https://cran.r-project.org/web/packages/rjags -======== ============= =============== -version versionsuffix toolchain -======== ============= =============== -``4-6`` ``-R-3.4.0`` ``intel/2017a`` -``4-6`` ``-R-3.4.3`` ``intel/2017b`` -``4-8`` ``-R-3.5.1`` ``foss/2018b`` -``4-9`` ``-R-3.6.0`` ``foss/2019a`` -``4-10`` ``foss/2019b`` -``4-10`` ``-R-4.0.0`` ``foss/2020a`` -======== ============= =============== +======== ============= ================================== +version versionsuffix toolchain +======== ============= ================================== +``4-6`` ``-R-3.4.0`` ``intel/2017a`` +``4-6`` ``-R-3.4.3`` ``intel/2017b`` +``4-8`` ``-R-3.5.1`` ``foss/2018b`` +``4-9`` ``-R-3.6.0`` ``foss/2019a`` +``4-10`` ``foss/2019b`` +``4-10`` ``-R-4.0.0`` ``foss/2020a`` +``4-10`` ``-R-4.0.3`` ``foss/2020b``, ``fosscuda/2020b`` +``4-10`` ``-R-4.0.4`` ``foss/2020b``, ``fosscuda/2020b`` +``4-10`` ``-R-4.0.5`` ``foss/2020b``, ``fosscuda/2020b`` +``4-10`` ``-R-4.1.0`` ``foss/2021a`` +======== ============= ================================== .. _list_software_Rmath_508: @@ -35529,7 +36768,7 @@ version toolchain *RSeQC* +++++++ -RSeQC provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. +RSeQC provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. *homepage*: http://rseqc.sourceforge.net/ @@ -35539,6 +36778,7 @@ version versionsuffix toolchain ``2.6.4`` ``-Python-2.7.12-R-3.3.1`` ``foss/2016b`` ``2.6.4`` ``-Python-2.7.14`` ``intel/2018a`` ``3.0.0`` ``-Python-3.6.6`` ``foss/2018b`` +``4.0.0`` ``foss/2021a`` ``4.0.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ========================== =============== @@ -35592,6 +36832,7 @@ version versionsuffix toolchain ``1.2.5042`` ``-Java-11`` ``foss/2019b`` ``1.3.959`` ``-Java-11-R-4.0.0`` ``foss/2020a`` ``1.3.1093`` ``-Java-11-R-4.0.0`` ``foss/2020a`` +``1.4.1717`` ``-Java-11-R-4.1.0`` ``foss/2021a`` ============ ==================== ================== @@ -35694,6 +36935,7 @@ version toolchain ``1.37.0`` ``GCCcore/8.3.0`` ``1.42.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.52.1`` ``GCCcore/10.3.0`` +``1.54.0`` ``GCCcore/11.2.0`` ========== ========================================================================== @@ -35703,7 +36945,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_Snippy_643` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -35890,12 +37132,12 @@ Filter SAM file for soft and hard clipped alignments. *homepage*: https://github.com/tseemann/samclip -========= ================ ================= -version versionsuffix toolchain -========= ================ ================= -``0.2`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -``0.4.0`` ``GCCcore/9.3.0`` -========= ================ ================= +========= ================ ===================================== +version versionsuffix toolchain +========= ================ ===================================== +``0.2`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``0.4.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========= ================ ===================================== .. _list_software_SAMtools_786: @@ -35926,7 +37168,7 @@ version versionsuffix toolchain ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.10`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ``1.11`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` -``1.12`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` ========== ================= ======================================================================================================================================= @@ -36038,11 +37280,11 @@ ScaFaCoS is a library of scalable fast coulomb solvers. *homepage*: http://www.scafacos.de/ -========= =============================== -version toolchain -========= =============================== -``1.0.1`` ``foss/2020a``, ``intel/2020a`` -========= =============================== +========= =============================================================== +version toolchain +========= =============================================================== +``1.0.1`` ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``intel/2020a`` +========= =============================================================== .. _list_software_ScaLAPACK_707: @@ -36072,7 +37314,7 @@ version versionsuffix toolchain ``2.1.0`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b`` ``2.1.0`` ``-bf`` ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020b`` ``2.1.0`` ``-bl`` ``gompi/2020b`` -``2.1.0`` ``-fb`` ``gompi/2021a`` +``2.1.0`` ``-fb`` ``gompi/2021.07``, ``gompi/2021a`` ``2.2`` ``-amd`` ``gompi/2020a`` ========= ================================= ============================================================================================================================================ @@ -36091,6 +37333,7 @@ version toolchain ======= ================================ ``2.3`` ``foss/2016a`` ``2.5`` ``gompi/2019a``, ``gompi/2020a`` +``2.6`` ``gompic/2020b`` ======= ================================ @@ -36126,6 +37369,22 @@ version toolchain ========= ============== +.. _list_software_Schrodinger_1144: + +*Schrodinger* ++++++++++++++ + +Schrodinger aims to provide integrated software solutions and services that truly meet its customers needs. We want to empower researchers around the world to achieve their goals of improving human health and quality of life through advanced computational techniques that transform the way chemists design compounds and materials. + +*homepage*: https://www.schrodinger.com/ + +========== ========== +version toolchain +========== ========== +``2020-4`` ``system`` +========== ========== + + .. _list_software_sciClone_816: *sciClone* @@ -36201,13 +37460,13 @@ Scikit-Build, or skbuild, is an improved build system generator for CPython C/C+ *homepage*: https://scikit-build.readthedocs.io/en/latest -========== ================= ============================================================================================ -version versionsuffix toolchain -========== ================= ============================================================================================ -``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` -``0.11.1`` ``GCCcore/10.3.0``, ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -========== ================= ============================================================================================ +========== ================= ================================================================================================================ +version versionsuffix toolchain +========== ================= ================================================================================================================ +``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``0.11.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +========== ================= ================================================================================================================ .. _list_software_scikit-cuda_1105: @@ -36470,6 +37729,7 @@ version versionsuffix toolchain ``3.1.2`` ``GCCcore/9.3.0`` ``4.0.1`` ``GCCcore/10.2.0`` ``4.1.0.post1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``4.2.0`` ``GCCcore/11.2.0`` =============== ======================= ================================================================================= @@ -36507,7 +37767,7 @@ version toolchain ========= ================================================== ``2.0.1`` ``foss/2016a`` ``6.0`` ``gompi/2019a``, ``gompi/2020a``, ``gompic/2019b`` -``7.0`` ``gompic/2020b`` +``7.0`` ``gompi/2021a``, ``gompic/2020b`` ========= ================================================== @@ -36579,6 +37839,7 @@ scVelo is a scalable toolkit for estimating and analyzing RNA velocities in sing version versionsuffix toolchain ========== ================= ============== ``0.1.24`` ``-Python-3.7.4`` ``foss/2019b`` +``0.2.3`` ``foss/2021a`` ========== ================= ============== @@ -36646,7 +37907,7 @@ version toolchain ``2.0.8`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``2.0.9`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.0.10`` ``GCCcore/8.3.0`` -``2.0.14`` ``GCCcore/10.2.0`` +``2.0.14`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========== ====================================================================== @@ -36785,12 +38046,12 @@ segemehl is a software to map short sequencer reads to reference genomes. Unli *homepage*: http://www.bioinf.uni-leipzig.de/Software/segemehl/ -========= ================================================ -version toolchain -========= ================================================ -``0.2.0`` ``foss/2016b``, ``intel/2017b``, ``intel/2018a`` -``0.3.4`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``foss/2018b`` -========= ================================================ +========= ============================================================= +version toolchain +========= ============================================================= +``0.2.0`` ``foss/2016b``, ``intel/2017b``, ``intel/2018a`` +``0.3.4`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``foss/2018b`` +========= ============================================================= .. _list_software_segmentation-models_1983: @@ -36985,11 +38246,11 @@ C++ interface to HTSlib, BWA-MEM and Fermi. *homepage*: https://github.com/walaj/SeqLib -========= ============= -version toolchain -========= ============= -``1.2.0`` ``GCC/9.3.0`` -========= ============= +========= ============================= +version toolchain +========= ============================= +``1.2.0`` ``GCC/10.2.0``, ``GCC/9.3.0`` +========= ============================= .. _list_software_Seqmagick_917: @@ -37051,11 +38312,11 @@ The serf library is a high performance C-based HTTP client library built upon t *homepage*: http://serf.apache.org/ -========= ================================================================================================================================================= -version toolchain -========= ================================================================================================================================================= -``1.3.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``intel/2017b``, ``iomkl/2018a`` -========= ================================================================================================================================================= +========= ===================================================================================================================================================================== +version toolchain +========= ===================================================================================================================================================================== +``1.3.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``intel/2017b``, ``iomkl/2018a`` +========= ===================================================================================================================================================================== .. _list_software_setuptools_1122: @@ -37236,13 +38497,14 @@ Shapely is a BSD-licensed Python package for manipulation and analysis of planar *homepage*: https://github.com/Toblerity/Shapely -========= ================= ====================================== -version versionsuffix toolchain -========= ================= ====================================== -``1.7.0`` ``-Python-3.7.2`` ``foss/2019a`` -``1.7.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``1.7.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` -========= ================= ====================================== +========= ================= ======================================================= +version versionsuffix toolchain +========= ================= ======================================================= +``1.7.0`` ``-Python-3.7.2`` ``foss/2019a`` +``1.7.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``1.7.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``1.8a1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` +========= ================= ======================================================= .. _list_software_sharutils_991: @@ -37335,11 +38597,12 @@ A std::streambuf wrapper for compression formats. *homepage*: https://github.com/jonathonl/shrinkwrap -============== ================= -version toolchain -============== ================= -``1.0.0-beta`` ``GCCcore/8.2.0`` -============== ================= +============== ================== +version toolchain +============== ================== +``1.0.0-beta`` ``GCCcore/8.2.0`` +``1.1.0`` ``GCCcore/10.2.0`` +============== ================== .. _list_software_Sibelia_697: @@ -37607,16 +38870,16 @@ SIONlib is a scalable I/O library for parallel access to task-local files. The *homepage*: https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html -========= ============= ======================================================== -version versionsuffix toolchain -========= ============= ======================================================== -``1.6.1`` ``foss/2016a`` -``1.6.1`` ``-tools`` ``foss/2016a`` -``1.7.1`` ``foss/2017a`` -``1.7.1`` ``-tools`` ``foss/2017a`` -``1.7.4`` ``-tools`` ``GCCcore/8.2.0`` -``1.7.6`` ``-tools`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ============= ======================================================== +========= ============= ============================================================================ +version versionsuffix toolchain +========= ============= ============================================================================ +``1.6.1`` ``foss/2016a`` +``1.6.1`` ``-tools`` ``foss/2016a`` +``1.7.1`` ``foss/2017a`` +``1.7.1`` ``-tools`` ``foss/2017a`` +``1.7.4`` ``-tools`` ``GCCcore/8.2.0`` +``1.7.6`` ``-tools`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ============= ============================================================================ .. _list_software_SIP_236: @@ -37691,6 +38954,22 @@ version toolchain ========= =============== +.. _list_software_sklearn-som_1132: + +*sklearn-som* ++++++++++++++ + +A simple, planar self-organizing map with methods similar to clustering methods in Scikit Learn. + +*homepage*: https://github.com/rileypsmith/sklearn-som + +========= ============== +version toolchain +========= ============== +``1.1.0`` ``foss/2020b`` +========= ============== + + .. _list_software_SLATEC_444: *SLATEC* @@ -37725,6 +39004,8 @@ version versionsuffix toolchain ``3.12.2`` ``-Python-2.7.16`` ``intel/2019b`` ``3.12.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.12.2`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``3.14.2`` ``foss/2020b`` +``3.15.1`` ``foss/2021a`` ========== ================== =============================== @@ -37742,6 +39023,7 @@ version versionsuffix toolchain ========== ================= ============== ``3.9.0`` ``-Python-3.6.4`` ``foss/2018a`` ``3.12.0`` ``-Python-3.7.4`` ``foss/2019b`` +``3.15.1`` ``foss/2021a`` ========== ================= ============== @@ -37852,11 +39134,11 @@ smith-waterman-gotoh alignment algorithm. *homepage*: https://github.com/ekg/smithwaterman -============ ================= -version toolchain -============ ================= -``20160702`` ``GCCcore/9.3.0`` -============ ================= +============ ===================================== +version toolchain +============ ===================================== +``20160702`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +============ ===================================== .. _list_software_Smoldyn_742: @@ -37909,6 +39191,7 @@ version versionsuffix toolchain ``5.7.1`` ``-Python-3.7.2`` ``foss/2019a`` ``5.26.1`` ``-Python-3.8.2`` ``intel/2020a`` ``6.1.0`` ``foss/2020b`` +``6.6.1`` ``foss/2021a`` ========== ================= =============================== @@ -37994,15 +39277,32 @@ version toolchain ``1.1.6`` ``system`` ``1.1.7`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``intel/2017b`` ``1.1.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``1.1.9`` ``GCCcore/11.2.0`` ========= ============================================================================================================ +.. _list_software_Snippy_643: + +*Snippy* +++++++++ + +Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). Rapid haploid variant calling and core genome alignment. + +*homepage*: https://github.com/tseemann/snippy + +========= ========================= ============= +version versionsuffix toolchain +========= ========================= ============= +``4.6.0`` ``-Java-13-Python-3.8.2`` ``GCC/9.3.0`` +========= ========================= ============= + + .. _list_software_snippy_675: *snippy* ++++++++ -Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). Rapid haploid variant calling and core genome alignment. +Rapid haploid variant calling and core genome alignment *homepage*: https://github.com/tseemann/snippy @@ -38010,6 +39310,7 @@ Snippy finds SNPs between a haploid reference genome and your NGS sequence read version versionsuffix toolchain ========= ================ ============== ``4.4.1`` ``-Perl-5.28.0`` ``foss/2018b`` +``4.6.0`` ``GCC/10.2.0`` ========= ================ ============== @@ -38022,11 +39323,11 @@ Finds SNP sites from a multi-FASTA alignment file. *homepage*: https://sanger-pathogens.github.io/snp-sites/ -========= ================= -version toolchain -========= ================= -``2.5.1`` ``GCCcore/9.3.0`` -========= ================= +========= ===================================== +version toolchain +========= ===================================== +``2.5.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========= ===================================== .. _list_software_snpEff_610: @@ -38034,19 +39335,20 @@ version toolchain *snpEff* ++++++++ -SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). +SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). *homepage*: https://pcingola.github.io/SnpEff/ -======== ========================= ================= -version versionsuffix toolchain -======== ========================= ================= -``3.6`` ``-Java-1.7.0_80`` ``system`` -``4.1d`` ``-Java-1.7.0_80`` ``system`` -``4.3t`` ``-Java-1.8`` ``system`` -``5.0`` ``-Java-13`` ``system`` -``5.0`` ``-Java-13-Python-3.8.2`` ``GCCcore/9.3.0`` -======== ========================= ================= +======== ========================= ================== +version versionsuffix toolchain +======== ========================= ================== +``3.6`` ``-Java-1.7.0_80`` ``system`` +``4.1d`` ``-Java-1.7.0_80`` ``system`` +``4.3t`` ``-Java-1.8`` ``system`` +``5.0`` ``-Java-13`` ``system`` +``5.0`` ``-Java-13-Python-3.8.2`` ``GCCcore/9.3.0`` +``5.0e`` ``-Java-13`` ``GCCcore/10.2.0`` +======== ========================= ================== .. _list_software_SNPhylo_685: @@ -38177,6 +39479,7 @@ SOCI is a database access library for C++ that makes the illusion of embedding S version toolchain ========= ================================= ``4.0.1`` ``GCC/10.2.0``, ``GCCcore/9.3.0`` +``4.0.2`` ``GCC/10.3.0`` ========= ================================= @@ -38212,6 +39515,22 @@ version toolchain ============ =============== +.. _list_software_SoQt_391: + +*SoQt* +++++++ + +SoQt is a Qt GUI component toolkit library for Coin. It is also compatible with SGI and TGS Open Inventor, and the API is based on the API of the InventorXt GUI component toolkit. + +*homepage*: https://coin3d.github.io/SoQt/html + +========= ============== +version toolchain +========= ============== +``1.6.0`` ``GCC/10.3.0`` +========= ============== + + .. _list_software_SortMeRNA_827: *SortMeRNA* @@ -38253,12 +39572,13 @@ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq *homepage*: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger -========= ============= -version toolchain -========= ============= -``1.1.0`` ``GCC/9.3.0`` -``1.2.2`` ``GCC/9.3.0`` -========= ============= +========= ============== +version toolchain +========= ============== +``1.1.0`` ``GCC/9.3.0`` +``1.2.2`` ``GCC/9.3.0`` +``1.3.0`` ``GCC/10.3.0`` +========= ============== .. _list_software_Spack_498: @@ -38276,6 +39596,7 @@ version toolchain ``0.10.0`` ``system`` ``0.11.2`` ``system`` ``0.12.1`` ``system`` +``0.16.2`` ``system`` ========== ========== @@ -38387,9 +39708,42 @@ A collection of all the estimation functions for spatial cross-sectional models version versionsuffix toolchain ========= ============= ============== ``1.1-5`` ``-R-3.6.2`` ``foss/2019b`` +``1.1-8`` ``-R-4.1.0`` ``foss/2021a`` ========= ============= ============== +.. _list_software_spdlog_649: + +*spdlog* +++++++++ + +Very fast, header-only/compiled, C++ logging library. + +*homepage*: https://github.com/gabime/spdlog + +========= ================== +version toolchain +========= ================== +``1.9.2`` ``GCCcore/10.3.0`` +========= ================== + + +.. _list_software_SpectrA_690: + +*SpectrA* ++++++++++ + +Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library. + +*homepage*: https://spectralib.org/ + +========= ============== +version toolchain +========= ============== +``1.0.0`` ``GCC/10.2.0`` +========= ============== + + .. _list_software_spectral.methods_1664: *spectral.methods* @@ -38450,19 +39804,20 @@ Spglib for Python. Spglib is a library for finding and handling crystal symmetri *homepage*: https://pypi.python.org/pypi/spglib -================ ================== =================================================== -version versionsuffix toolchain -================ ================== =================================================== -``1.9.4.2`` ``-Python-2.7.12`` ``intel/2016b`` -``1.9.5`` ``-Python-2.7.12`` ``intel/2016b`` -``1.9.9.38`` ``-Python-2.7.13`` ``intel/2017a`` -``1.10.0.2`` ``-Python-2.7.14`` ``intel/2017b`` -``1.10.0.2`` ``-Python-3.6.3`` ``intel/2017b`` -``1.14.1.post0`` ``-Python-3.7.2`` ``intel/2019a`` -``1.16.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``1.16.0`` ``-Python-3.7.4`` ``intel/2019b`` -``1.16.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -================ ================== =================================================== +================ ================== ======================================================== +version versionsuffix toolchain +================ ================== ======================================================== +``1.9.4.2`` ``-Python-2.7.12`` ``intel/2016b`` +``1.9.5`` ``-Python-2.7.12`` ``intel/2016b`` +``1.9.9.38`` ``-Python-2.7.13`` ``intel/2017a`` +``1.10.0.2`` ``-Python-2.7.14`` ``intel/2017b`` +``1.10.0.2`` ``-Python-3.6.3`` ``intel/2017b`` +``1.14.1.post0`` ``-Python-3.7.2`` ``intel/2019a`` +``1.16.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``1.16.0`` ``-Python-3.7.4`` ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` +``1.16.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.16.1`` ``foss/2021a`` +================ ================== ======================================================== .. _list_software_Sphinx_634: @@ -38686,6 +40041,7 @@ version toolchain ``3.31.1`` ``GCCcore/9.3.0`` ``3.33.0`` ``GCCcore/10.2.0`` ``3.35.4`` ``GCCcore/10.3.0`` +``3.36`` ``GCCcore/11.2.0`` ============ ==================================================================================================================================================================== @@ -38809,11 +40165,11 @@ SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Si *homepage*: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library -======= ================= -version toolchain -======= ================= -``1.1`` ``GCCcore/9.3.0`` -======= ================= +======= ===================================== +version toolchain +======= ===================================== +``1.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +======= ===================================== .. _list_software_Stack_502: @@ -38946,6 +40302,7 @@ version toolchain ``2.7.6a`` ``GCC/10.2.0``, ``GCC/9.3.0`` ``2.7.7a`` ``GCC/10.2.0``, ``GCC/9.3.0`` ``2.7.8a`` ``GCC/10.2.0`` +``2.7.9a`` ``GCC/10.3.0`` ========== ============================================================== @@ -39039,6 +40396,7 @@ version versionsuffix toolchain ``0.11.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``0.11.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``0.12.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``0.12.2`` ``foss/2021a`` ========== ================== =================================================== @@ -39147,6 +40505,7 @@ version toolchain ``2.1.1`` ``GCC/8.3.0`` ``2.1.3`` ``GCC/8.3.0``, ``GCC/9.3.0`` ``2.1.4`` ``GCC/8.3.0``, ``GCC/9.3.0`` +``2.1.7`` ``GCC/10.3.0`` ========== ================================== @@ -39199,6 +40558,7 @@ version toolchain ``1.6.4`` ``foss/2018b`` ``2.0.0`` ``GCC/7.3.0-2.30``, ``GCC/8.3.0`` ``2.0.2`` ``GCC/10.2.0`` +``2.0.3`` ``GCC/10.3.0`` ============ ================================= @@ -39211,16 +40571,16 @@ Subversion is an open source version control system. *homepage*: http://subversion.apache.org/ -========== ===================================== -version toolchain -========== ===================================== -``1.9.7`` ``iomkl/2018a`` -``1.9.9`` ``GCCcore/7.3.0`` -``1.10.0`` ``foss/2017b``, ``intel/2017b`` -``1.12.0`` ``GCCcore/8.2.0`` -``1.14.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``1.14.1`` ``GCCcore/10.3.0`` -========== ===================================== +========== ====================================== +version toolchain +========== ====================================== +``1.9.7`` ``iomkl/2018a`` +``1.9.9`` ``GCCcore/7.3.0`` +``1.10.0`` ``foss/2017b``, ``intel/2017b`` +``1.12.0`` ``GCCcore/8.2.0`` +``1.14.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.14.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ====================================== .. _list_software_suds_447: @@ -39263,7 +40623,7 @@ version versionsuffix toolchain ``5.4.0`` ``-METIS-5.1.0`` ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` ``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b``, ``intel/2019b`` ``5.7.1`` ``-METIS-5.1.0`` ``foss/2020a``, ``intel/2020a`` -``5.8.1`` ``-METIS-5.1.0`` ``foss/2020b`` +``5.8.1`` ``-METIS-5.1.0`` ``foss/2020b``, ``intel/2020b`` ``5.10.1`` ``-METIS-5.1.0`` ``foss/2021a`` ========== =================== ================================================================================================= @@ -39547,7 +40907,7 @@ version versionsuffix toolchain ``3.0.12`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.0.12`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``4.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.0.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``4.0.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ============================ ================================================================ @@ -39572,7 +40932,7 @@ version toolchain *SymEngine* +++++++++++ -SymEngine is a standalone fast C++ symbolic manipulation library. +SymEngine is a standalone fast C++ symbolic manipulation library *homepage*: https://github.com/symengine/symengine @@ -39581,9 +40941,26 @@ version versionsuffix toolchain ========= ============= ==================== ``0.3.0`` ``-20181006`` ``intel/2018a`` ``0.4.0`` ``GCC/8.2.0-2.31.1`` +``0.7.0`` ``GCC/10.3.0`` ========= ============= ==================== +.. _list_software_SymEngine-python_1630: + +*SymEngine-python* +++++++++++++++++++ + +Python wrappers to the C++ library SymEngine, a fast C++ symbolic manipulation library. + +*homepage*: https://github.com/symengine/symengine.py + +========= ============== +version toolchain +========= ============== +``0.7.2`` ``GCC/10.3.0`` +========= ============== + + .. _list_software_SYMPHONY_647: *SYMPHONY* @@ -39620,11 +40997,27 @@ version versionsuffix toolchain ``1.4`` ``foss/2019a``, ``intel/2019a`` ``1.5.1`` ``-Python-3.7.4`` ``foss/2019b`` ``1.6.2`` ``-Python-3.8.2`` ``foss/2020a`` -``1.7.1`` ``foss/2020b`` +``1.7.1`` ``foss/2020b``, ``intel/2020b`` ``1.8`` ``foss/2021a`` ========= ================== =============================== +.. _list_software_SyRI_359: + +*SyRI* +++++++ + +Synteny and Rearrangement Identifier (SyRI). + +*homepage*: https://schneebergerlab.github.io/syri/ + +======= ============== +version toolchain +======= ============== +``1.4`` ``foss/2021a`` +======= ============== + + .. _list_software_Szip_422: *Szip* @@ -39638,7 +41031,7 @@ Szip compression software, providing lossless compression of scientific data version toolchain ========= ============================================================================================================================================================================================================================================================================================= ``2.1`` ``GCC/4.8.1``, ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``gmpolf/2017.10``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================================================================================================================================================================================================= @@ -39648,7 +41041,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_typing-extensions_1816` +:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` .. _list_software_tabix_536: @@ -39660,11 +41053,11 @@ Generic indexer for TAB-delimited genome position files *homepage*: http://samtools.sourceforge.net -========= ========================================================================================================= -version toolchain -========= ========================================================================================================= -``0.2.6`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``intel/2016a``, ``intel/2016b`` -========= ========================================================================================================= +========= ================================================================================================================================================ +version toolchain +========= ================================================================================================================================================ +``0.2.6`` ``GCCcore/10.2.0``, ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``intel/2016a``, ``intel/2016b`` +========= ================================================================================================================================================ .. _list_software_tabixpp_760: @@ -39886,7 +41279,7 @@ version toolchain ``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``8.6.10`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``8.6.11`` ``GCCcore/10.3.0`` +``8.6.11`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ========================================================================================================================================================================= @@ -39899,12 +41292,12 @@ TCLAP is a small, flexible library that provides a simple interface for defining *homepage*: http://tclap.sourceforge.net/ -========= ================= -version toolchain -========= ================= -``1.2.2`` ``GCCcore/8.3.0`` -``1.2.4`` ``GCCcore/9.3.0`` -========= ================= +========= ===================================== +version toolchain +========= ===================================== +``1.2.2`` ``GCCcore/8.3.0`` +``1.2.4`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +========= ===================================== .. _list_software_tcsh_434: @@ -39923,6 +41316,7 @@ version toolchain ``6.20.00`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``6.22.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``6.22.03`` ``GCCcore/10.2.0`` +``6.22.04`` ``GCCcore/10.3.0`` =========== ======================================================= @@ -40051,6 +41445,8 @@ version versionsuffix toolchain ``2.4.1`` ``foss/2020b``, ``fosscuda/2020b`` ``2.4.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``2.5.0`` ``foss/2020b``, ``fosscuda/2020b`` +``2.6.0`` ``foss/2021a`` +``2.6.0`` ``-CUDA-11.3.1`` ``foss/2021a`` ========== ============================= =================================================== @@ -40164,11 +41560,12 @@ A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator *homepage*: http://wias-berlin.de/software/index.jsp?id=TetGen -========= ================= -version toolchain -========= ================= -``1.5.0`` ``GCCcore/6.4.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``1.5.0`` ``GCCcore/6.4.0`` +``1.6.0`` ``GCCcore/10.2.0`` +========= ================== .. _list_software_TEToolkit_895: @@ -40413,12 +41810,12 @@ The `time' command runs another program, then displays information about the res *homepage*: https://www.gnu.org/software/time/ -======= =========================================================================== -version toolchain -======= =========================================================================== -``1.7`` ``system`` -``1.9`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= =========================================================================== +======= =================================================================================================================== +version toolchain +======= =================================================================================================================== +``1.7`` ``system`` +``1.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= =================================================================================================================== .. _list_software_TINKER_461: @@ -40477,7 +41874,7 @@ version versionsuffix toolchain ``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2018a``, ``iomkl/2018a`` ``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``8.6.10`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``8.6.11`` ``GCCcore/10.3.0`` +``8.6.11`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ================= ================================================================================================================================================ @@ -40508,6 +41905,8 @@ version versionsuffix toolchain ``3.7.4`` ``GCCcore/8.3.0`` ``3.8.2`` ``GCCcore/9.3.0`` ``3.8.6`` ``GCCcore/10.2.0`` +``3.9.5`` ``GCCcore/10.3.0`` +``3.9.6`` ``GCCcore/11.2.0`` ========== ================== ========================================================================================================= @@ -40552,16 +41951,16 @@ tmux is a terminal multiplexer: it enables a number of terminals to be created, *homepage*: https://github.com/tmux/tmux/ -======== ===================================== -version toolchain -======== ===================================== -``1.9a`` ``GCC/4.9.2`` -``2.2`` ``GCCcore/4.9.3`` -``2.3`` ``GCC/5.4.0-2.26``, ``system`` -``3.1c`` ``GCCcore/8.3.0`` -``3.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.2a`` ``GCCcore/10.3.0`` -======== ===================================== +======== ====================================== +version toolchain +======== ====================================== +``1.9a`` ``GCC/4.9.2`` +``2.2`` ``GCCcore/4.9.3`` +``2.3`` ``GCC/5.4.0-2.26``, ``system`` +``3.1c`` ``GCCcore/8.3.0`` +``3.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.2a`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +======== ====================================== .. _list_software_ToFu_382: @@ -40651,6 +42050,22 @@ version versionsuffix toolchain ========= =============================== ================================== +.. _list_software_torchinfo_972: + +*torchinfo* ++++++++++++ + +" Torchinfo provides information complementary to what is provided by print(your_model) in PyTorch, similar to Tensorflow's model.summary() API to view the visualization of the model, which is helpful while debugging your network. + +*homepage*: https://github.com/TylerYep/torchinfo + +========= ================== ================================== +version versionsuffix toolchain +========= ================== ================================== +``1.5.2`` ``-PyTorch-1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` +========= ================== ================================== + + .. _list_software_torchtext_997: *torchtext* @@ -40666,6 +42081,7 @@ version versionsuffix toolchain ``0.5.0`` ``-PyTorch-1.4.0-Python-3.7.4`` ``fosscuda/2019b`` ``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` ``0.8.1`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` +``0.9.1`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` ========= =============================== ================================== @@ -40693,6 +42109,7 @@ version versionsuffix toolchain ``0.8.2`` ``-PyTorch-1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` ``0.8.2`` ``-Python-3.7.4-PyTorch-1.7.1`` ``fosscuda/2019b`` ``0.9.1`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` +``0.9.1`` ``-Python-3.7.4-PyTorch-1.8.1`` ``fosscuda/2019b`` ========= ==================================== ================================== @@ -40736,6 +42153,8 @@ version versionsuffix toolchain ``4.51.0`` ``-Python-3.8.2`` ``intel/2020a`` ``4.56.2`` ``GCCcore/10.2.0`` ``4.60.0`` ``GCCcore/10.2.0`` +``4.61.1`` ``GCCcore/10.3.0`` +``4.61.2`` ``GCCcore/10.3.0`` ========== ================== =============================== @@ -40836,6 +42255,22 @@ version versionsuffix toolchain ========= =============== ========== +.. _list_software_TRAVIS-Analyzer_1356: + +*TRAVIS-Analyzer* ++++++++++++++++++ + +TRAVIS is a free tool for analyzing and visualizing trajectories from all kinds of Molecular Dynamics or Monte Carlo simulations. + +*homepage*: http://www.travis-analyzer.de/ + +========== ============== +version toolchain +========== ============== +``210521`` ``GCC/10.3.0`` +========== ============== + + .. _list_software_treatSens_953: *treatSens* @@ -41243,6 +42678,22 @@ version versionsuffix toolchain ============ ================== =============== +.. _list_software_TWL-NINJA_660: + +*TWL-NINJA* ++++++++++++ + +Nearly Infinite Neighbor Joining Application. + +*homepage*: https://github.com/TravisWheelerLab/NINJA + +===================== ============== +version toolchain +===================== ============== +``0.97-cluster_only`` ``GCC/10.2.0`` +===================== ============== + + .. _list_software_typing-extensions_1816: *typing-extensions* @@ -41268,7 +42719,7 @@ version versionsuffix toolchain --- -:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_UCX-CUDA_570` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_unimap_650` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` +:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_UCX-CUDA_570` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_unimap_650` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_UShER_423` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` .. _list_software_UCLUST_480: @@ -41309,6 +42760,7 @@ version versionsuffix toolchain ``1.9.0`` ``GCCcore/10.2.0`` ``1.9.0`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` ``1.10.0`` ``GCCcore/10.3.0`` +``1.11.0`` ``GCCcore/11.2.0`` ============ ================ ======================================================= @@ -41325,6 +42777,7 @@ Unified Communication X An open-source production grade communication framework version versionsuffix toolchain ========== ================ ================== ``1.10.0`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` +``1.11.0`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` ========== ================ ================== @@ -41361,7 +42814,7 @@ version toolchain ``2.2.24`` ``intel/2017a`` ``2.2.25`` ``foss/2017b``, ``intel/2017b`` ``2.2.26`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``2.2.28`` ``GCCcore/10.3.0`` +``2.2.28`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== =============================================================================================================================================================================================== @@ -41554,12 +43007,13 @@ RAR is a powerful archive manager. *homepage*: https://www.rarlab.com/ -========= ================= -version toolchain -========= ================= -``5.6.1`` ``GCCcore/7.3.0`` -``5.7.3`` ``GCCcore/8.2.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``5.6.1`` ``GCCcore/7.3.0`` +``5.7.3`` ``GCCcore/8.2.0`` +``6.0.2`` ``GCCcore/10.2.0`` +========= ================== .. _list_software_UnZip_502: @@ -41571,11 +43025,11 @@ UnZip is an extraction utility for archives compressed in .zip format (also call *homepage*: http://www.info-zip.org/UnZip.html -======= ===================================================================================================================================== -version toolchain -======= ===================================================================================================================================== -``6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ===================================================================================================================================== +======= ========================================================================================================================================================= +version toolchain +======= ========================================================================================================================================================= +``6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ========================================================================================================================================================= .. _list_software_UQTk_357: @@ -41613,6 +43067,22 @@ version versionsuffix toolchain =================== =============== ========== +.. _list_software_UShER_423: + +*UShER* ++++++++ + +UShER is now a package consisting of a family of programs for rapid phylogenetic analyses, particularly suitable for the SARS-CoV-2 genomes. + +*homepage*: https://github.com/yatisht/usher + +========= =============== +version toolchain +========= =============== +``0.4.1`` ``gompi/2020b`` +========= =============== + + .. _list_software_USPEX_405: *USPEX* @@ -41644,7 +43114,7 @@ version toolchain ``2.2.0`` ``GCCcore/6.4.0`` ``2.3.0`` ``GCCcore/8.2.0`` ``2.5.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.6.1`` ``GCCcore/10.3.0`` +``2.6.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ======================================================== @@ -41675,6 +43145,7 @@ version toolchain ``2.34`` ``GCCcore/8.3.0`` ``2.35`` ``GCCcore/9.3.0`` ``2.36`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.37`` ``GCCcore/11.2.0`` ========== ====================================== @@ -41684,7 +43155,7 @@ version toolchain --- -:ref:`list_software_V8_142` - :ref:`list_software_Vala_388` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcflib_630` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VMD_231` - :ref:`list_software_voltools_898` - :ref:`list_software_vorbis-tools_1267` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` +:ref:`list_software_V8_142` - :ref:`list_software_Vala_388` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_Vampire_724` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VBZ-Compression_1457` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcflib_630` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VisPy_507` - :ref:`list_software_VMD_231` - :ref:`list_software_voltools_898` - :ref:`list_software_vorbis-tools_1267` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` .. _list_software_V8_142: @@ -41759,6 +43230,22 @@ version versionsuffix toolchain ========= ============= ========== +.. _list_software_Vampire_724: + +*Vampire* ++++++++++ + +The Vampire Theorem Prover. + +*homepage*: https://vprover.github.io/ + +========= ================== +version toolchain +========= ================== +``4.5.1`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_VarDict_685: *VarDict* @@ -41873,6 +43360,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_VBZ-Compression_1457: + +*VBZ-Compression* ++++++++++++++++++ + +VBZ compression HDF5 plugin for nanopolish + +*homepage*: https://github.com/nanoporetech/vbz_compression + +========= =============== +version toolchain +========= =============== +``1.0.1`` ``gompi/2020b`` +========= =============== + + .. _list_software_VCF-kit_596: *VCF-kit* @@ -41898,11 +43401,12 @@ vcflib provides methods to manipulate and interpret sequence variation as it can *homepage*: https://github.com/vcflib/vcflib -========= ================= ============= -version versionsuffix toolchain -========= ================= ============= -``1.0.2`` ``-Python-3.8.2`` ``GCC/9.3.0`` -========= ================= ============= +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.0.2`` ``GCC/10.2.0`` +``1.0.2`` ``-Python-3.8.2`` ``GCC/9.3.0`` +========= ================= ============== .. _list_software_vcfnp_541: @@ -41930,16 +43434,16 @@ The aim of VCFtools is to provide easily accessible methods for working with c *homepage*: https://vcftools.github.io -========== ================ ===================================================================== -version versionsuffix toolchain -========== ================ ===================================================================== -``0.1.14`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` -``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` -``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` -``0.1.16`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` -``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` -========== ================ ===================================================================== +========== ================ ===================================================================================== +version versionsuffix toolchain +========== ================ ===================================================================================== +``0.1.14`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` +``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` +``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` +``0.1.16`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` +``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` +========== ================ ===================================================================================== .. _list_software_VEGAS_374: @@ -41970,6 +43474,7 @@ Velocyto is a library for the analysis of RNA velocity. =========== ================= =============== version versionsuffix toolchain =========== ================= =============== +``0.17.17`` ``foss/2021a`` ``0.17.17`` ``-Python-3.8.2`` ``intel/2020a`` =========== ================= =============== @@ -42116,6 +43621,22 @@ version toolchain ========= ================= +.. _list_software_VisPy_507: + +*VisPy* ++++++++ + +VisPy is a high-performance interactive 2D/3D data visualization library leveraging the computational power of modern Graphics Processing Units (GPUs) through the OpenGL library to display very large datasets. + +*homepage*: https://vispy.org + +========= =============================== +version toolchain +========= =============================== +``0.6.6`` ``foss/2020b``, ``intel/2020b`` +========= =============================== + + .. _list_software_VMD_231: *VMD* @@ -42161,11 +43682,11 @@ Command-line tools for creating and playing Ogg Vorbis files. *homepage*: https://xiph.org/vorbis/ -========= ====================================== -version toolchain -========= ====================================== -``1.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========= ====================================== +========= ========================================================== +version toolchain +========= ========================================================== +``1.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ========================================================== .. _list_software_Voro++_508: @@ -42177,11 +43698,11 @@ Voro++ is a software library for carrying out three-dimensional computations of *homepage*: http://math.lbl.gov/voro++/ -========= ====================================================================================================== -version toolchain -========= ====================================================================================================== -``0.4.6`` ``GCCcore/6.4.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2019b``, ``intel/2016a``, ``intel/2019b`` -========= ====================================================================================================== +========= ============================================================================================================================================== +version toolchain +========= ============================================================================================================================================== +``0.4.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2019b``, ``intel/2016a``, ``intel/2019b`` +========= ============================================================================================================================================== .. _list_software_vsc-base_788: @@ -42334,11 +43855,11 @@ A tool set for short variant discovery in genetic sequence data. *homepage*: http://genome.sph.umich.edu/wiki/Vt -=========== ============================= -version toolchain -=========== ============================= -``0.57721`` ``GCC/9.3.0``, ``foss/2018b`` -=========== ============================= +=========== ============================================= +version toolchain +=========== ============================================= +``0.57721`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``foss/2018b`` +=========== ============================================= .. _list_software_VTK_245: @@ -42402,6 +43923,7 @@ version toolchain ``2019_update3`` ``system`` ``2019_update5`` ``system`` ``2020_update3`` ``system`` +``2021.6.0`` ``system`` ================= ========== @@ -42443,7 +43965,7 @@ version toolchain --- -:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_WCT_238` - :ref:`list_software_wcwidth_762` - :ref:`list_software_webin-cli_890` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_WHAM_301` - :ref:`list_software_WhatsHap_800` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` +:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_WCT_238` - :ref:`list_software_wcwidth_762` - :ref:`list_software_webin-cli_890` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wgsim_551` - :ref:`list_software_WHAM_301` - :ref:`list_software_WhatsHap_800` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` .. _list_software_wandb_524: @@ -42621,6 +44143,22 @@ version toolchain ========== ===================================== +.. _list_software_wgsim_551: + +*wgsim* ++++++++ + +Wgsim is a small tool for simulating sequence reads from a reference genome. + +*homepage*: https://github.com/lh3/wgsim/ + +============ ============== +version toolchain +============ ============== +``20111017`` ``GCC/10.2.0`` +============ ============== + + .. _list_software_WHAM_301: *WHAM* @@ -42695,6 +44233,8 @@ version toolchain ``17.1`` ``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` ``18.1`` ``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` ``19.1`` ``intel/2019a`` +``19.2`` ``intel/2020b`` +``21.1`` ``intel/2021a`` ======== ================================================ @@ -42819,6 +44359,7 @@ version versionsuffix toolchain ``4.0.1`` ``-dmpar`` ``intel/2018b`` ``4.0.2`` ``-dmpar`` ``foss/2018b`` ``4.1`` ``-dmpar`` ``intel/2019b`` +``4.2`` ``-dmpar`` ``foss/2020b`` ========= ============= =============== @@ -42829,7 +44370,7 @@ version versionsuffix toolchain The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. -*homepage*: http://www.wrf-model.org +*homepage*: https://www.wrf-model.org =========== ============= ================================================================ version versionsuffix toolchain @@ -42840,6 +44381,8 @@ version versionsuffix toolchain ``4.0.2`` ``-dmpar`` ``foss/2018b`` ``4.1.3`` ``-dm+sm`` ``intel/2019b`` ``4.1.3`` ``-dmpar`` ``foss/2019b``, ``intel/2019b`` +``4.2.2`` ``-dmpar`` ``foss/2020b`` +``4.3`` ``-dmpar`` ``foss/2021a`` =========== ============= ================================================================ @@ -42948,6 +44491,7 @@ version toolchain ``3.0.4`` ``GCC/8.2.0-2.31.1`` ``3.1.3`` ``GCC/8.3.0`` ``3.1.4`` ``GCC/10.2.0`` +``3.1.5`` ``GCC/10.3.0`` ========= ==================== @@ -42957,7 +44501,7 @@ version toolchain --- -:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_XZ_178` +:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xTB_270` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_XZ_178` .. _list_software_X11_186: @@ -42983,6 +44527,7 @@ version toolchain ``20200222`` ``GCCcore/9.3.0`` ``20201008`` ``GCCcore/10.2.0`` ``20210518`` ``GCCcore/10.3.0`` +``20210802`` ``GCCcore/11.2.0`` ============ ================================================== @@ -43013,6 +44558,7 @@ version toolchain ``20191217`` ``GCCcore/9.3.0`` ``20201026`` ``GCCcore/10.2.0`` ``20210414`` ``GCCcore/10.3.0`` +``20210613`` ``GCCcore/11.2.0`` ============ ================================= @@ -43025,19 +44571,19 @@ x265 is a free software library and application for encoding video streams into *homepage*: https://x265.org/ -======= ===================================== -version toolchain -======= ===================================== -``2.4`` ``foss/2016b`` -``2.5`` ``intel/2017a`` -``2.6`` ``GCCcore/6.4.0``, ``intel/2017b`` -``2.7`` ``GCCcore/6.4.0`` -``2.9`` ``GCCcore/7.3.0`` -``3.0`` ``GCCcore/8.2.0`` -``3.2`` ``GCCcore/8.3.0`` -``3.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.5`` ``GCCcore/10.3.0`` -======= ===================================== +======= ====================================== +version toolchain +======= ====================================== +``2.4`` ``foss/2016b`` +``2.5`` ``intel/2017a`` +``2.6`` ``GCCcore/6.4.0``, ``intel/2017b`` +``2.7`` ``GCCcore/6.4.0`` +``2.9`` ``GCCcore/7.3.0`` +``3.0`` ``GCCcore/8.2.0`` +``3.2`` ``GCCcore/8.3.0`` +``3.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.5`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +======= ====================================== .. _list_software_XALT_313: @@ -43065,23 +44611,24 @@ xarray (formerly xray) is an open source project and Python package that aims to *homepage*: https://github.com/pydata/xarray -========== ================== =================================== -version versionsuffix toolchain -========== ================== =================================== -``0.9.5`` ``-Python-2.7.13`` ``intel/2017a`` -``0.9.5`` ``-Python-3.6.1`` ``intel/2017a`` -``0.9.6`` ``-Python-2.7.13`` ``intel/2017a`` -``0.10.0`` ``-Python-2.7.14`` ``intel/2017b`` -``0.10.0`` ``-Python-3.6.3`` ``intel/2017b`` -``0.10.3`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.4`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.8`` ``-Python-3.6.4`` ``intel/2018a`` -``0.12.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` -``0.15.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``0.16.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``0.16.2`` ``fosscuda/2020b``, ``intel/2020b`` -========== ================== =================================== +========== ================== =================================================== +version versionsuffix toolchain +========== ================== =================================================== +``0.9.5`` ``-Python-2.7.13`` ``intel/2017a`` +``0.9.5`` ``-Python-3.6.1`` ``intel/2017a`` +``0.9.6`` ``-Python-2.7.13`` ``intel/2017a`` +``0.10.0`` ``-Python-2.7.14`` ``intel/2017b`` +``0.10.0`` ``-Python-3.6.3`` ``intel/2017b`` +``0.10.3`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.4`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.8`` ``-Python-3.6.4`` ``intel/2018a`` +``0.12.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` +``0.15.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.16.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.16.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``0.19.0`` ``foss/2021a`` +========== ================== =================================================== .. _list_software_xbitmaps_872: @@ -43259,14 +44806,14 @@ Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerce *homepage*: https://xerces.apache.org/xerces-c/ -========= ===================================== -version toolchain -========= ===================================== -``3.1.4`` ``GCCcore/6.4.0`` -``3.2.0`` ``GCCcore/7.3.0`` -``3.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.2.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========= ===================================== +========= ============================================================================= +version toolchain +========= ============================================================================= +``3.1.4`` ``GCCcore/6.4.0`` +``3.2.0`` ``GCCcore/7.3.0`` +``3.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.2.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========= ============================================================================= .. _list_software_xESMF_419: @@ -43384,6 +44931,7 @@ A Python module for creating Excel XLSX files version toolchain ========= ================== ``1.4.0`` ``GCCcore/10.2.0`` +``1.4.4`` ``GCCcore/10.3.0`` ========= ================== @@ -43450,7 +44998,7 @@ version versionsuffix toolchain This is a Perl extension interface to James Clark's XML parser, expat. -*homepage*: http://search.cpan.org/~toddr/XML-Parser-2.41/ +*homepage*: https://search.cpan.org/~toddr/XML-Parser-2.46/ =========== ================ ====================================================================================== version versionsuffix toolchain @@ -43462,6 +45010,7 @@ version versionsuffix toolchain ``2.44_01`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` ``2.44_01`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` ``2.44_01`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``2.46`` ``-Perl-5.32.1`` ``GCCcore/10.3.0`` =========== ================ ====================================================================================== @@ -43545,7 +45094,7 @@ version toolchain ``1.19.0`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``1.19.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.19.2`` ``GCCcore/10.2.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -``1.19.3`` ``GCCcore/10.3.0`` +``1.19.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ==================================================================================================================================== @@ -43565,7 +45114,7 @@ version versionsuffix toolchain ``1.2.2`` ``-X11-20180131`` ``GCCcore/6.4.0`` ``1.2.3`` ``GCCcore/7.3.0`` ``1.2.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ================= ======================================================================================================================= @@ -43578,13 +45127,13 @@ X protocol and ancillary headers *homepage*: https://www.freedesktop.org/wiki/Software/xlibs -========== ===================================================================================================================================== -version toolchain -========== ===================================================================================================================================== -``7.0.28`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``7.0.29`` ``intel/2016a`` -``7.0.31`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ===================================================================================================================================== +========== ========================================================================================================================================================= +version toolchain +========== ========================================================================================================================================================= +``7.0.28`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``7.0.29`` ``intel/2016a`` +``7.0.31`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ========================================================================================================================================================= .. _list_software_XSD_239: @@ -43619,6 +45168,22 @@ version toolchain ============== ========================================================== +.. _list_software_xTB_270: + +*xTB* ++++++ + +Semiempirical Extended Tight-Binding Program Package. + +*homepage*: https://xtb-docs.readthedocs.io + +========= =============== +version toolchain +========= =============== +``6.4.1`` ``intel/2021a`` +========= =============== + + .. _list_software_xtb_334: *xtb* @@ -43667,6 +45232,7 @@ version toolchain ``1.20.8`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``1.20.9`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``1.20.11`` ``GCCcore/10.3.0`` +``1.20.13`` ``GCCcore/11.2.0`` =========== ===================================== @@ -43688,7 +45254,7 @@ version versionsuffix toolchain ``5.2.2`` ``-gettext-0.19.7`` ``foss/2016a``, ``intel/2016a`` ``5.2.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``gimkl/2017a`` ``5.2.4`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` -``5.2.5`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``5.2.5`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ========= =================== =========================================================================================================================================================== @@ -43698,7 +45264,7 @@ version versionsuffix toolchain --- -:ref:`list_software_YACS_304` - :ref:`list_software_Yade_387` - :ref:`list_software_yaff_422` - :ref:`list_software_Yambo_504` - :ref:`list_software_YANK_307` - :ref:`list_software_YAPS_317` - :ref:`list_software_Yasm_410` - :ref:`list_software_YAXT_326` +:ref:`list_software_YACS_304` - :ref:`list_software_Yade_387` - :ref:`list_software_yaff_422` - :ref:`list_software_Yambo_504` - :ref:`list_software_YANK_307` - :ref:`list_software_YAPS_317` - :ref:`list_software_Yasm_410` - :ref:`list_software_YAXT_326` - :ref:`list_software_Yices_509` .. _list_software_YACS_304: @@ -43710,11 +45276,11 @@ YACS was created as a lightweight library to define and manage system configurat *homepage*: https://github.com/rbgirshick/yacs -========= ===================================== -version toolchain -========= ===================================== -``0.1.8`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` -========= ===================================== +========= ============================================================================= +version toolchain +========= ============================================================================= +``0.1.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` +========= ============================================================================= .. _list_software_Yade_387: @@ -43820,11 +45386,11 @@ Yasm: Complete rewrite of the NASM assembler with BSD license *homepage*: http://www.tortall.net/projects/yasm/ -========= =========================================================================================================================================================================================================================================================================== -version toolchain -========= =========================================================================================================================================================================================================================================================================== -``1.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -========= =========================================================================================================================================================================================================================================================================== +========= =============================================================================================================================================================================================================================================================================================== +version toolchain +========= =============================================================================================================================================================================================================================================================================================== +``1.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +========= =============================================================================================================================================================================================================================================================================================== .. _list_software_YAXT_326: @@ -43843,9 +45409,26 @@ version toolchain ``0.6.0`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``0.6.2`` ``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` ``0.9.0`` ``gompi/2020b`` +``0.9.1`` ``gompi/2021a`` ========= ================================================= +.. _list_software_Yices_509: + +*Yices* ++++++++ + +Yices 2 is an SMT solver that decides the satisfiability of formulas containing uninterpreted function symbols with equality, real and integer arithmetic, bitvectors, scalar types, and tuples. Yices 2 supports both linear and nonlinear arithmetic. + +*homepage*: https://yices.csl.sri.com/index.html + +========= ================== +version toolchain +========= ================== +``2.6.2`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_letter_z: *Z* @@ -43910,7 +45493,7 @@ version toolchain ``4.2.5`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` ``4.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.3.3`` ``GCCcore/10.2.0`` -``4.3.4`` ``GCCcore/10.3.0`` +``4.3.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ========================================================================================================= @@ -43939,11 +45522,11 @@ Zip is a compression and file packaging/archive utility. Although highly compati *homepage*: http://www.info-zip.org/Zip.html -======= =============================================================================================== -version toolchain -======= =============================================================================================== -``3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= =============================================================================================== +======= ====================================================================================================================================== +version toolchain +======= ====================================================================================================================================== +``3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ====================================================================================================================================== .. _list_software_zlib_433: @@ -43961,7 +45544,7 @@ version toolchain ``1.2.7`` ``GCC/4.8.1``, ``GCC/4.8.2`` ``1.2.8`` ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.2.10`` ``system`` -``1.2.11`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` +``1.2.11`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -44033,5 +45616,6 @@ version toolchain ``1.4.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.4.5`` ``GCCcore/10.2.0`` ``1.4.9`` ``GCCcore/10.3.0`` +``1.5.0`` ``GCCcore/11.2.0`` ========= ==================================================== diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index c7328338..69d7d6af 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -10,6 +10,7 @@ * EB_Anaconda * EB_AOMP * EB_CPLEX + * EB_CRISPR_minus_DAV * EB_CUDA * EB_EPD * EB_IMOD @@ -34,6 +35,7 @@ * EB_MATLAB * EB_MCR * EB_NVHPC + * EB_ORCA * EB_PGI * EB_Samcef * EB_Stata @@ -209,6 +211,7 @@ * EB_mutil * EB_MXNet * EB_NAMD + * EB_ORCA * PerlModule * SystemMPI @@ -265,6 +268,7 @@ * EB_dm_minus_reverb * EB_EasyBuildMeta * EB_EggLib + * EB_jaxlib * EB_libxml2 * EB_Metagenome_Atlas * EB_netcdf4_minus_python @@ -354,6 +358,7 @@ * EB_MATLAB * EB_MCR * EB_NVHPC + * EB_ORCA * EB_PGI * EB_Samcef * EB_Stata @@ -375,6 +380,7 @@ * EB_MTL4 * EB_picard * EB_RepeatMasker + * EB_RepeatModeler * Waf @@ -399,6 +405,7 @@ * EB_dm_minus_reverb * EB_EasyBuildMeta * EB_EggLib + * EB_jaxlib * EB_libxml2 * EB_Metagenome_Atlas * EB_netcdf4_minus_python diff --git a/docs/version-specific/easyconfig_parameters.rst b/docs/version-specific/easyconfig_parameters.rst index 439022f4..cf020344 100644 --- a/docs/version-specific/easyconfig_parameters.rst +++ b/docs/version-specific/easyconfig_parameters.rst @@ -51,6 +51,7 @@ build parameters ``easyblock`` EasyBlock to use for building; if set to None, an easyblock is selected based on the software name None ``easybuild_version`` EasyBuild-version this spec-file was written for None ``enhance_sanity_check`` Indicate that additional sanity check commands & paths should enhance the existin sanity check, not replace it False +``fix_bash_shebang_for`` List of files for which Bash shebang should be fixed to '#!/usr/bin/env bash' (glob patterns supported) None ``fix_perl_shebang_for`` List of files for which Perl shebang should be fixed to '#!/usr/bin/env perl' (glob patterns supported) None ``fix_python_shebang_for`` List of files for which Python shebang should be fixed to '#!/usr/bin/env python' (glob patterns supported) None ``github_account`` GitHub account name to be used to resolve template values in source URLs "%(namelower)s" diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index 911e781f..a0398593 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -330,61 +330,57 @@ Build a Python package and module with cmake. Some packages use cmake to first build and install C Python packages and then put the Python package in lib/pythonX.Y/site-packages. - We install this in a seperate location and generate a module file - which sets the PYTHONPATH. - - We use the default CMake implementation, and use make_module_extra from PythonPackage. + We use the default CMake implementation, and use make_module_extra from PythonPackage + to generate a module file which sets the PYTHONPATH. Extra easyconfig parameters specific to ``CMakePythonPackage`` easyblock ------------------------------------------------------------------------ -======================== ================================================================================================================================================================================================== ======================================================================= -easyconfig parameter description default value -======================== ================================================================================================================================================================================================== ======================================================================= -``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` -``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` -``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``configure_cmd`` Configure command to use ``"cmake"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``generator`` Build file generator to use. None to use CMakes default ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``separate_build_dir`` Perform build in a separate directory ``True`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``srcdir`` Source directory location to provide to cmake command ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== ================================================================================================================================================================================================== ======================================================================= +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` +``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``configure_cmd`` Configure command to use ``"cmake"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``generator`` Build file generator to use. None to use CMakes default ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Build command to use ``"make install"`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``None`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``separate_build_dir`` Perform build in a separate directory ``True`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``srcdir`` Source directory location to provide to cmake command ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= Customised steps in ``CMakePythonPackage`` easyblock ---------------------------------------------------- -* ``build_step`` - Build Python package with cmake * ``configure_step`` - Main configuration using cmake -* ``install_step`` - Install with cmake install +* ``install_step`` - Main configuration using cmake .. _CmdCp: @@ -541,41 +537,40 @@ Build a Python package and module with 'python configure/make/make install'. Extra easyconfig parameters specific to ``ConfigureMakePythonPackage`` easyblock -------------------------------------------------------------------------------- -======================== =================================================================================================================================================================================================== ======================================================================= -easyconfig parameter description default value -======================== =================================================================================================================================================================================================== ======================================================================= -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``configure_cmd`` Configure command to use ``"./configure"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== =================================================================================================================================================================================================== ======================================================================= +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``configure_cmd`` Configure command to use ``"./configure"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Build command to use ``"make install"`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= Customised steps in ``ConfigureMakePythonPackage`` easyblock ------------------------------------------------------------ @@ -653,32 +648,31 @@ Extends PythonPackage to add a Fortran compiler to the make call Extra easyconfig parameters specific to ``FortranPythonPackage`` easyblock -------------------------------------------------------------------------- -======================== ========================================================================================================================================================== ======================================================================= -easyconfig parameter description default value -======================== ========================================================================================================================================================== ======================================================================= -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== ========================================================================================================================================================== ======================================================================= +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= Customised steps in ``FortranPythonPackage`` easyblock ------------------------------------------------------ @@ -944,37 +938,36 @@ Bundle of modules: only generate module files, nothing to build/install Extra easyconfig parameters specific to ``PythonBundle`` easyblock ------------------------------------------------------------------ -=========================== ========================================================================================================================================================== ======================================================================= -easyconfig parameter description default value -=========================== ========================================================================================================================================================== ======================================================================= -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -=========================== ========================================================================================================================================================== ======================================================================= +=========================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +=========================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` +=========================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= .. _PythonPackage: @@ -988,32 +981,31 @@ Builds and installs a Python package, and provides a dedicated module file. Extra easyconfig parameters specific to ``PythonPackage`` easyblock ------------------------------------------------------------------- -======================== ========================================================================================================================================================== ======================================================================= -easyconfig parameter description default value -======================== ========================================================================================================================================================== ======================================================================= -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== ========================================================================================================================================================== ======================================================================= +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= Customised steps in ``PythonPackage`` easyblock ----------------------------------------------- @@ -1294,32 +1286,31 @@ Support for install VSC Python packages. Extra easyconfig parameters specific to ``VSCPythonPackage`` easyblock ---------------------------------------------------------------------- -======================== ========================================================================================================================================================== ======================================================================= -easyconfig parameter description default value -======================== ========================================================================================================================================================== ======================================================================= -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== ========================================================================================================================================================== ======================================================================= +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= .. _VersionIndependentPythonPackage: @@ -1333,32 +1324,31 @@ Support for building/installing python packages without requiring a specific pyt Extra easyconfig parameters specific to ``VersionIndependentPythonPackage`` easyblock ------------------------------------------------------------------------------------- -======================== ========================================================================================================================================================== ======================================================================= -easyconfig parameter description default value -======================== ========================================================================================================================================================== ======================================================================= -``buildcmd`` Command to pass to setup.py to build the extension ``"build"`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_easy_install`` Install using '%(python)s setup.py easy_install --prefix=%(prefix)s %(installopts)s %(loc)s' (deprecated) ``False`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``use_setup_py_develop`` Install using '%(python)s setup.py develop --prefix=%(prefix)s %(installopts)s' (deprecated) ``False`` -``zipped_egg`` Install as a zipped eggs (requires use_easy_install) ``False`` -======================== ========================================================================================================================================================== ======================================================================= +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` +======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= Customised steps in ``VersionIndependentPythonPackage`` easyblock ----------------------------------------------------------------- diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index 1c74dd02..bbedea28 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -281,6 +281,7 @@ Option flag Opt ``--extra-modules=EXTRA-MODULES`` List of extra modules to load after setting up the build environment (type comma-separated list) ``--fetch`` Allow downloading sources ignoring OS and modules tool dependencies, implies --stop=fetch, --ignore-osdeps and ignore modules tool (default: False) ``--filter-deps=FILTER-DEPS`` List of dependencies that you do *not* want to install with EasyBuild, because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses) (type comma-separated list) +``--filter-ecs=FILTER-ECS`` List of easyconfigs (given as glob patterns) to *ignore* when given on command line or auto-selected when building with --from-pr. (e.g. --filter-ecs=*intel*) (type comma-separated list) ``--filter-env-vars=FILTER-ENV-VARS`` List of names of environment variables that should *not* be defined/updated by module files generated by EasyBuild (type comma-separated list) ``--fixed-installdir-naming-scheme`` Use fixed naming scheme for installation directories (default: True; disable with --disable-fixed-installdir-naming-scheme) ``--force-download=FORCE-DOWNLOAD`` Force re-downloading of sources and/or patches, even if they are available already in source path (type choice; default: sources) (choices: all, patches, sources) diff --git a/docs/version-specific/toolchain_opts.rst b/docs/version-specific/toolchain_opts.rst index e0b40376..343ef171 100644 --- a/docs/version-specific/toolchain_opts.rst +++ b/docs/version-specific/toolchain_opts.rst @@ -5,7 +5,7 @@ Available toolchain options (by toolchain) *(see also* ``eb --avail-toolchain-opts `` *)* -ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iiblf_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - nvompic_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ +ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iiblf_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - nvompic_ - nvpsmpic_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ .. _ClangGCC: @@ -3457,6 +3457,49 @@ option description ========================= ======================================================================= ========= +.. _nvpsmpic: + +Available options for nvpsmpic toolchain +---------------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + .. _pmkl: Available options for pmkl toolchain diff --git a/docs/version-specific/toolchains.rst b/docs/version-specific/toolchains.rst index b6beba4a..a990050c 100644 --- a/docs/version-specific/toolchains.rst +++ b/docs/version-specific/toolchains.rst @@ -81,6 +81,7 @@ Name Compiler(s) MPI Linear algebra **ismkl** icc, ifort MPICH2 imkl imkl **NVHPC** NVHPC *(none)* *(none)* *(none)* **nvompic** NVHPC OpenMPI *(none)* *(none)* +**nvpsmpic** NVHPC psmpi *(none)* *(none)* **PGI** PGI *(none)* *(none)* *(none)* **pmkl** PGI *(none)* imkl imkl **pomkl** PGI OpenMPI imkl imkl From b60f6b39af014bdee59ddc5e319fa23f766d5eb3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 7 Sep 2021 10:12:13 +0800 Subject: [PATCH 165/286] update release notes and changelog for EasyBuild v4.4.2 + bump version to 4.4.2 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 239 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 239 insertions(+), 5 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 2ce0810e..a38ecb5e 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20210907.01** (`Sep 7th 2021`): update release notes for EasyBuild v4.4.2 (see :ref:`release_notes_eb442`) * **release 20210706.01** (`Jul 6th 2021`): update release notes for EasyBuild v4.4.1 (see :ref:`release_notes_eb441`) * **release 20210602.01** (`Jun 2nd 2021`): update release notes for EasyBuild v4.4.0 (see :ref:`release_notes_eb440`) * **release 20210409.01** (`Apr 9th 2021`): update release notes for EasyBuild v4.3.4 (see :ref:`release_notes_eb434`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 1cc08a9b..77d8af15 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,245 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,388** different software packages, -including 36 different (compiler) toolchains. It contains 237 software-specific easyblocks and 37 generic easyblocks, -alongside 12,607 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,467** different software packages, +including 36 different (compiler) toolchains. It contains 241 software-specific easyblocks and 37 generic easyblocks, +alongside 13,265 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb442: + +EasyBuild v4.4.2 (September 7th 2021) +------------------------------------- + +bugfix/update release + +**framework** + +* various enhancements, including: + + * add per-extension timing in output produced by ``eb`` command (`#3734 `_) + * add definition for new toolchain ``nvpsmpic`` (NVHPC + ParaStationMPI + CUDA) (`#3736 `_) + * include list of missing libraries in warning about missing FFTW libraries in ``imkl`` toolchain component (`#3776 `_) + * check for recursive symlinks by default before copying a folder (`#3784 `_) + * add ``--filter-ecs`` configuration option to filter out easyconfigs from set of easyconfigs to install (`#3796 `_) + * check type of ``source_tmpl`` value for extensions, ensure it's a string value (not a list) (`#3799 `_) + * also define ``$BLAS_SHARED_LIBS`` & co in build environment (analogous to ``$BLAS_STATIC_LIBS``) (`#3800 `_) + * report use of ``--ignore-test-failure`` in success message in output (`#3806 `_) + * add ``get_cuda_cc_template_value`` method to ``EasyConfig`` class (`#3807 `_) + * add support for ``fix_bash_shebang_for`` (`#3808 `_) + * pick up ``$MODULES_CMD`` to facilitate using Environment Modules 4.x as modules tool (`#3816 `_) + * use more sensible branch name for creating easyblocks PR with ``--new-pr`` (`#3817 `_) + +* various bug fixes, including: + + * remove Python 2.6 from list of supported Python versions in ``setup.py ``(`#3767 `_) + * don't add directory that doesn't include any files to ``$PATH`` or ``$LD_LIBRARY_PATH`` (`#3769 `_) + * make logdir writable also when ``--stop``/``--fetch`` is used and ``--read-only-installdir`` is enabled (`#3771 `_) + * fix forgotten renaming of ``l`` to ``char`` in ``__init__.py`` that is created for included Python modules (`#3773 `_) + * fix ``verify_imports`` by deleting all imported modules before re-importing them one by one (`#3780 `_) + * fix ``ignore_test_failure`` not set for Extension instances (`#3782 `_) + * update ``iompi`` toolchain to ``intel-compiler`` subtoolchain for oneAPI versions (>= ``iompi`` 2020.12) (`#3785 `_) + * don't parse patch files as easyconfigs when searching for where patch file is used (`#3786 `_) + * make sure git clone with a tag argument actually downloads a tag (`#3795 `_) + * fix CI by excluding GC3Pie 2.6.7 (which is broken with Python 2) and improve error reporting for option parsing (`#3798 `_) + * correctly resolve templates for patches in extensions when uploading to GitHub (`#3805 `_) + * add ``--easystack`` to ignored options when submitting job (`#3813 `_) + +* other changes: + + * speed up tests by caching checked paths in ``set_tmpdir`` + less test cases for ``test_compiler_dependent_optarch`` (`#3802 `_) + * speed up ``set_parallel`` method in ``EasyBlock`` class (`#3812 `_) + +**easyblocks** + +* 4 new software-specific easyblocks: + + * CRISPR-DAV (`#2487 `_), jaxlib (`#2545 `_), ORCA (`#2504 `_), RepeatModeler (`#2470 `_) + +* minor enhancements, including: + + * update ABAQUS easyblock to support installation of v2020 (`#2034 `_) + * enable make check and sanity check exec for OpenMPI (`#2444 `_) + * fixed sanity check for later versions of Molpro (`#2499 `_) + * add Ampere to known GPU architectures for Kokkos in LAMMPS easyblock (`#2510 `_) + * update sanity check in ESMF easyblock to take into account new binary names from version 8.1.0 onwards (`#2512 `_) + * use ``report_test_failure`` in TensorFlow easyblock (`#2519 `_) + * add support for imkl 2021.x in easyblocks for + + * Amber (`#2527 `_), BerkeleyGW (`#2528 `_), CP2K (`#2529 `_), FreeFEM (`#2530 `_), GROMACS (`#2531 `_), numexpr (`#2532 `_) + + * add ``install_src`` option and enhance ``buildcmd`` option in PythonPackage easyblock (`#2534 `_) + * make sure AOCC commands like clang/flang pick up ``GCCcore`` as GCC toolchain (`#2538 `_) + * create ``CMakeConfig`` files for tbb >= 2020 (`#2539 `_) + * find source dir for libunwind when building ldd for Clang versions >= 12.0.1 (`#2540 `_) + * fix motorBike test in sanity check for OpenFOAM 9 (`#2544 `_) + * generate and install pkg-config files for OpenSSL wrapper (`#2549 `_) + * don't run ``setup.py config`` for numpy >= 1.21, since it's no longer supported (`#2554 `_) + * update WIEK2k easyblock to handle new Intel versions, WIEN2k v21, Perl dependency, and tuning of dimension parameters (`#2558 `_) + * remove PCRE from list of system libraries for TensorFlow 2.6.0 (`#2559 `_) + * add support for also installing Tosca component in ABAQUS (`#2560 `_) + * update ABAQUS easyblock to support installing of version 2021 with hot fixes (`#2562 `_) + * update sanity check in VTune easyblock for 2021.x versions (`#2563 `_) + +* various bug fixes, including: + + * handle failure of running ``nvidia-smi`` in TensorFlow tests (`#2506 `_) + * remove Python 2.6 from list of supported Python versions in ``setup.py`` (`#2507 `_) + * clean up installation of Tkinter (`#2509 `_) + * remove redundant ``$CPATH`` entry of tbb modules + fix ``--module-only`` (`#2511 `_) + * honor ``--ignore-test-failure`` in PythonPackage (`#2516 `_) + * use correct GTK+ version for OpenCV based on dependencies (`#2520 `_) + * ensure Python prep is done in sanity check + support debug builds in TensorFlow easyblock (`#2522 `_) + * correct cleanup of single-letter local variable in ``__init__`` of ``easybuild.easyblocks`` (`#2524 `_) + * reset runtest to ``None`` in CMakePythonPackage (`#2536 `_) + * set ``$I_MPI_ROOT`` correctly for 2021.x in impi easyblock (`#2537 `_) + * let Bundle easyblock pick up custom easyblock for components based on name if no easyblock is specified explicitly (`#2543 `_, `#2547 `_) + * explicitly use only OpenBLAS for PyTorch if MKL is not used (`#2448 `_) + * keep symlinks in cuDNN installations (`#2550 `_) + * use ``${BLAS,LAPACK}_SHARED_LIBS`` in GROMACS easyblock for FlexiBLAS-based toolchains (`#2552 `_) + * copy the list to avoid changing the original lists in ``DEFAULT_TARGETS_MAP`` for Clang and LLVM (`#2556 `_) + * fix ``pathsep`` ``join`` bug that breaks installation of CUDA versions < 10.1 if ``$PERL5LIB`` is defined (`#2561 `_) + +* other changes: + + * simplify Boost easyblock (`#2513 `_) + * remove deprecated options from PythonPackage (`#2535 `_) + +**easyconfigs** + +* added easyconfig for foss/2021.07 (candidate for foss/2021b) (`#13788 `_) and iomkl/2021a (`#13521 `_) toolchains + +* added example easyconfig files for 79 new software packages: + + * AlphaFold (`#13867 `_), andi (`#13768 `_), aria2 (`#13709 `_), AUTO-07p (`#13831 `_), babl (`#13216 `_), BAli-Phy (`#13484 `_), + biogeme (`#13735 `_), Bio-SearchIO-hmmer (`#13419 `_), BuDDy (`#13907 `_), c-ares (`#13709 `_), CellRank (`#13408 `_), Coin (`#13818 `_), + Co-phylog (`#13769 `_), cppy (`#13823 `_), CREST (`#13648 `_), CRISPR-DAV (`#13139 `_), CSBLAST (`#13794 `_), DGL (`#13793 `_), + DistributedStream (`#13659 `_), Excel-Writer-XLSX (`#13139 `_), FBPIC (`#13500 `_), freebayes (`#12859 `_), freud-analysis (`#13354 `_), + fumi_tools (`#13517 `_), GEGL (`#13216 `_), GIMP (`#13216 `_), glib-networking (`#13216 `_), GOATOOLS (#13364, `#13629 `_), + gofasta (`#13651 `_), GTK2 (`#13900 `_), GTK3 (`#13900 `_), Highway (`#13453 `_), hipSYCL (`#13837 `_), ISA-L (`#13663 `_), jax (`#13760 `_), + JSON-GLib (`#13216 `_), Kalign (`#13463 `_), LADR (`#13351 `_), lDDT (`#13794 `_), libdivsufsort (`#13768 `_), libjxl (`#13453 `_, `#13829 `_), + libmypaint (`#13216 `_), libtecla (`#13908 `_), lie_learn (`#13793 `_), longestrunsubsequence (`#13800 `_), Maude (`#13909 `_), + mimalloc (`#13726 `_), MINPACK (`#13802 `_), Mish-Cuda (`#13759 `_, `#13784 `_), muparserx (`#13779 `_), nlohmann_json (`#13777 `_), + OpenStackClient (`#13644 `_), OSPRay (`#12852 `_), pandapower (`#13687 `_), pangolin (`#13733 `_, `#13848 `_), PSIPRED (`#13794 `_), + PYPOWER (`#13689 `_), PyPSA (`#13673 `_), PyRosetta (`#13793 `_), pysamstats (`#13139 `_), pytest-benchmark (`#13622 `_), + python-isal (`#13663 `_), QCxMS (`#13650 `_), RepeatModeler (`#13126 `_), Schrodinger (`#11698 `_), sklearn-som (`#13699 `_), + SoQt (`#13818 `_), spdlog (`#13778 `_), SpectrA (`#13743 `_), SymEngine-python (`#13652 `_), SyRI (`#13800 `_), torchinfo (`#13662 `_), + TRAVIS-Analyzer (`#13503 `_), UShER (`#13708 `_), Vampire (`#13352 `_), VBZ-Compression (`#13536 `_), VisPy (`#13468 `_), + wgsim (`#13475 `_), Yices (`#13906 `_) + +* added additional easyconfigs for various supported software packages, including: + + * ABAQUS 2020.eb, ANTs 2.3.5, AOCC 3.1.0, Arb 2.19.0, archspec 0.1.2, Armadillo 10.5.3, ASE 3.22.0, + Autotools 20210726, BamTools 2.5.2, bgen 4.1.3, Biopython 1.79, bitarray 1.5.3, Boost 1.76.0, Bowtie2 2.4.4, + bpytop 1.0.67, Cartopy 0.19.0.post1, Centrifuge 1.0.4, Clang 12.0.1, CMake 3.21.1, CRISPResso2 2.2.1, CUDA 11.4.1, + cuDNN 8.2.2.26, cURL 7.78.0, cutadapt 3.4, DIAMOND 2.0.11, DROP 1.1.0, Dsuite 20210718, dtcmp 1.1.2, ecCodes 2.22.1, + Elk 7.2.42, ESMF 8.1.1, expat 2.4.1, fastq-tools 0.8.3, Fiona 1.8.20, FLINT 2.7.1, g2clib 1.6.3, g2lib 3.2.0, + GCC(core) 11.2.0, GDCM 3.0.8, GDRCopy 2.3, GenomeTools 1.6.2, GffCompare 0.12.2, gffread 0.12.7, GLib 2.69.1, + GMT 6.2.0, Go 1.16.6, GPAW 21.6.0, Gradle 6.9.1.eb, GROMACS 2021.3, HarfBuzz 2.8.2, HDF5 1.12.1, Horovod 0.22.1, + hwloc 2.5.0, hypothesis 6.14.6, igraph 0.9.4, ImageMagick 7.1.0, IMOD 4.11.5, IPython 7.26.0, Java 16, + Julia 1.6.2, JupyterHub 1.4.1, JupyterLab 3.1.6, Kent_tools 418, lavaan 0.6-9, libfabric 1.13.0, libffcall 2.4, + libffi 3.4.2, libgeotiff 1.7.0, libRmath 4.1.0, LIBSVM 3.25, LibTIFF 4.3.0, likwid 5.2.0, LLVM 12.0.1, LMDB 0.9.29, + magma 2.6.1, MariaDB 10.6.4, MATIO 1.5.21, matplotlib 3.4.2, MEGA 10.0.5, Mesa 21.1.7, Meson 0.59.1, + Metal 2020-05-05, Mini-XML 3.2, molmod 1.4.8, MPICH 3.4.2, nanopolish 0.13.3, NCCL 2.10.3, ncdu 1.16, NCO 5.0.1, + neptune-client 0.10.5, netcdf4-python 1.5.7, networkx 2.5.1, nodejs 14.17.6, NSPR 4.32, NSS 3.69, NVHPC 21.7, + OpenBLAS 0.3.17, OpenEXR 3.1.1, OpenFOAM 9, OpenFOAM v2106, OpenMM 7.5.1, OpenMolcas 21.06, openpyxl 3.0.7, + Pango 1.48.8, parallel 20210722, Paraver 4.9.2, ParaView 5.9.1, patchelf 0.13, PCRE2 10.37, PCRE 8.45, Perl 5.34.0, + PETSc 3.15.1, petsc4py 3.15.0, Pillow 8.3.1, Pillow-SIMD 8.3.1, plotly.py 5.1.0, PLUMED 2.7.2, PMIx 4.1.0, + poppler 21.06.1, PostgreSQL 13.3, preseq 3.1.2, pybind11 2.7.1, pyFFTW 0.12.0, PyGEOS 0.10.2, Pyomo 6.0.1, + PyQt5 5.15.4, pyshp 2.1.3, Python 3.9.6, python-igraph 0.9.6, QTLtools 1.3.1, RAxML-NG 1.0.3, + R-bundle-Bioconductor 3.13, re2c 2.2, ReFrame 3.8.0., RStudio-Server 1.4.1717, Rust 1.54.0, Scalasca 2.6, + scVelo 0.2.3, Shapely 1.8a1, shrinkwrap 1.1.0, SLEPc 3.15.1, slepc4py 3.15.1, snakemake 6.6.1, snappy 1.1.9, + snippy 4.6.0, snpEff 5.0e, SOCI 4.0.2, SpaceRanger 1.3.0, Spack 0.16.2, spatialreg 1.1-8, + spglib-python 1.16.1, SQLite 3.36, STAR 2.7.9a, statsmodels 0.12.2, StringTie 2.1.7, Subread 2.0.3, SymEngine 0.7.0, + TensorFlow 2.6.0, TetGen 1.6.0, Tkinter 3.9.6, torchtext 0.9.1, tqdm 4.61.2, UCX 1.11.0, UCX-CUDA 1.11.0, + unrar 6.0.2, util-linux 2.37, VTune 2021.6.0, WIEN2k 21.1, WPS 4.2, WRF 4.3, X11 20210802, + x264 20210613, xarray 0.19.0, XlsxWriter 1.4.4, XML-Parser 2.46, zstd 1.5.0 + +* minor enhancements, including: + + * add extensions to recent R v4.x easyconfigs: PCAmatchR (`#13448 `_), hal9001 (`#13451 `_), cobalt (`#13544 `_), CBPS (`#13549 `_), + SBdecomp (`#13565 `_), lwgeom (`#13674 `_), naturalsort (`#13762 `_), finalfit + gtsummary (`#13766 `_) + * add VBZ compress capability to nanopolish 0.13.3 (for fast5 files) (`#13536 `_) + * add CMake build dependency to easyconfig for tbb 2020.03 (`#13704 `_) + * also build shared libs for MUMPS 5.3.5 (`#13702 `_) and 5.4.0 (`#13705 `_) + * add dependency on pkg-config to OpenSSL wrappers (`#13765 `_) + +* various bug fixes, including: + + * fix LAMMPS 3Mar2020 easyconfigs using intel toolchain on AMD CPUs by patching out hardcoded ``-xHost`` (`#11577 `_) + * fix sanity check error for OpenCV v4.5.1 by adding (and using) freetype and HarfBuzz dependencies (`#12517 `_) + * add patches for TensorFlow 1.13.1 to fix installation (`#13326 `_) + * remove Python 2.6 from list of supported Python versions in ``setup.py`` (`#13349 `_) + * switch back to Bundle easyblock for PyQt5 5.15.1 + add back source URLs for components (`#13371 `_) + * add pkg-config build dependency for GDAL 3.2.1 (`#13383 `_, `#13808 `_), Rust (`#13538 `_), GenomeTools (`#13805 `_), x264 (`#13834 `_) + * add missing Python 3 build dependency for Rust v1.52.1 (`#13399 `_) + * fix order of cffi extension in old Python easyconfigs (`#13400 `_) + * patch out ``__asm__`` use in ctffind to avoid build failure on ppc64le (`#13409 `_) + * disable building man pages in Gdk-Pixbuf (`#13410 `_) + * add missing Bio-Search-hmmer dependency for prokka (`#13419 `_) + * avoid downloading old numpy version during install for h5py (`#13428 `_) + * add patch for Qt5 5.8.0 to fix compilation failure in webkit (`#13434 `_) + * avoid downloading and building freetype and qhull for matplotlib 3.4.2 (`#13437 `_) + * fix order of components in recent GTK+ easyconfigs to avoid dependency on system GTK+ in GTK+ themes (`#13449 `_) + * fix Python 2.7.13 easyconfigs by adding missing extensions (`#13456 `_) + * add TensorFlow patch to fix crash on shutdown (`#13462 `_) + * allow for non-x86_64 in ``postinstallcmds`` for CuPy (`#13501 `_) + * disable default EULA acceptance in easyconfig for NVHPC v21.5 (`#13516 `_) + * fix error with p7zip's 7z command not finding ``7z.dll`` (`#13542 `_) + * patch MaxBin2 Perl script to use provided Perl dependency (`#13551 `_) + * add missing zlib dependency to libarchive (`#13579 `_) + * fix pkgconfig version in patch for bzip 1.0.8 (+ add easyconfig with GCCcore/11.2.0 toolchain) (`#13581 `_) + * fix build of DIRAC 19.0 easyconfig with high compiler optimizations (`#13613 `_) + * fix source URLs and add alternative checksum for Hypre 2.15.1 (since it moved to a different GitHub repo) (`#13616 `_) + * add new source URL for Mesa easyconfigs using 2017b toolchain (`#13617 `_) + * avoid ``MPICXX`` dependency in SimpleElastics ITK (`#13623 `_) + * add upstream patch for GCC 9.x, 10.x, 11.x to avoid spurious FPE on avx512 (affects UCX) (`#13628 `_) + * add patch for ctffind 4.1.14 to declare functions without return as void (fixes segfault) (`#13665 `_) + * enable EGL in recent libepoxy ECs (`#13684 `_) + * remove unused ``buildcmd`` from libgpuarray easyconfigs (`#13720 `_) + * add patch to fix building Qt5.10.1 against newer glibc (`#13730 `_) + * add Python 3 as a builddependency to recent fontconfig easyconfigs (`#13731 `_) + * update source_URL in BLAST 2.2.26 easyconfig (`#13732 `_) + * restore error message on failing easyconfigs test suite, required by bot to determine end of output of test suite (`#13745 `_, `#13770 `_) + * add Perl build dependency to recent Clang easyconfigs (`#13746 `_) + * disable using system Valgrind in the json-c tests (`#13750 `_) + * use Archive source URL for spatstat.geom extension in Seurat (`#13761 `_) + * add ld.gold relocts patch to binutils 2.30 (`#13785 `_) + * add missing Python + Zip build dependencies for old Bazel versions used as build dep for TensorFlow 1.12.0 + 1.13.1 (`#13786 `_) + * add alternative checksum for AFNI 18.3.00 (`#13790 `_) + * update tensorflow-probability easyconfigs to include ``--release`` flag in ``installopts`` (`#13810 `_) + * fix source URL for DB 18.1.32 (`#13813 `_) + * add missing cppy build dependency for matplotlib 3.4.2 (`#13823 `_) + * disable bash completion in recent x264 easyconfigs (`#13834 `_) + * add Perl as build dependency for ELPA 2021.05.001 + patch to fix hardcoded ``/usr/bin/perl`` (`#13835 `_) + * add archive source URL to Spark 3.x easyconfigs to fix broken download (`#13842 `_) + * fix PCRE dependency for GDAL 3.2.1 and 3.3.0, don't use PCRE2 (`#13861 `_) + * add Perl build dependency for HMMER 3.3.2 + patch to ensure it is used (`#13870 `_) + * stick to intel-compilers toolchain for DFT-D3 v3.2.0 (`#13878 `_) + * add missing flex build dependency for leidenalg (`#13884 `_) + * update CMake build dependency for Eigen 3.3.4 + 3.3.5 (`#13889 `_) + * fix source URL for Yasm 1.3.0 (+ add missing checksum) (`#13901 `_) + * update to more recent Meson build dependency for GCCcore/8.3.0 easyconfigs to fix failing RPATH sanity check (`#13910 `_) + * fix shebang for RepeatMasker 4.1.2-p1 Perl script (`#13911 `_) + +* other changes: + + * use custom ORCA easyblock in easyconfigs for ORCA v4.x (`#13348 `_) + * move archived easyconfig files to correct ``__archive__`` folder (`#13422 `_) + * rename NINJA to TWL-NINJA to avoid nameclash (`#13529 `_) + * remove superfluous ``configopts`` and add sanity checks/checksums in CLHEP easyconfigs (`#13614 `_) + * remove superfluous ``-DCMAKE_BUILD_TYPE`` configuration option in Arrow easyconfigs (`#13615 `_) + * switch ITK easyconfigs to CMakePythonPackage easyblock, also enable ``-DITK_USE_SYSTEM_HDF5`` configuration option, fix download URLs (`#13619 `_) + * use ``build_type`` instead of ``-DCMAKE_BUILD_TYPE=RELEASE`` in ``configopts`` in MMseqs2 easyconfigs (`#13620 `_) + * avoid using system GTK+3 and remove ``-DCMAKE_BUILD_TYPE=RELEASE`` configure option in OpenCV easyconfigs (`#13621 `_) + * remove ``-DCMAKE_BUILD_TYPE=RELEASE`` configure option and add checksums in LLVM easyconfigs (`#13624 `_) + * create libtinfo symlinks in easyconfigs for ncurses with system toolchain (`#13658 `_), 6.1 (`#13661 `_) and 6.2 (`#13660 `_) + * increase test timeouts for PyTorch 1.8.1 and 1.9.0 (`#13700 `_) + * rename CUDAcore to CUDA for v11.3.1 and v11.4.1 after merging foss/fosscuda, to ensure that ``get_software_root('CUDA')`` used in easyblocks works (`#13874 `_) + * use CUDA instead of CUDAcore in recent NVHPC comments (`#13875 `_) + + .. _release_notes_eb441: EasyBuild v4.4.1 (July 6th 2021) diff --git a/docs/conf.py b/docs/conf.py index 12f4879b..6d17cf87 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.4.1' # this is meant to reference the version of EasyBuild +version = '4.4.2' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20210706.0' # this is meant to reference the version of the documentation itself +release = '20210907.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 96b7a1fc5aae3d6017fcc3e1d369b04a240db20f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 7 Sep 2021 15:14:46 +0800 Subject: [PATCH 166/286] bump version to 4.4.2 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 42c10609..1c691a89 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.4.1' +VERSION = '4.4.2' # Utility function to read README file From 6bfb5f356cc8eaad1bd5c4a4c6c56b85793f10de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Sep 2021 10:52:48 +0200 Subject: [PATCH 167/286] fix typos in 4.4.2 release notes --- docs/Release_notes.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 77d8af15..80c076d3 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -35,7 +35,7 @@ bugfix/update release * various bug fixes, including: - * remove Python 2.6 from list of supported Python versions in ``setup.py ``(`#3767 `_) + * remove Python 2.6 from list of supported Python versions in ``setup.py`` (`#3767 `_) * don't add directory that doesn't include any files to ``$PATH`` or ``$LD_LIBRARY_PATH`` (`#3769 `_) * make logdir writable also when ``--stop``/``--fetch`` is used and ``--read-only-installdir`` is enabled (`#3771 `_) * fix forgotten renaming of ``l`` to ``char`` in ``__init__.py`` that is created for included Python modules (`#3773 `_) @@ -78,7 +78,7 @@ bugfix/update release * fix motorBike test in sanity check for OpenFOAM 9 (`#2544 `_) * generate and install pkg-config files for OpenSSL wrapper (`#2549 `_) * don't run ``setup.py config`` for numpy >= 1.21, since it's no longer supported (`#2554 `_) - * update WIEK2k easyblock to handle new Intel versions, WIEN2k v21, Perl dependency, and tuning of dimension parameters (`#2558 `_) + * update WIEN2k easyblock to handle new Intel versions, WIEN2k v21, Perl dependency, and tuning of dimension parameters (`#2558 `_) * remove PCRE from list of system libraries for TensorFlow 2.6.0 (`#2559 `_) * add support for also installing Tosca component in ABAQUS (`#2560 `_) * update ABAQUS easyblock to support installing of version 2021 with hot fixes (`#2562 `_) From cb708cf3055cf674c9f244cc8f6f9bec4a893e23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Oct 2021 09:53:57 +0200 Subject: [PATCH 168/286] update overview of common toolchains with foss/2021b and intel/2021b --- docs/Common-toolchains.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/Common-toolchains.rst b/docs/Common-toolchains.rst index 92ff62d4..2d1c80e3 100644 --- a/docs/Common-toolchains.rst +++ b/docs/Common-toolchains.rst @@ -182,6 +182,8 @@ Component versions in ``foss`` toolchain +----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ | ``2021a`` | May '21 | 2.36.1 | 10.3.0 | 4.1.1 | 3.0.4 | 0.3.15 | (incl. with OpenBLAS) | 2.1.0 | 3.3.9 | +----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2021b`` | Oct '21 | 2.37 | 11.2.0 | 4.1.1 | 3.0.4 | 0.3.18 | (incl. with OpenBLAS) | 2.1.0 | 3.3.10 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ *(components marked with* * *were patched)* @@ -222,6 +224,8 @@ Component versions in ``intel`` toolchain +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ | ``2021a`` | May'21 | 2.36.1 | 10.3.0 | 2021.2.0 | 2021.2.0 | 2021.2.0 | +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ +| ``2021b`` | Oct'21 | 2.37 | 11.2.0 | 2021.4.0 | 2021.4.0 | 2021.4.0 | ++----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ ``(*)``: This toolchain is deprecated, see :ref:`deprecated_easyconfigs_toolchains` for more information. From 52a03816ba02b1121cde683e03dfc14a0f179698 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Oct 2021 10:27:55 +0200 Subject: [PATCH 169/286] auto-update documentation for EasyBuild v4.5.0 --- docs/version-specific/Supported_software.rst | 1827 ++++++++++++----- docs/version-specific/easyblocks.rst | 6 +- .../version-specific/easyconfig_constants.rst | 2 +- docs/version-specific/generic_easyblocks.rst | 203 +- docs/version-specific/help.rst | 10 +- docs/version-specific/toolchain_opts.rst | 48 +- docs/version-specific/toolchains.rst | 1 - 7 files changed, 1384 insertions(+), 713 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 23b3cd33..ef0a9c6a 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2469 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2506 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -153,6 +153,22 @@ version versionsuffix toolchain ========= ================ =============== +.. _list_software_abTEM_425: + +*abTEM* ++++++++ + +abTEM provides a Python API for running simulations of Transmission Electron Microscopy images. + +*homepage*: https://github.com/jacobjma/abTEM + +============ =============== ================== +version versionsuffix toolchain +============ =============== ================== +``1.0.0b24`` ``-ASE-3.22.0`` ``fosscuda/2020b`` +============ =============== ================== + + .. _list_software_ABySS_418: *ABySS* @@ -249,14 +265,14 @@ AdapterRemoval searches for and removes remnant adapter sequences from High-Thr *homepage*: https://github.com/MikkelSchubert/adapterremoval -========= ============== -version toolchain -========= ============== -``2.2.0`` ``foss/2016b`` -``2.2.2`` ``foss/2018b`` -``2.3.1`` ``foss/2018b`` -``2.3.2`` ``GCC/10.3.0`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``2.2.0`` ``foss/2016b`` +``2.2.2`` ``foss/2018b`` +``2.3.1`` ``foss/2018b`` +``2.3.2`` ``GCC/10.2.0``, ``GCC/10.3.0`` +========= ============================== .. _list_software_ADDA_266: @@ -335,7 +351,7 @@ version versionsuffix toolchain ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. -*homepage*: http://software.genetics.ucla.edu/admixture +*homepage*: https://dalexander.github.io/admixture/ ========= ========== version toolchain @@ -580,6 +596,7 @@ AlphaFold can predict protein structures with atomic accuracy even where no simi version toolchain ========= ================================== ``2.0.0`` ``foss/2020b``, ``fosscuda/2020b`` +``2.0.1`` ``foss/2020b``, ``fosscuda/2020b`` ========= ================================== @@ -1570,9 +1587,26 @@ Initial implementation of an ARTIC bioinformatics platform for nanopore sequenc version versionsuffix toolchain ============== ================= ============== ``2020.04.13`` ``-Python-3.6.6`` ``foss/2018b`` +``2021.06.24`` ``foss/2020b`` ============== ================= ============== +.. _list_software_ARTS_314: + +*ARTS* +++++++ + +ARTS is a radiative transfer model for the millimeter and sub-millimeter spectral range. There are a number of models mostly developed explicitly for the different sensors. + +*homepage*: http://www.radiativetransfer.org/ + +========== =============== +version toolchain +========== =============== +``2.2.64`` ``gompi/2019a`` +========== =============== + + .. _list_software_ArviZ_492: *ArviZ* @@ -1639,35 +1673,35 @@ ASE is a python package providing an open source Atomic Simulation Environment *homepage*: https://wiki.fysik.dtu.dk/ase/ -============== ================== =================================================== -version versionsuffix toolchain -============== ================== =================================================== -``3.9.1.4567`` ``-Python-2.7.11`` ``intel/2016a`` -``3.10.0`` ``-Python-2.7.11`` ``intel/2016.02-GCC-4.9`` -``3.11.0`` ``-Python-2.7.12`` ``intel/2016b`` -``3.13.0`` ``-Python-2.7.12`` ``foss/2016b`` -``3.13.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.15.0`` ``-Python-2.7.12`` ``foss/2016b`` -``3.15.0`` ``-Python-2.7.14`` ``intel/2017b`` -``3.15.0`` ``-Python-3.5.2`` ``foss/2016b`` -``3.15.0`` ``-Python-3.6.2`` ``foss/2017b`` -``3.15.0`` ``-Python-3.6.3`` ``foss/2017b`` -``3.16.2`` ``-Python-3.6.4`` ``iomkl/2018.02``, ``iomkl/2018a`` -``3.16.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.17.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.17.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.18.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.18.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``3.19.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``3.20.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``3.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``3.20.1`` ``-Python-3.8.2`` ``intel/2020a`` -``3.21.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``3.21.1`` ``-Python-3.8.2`` ``foss/2020a`` -``3.22.0`` ``foss/2021a`` -============== ================== =================================================== +============== ================== =================================================================== +version versionsuffix toolchain +============== ================== =================================================================== +``3.9.1.4567`` ``-Python-2.7.11`` ``intel/2016a`` +``3.10.0`` ``-Python-2.7.11`` ``intel/2016.02-GCC-4.9`` +``3.11.0`` ``-Python-2.7.12`` ``intel/2016b`` +``3.13.0`` ``-Python-2.7.12`` ``foss/2016b`` +``3.13.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.15.0`` ``-Python-2.7.12`` ``foss/2016b`` +``3.15.0`` ``-Python-2.7.14`` ``intel/2017b`` +``3.15.0`` ``-Python-3.5.2`` ``foss/2016b`` +``3.15.0`` ``-Python-3.6.2`` ``foss/2017b`` +``3.15.0`` ``-Python-3.6.3`` ``foss/2017b`` +``3.16.2`` ``-Python-3.6.4`` ``iomkl/2018.02``, ``iomkl/2018a`` +``3.16.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``3.17.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``3.17.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.18.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.18.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``3.19.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``3.20.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``3.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.20.1`` ``-Python-3.8.2`` ``intel/2020a`` +``3.21.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``3.21.1`` ``-Python-3.8.2`` ``foss/2020a`` +``3.22.0`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b``, ``intel/2020b`` +============== ================== =================================================================== .. _list_software_ASHS_303: @@ -2096,6 +2130,22 @@ version versionsuffix toolchain ========= ============== ========== +.. _list_software_AutoGeneS_875: + +*AutoGeneS* ++++++++++++ + +AutoGeneS automatically extracts informative genes and reveals the cellular heterogeneity of bulk RNA samples. + +*homepage*: https://github.com/theislab/AutoGeneS + +========= ============== +version toolchain +========= ============== +``1.0.4`` ``foss/2020b`` +========= ============== + + .. _list_software_AutoGrid_799: *AutoGrid* @@ -2217,7 +2267,7 @@ version versionsuffix toolchain --- -:ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` +:ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` .. _list_software_babl_401: @@ -2456,6 +2506,22 @@ version toolchain ======= ============= +.. _list_software_bashplotlib_1172: + +*bashplotlib* ++++++++++++++ + +bashplotlib is a python package and command line tool for making basic plots in the terminal. It's a quick way to visualize data when you don't have a GUI. + +*homepage*: https://github.com/glamp/bashplotlib + +========= ================== +version toolchain +========= ================== +``0.6.5`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_bat_311: *bat* @@ -2562,29 +2628,29 @@ Bazel is a build tool that builds code quickly and reliably. It is used to build *homepage*: https://bazel.io/ -========== ============= ====================================== -version versionsuffix toolchain -========== ============= ====================================== -``0.4.4`` ``system`` -``0.7.0`` ``GCCcore/6.4.0`` -``0.10.0`` ``GCCcore/6.4.0`` -``0.11.0`` ``GCCcore/6.4.0`` -``0.11.1`` ``GCCcore/6.4.0`` -``0.12.0`` ``GCCcore/6.4.0`` -``0.16.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``0.18.0`` ``GCCcore/7.3.0`` -``0.20.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``0.25.2`` ``GCCcore/8.2.0`` -``0.26.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.29.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.29.1`` ``-Java-1.8`` ``GCCcore/9.3.0`` -``1.1.0`` ``GCCcore/8.3.0`` -``2.0.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` -``3.4.1`` ``GCCcore/8.3.0`` -``3.6.0`` ``GCCcore/9.3.0`` -``3.7.1`` ``GCCcore/8.3.0`` -``3.7.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========== ============= ====================================== +========== ============= ========================================================= +version versionsuffix toolchain +========== ============= ========================================================= +``0.4.4`` ``system`` +``0.7.0`` ``GCCcore/6.4.0`` +``0.10.0`` ``GCCcore/6.4.0`` +``0.11.0`` ``GCCcore/6.4.0`` +``0.11.1`` ``GCCcore/6.4.0`` +``0.12.0`` ``GCCcore/6.4.0`` +``0.16.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``0.18.0`` ``GCCcore/7.3.0`` +``0.20.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``0.25.2`` ``GCCcore/8.2.0`` +``0.26.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.29.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.29.1`` ``-Java-1.8`` ``GCCcore/9.3.0`` +``1.1.0`` ``GCCcore/8.3.0`` +``2.0.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +``3.4.1`` ``GCCcore/8.3.0`` +``3.6.0`` ``GCCcore/9.3.0`` +``3.7.1`` ``GCCcore/8.3.0`` +``3.7.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0`` +========== ============= ========================================================= .. _list_software_bbcp_407: @@ -2610,13 +2676,13 @@ version versionsuffix toolchain bbFTP is a file transfer software. It implements its own transfer protocol, which is optimized for large files (larger than 2GB) and secure as it does not read the password in a file and encrypts the connection information. bbFTP main features are: * Encoded username and password at connection * SSH and Certificate authentication modules * Multi-stream transfer * Big windows as defined in RFC1323 * On-the-fly data compression * Automatic retry * Customizable time-outs * Transfer simulation * AFS authentication integration * RFIO interface -*homepage*: http://doc.in2p3.fr/bbftp/ +*homepage*: https://software.in2p3.fr/bbftp/ -========= =============== -version toolchain -========= =============== -``3.2.1`` ``intel/2016a`` -========= =============== +========= ============================================== +version toolchain +========= ============================================== +``3.2.1`` ``GCCcore/9.3.0``, ``intel/2016a``, ``system`` +========= ============================================== .. _list_software_BBMap_418: @@ -2944,6 +3010,7 @@ version versionsuffix toolchain ``1.2.0`` ``intel/2017a``, ``intel/2018a`` ``2.0.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.0.1`` ``foss/2021a`` ============= ================= ================================================================ @@ -3231,22 +3298,22 @@ Bioperl is the product of a community effort to produce Perl code which is usefu *homepage*: https://bioperl.org/ -=========== ================ =============================== -version versionsuffix toolchain -=========== ================ =============================== -``1.6.924`` ``-Perl-5.20.3`` ``intel/2016a`` -``1.6.924`` ``-Perl-5.22.1`` ``foss/2016a`` -``1.7.0`` ``-Perl-5.24.0`` ``foss/2016b`` -``1.7.1`` ``-Perl-5.24.0`` ``intel/2016b`` -``1.7.1`` ``-Perl-5.24.1`` ``intel/2017a`` -``1.7.2`` ``GCCcore/8.3.0`` -``1.7.2`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``1.7.2`` ``-Perl-5.26.1`` ``intel/2018a`` -``1.7.2`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` -``1.7.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -``1.7.7`` ``GCCcore/9.3.0`` -``1.7.8`` ``GCCcore/10.2.0`` -=========== ================ =============================== +=========== ================ ====================================== +version versionsuffix toolchain +=========== ================ ====================================== +``1.6.924`` ``-Perl-5.20.3`` ``intel/2016a`` +``1.6.924`` ``-Perl-5.22.1`` ``foss/2016a`` +``1.7.0`` ``-Perl-5.24.0`` ``foss/2016b`` +``1.7.1`` ``-Perl-5.24.0`` ``intel/2016b`` +``1.7.1`` ``-Perl-5.24.1`` ``intel/2017a`` +``1.7.2`` ``GCCcore/8.3.0`` +``1.7.2`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``1.7.2`` ``-Perl-5.26.1`` ``intel/2018a`` +``1.7.2`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` +``1.7.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``1.7.7`` ``GCCcore/9.3.0`` +``1.7.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +=========== ================ ====================================== .. _list_software_BioPP_442: @@ -3385,7 +3452,7 @@ version toolchain ``3.2.2`` ``GCCcore/7.4.0`` ``3.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` ``3.5.2`` ``system`` -``3.5.3`` ``GCCcore/9.3.0``, ``system`` +``3.5.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0``, ``system`` ``3.6.1`` ``GCCcore/10.1.0`` ``3.7.1`` ``GCCcore/10.2.0``, ``system`` ``3.7.6`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0``, ``system`` @@ -3503,7 +3570,7 @@ version versionsuffix toolchain ``2.8.1`` ``foss/2018b`` ``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a``, ``iimpi/2019b`` ``2.10.1`` ``gompi/2020a``, ``iimpi/2020a`` -``2.11.0`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b`` +``2.11.0`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a`` ========== ================== ================================================================== @@ -3552,18 +3619,18 @@ AMD's fork of BLIS. BLIS is a portable software framework for instantiating high *homepage*: https://developer.amd.com/amd-cpu-libraries/blas-library/ -========= ============= ====================================== -version versionsuffix toolchain -========= ============= ====================================== -``0.3.2`` ``GCC/7.3.0-2.30`` -``0.6.0`` ``GCC/8.3.0-2.32`` -``0.8.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``0.8.1`` ``GCCcore/10.3.0`` -``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` -``2.2`` ``-amd`` ``GCCcore/9.3.0`` -``3.0`` ``-amd`` ``GCCcore/10.3.0`` -``3.0.1`` ``-amd`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========= ============= ====================================== +========= ============= ================================================== +version versionsuffix toolchain +========= ============= ================================================== +``0.3.2`` ``GCC/7.3.0-2.30`` +``0.6.0`` ``GCC/8.3.0-2.32`` +``0.8.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``0.8.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCCcore/10.3.0`` +``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` +``2.2`` ``-amd`` ``GCCcore/9.3.0`` +``3.0`` ``-amd`` ``GCCcore/10.3.0`` +``3.0.1`` ``-amd`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ============= ================================================== .. _list_software_Blitz++_603: @@ -3689,6 +3756,7 @@ version versionsuffix toolchain ``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``2.0.2`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``2.2.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``2.4.1`` ``foss/2021a`` =========== ================== =================================================== @@ -3844,6 +3912,7 @@ version versionsuffix toolchain ``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` ``1.72.0`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a`` ``1.74.0`` ``GCC/10.2.0`` +``1.76.0`` ``GCC/10.3.0`` ========== ================== ==================================================================== @@ -4035,11 +4104,11 @@ Brotli is a generic-purpose lossless compression algorithm that compresses data *homepage*: https://github.com/google/brotli -========= ===================================== -version toolchain -========= ===================================== -``1.0.9`` ``GCCcore/10.3.0``, ``GCCcore/8.3.0`` -========= ===================================== +========= ============================================================================= +version toolchain +========= ============================================================================= +``1.0.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` +========= ============================================================================= .. _list_software_bsddb3_562: @@ -4150,11 +4219,12 @@ This module sets a group of environment variables for compilers, linkers, maths *homepage*: None -=========== ================================================================================================================================================================================================================================================================================================================================ -version toolchain -=========== ================================================================================================================================================================================================================================================================================================================================ -``default`` ``FCC/4.5.0``, ``Fujitsu/21.05``, ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b`` -=========== ================================================================================================================================================================================================================================================================================================================================ +=========== ================ ================================================================================================================================================================================================================================================================================================================================================================= +version versionsuffix toolchain +=========== ================ ================================================================================================================================================================================================================================================================================================================================================================= +``default`` ``FCC/4.5.0``, ``Fujitsu/21.05``, ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b`` +``default`` ``-CUDA-11.3.1`` ``foss/2021a`` +=========== ================ ================================================================================================================================================================================================================================================================================================================================================================= .. _list_software_Bullet_616: @@ -4271,12 +4341,12 @@ The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl *homepage*: https://core.tcl-lang.org/bwidget/home -========== ==================================== -version toolchain -========== ==================================== -``1.9.13`` ``GCCcore/8.2.0`` -``1.9.14`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ==================================== +========== ======================================================== +version toolchain +========== ======================================================== +``1.9.13`` ``GCCcore/8.2.0`` +``1.9.14`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ======================================================== .. _list_software_BWISE_378: @@ -4381,7 +4451,7 @@ bzip2 is a freely available, patent free, high-quality data compressor. It typi version toolchain ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.0.6`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -4391,7 +4461,7 @@ version toolchain --- -:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_c-ares_571: @@ -4604,6 +4674,7 @@ version versionsuffix toolchain ``1.9`` ``-Java-11`` ``GCCcore/8.3.0`` ``2.1.1`` ``GCCcore/10.2.0`` ``2.1.1`` ``-Java-11`` ``GCCcore/9.3.0`` +``2.2`` ``GCCcore/10.3.0`` ========= ================ =============================== @@ -4706,6 +4777,7 @@ version versionsuffix toolchain ``0.18.0`` ``-Python-3.7.4`` ``foss/2019b`` ``0.18.0`` ``-Python-3.8.2`` ``foss/2020a`` ``0.19.0.post1`` ``foss/2020b``, ``intel/2020b`` +``0.20.0`` ``foss/2021a`` ================ ================= =============================== @@ -4851,12 +4923,12 @@ Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming *homepage*: https://github.com/coin-or/Cbc -========== ============== -version toolchain -========== ============== -``2.10.3`` ``foss/2018b`` -``2.10.5`` ``foss/2020b`` -========== ============== +========== ============================== +version toolchain +========== ============================== +``2.10.3`` ``foss/2018b`` +``2.10.5`` ``foss/2020b``, ``foss/2021a`` +========== ============================== .. _list_software_CBLAS_357: @@ -4971,14 +5043,14 @@ CD-HIT is a very widely used program for clustering and comparing protein or nu *homepage*: https://github.com/weizhongli/cdhit -========= ============== ===================================================================================== -version versionsuffix toolchain -========= ============== ===================================================================================== -``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` -``4.6.6`` ``foss/2016b`` -``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` -``4.8.1`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` -========= ============== ===================================================================================== +========= ============== ===================================================================================================== +version versionsuffix toolchain +========= ============== ===================================================================================================== +``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` +``4.6.6`` ``foss/2016b`` +``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` +``4.8.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` +========= ============== ===================================================================================================== .. _list_software_CDAT_284: @@ -5354,12 +5426,12 @@ The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that *homepage*: https://github.com/coin-or/Cgl -========== ============== -version toolchain -========== ============== -``0.60.2`` ``foss/2018b`` -``0.60.3`` ``foss/2020b`` -========== ============== +========== ============================== +version toolchain +========== ============================== +``0.60.2`` ``foss/2018b`` +``0.60.3`` ``foss/2020b``, ``foss/2021a`` +========== ============================== .. _list_software_CGmapTools_985: @@ -5751,6 +5823,22 @@ version versionsuffix toolchain ========= ================ =============== +.. _list_software_CIRI-long_772: + +*CIRI-long* ++++++++++++ + +Circular RNA Identification for Long-Reads Nanopore Sequencing Data + +*homepage*: https://github.com/bioinfo-biols/CIRI-long/ + +========= ============== +version toolchain +========= ============== +``1.0.2`` ``foss/2020b`` +========= ============== + + .. _list_software_cisTEM_549: *cisTEM* @@ -5821,7 +5909,7 @@ version versionsuffix toolchain ``10.0.1`` ``GCCcore/9.3.0`` ``11.0.0`` ``GCCcore/9.3.0`` ``11.0.1`` ``GCCcore/10.2.0``, ``gcccuda/2020b`` -``12.0.1`` ``GCCcore/10.3.0`` +``12.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ================== ====================================== @@ -5939,12 +6027,12 @@ Clp (Coin-or linear programming) is an open-source linear programming solver. It *homepage*: https://github.com/coin-or/Clp -========== ============== -version toolchain -========== ============== -``1.17.3`` ``foss/2018b`` -``1.17.6`` ``foss/2020b`` -========== ============== +========== ============================== +version toolchain +========== ============================== +``1.17.3`` ``foss/2018b`` +``1.17.6`` ``foss/2020b``, ``foss/2021a`` +========== ============================== .. _list_software_Clustal-Omega_1262: @@ -5973,11 +6061,11 @@ ClustalW2 is a general purpose multiple sequence alignment program for DNA or pr *homepage*: https://www.ebi.ac.uk/Tools/msa/clustalw2/ -======= =========================================================================================================================================== -version toolchain -======= =========================================================================================================================================== -``2.1`` ``GCC/10.3.0``, ``foss/2016b``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b``, ``intel/2020a`` -======= =========================================================================================================================================== +======= =========================================================================================================================================================== +version toolchain +======= =========================================================================================================================================================== +``2.1`` ``GCC/10.3.0``, ``foss/2016b``, ``foss/2018b``, ``foss/2021a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b``, ``intel/2020a`` +======= =========================================================================================================================================================== .. _list_software_Cluster-Buster_1412: @@ -6205,12 +6293,12 @@ CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functi *homepage*: https://github.com/coin-or/CoinUtils -========== ================================= -version toolchain -========== ================================= -``2.11.3`` ``GCCcore/7.3.0``, ``foss/2018b`` -``2.11.4`` ``GCCcore/10.2.0`` -========== ================================= +========== ================================== +version toolchain +========== ================================== +``2.11.3`` ``GCCcore/7.3.0``, ``foss/2018b`` +``2.11.4`` ``GCC/10.3.0``, ``GCCcore/10.2.0`` +========== ================================== .. _list_software_Commet_613: @@ -6508,6 +6596,7 @@ version versionsuffix toolchain ``7.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` ``7.1`` ``-psmp`` ``foss/2020b`` ``8.1`` ``foss/2020b`` +``8.2`` ``foss/2021a`` ======= ============= ================================================================================= @@ -6683,12 +6772,12 @@ Conditional Reciprocal Best BLAST - high confidence ortholog assignment. CRB-BL *homepage*: https://github.com/cboursnell/crb-blast -========= =============== =============== -version versionsuffix toolchain -========= =============== =============== -``0.6.9`` ``intel/2017a`` -``0.6.9`` ``-Ruby-2.6.1`` ``foss/2018b`` -========= =============== =============== +========= =============== ================================ +version versionsuffix toolchain +========= =============== ================================ +``0.6.9`` ``gompi/2021a``, ``intel/2017a`` +``0.6.9`` ``-Ruby-2.6.1`` ``foss/2018b`` +========= =============== ================================ .. _list_software_CREST_385: @@ -7053,6 +7142,7 @@ version toolchain ``11.1.1`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` ``11.3.1`` ``system`` ``11.4.1`` ``system`` +``11.4.2`` ``system`` ================= ========================================================================== @@ -7247,7 +7337,7 @@ version versionsuffix toolchain ``2.8`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``2.10`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``2.10`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``3.4`` ``GCCcore/10.3.0`` +``3.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ================== ================================================ @@ -7417,7 +7507,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` .. _list_software_dadi_402: @@ -7461,11 +7551,12 @@ The Dalton code is a powerful tool for a wide range of molecular properties at *homepage*: https://daltonprogram.org/ -======== ============= =============== -version versionsuffix toolchain -======== ============= =============== -``2016`` ``-i8`` ``intel/2017b`` -======== ============= =============== +========== ============= =============== +version versionsuffix toolchain +========== ============= =============== +``2016`` ``-i8`` ``intel/2017b`` +``2020.0`` ``foss/2021a`` +========== ============= =============== .. _list_software_damageproto_1171: @@ -7563,6 +7654,7 @@ version versionsuffix toolchain ``2.8.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``2.18.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``2021.2.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``2021.9.1`` ``foss/2021a`` ============ ================== =================================================== @@ -7609,16 +7701,16 @@ Berkeley DB enables the development of custom data management solutions, withou *homepage*: http://www.oracle.com/technetwork/products/berkeleydb -=========== ========================================================================= -version toolchain -=========== ========================================================================= -``4.8.30`` ``intel/2016a`` -``6.2.23`` ``foss/2016a`` -``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` -``18.1.25`` ``GCCcore/7.3.0`` -``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``18.1.40`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -=========== ========================================================================= +=========== =============================================================================================================== +version toolchain +=========== =============================================================================================================== +``4.8.30`` ``intel/2016a`` +``6.2.23`` ``foss/2016a`` +``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` +``18.1.25`` ``GCCcore/7.3.0`` +``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``18.1.40`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +=========== =============================================================================================================== .. _list_software_DB_File_613: @@ -7637,6 +7729,7 @@ version versionsuffix toolchain ``1.835`` ``-Perl-5.20.3`` ``intel/2016a`` ``1.835`` ``-Perl-5.22.1`` ``foss/2016a`` ``1.855`` ``GCCcore/10.2.0`` +``1.856`` ``GCCcore/10.3.0`` ========= ================ ================== @@ -7755,6 +7848,7 @@ version toolchain ========= ==================================== ``3.6.3`` ``GCCcore/7.3.0`` ``3.6.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.6.6`` ``GCCcore/10.3.0`` ========= ==================================== @@ -8025,6 +8119,22 @@ version toolchain ========= ===================================================================================== +.. _list_software_DFT-D4_387: + +*DFT-D4* +++++++++ + +Generally Applicable Atomic-Charge Dependent London Dispersion Correction. + +*homepage*: https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4 + +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``3.2.0`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =============== + + .. _list_software_DFTB+_331: *DFTB+* @@ -8663,7 +8773,7 @@ version versionsuffix toolchain --- -:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Excel-Writer-XLSX_1559` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_ELSI-RCI_568` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESL-Bundle_875` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Excel-Writer-XLSX_1559` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_expecttest_1097` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_E-ANTIC_481: @@ -8810,6 +8920,7 @@ version toolchain ``4.3.4`` ``system`` ``4.4.0`` ``system`` ``4.4.1`` ``system`` +``4.4.2`` ``system`` ========== ========== @@ -8904,6 +9015,7 @@ version versionsuffix toolchain ``1.3.8.post1`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ``1.3.8.post1`` ``-Python-3.8.2`` ``GCC/9.3.0`` ``1.3.8.post2`` ``-Python-3.8.2`` ``iccifort/2020.1.217`` +``1.3.9`` ``GCC/10.2.0`` =============== ================= ====================================== @@ -8949,24 +9061,24 @@ Eigen is a C++ template library for linear algebra: matrices, vectors, numerical *homepage*: https://eigen.tuxfamily.org -========== =========================================== -version toolchain -========== =========================================== -``3.2.3`` ``foss/2016a``, ``foss/2016b`` -``3.2.5`` ``system`` -``3.2.6`` ``system`` -``3.2.7`` ``foss/2016a``, ``intel/2016a`` -``3.2.8`` ``foss/2016a``, ``intel/2016a``, ``system`` -``3.2.9`` ``foss/2016b``, ``intel/2016b`` -``3.2.10`` ``intel/2016b`` -``3.3.2`` ``foss/2016b``, ``intel/2016b`` -``3.3.3`` ``GCCcore/6.3.0``, ``intel/2016b`` -``3.3.4`` ``system`` -``3.3.5`` ``system`` -``3.3.7`` ``GCCcore/9.3.0``, ``system`` -``3.3.8`` ``GCCcore/10.2.0`` -``3.3.9`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========== =========================================== +========== ========================================================== +version toolchain +========== ========================================================== +``3.2.3`` ``foss/2016a``, ``foss/2016b`` +``3.2.5`` ``system`` +``3.2.6`` ``system`` +``3.2.7`` ``foss/2016a``, ``intel/2016a`` +``3.2.8`` ``foss/2016a``, ``intel/2016a``, ``system`` +``3.2.9`` ``foss/2016b``, ``intel/2016b`` +``3.2.10`` ``intel/2016b`` +``3.3.2`` ``foss/2016b``, ``intel/2016b`` +``3.3.3`` ``GCCcore/6.3.0``, ``intel/2016b`` +``3.3.4`` ``system`` +``3.3.5`` ``system`` +``3.3.7`` ``GCCcore/9.3.0``, ``system`` +``3.3.8`` ``GCCcore/10.2.0`` +``3.3.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ========================================================== .. _list_software_EIGENSOFT_676: @@ -9063,7 +9175,7 @@ version toolchain ``2019.11.001`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a``, ``iomkl/2019b`` ``2020.05.001`` ``intel/2020a`` ``2020.11.001`` ``foss/2020b``, ``intel/2020b`` -``2021.05.001`` ``foss/2021a``, ``intel/2021a`` +``2021.05.001`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` =================== ================================================================================= @@ -9092,12 +9204,30 @@ ELSI provides and enhances scalable, open-source software library solutions for *homepage*: https://wordpress.elsi-interchange.org/ -========= ============= =============== -version versionsuffix toolchain -========= ============= =============== -``2.5.0`` ``intel/2019b`` -``2.5.0`` ``-PEXSI`` ``intel/2019b`` -========= ============= =============== +========= ============= =============================== +version versionsuffix toolchain +========= ============= =============================== +``2.5.0`` ``intel/2019b`` +``2.5.0`` ``-PEXSI`` ``intel/2019b`` +``2.6.4`` ``-PEXSI`` ``foss/2020b``, ``intel/2020b`` +``2.7.1`` ``-PEXSI`` ``foss/2021a``, ``intel/2021a`` +========= ============= =============================== + + +.. _list_software_ELSI-RCI_568: + +*ELSI-RCI* +++++++++++ + +ELSI-RCI provides and enhances open-source software packages which iteratively solve or circumvent eigenvalue problems in self-consistent field calculations based on the Kohn-Sham density-functional theory. + +*homepage*: https://wordpress.elsi-interchange.org/ + +========= =============================== +version toolchain +========= =============================== +``0.1.0`` ``foss/2020b``, ``intel/2020b`` +========= =============================== .. _list_software_Emacs_489: @@ -9150,14 +9280,14 @@ EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a fre *homepage*: http://emboss.sourceforge.net/ -========= ================= ================================================================================================================================ -version versionsuffix toolchain -========= ================= ================================================================================================================================ -``6.6.0`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` -``6.6.0`` ``-Java-11`` ``GCC/8.3.0`` -``6.6.0`` ``-Java-13`` ``GCC/10.2.0`` -``6.6.0`` ``-X11-20170314`` ``intel/2017a`` -========= ================= ================================================================================================================================ +========= ================= ================================================================================================================================================ +version versionsuffix toolchain +========= ================= ================================================================================================================================================ +``6.6.0`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018b``, ``foss/2021a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` +``6.6.0`` ``-Java-11`` ``GCC/8.3.0`` +``6.6.0`` ``-Java-13`` ``GCC/10.2.0`` +``6.6.0`` ``-X11-20170314`` ``intel/2017a`` +========= ================= ================================================================================================================================================ .. _list_software_emcee_511: @@ -9309,6 +9439,22 @@ version versionsuffix toolchain ========= ============= =============== +.. _list_software_ESL-Bundle_875: + +*ESL-Bundle* +++++++++++++ + +The ESL Bundle is a collection of libraries and utilities broadly used in electronic structure calculations, put together to make their use easier by researchers and scientific software developers. ESL stands for Electronic Structure Library, an initiative which distributes quality software and promotes open standards for high-performance computing applications in the field of electronic structure calculations. + +*homepage*: https://esl.cecam.org + +========= =============================== +version toolchain +========= =============================== +``0.6.1`` ``foss/2020b``, ``intel/2020b`` +========= =============================== + + .. _list_software_ESMF_299: *ESMF* @@ -9411,6 +9557,7 @@ version versionsuffix toolchain ============ ================== =============== ``3.0.0b36`` ``-Python-2.7.12`` ``intel/2016b`` ``3.1.1`` ``-Python-3.6.6`` ``foss/2018b`` +``3.1.2`` ``foss/2020b`` ``3.1.2`` ``-Python-3.8.2`` ``foss/2020a`` ============ ================== =============== @@ -9554,11 +9701,11 @@ Exonerate is a generic tool for pairwise sequence comparison. It allows you to *homepage*: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate -========= ============================================================================================================================================================================================================= -version toolchain -========= ============================================================================================================================================================================================================= -``2.4.0`` ``GCC/10.2.0``, ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a`` -========= ============================================================================================================================================================================================================= +========= ============================================================================================================================================================================================================================= +version toolchain +========= ============================================================================================================================================================================================================================= +``2.4.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a`` +========= ============================================================================================================================================================================================================================= .. _list_software_expat_546: @@ -9601,6 +9748,22 @@ version toolchain ========== ==================================== +.. _list_software_expecttest_1097: + +*expecttest* +++++++++++++ + +This library implements expect tests (also known as "golden" tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output. If the output of the test changes, you can rerun the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output. + +*homepage*: https://github.com/ezyang/expecttest + +========= ================== +version toolchain +========= ================== +``0.1.3`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_eXpress_746: *eXpress* @@ -9641,7 +9804,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -9835,12 +9998,12 @@ FastME: a comprehensive, accurate and fast distance-based phylogeny inference pr *homepage*: http://www.atgc-montpellier.fr/fastme/ -=========== ======================================================================== -version toolchain -=========== ======================================================================== -``2.1.5`` ``foss/2016a`` -``2.1.6.1`` ``GCC/8.3.0``, ``iccifort/2019.5.281``, ``intel/2018a``, ``intel/2018b`` -=========== ======================================================================== +=========== ======================================================================================== +version toolchain +=========== ======================================================================================== +``2.1.5`` ``foss/2016a`` +``2.1.6.1`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``iccifort/2019.5.281``, ``intel/2018a``, ``intel/2018b`` +=========== ======================================================================================== .. _list_software_fastp_542: @@ -10168,6 +10331,22 @@ version toolchain ========= ========== +.. _list_software_fdict_522: + +*fdict* ++++++++ + +A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. + +*homepage*: https://github.com/zerothi/fdict + +========= ======================================= +version toolchain +========= ======================================= +``0.8.0`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +========= ======================================= + + .. _list_software_FDS_221: *FDS* @@ -10448,21 +10627,22 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: https://www.fftw.org -========= ============= ======================================================================================================================================================================================================================================================================================================================= -version versionsuffix toolchain -========= ============= ======================================================================================================================================================================================================================================================================================================================= -``1.0.0`` ``-fujitsu`` ``FCC/4.5.0`` -``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` -``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` -``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` -``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` -``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` -``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` -``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``iomkl/2018b`` -``3.3.8`` ``-amd`` ``gompi/2020a`` -``3.3.8`` ``-serial`` ``GCC/9.3.0`` -``3.3.9`` ``gompi/2021.07``, ``gompi/2021a``, ``intel/2021a`` -========= ============= ======================================================================================================================================================================================================================================================================================================================= +========== ============= ======================================================================================================================================================================================================================================================================================================================= +version versionsuffix toolchain +========== ============= ======================================================================================================================================================================================================================================================================================================================= +``1.0.0`` ``-fujitsu`` ``FCC/4.5.0`` +``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` +``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` +``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` +``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` +``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` +``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` +``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``iomkl/2018b`` +``3.3.8`` ``-amd`` ``gompi/2020a`` +``3.3.8`` ``-serial`` ``GCC/9.3.0`` +``3.3.9`` ``gompi/2021a``, ``intel/2021a`` +``3.3.10`` ``gompi/2021b``, ``iimpi/2021b`` +========== ============= ======================================================================================================================================================================================================================================================================================================================= .. _list_software_fgbio_519: @@ -10733,7 +10913,7 @@ version versionsuffix toolchain ``1.8.13`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``1.8.13.post1`` ``-Python-3.7.2`` ``foss/2019a`` ``1.8.16`` ``-Python-3.8.2`` ``foss/2020a`` -``1.8.20`` ``foss/2020b``, ``intel/2020b`` +``1.8.20`` ``foss/2020b``, ``foss/2021a``, ``intel/2020b`` ================ ================= =================================================== @@ -11074,6 +11254,22 @@ version toolchain ========= =============================================================================================== +.. _list_software_flook_539: + +*flook* ++++++++ + +The fortran-Lua-hook library. + +*homepage*: https://github.com/ElectronicStructureLibrary/flook + +========= ======================================= +version toolchain +========= ======================================= +``0.8.1`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +========= ======================================= + + .. _list_software_FLTK_305: *FLTK* @@ -11278,8 +11474,8 @@ version toolchain ``2019b`` ``system`` ``2020a`` ``system`` ``2020b`` ``system`` -``2021.07`` ``system`` ``2021a`` ``system`` +``2021b`` ``system`` =========== ========== @@ -11541,6 +11737,22 @@ version versionsuffix toolchain ========= =================== ========== +.. _list_software_FreeTDS_621: + +*FreeTDS* ++++++++++ + +FreeTDS is a set of libraries for Unix and Linux that allows your programs to natively talk to Microsoft SQL Server and Sybase databases. + +*homepage*: https://www.freetds.org/ + +========= ================== +version toolchain +========= ================== +``1.3.3`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_freetype_868: *freetype* @@ -12515,14 +12727,15 @@ GD.pm - Interface to Gd Graphics Library *homepage*: https://github.com/lstein/Perl-GD -======== ================ ================= -version versionsuffix toolchain -======== ================ ================= -``2.66`` ``-Perl-5.24.0`` ``foss/2016b`` -``2.68`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``2.69`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -``2.71`` ``GCCcore/9.3.0`` -======== ================ ================= +======== ================ ================== +version versionsuffix toolchain +======== ================ ================== +``2.66`` ``-Perl-5.24.0`` ``foss/2016b`` +``2.68`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``2.69`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``2.71`` ``GCCcore/9.3.0`` +``2.73`` ``GCCcore/10.3.0`` +======== ================ ================== .. _list_software_GDAL_280: @@ -12561,6 +12774,7 @@ version versionsuffix toolchain ``3.0.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``3.2.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``3.3.0`` ``foss/2021a`` +``3.3.2`` ``foss/2021b`` ========= ============================== ================================================================ @@ -12753,6 +12967,7 @@ version versionsuffix toolchain ======= ================ ====================================== ``2.1`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` ``2.1`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` +``2.1`` ``-CUDA-11.2.1`` ``GCCcore/10.2.0`` ``2.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``2.3`` ``GCCcore/11.2.0`` ======= ================ ====================================== @@ -13300,13 +13515,13 @@ The gflags package contains a C++ library that implements commandline flags proc *homepage*: https://github.com/gflags/gflags -========= =========================================================================== -version toolchain -========= =========================================================================== -``2.1.2`` ``foss/2016a`` -``2.2.1`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` -``2.2.2`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= =========================================================================== +========= =================================================================================================================== +version toolchain +========= =================================================================================================================== +``2.1.2`` ``foss/2016a`` +``2.2.1`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` +``2.2.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= =================================================================================================================== .. _list_software_GFOLD_364: @@ -13724,9 +13939,9 @@ The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C version versionsuffix toolchain ========= ============= =============================================================================================================== ``2.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b`` -``2.2.0`` ``-egl`` ``GCCcore/10.2.0`` -``2.2.0`` ``-glx`` ``GCCcore/10.2.0`` -``2.2.0`` ``-osmesa`` ``GCCcore/10.2.0`` +``2.2.0`` ``-egl`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` +``2.2.0`` ``-glx`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` +``2.2.0`` ``-osmesa`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` ========= ============= =============================================================================================================== @@ -14318,6 +14533,7 @@ version versionsuffix toolchain ``2020.06`` ``-amd`` ``system`` ``2020.11`` ``system`` ``2020b`` ``system`` +``2021a`` ``system`` =========== ============= ========== @@ -14449,8 +14665,8 @@ version versionsuffix toolchain ``2019b`` ``system`` ``2020a`` ``system`` ``2020b`` ``system`` -``2021.07`` ``system`` ``2021a`` ``system`` +``2021b`` ``system`` ``system`` ``-2.29`` ``system`` =========== ============= ========== @@ -14564,6 +14780,7 @@ version versionsuffix toolchain ``20.10.0`` ``-ASE-3.20.1-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``21.1.0`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` ``21.6.0`` ``foss/2021a`` +``21.6.0`` ``-ASE-3.22.0`` ``foss/2020b``, ``intel/2020b`` =========== ============================ =============================== @@ -15095,6 +15312,7 @@ version versionsuffix toolchain ``2021`` ``foss/2020b``, ``fosscuda/2020b`` ``2021.2`` ``fosscuda/2020b`` ``2021.3`` ``foss/2021a`` +``2021.3`` ``-CUDA-11.3.1`` ``foss/2021a`` ========== ================= ============================================================================================================ @@ -15294,6 +15512,7 @@ version versionsuffix toolchain ``1.0.2`` ``-Python-3.7.4`` ``intel/2019b`` ``1.3.0`` ``-Python-3.8.2`` ``intel/2020a`` ``1.5.0`` ``intel/2020b`` +``1.7.0`` ``intel/2020b`` ========= ================== =============================== @@ -15481,24 +15700,24 @@ The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. *homepage*: https://www.gurobi.com -========= ================= =============================== -version versionsuffix toolchain -========= ================= =============================== -``6.5.1`` ``system`` -``6.5.2`` ``system`` -``7.0.1`` ``system`` -``7.5.2`` ``system`` -``7.5.2`` ``-Python-3.6.4`` ``intel/2018a`` -``8.1.1`` ``system`` -``9.0.0`` ``system`` -``9.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``9.0.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``9.0.1`` ``system`` -``9.0.3`` ``GCCcore/10.2.0``, ``system`` -``9.1.0`` ``system`` -``9.1.1`` ``GCCcore/10.2.0`` -``9.1.2`` ``GCCcore/10.2.0``, ``system`` -========= ================= =============================== +========= ================= ================================================== +version versionsuffix toolchain +========= ================= ================================================== +``6.5.1`` ``system`` +``6.5.2`` ``system`` +``7.0.1`` ``system`` +``7.5.2`` ``system`` +``7.5.2`` ``-Python-3.6.4`` ``intel/2018a`` +``8.1.1`` ``system`` +``9.0.0`` ``system`` +``9.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``9.0.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``9.0.1`` ``system`` +``9.0.3`` ``GCCcore/10.2.0``, ``system`` +``9.1.0`` ``system`` +``9.1.1`` ``GCCcore/10.2.0`` +``9.1.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``system`` +========= ================= ================================================== .. _list_software_gzip_442: @@ -15525,7 +15744,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -15777,6 +15996,22 @@ version toolchain ========= ========== +.. _list_software_HDBSCAN_499: + +*HDBSCAN* ++++++++++ + +The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library provides a high performance implementation of this algorithm, along with tools for analysing the resulting clustering. + +*homepage*: http://hdbscan.readthedocs.io/en/latest/ + +========== ============== +version toolchain +========== ============== +``0.8.27`` ``foss/2021a`` +========== ============== + + .. _list_software_HDDM_285: *HDDM* @@ -15880,7 +16115,7 @@ version versionsuffix toolchain ``1.10.6`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpic/2020a`` ``1.10.7`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpic/2020b`` ``1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` -``1.12.1`` ``gompi/2021a`` +``1.12.1`` ``gompi/2021a``, ``gompi/2021b`` ================= ============= ================================================================================================================================================================================================================== @@ -16015,13 +16250,14 @@ The HH-suite is an open-source software package for sensitive protein sequence *homepage*: https://github.com/soedinglab/hh-suite -============== ================================================= -version toolchain -============== ================================================= -``3.0-beta.3`` ``intel/2018a`` -``3.2.0`` ``foss/2019b``, ``fosscuda/2019b`` -``3.3.0`` ``foss/2020a``, ``gompi/2020b``, ``gompic/2020b`` -============== ================================================= +============== ================= ================================================================== +version versionsuffix toolchain +============== ================= ================================================================== +``3.0-beta.3`` ``intel/2018a`` +``3.2.0`` ``foss/2019b``, ``fosscuda/2019b`` +``3.3.0`` ``foss/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b`` +``3.3.0`` ``-Python-3.7.4`` ``gompic/2019b`` +============== ================= ================================================================== .. _list_software_HiC-Pro_594: @@ -16233,11 +16469,11 @@ HMMER is used for searching sequence databases for sequence homologs, and for m *homepage*: http://hmmer.org -========= ============= -version toolchain -========= ============= -``2.3.2`` ``GCC/8.3.0`` -========= ============= +========= ============================= +version toolchain +========= ============================= +``2.3.2`` ``GCC/10.3.0``, ``GCC/8.3.0`` +========= ============================= .. _list_software_hmmlearn_852: @@ -16300,6 +16536,8 @@ version versionsuffix toolchain ``0.21.3`` ``-TensorFlow-2.3.1-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` ``0.22.0`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` ``0.22.1`` ``-CUDA-11.3.1-TensorFlow-2.6.0`` ``foss/2021a`` +``0.22.1`` ``-TensorFlow-2.5.0`` ``fosscuda/2020b`` +``0.22.1`` ``-TensorFlow-2.5.0-Python-3.7.4`` ``fosscuda/2019b`` ========== =================================== ================================== @@ -16329,12 +16567,12 @@ The HPCG Benchmark project is an effort to create a more relevant metric for ran *homepage*: https://software.sandia.gov/hpcg -======= ================================================================================== -version toolchain -======= ================================================================================== -``3.0`` ``foss/2016b``, ``foss/2018b``, ``intel/2018b`` -``3.1`` ``foss/2018b``, ``foss/2021.07``, ``foss/2021a``, ``intel/2018b``, ``intel/2021a`` -======= ================================================================================== +======= ================================================================================================= +version toolchain +======= ================================================================================================= +``3.0`` ``foss/2016b``, ``foss/2018b``, ``intel/2018b`` +``3.1`` ``foss/2018b``, ``foss/2021a``, ``foss/2021b``, ``intel/2018b``, ``intel/2021a``, ``intel/2021b`` +======= ================================================================================================= .. _list_software_HPCX_307: @@ -16366,6 +16604,7 @@ Highly parallel density based spatial clustering for application with noise version toolchain ============ ============== ``20171110`` ``foss/2017b`` +``20210826`` ``foss/2020b`` ============ ============== @@ -16383,7 +16622,7 @@ version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021.07``, ``foss/2021a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -16667,7 +16906,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -17171,6 +17410,7 @@ version versionsuffix toolchain ``2020a`` ``system`` ``2020b`` ``system`` ``2021a`` ``system`` +``2021b`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ===================== ==================== ========== @@ -17259,6 +17499,7 @@ version versionsuffix toolchain ========= ================= =============================== ``2.3.0`` ``-Python-3.6.4`` ``intel/2018a`` ``2.5.0`` ``foss/2019a`` +``2.9.0`` ``fosscuda/2020b`` ``2.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========= ================= =============================== @@ -17272,13 +17513,14 @@ Image Processing and Analysis in Java *homepage*: https://imagej.nih.gov/ij -========= ========== -version toolchain -========= ========== -``1.51a`` ``system`` -``1.51i`` ``system`` -``1.51k`` ``system`` -========= ========== +========= ============= ========== +version versionsuffix toolchain +========= ============= ========== +``1.51a`` ``system`` +``1.51i`` ``system`` +``1.51k`` ``system`` +``1.52q`` ``-Java-1.8`` ``system`` +========= ============= ========== .. _list_software_ImageMagick_1071: @@ -17424,12 +17666,30 @@ version versionsuffix toolchain ``2019.5.281`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b``, ``iompi/2019b`` ``2020.0.166`` ``iimpi/2020.00`` ``2020.1.217`` ``gompi/2020a``, ``iimpi/2020.06-impi-18.5``, ``iimpi/2020a``, ``iimpic/2020a``, ``iompi/2020a`` -``2020.4.304`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpic/2020b``, ``iompi/2020b`` +``2020.4.304`` ``NVHPC/21.2``, ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpic/2020b``, ``iompi/2020b`` ``2021.1.1`` ``iimpi/2020.12`` ``2021.2.0`` ``gompi/2021a``, ``iimpi/2021a``, ``iompi/2021a`` +``2021.3.0`` ``gompi/2021a`` +``2021.4.0`` ``system`` ============== ============= ====================================================================================================================================================================================================================================================================== +.. _list_software_imkl-FFTW_785: + +*imkl-FFTW* ++++++++++++ + +FFTW interfaces using Intel oneAPI Math Kernel Library + +*homepage*: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html + +============ ================================ +version toolchain +============ ================================ +``2021.4.0`` ``gompi/2021b``, ``iimpi/2021b`` +============ ================================ + + .. _list_software_Imlib2_543: *Imlib2* @@ -17526,6 +17786,8 @@ version versionsuffix toolchain ``2019.12.320`` ``iccifort/2020.4.304`` ``2021.1.1`` ``intel-compilers/2021.1.2`` ``2021.2.0`` ``intel-compilers/2021.2.0`` +``2021.3.0`` ``intel-compilers/2021.3.0`` +``2021.4.0`` ``intel-compilers/2021.4.0`` ``system`` ``iccifort/system-GCC-system-2.29`` =============== ============= ================================================================================================================================================================================================================================ @@ -17767,6 +18029,7 @@ version versionsuffix toolchain ``2020a`` ``system`` ``2020b`` ``system`` ``2021a`` ``system`` +``2021b`` ``system`` ===================== ============= ========== @@ -17785,6 +18048,7 @@ version toolchain ``2021.1.2`` ``system`` ``2021.2.0`` ``system`` ``2021.3.0`` ``system`` +``2021.4.0`` ``system`` ============ ========== @@ -18192,7 +18456,7 @@ version versionsuffix toolchain ``1.5.5`` ``-omp-mpi`` ``foss/2016a`` ``1.6.6`` ``intel/2018a`` ``1.6.12`` ``foss/2018b``, ``foss/2020a``, ``intel/2019b`` -``2.1.2`` ``foss/2020a`` +``2.1.2`` ``foss/2020a``, ``gompi/2020b`` ========== ============= =============================================== @@ -18241,11 +18505,11 @@ Intelligent Storage Acceleration Library *homepage*: https://github.com/intel/isa-l -========== ================== -version toolchain -========== ================== -``2.30.0`` ``GCCcore/10.3.0`` -========== ================== +========== ====================================== +version toolchain +========== ====================================== +``2.30.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========== ====================================== .. _list_software_ISL_232: @@ -18269,6 +18533,22 @@ version toolchain ======== ========================================================= +.. _list_software_isoCirc_716: + +*isoCirc* ++++++++++ + +isoCirc: computational pipeline to identify high-confidence BSJs and full-length circRNA isoforms from isoCirc long-read data + +*homepage*: https://github.com/Xinglab/isoCirc + +========= ============== +version toolchain +========= ============== +``1.0.4`` ``foss/2020b`` +========= ============== + + .. _list_software_ispc_431: *ispc* @@ -18330,6 +18610,7 @@ version versionsuffix toolchain ``4.13.1`` ``-Python-2.7.15`` ``foss/2018b`` ``4.13.1`` ``-Python-3.6.4`` ``foss/2018a`` ``4.13.1`` ``-Python-3.6.6`` ``foss/2018b`` +``4.13.1`` ``-Python-3.7.4`` ``foss/2019b`` ``5.0.1`` ``-Python-3.7.2`` ``foss/2019a`` ``5.0.1`` ``-Python-3.7.4`` ``foss/2019b`` ``5.0b01`` ``-Python-3.6.6`` ``foss/2018b`` @@ -18544,7 +18825,7 @@ version versionsuffix toolchain *jax* +++++ -Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more +Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more *homepage*: https://pypi.python.org/pypi/jax @@ -18552,6 +18833,7 @@ Composable transformations of Python+NumPy programs: differentiate, vectorize, J version toolchain ========== ================================== ``0.2.19`` ``foss/2020b``, ``fosscuda/2020b`` +``0.2.20`` ``foss/2021a`` ========== ================================== @@ -18580,11 +18862,11 @@ JBIG-KIT is a software implementation of the JBIG1 data compression standard (I *homepage*: https://www.cl.cam.ac.uk/~mgk25/jbigkit/ -======= ================================================================================================================== -version toolchain -======= ================================================================================================================== -``2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ================================================================================================================== +======= ====================================================================================================================================== +version toolchain +======= ====================================================================================================================================== +``2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ====================================================================================================================================== .. _list_software_Jellyfish_938: @@ -18962,12 +19244,12 @@ Kalign is a fast multiple sequence alignment program for biological sequences. *homepage*: https://github.com/TimoLassmann/kalign -========= ================== -version toolchain -========= ================== -``2.0.4`` ``GCCcore/10.2.0`` -``3.3.1`` ``GCCcore/10.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``2.0.4`` ``GCCcore/10.2.0`` +``3.3.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_kallisto_867: @@ -19274,6 +19556,7 @@ version versionsuffix toolchain ``2.0.9-beta`` ``-Perl-5.28.0`` ``foss/2018b`` ``2.0.9-beta`` ``-Perl-5.30.2`` ``gompi/2020a`` ``2.1.1`` ``gompi/2020b`` +``2.1.2`` ``gompi/2021a`` ============== ================ =============== @@ -19381,7 +19664,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libfdf_615` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libmbd_618` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpspio_866` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libSBML_613` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_longread_umi_1270` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -19619,6 +19902,7 @@ version versionsuffix toolchain ========= ================= ================================== ``0.8.2`` ``-Python-3.8.2`` ``foss/2020a`` ``0.8.3`` ``foss/2020b``, ``fosscuda/2020b`` +``0.8.7`` ``foss/2021a`` ========= ================= ================================== @@ -19942,6 +20226,7 @@ libctl is a free Guile-based library implementing flexible control files for sci version toolchain ========= ================= ``3.2.2`` ``foss/2016a`` +``4.0.0`` ``intel/2020a`` ``4.1.3`` ``GCCcore/6.4.0`` ========= ================= @@ -20153,9 +20438,27 @@ version toolchain ``1.11.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``1.12.1`` ``GCCcore/10.3.0`` ``1.13.0`` ``GCCcore/11.2.0`` +``1.13.1`` ``GCCcore/11.2.0`` +``1.13.2`` ``GCCcore/11.2.0`` ========== ===================================== +.. _list_software_libfdf_615: + +*libfdf* +++++++++ + +LibFDF provides a Fortran API to parse files in the Flexible Data Format (FDF). + +*homepage*: https://launchpad.net/libfdf + +========= ============= ======================================= +version versionsuffix toolchain +========= ============= ======================================= +``0.2.2`` ``-serial`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +========= ============= ======================================= + + .. _list_software_libffcall_927: *libffcall* @@ -20201,13 +20504,13 @@ libFLAME is a portable library for dense matrix computations, providing much of *homepage*: https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame -========= ============= ===================================== -version versionsuffix toolchain -========= ============= ===================================== -``1.0`` ``-amd`` ``GCC/7.3.0-2.30`` -``2.2`` ``-amd`` ``GCCcore/9.3.0`` -``5.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========= ============= ===================================== +========= ============= ========================================================================= +version versionsuffix toolchain +========= ============= ========================================================================= +``1.0`` ``-amd`` ``GCC/7.3.0-2.30`` +``2.2`` ``-amd`` ``GCCcore/9.3.0`` +``5.2.0`` ``GCC/10.3.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +========= ============= ========================================================================= .. _list_software_libfontenc_1060: @@ -20420,15 +20723,16 @@ version versionsuffix toolchain *libGridXC* +++++++++++ -A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems. It is based on SiestaXC. +A library to compute the exchange and correlation energy and potential in spherical (i.e. atoms) or periodic systems. -*homepage*: https://launchpad.net/libgridxc +*homepage*: https://gitlab.com/siesta-project/libraries/libgridxc -========= =============== -version toolchain -========= =============== -``0.8.5`` ``iimpi/2019b`` -========= =============== +========= ================================ +version toolchain +========= ================================ +``0.8.5`` ``iimpi/2019b`` +``0.9.6`` ``gompi/2020b``, ``iimpi/2020b`` +========= ================================ .. _list_software_libgtextutils_1428: @@ -20456,11 +20760,11 @@ libHaru is a free, cross platform, open source library for generating PDF files. *homepage*: http://libharu.org/ -========= ============================================================================================================================================= -version toolchain -========= ============================================================================================================================================= -``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2017a``, ``intel/2018b`` -========= ============================================================================================================================================= +========= ============================================================================================================================================================= +version toolchain +========= ============================================================================================================================================================= +``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2021a``, ``intel/2017a``, ``intel/2018b`` +========= ============================================================================================================================================================= .. _list_software_libibmad_820: @@ -20583,7 +20887,7 @@ version versionsuffix toolchain ``2.1.0`` ``intel/2016b`` ``2.4.2`` ``intel/2018a`` ``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` -``2.6.0`` ``-lmax-6-cp2k`` ``GCC/10.2.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a`` +``2.6.0`` ``-lmax-6-cp2k`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a`` ========= ================ =================================================================================================================================================================================================== @@ -20678,6 +20982,22 @@ version toolchain =========== =============== +.. _list_software_libmbd_618: + +*libmbd* +++++++++ + +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. + +*homepage*: https://libmbd.github.io/index.html + +========== ================================================================ +version toolchain +========== ================================================================ +``0.10.4`` ``foss/2020b``, ``foss/2021a``, ``intel/2020b``, ``intel/2021a`` +========== ================================================================ + + .. _list_software_libMemcached_1198: *libMemcached* @@ -20898,11 +21218,12 @@ LibPSML provides a Fortran API to parse files in the PSeudopotential Markup Lan *homepage*: https://launchpad.net/libpsml -========= ============================== -version toolchain -========= ============================== -``1.1.7`` ``foss/2016b``, ``foss/2017a`` -========= ============================== +========== ======================================= +version toolchain +========== ======================================= +``1.1.7`` ``foss/2016b``, ``foss/2017a`` +``1.1.10`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +========== ======================================= .. _list_software_libpsortb_977: @@ -20921,6 +21242,22 @@ version toolchain ======= ============== +.. _list_software_libpspio_866: + +*libpspio* +++++++++++ + +libpspio is a library to read and write pseudopotentials in multiple formats. + +*homepage*: https://gitlab.e-cam2020.eu/esl/pspio/ + +========= ======================================= +version toolchain +========= ======================================= +``0.2.4`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +========= ======================================= + + .. _list_software_libpthread-stubs_1661: *libpthread-stubs* @@ -21060,6 +21397,22 @@ version toolchain ========= ================= +.. _list_software_libSBML_613: + +*libSBML* ++++++++++ + +libSBML (Systems Biology Markup Language library) is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It's not an application itself (though it does come with example programs), but rather a library you embed in your own applications. + +*homepage*: http://sbml.org/Software/libSBML + +========== ============== +version toolchain +========== ============== +``5.19.0`` ``GCC/10.3.0`` +========== ============== + + .. _list_software_libsigc++_819: *libsigc++* @@ -21177,12 +21530,13 @@ version toolchain C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API -*homepage*: http://libspatialindex.github.io +*homepage*: https://libspatialindex.org ========= ====================================================================================== version toolchain ========= ====================================================================================== ``1.8.5`` ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2018a`` +``1.9.3`` ``GCCcore/11.2.0`` ========= ====================================================================================== @@ -21432,11 +21786,11 @@ Portable uuid C library *homepage*: http://sourceforge.net/projects/libuuid/ -========= ========================================================================================================= -version toolchain -========= ========================================================================================================= -``1.0.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2016a``, ``intel/2017a``, ``intel/2017b`` -========= ========================================================================================================= +========= ============================================================================================================================ +version toolchain +========= ============================================================================================================================ +``1.0.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``intel/2017a``, ``intel/2017b`` +========= ============================================================================================================================ .. _list_software_libuv_546: @@ -21464,12 +21818,12 @@ libvdwxc is a general library for evaluating energy and potential for exchange-c *homepage*: https://libvdwxc.org -========= ============================================================================== -version toolchain -========= ============================================================================== -``0.3.2`` ``foss/2018b`` -``0.4.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a`` -========= ============================================================================== +========= ================================================================================================================ +version toolchain +========= ================================================================================================================ +``0.3.2`` ``foss/2018b`` +``0.4.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``intel/2020b``, ``intel/2021a`` +========= ================================================================================================================ .. _list_software_libvorbis_972: @@ -21562,6 +21916,7 @@ version toolchain ``5.1.2`` ``GCC/10.2.0`` ``5.1.3`` ``GCC/10.2.0`` ``5.1.5`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` +``5.1.6`` ``GCC/11.2.0`` ========= ===================================================================================================================================================================================================================================== @@ -21928,6 +22283,7 @@ version toolchain ``1.8.3`` ``foss/2018a``, ``intel/2018a`` ``1.10`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.16.1`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` +``1.16.2`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` ========== =============================================================================================== @@ -22037,14 +22393,15 @@ version versionsuffix toolchain *lifelines* +++++++++++ -lifelines is a pure Python implementation of the best parts of survival analysis +lifelines is a complete survival analysis library, written in pure Python. -*homepage*: https://lifelines.readthedocs.io +*homepage*: https://lifelines.readthedocs.io/en/latest/ ========== ================= ================== version versionsuffix toolchain ========== ================= ================== ``0.22.8`` ``-Python-3.7.2`` ``fosscuda/2019a`` +``0.26.3`` ``fosscuda/2020b`` ========== ================= ================== @@ -22439,6 +22796,22 @@ version toolchain ========= ================== +.. _list_software_longread_umi_1270: + +*longread_umi* +++++++++++++++ + +A collection of scripts for processing longread UMI data. + +*homepage*: https://github.com/SorenKarst/longread_umi + +========= ============== +version toolchain +========= ============== +``0.3.2`` ``foss/2020b`` +========= ============== + + .. _list_software_Longshot_846: *Longshot* @@ -22453,6 +22826,7 @@ version toolchain ========= ===================================== ``0.3.4`` ``GCCcore/8.2.0`` ``0.4.1`` ``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` +``0.4.3`` ``GCCcore/10.2.0`` ========= ===================================== @@ -22551,11 +22925,12 @@ Least-squares methods to estimate rates and dates from phylogenies *homepage*: https://github.com/tothuhien/lsd2 -========= ================= -version toolchain -========= ================= -``1.9.7`` ``GCCcore/9.3.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``1.9.7`` ``GCCcore/9.3.0`` +``2.2`` ``GCCcore/10.2.0`` +========= ================== .. _list_software_LSMS_319: @@ -22799,7 +23174,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -22877,9 +23252,9 @@ version toolchain *MAFFT* +++++++ -MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. +MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc. -*homepage*: https://mafft.cbrc.jp/alignment/software/source.html +*homepage*: https://mafft.cbrc.jp/alignment/software/ ========= ==================== ======================================================================================= version versionsuffix toolchain @@ -22891,7 +23266,8 @@ version versionsuffix toolchain ``7.453`` ``-with-extensions`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``gompi/2020a``, ``iccifort/2019.5.281``, ``iimpi/2020a`` ``7.470`` ``-with-extensions`` ``GCC/9.3.0``, ``gompi/2020a`` ``7.471`` ``-with-extensions`` ``iimpi/2020a`` -``7.475`` ``-with-extensions`` ``gompi/2020b`` +``7.475`` ``-with-extensions`` ``GCC/10.2.0``, ``gompi/2020b`` +``7.487`` ``-with-extensions`` ``gompi/2021a`` ========= ==================== ======================================================================================= @@ -23433,7 +23809,7 @@ version versionsuffix toolchain ``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` ``3.2.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``3.3.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -``3.4.2`` ``foss/2021a`` +``3.4.2`` ``foss/2021a``, ``intel/2021a`` ========= ================================= ======================================================================== @@ -23666,14 +24042,14 @@ The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable *homepage*: http://micans.org/mcl/ -========== ================ ===================================================================== -version versionsuffix toolchain -========== ================ ===================================================================== -``02.063`` ``intel/2016b`` -``14.137`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``intel/2016b`` -``14.137`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``14.137`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -========== ================ ===================================================================== +========== ================ ========================================================================================= +version versionsuffix toolchain +========== ================ ========================================================================================= +``02.063`` ``intel/2016b`` +``14.137`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``intel/2016b`` +``14.137`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``14.137`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +========== ================ ========================================================================================= .. _list_software_MCR_226: @@ -23844,6 +24220,7 @@ version versionsuffix toolchain ``1.1.1`` ``-Python-3.7.4`` ``foss/2019b`` ``1.1.3`` ``-Python-3.7.4`` ``foss/2019b`` ``1.2.0`` ``-Python-3.7.4`` ``foss/2019b`` +``1.4.3`` ``foss/2020b`` ``1.4.3`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================= ============== @@ -23893,6 +24270,7 @@ Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation softwar version versionsuffix toolchain ========= ================== =============================================== ``1.3`` ``foss/2016a`` +``1.4.3`` ``intel/2020a`` ``1.6.0`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2018a`` ========= ================== =============================================== @@ -23993,7 +24371,7 @@ version versionsuffix toolchain The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo. -*homepage*: http://meme-suite.org +*homepage*: https://meme-suite.org/meme/index.html ========= ============================== =============================== version versionsuffix toolchain @@ -24002,6 +24380,7 @@ version versionsuffix toolchain ``5.0.4`` ``-Perl-5.26.0-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``5.1.1`` ``-Python-3.6.6`` ``foss/2018b`` ``5.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``5.4.1`` ``GCC/10.3.0`` ========= ============================== =============================== @@ -24118,6 +24497,22 @@ version toolchain ========== ==================================================================== +.. _list_software_Mesa-demos_971: + +*Mesa-demos* +++++++++++++ + +Mesa utility and demo programs, including glxinfo and eglinfo. + +*homepage*: https://www.mesa3d.org/ + +========= ================== +version toolchain +========= ================== +``8.4.0`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_meshalyzer_1092: *meshalyzer* @@ -24893,6 +25288,22 @@ version versionsuffix toolchain ========== =================== ========== +.. _list_software_MixMHC2pred_995: + +*MixMHC2pred* ++++++++++++++ + +MixMHC2pred is a predictor of HLA class II ligands and epitopes. It is described in publication Racle, J., et al. Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes + +*homepage*: https://github.com/GfellerLab/MixMHC2pred + +======= ========== +version toolchain +======= ========== +``1.2`` ``system`` +======= ========== + + .. _list_software_mkl-dnn_689: *mkl-dnn* @@ -25019,16 +25430,17 @@ MMseqs2: ultra fast and sensitive search and clustering suite *homepage*: https://mmseqs.com -============ ================================ -version toolchain -============ ================================ -``1-c7a89`` ``foss/2016b`` -``5-9375b`` ``intel/2018a`` -``8-fac81`` ``intel/2018b`` -``10-6d92c`` ``gompi/2019b``, ``iimpi/2019b`` -``11-e1a1c`` ``iimpi/2019b`` -``13-45111`` ``gompi/2020b`` -============ ================================ +===================== ================================ +version toolchain +===================== ================================ +``1-c7a89`` ``foss/2016b`` +``5-9375b`` ``intel/2018a`` +``8-fac81`` ``intel/2018b`` +``10-6d92c`` ``gompi/2019b``, ``iimpi/2019b`` +``11-e1a1c`` ``iimpi/2019b`` +``13-45111`` ``gompi/2020b`` +``13-45111-20211006`` ``gompi/2020b`` +===================== ================================ .. _list_software_mmtf-cpp_804: @@ -25354,6 +25766,7 @@ version toolchain ``1.3.1`` ``GCCcore/8.3.0`` ``1.3.2`` ``GCCcore/8.3.0`` ``1.4.2`` ``GCCcore/10.2.0`` +``1.4.4`` ``GCCcore/10.2.0`` ========= ================== @@ -25929,13 +26342,13 @@ MUSCLE is one of the best-performing multiple alignment programs according to *homepage*: https://drive5.com/muscle/ -============ =============== ====================================================================================================================================== -version versionsuffix toolchain -============ =============== ====================================================================================================================================== -``3.8.31`` ``GCC/7.3.0-2.30``, ``foss/2016a``, ``foss/2017b``, ``foss/2018a``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``3.8.31`` ``-i86linux64`` ``system`` -``3.8.1551`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` -============ =============== ====================================================================================================================================== +============ =============== ========================================================================================================================================================== +version versionsuffix toolchain +============ =============== ========================================================================================================================================================== +``3.8.31`` ``GCC/7.3.0-2.30``, ``GCCcore/10.2.0``, ``foss/2016a``, ``foss/2017b``, ``foss/2018a``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``3.8.31`` ``-i86linux64`` ``system`` +``3.8.1551`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` +============ =============== ========================================================================================================================================================== .. _list_software_MuSiC_449: @@ -26229,7 +26642,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -26591,6 +27004,7 @@ version versionsuffix toolchain ``2.9.9`` ``-CUDA-11.3.1`` ``system`` ``2.10.3`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` ``2.10.3`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` +``2.11.4`` ``gcccuda/2019b`` ========== =================== ============================== @@ -26939,6 +27353,7 @@ version versionsuffix toolchain ``4.7.1`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` ``4.7.4`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2020b`` ``4.8.0`` ``gompi/2021a``, ``iimpi/2021a`` +``4.8.1`` ``gompi/2021b`` =========== ================ ========================================================================================================================== @@ -27197,6 +27612,8 @@ version versionsuffix toolchain ``2.4`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` ``2.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``2.5.1`` ``foss/2021a`` +``2.6.2`` ``foss/2020b`` +``2.6.3`` ``foss/2021a`` ========= ================== ======================================================================== @@ -27268,6 +27685,7 @@ version toolchain ``20.04.1`` ``system`` ``20.10.0`` ``system`` ``21.03.0`` ``system`` +``21.08.0`` ``system`` =========== ========== @@ -27950,6 +28368,23 @@ version toolchain ========== ==================== +.. _list_software_NTPoly_582: + +*NTPoly* +++++++++ + +is a massively parallel library for computing the functions of sparse, symmetric matrices based on polynomial expansions. For sufficiently sparse matrices, most of the matrix functions in NTPoly can be computed in linear time. + +*homepage*: https://github.com/william-dawson/NTPoly + +========= =============================== +version toolchain +========= =============================== +``2.5.1`` ``foss/2020b``, ``intel/2020b`` +``2.7.0`` ``foss/2021a``, ``intel/2021a`` +========= =============================== + + .. _list_software_numactl_756: *numactl* @@ -28108,6 +28543,7 @@ version versionsuffix toolc ``6.6.revision27746`` ``-2015-10-20-patches-20170814-Python-2.7.13`` ``intel/2017a`` ``6.8.revision47`` ``-2017-12-14-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` ``7.0.0`` ``-Python-3.7.4`` ``intel/2019b`` +``7.0.2`` ``intel/2021a`` ``7.0.2`` ``-Python-3.7.4`` ``intel/2019b`` ===================== ============================================== ================================ @@ -28134,7 +28570,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSceneGraph_1394` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -28446,6 +28882,7 @@ version versionsuffix toolchain ``0.3.12`` ``GCC/10.2.0`` ``0.3.15`` ``GCC/10.3.0`` ``0.3.17`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``0.3.18`` ``GCC/11.2.0`` ========== ================= ========================================================== @@ -28531,6 +28968,8 @@ version versionsuffix toolchain ``4.2.0`` ``-Python-3.8.2`` ``foss/2020a`` ``4.2.0`` ``-Python-3.8.2-contrib`` ``foss/2020a`` ``4.5.1`` ``-contrib`` ``foss/2020b``, ``fosscuda/2020b`` +``4.5.3`` ``-CUDA-11.3.1-contrib`` ``foss/2021a`` +``4.5.3`` ``-contrib`` ``foss/2021a`` ========== ========================= ================================================================ @@ -28788,47 +29227,48 @@ The Open MPI Project is an open source MPI implementation. *homepage*: http://www.open-mpi.org/ -========== ============= ==================================================================================================================== -version versionsuffix toolchain -========== ============= ==================================================================================================================== -``1.6.5`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.3`` -``1.6.5`` ``-no-OFED`` ``GCC/4.8.1``, ``GCC/4.8.2`` -``1.7.3`` ``GCC/4.8.2`` -``1.8.1`` ``GCC/4.8.3`` -``1.8.3`` ``GCC/4.9.2`` -``1.8.4`` ``GCC/4.8.4``, ``GCC/4.9.2`` -``1.8.5`` ``GNU/4.9.2-2.25`` -``1.8.6`` ``GNU/4.9.3-2.25`` -``1.8.8`` ``GNU/4.9.3-2.25`` -``1.10.1`` ``GCC/4.9.3-2.25`` -``1.10.2`` ``GCC/4.9.3-2.25``, ``GCC/5.3.0-2.26``, ``GCC/6.1.0-2.27``, ``PGI/16.3-GCC-4.9.3-2.25``, ``PGI/16.4-GCC-5.3.0-2.26`` -``1.10.3`` ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` -``1.10.4`` ``PGI/16.7-GCC-5.4.0-2.26``, ``iccifort/2016.3.210-GCC-4.9.3-2.25`` -``2.0.0`` ``GCC/5.2.0`` -``2.0.1`` ``GCC/6.2.0-2.27``, ``iccifort/2017.1.132-GCC-5.4.0-2.26`` -``2.0.2`` ``GCC/6.3.0-2.27``, ``iccifort/2017.1.132-GCC-6.3.0-2.27`` -``2.0.2`` ``-opa`` ``GCC/6.3.0-2.27`` -``2.1.0`` ``GCC/6.3.0-2.28`` -``2.1.1`` ``GCC/6.4.0-2.28``, ``gcccuda/2017b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` -``2.1.2`` ``GCC/6.4.0-2.28``, ``gcccuda/2018a``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` -``2.1.3`` ``iccifort/2018.2.199-GCC-6.4.0-2.28`` -``3.0.0`` ``GCC/7.2.0-2.29`` -``3.1.0`` ``GCC/7.3.0-2.30`` -``3.1.1`` ``GCC/7.3.0-2.30``, ``gcccuda/2018b``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` -``3.1.2`` ``GCC/8.2.0-2.31.1`` -``3.1.3`` ``GCC/8.2.0-2.31.1``, ``gcccuda/2019a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``3.1.4`` ``GCC/8.3.0``, ``GCC/8.3.0-2.32``, ``gcccuda/2019b``, ``iccifort/2019.5.281`` -``4.0.0`` ``GCC/8.2.0-2.31.1`` -``4.0.0`` ``-hpcx`` ``GCC/8.2.0-2.31.1`` -``4.0.1`` ``GCC/8.3.0-2.32`` -``4.0.2`` ``GCC/9.2.0-2.32`` -``4.0.3`` ``GCC/9.3.0``, ``gcccuda/2020a``, ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` -``4.0.5`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` -``4.0.6`` ``GCC/10.3.0`` -``4.1.0`` ``GCC/10.2.0`` -``4.1.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0`` -``system`` ``GCC/system-2.29`` -========== ============= ==================================================================================================================== +========== ================ ==================================================================================================================== +version versionsuffix toolchain +========== ================ ==================================================================================================================== +``1.6.5`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.3`` +``1.6.5`` ``-no-OFED`` ``GCC/4.8.1``, ``GCC/4.8.2`` +``1.7.3`` ``GCC/4.8.2`` +``1.8.1`` ``GCC/4.8.3`` +``1.8.3`` ``GCC/4.9.2`` +``1.8.4`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``1.8.5`` ``GNU/4.9.2-2.25`` +``1.8.6`` ``GNU/4.9.3-2.25`` +``1.8.8`` ``GNU/4.9.3-2.25`` +``1.10.1`` ``GCC/4.9.3-2.25`` +``1.10.2`` ``GCC/4.9.3-2.25``, ``GCC/5.3.0-2.26``, ``GCC/6.1.0-2.27``, ``PGI/16.3-GCC-4.9.3-2.25``, ``PGI/16.4-GCC-5.3.0-2.26`` +``1.10.3`` ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` +``1.10.4`` ``PGI/16.7-GCC-5.4.0-2.26``, ``iccifort/2016.3.210-GCC-4.9.3-2.25`` +``2.0.0`` ``GCC/5.2.0`` +``2.0.1`` ``GCC/6.2.0-2.27``, ``iccifort/2017.1.132-GCC-5.4.0-2.26`` +``2.0.2`` ``GCC/6.3.0-2.27``, ``iccifort/2017.1.132-GCC-6.3.0-2.27`` +``2.0.2`` ``-opa`` ``GCC/6.3.0-2.27`` +``2.1.0`` ``GCC/6.3.0-2.28`` +``2.1.1`` ``GCC/6.4.0-2.28``, ``gcccuda/2017b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +``2.1.2`` ``GCC/6.4.0-2.28``, ``gcccuda/2018a``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` +``2.1.3`` ``iccifort/2018.2.199-GCC-6.4.0-2.28`` +``3.0.0`` ``GCC/7.2.0-2.29`` +``3.1.0`` ``GCC/7.3.0-2.30`` +``3.1.1`` ``GCC/7.3.0-2.30``, ``gcccuda/2018b``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` +``3.1.2`` ``GCC/8.2.0-2.31.1`` +``3.1.3`` ``GCC/8.2.0-2.31.1``, ``gcccuda/2019a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``3.1.4`` ``GCC/8.3.0``, ``GCC/8.3.0-2.32``, ``gcccuda/2019b``, ``iccifort/2019.5.281`` +``4.0.0`` ``GCC/8.2.0-2.31.1`` +``4.0.0`` ``-hpcx`` ``GCC/8.2.0-2.31.1`` +``4.0.1`` ``GCC/8.3.0-2.32`` +``4.0.2`` ``GCC/9.2.0-2.32`` +``4.0.3`` ``GCC/9.3.0``, ``gcccuda/2020a``, ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` +``4.0.5`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` +``4.0.5`` ``-CUDA-11.2.1`` ``NVHPC/21.2`` +``4.0.6`` ``GCC/10.3.0`` +``4.1.0`` ``GCC/10.2.0`` +``4.1.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0`` +``system`` ``GCC/system-2.29`` +========== ================ ==================================================================================================================== .. _list_software_OpenMS_562: @@ -28931,6 +29371,22 @@ version versionsuffix toolchain ========= =================== ========== +.. _list_software_OpenSceneGraph_1394: + +*OpenSceneGraph* +++++++++++++++++ + +The OpenSceneGraph is an open source high performance 3D graphics toolkit, used by application developers in fields such as visual simulation, games, virtual reality, scientific visualization and modelling. Written entirely in Standard C++ and OpenGL it runs on all Windows platforms, OSX, GNU/Linux, IRIX, Solaris, HP-Ux, AIX and FreeBSD operating systems. The OpenSceneGraph is now well established as the world leading scene graph technology, used widely in the vis-sim, space, scientific, oil-gas, games and virtual reality industries. + +*homepage*: http://www.openscenegraph.org/ + +========= ============== +version toolchain +========= ============== +``3.6.5`` ``foss/2021a`` +========= ============== + + .. _list_software_OpenSees_802: *OpenSees* @@ -29185,6 +29641,8 @@ version versionsuffix toolchain ``2.3.3`` ``-Python-2.7.15`` ``intel/2018b`` ``2.3.8`` ``-Python-2.7.16`` ``foss/2019b`` ``2.3.11`` ``-Python-3.7.4`` ``intel/2019b`` +``2.5.2`` ``foss/2020b`` +``2.5.4`` ``foss/2020b`` ========== ================== =============== @@ -29214,12 +29672,12 @@ Osi (Open Solver Interface) provides an abstract base class to a generic linear *homepage*: https://github.com/coin-or/Osi -=========== ================================= -version toolchain -=========== ================================= -``0.108.5`` ``GCCcore/7.3.0``, ``foss/2018b`` -``0.108.6`` ``GCCcore/10.2.0`` -=========== ================================= +=========== ================================== +version toolchain +=========== ================================== +``0.108.5`` ``GCCcore/7.3.0``, ``foss/2018b`` +``0.108.6`` ``GCC/10.3.0``, ``GCCcore/10.2.0`` +=========== ================================== .. _list_software_OSPRay_542: @@ -29254,8 +29712,9 @@ version versionsuffix toolchain ``5.6.2`` ``gompi/2019a`` ``5.6.3`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2019b``, ``iimpic/2020a`` ``5.7`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b`` -``5.7.1`` ``ffmpi/4.5.0``, ``gompi/2021.07``, ``gompi/2021a``, ``iimpi/2021a``, ``iompi/2021a`` +``5.7.1`` ``ffmpi/4.5.0``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021a``, ``iompi/2021a`` ``5.7.1`` ``-CUDA-11.3.1`` ``gompi/2021a`` +``5.8`` ``iimpi/2021b`` ========= ================ ============================================================================================================================================================================================= @@ -29316,7 +29775,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAML_298` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -29457,6 +29916,22 @@ version toolchain ======== ========================================================== +.. _list_software_panaroo_752: + +*panaroo* ++++++++++ + +A pangenome analysis pipeline. + +*homepage*: https://gtonkinhill.github.io/panaroo/ + +========= ============== +version toolchain +========= ============== +``1.2.8`` ``foss/2020b`` +========= ============== + + .. _list_software_pandapower_1073: *pandapower* @@ -30216,6 +30691,22 @@ version toolchain ========= ================= +.. _list_software_PEPT_313: + +*PEPT* +++++++ + +A Python library that integrates all the tools necessary to perform research using Positron Emission Particle Tracking (PEPT). The library includes algorithms for the location, identification and tracking of particles, in addition to tools for visualisation and analysis, and utilities allowing the realistic simulation of PEPT data. + +*homepage*: https://pept.readthedocs.io/en/latest/ + +========= ============== +version toolchain +========= ============== +``0.4.1`` ``foss/2021a`` +========= ============== + + .. _list_software_Percolator_1051: *Percolator* @@ -30697,6 +31188,7 @@ Phylogenetic estimation using (Maximum) Likelihood version toolchain ================ ============== ``3.3.20190321`` ``foss/2018b`` +``3.3.20200621`` ``foss/2020b`` ================ ============== @@ -31723,6 +32215,7 @@ version versionsuffix toolchain ``12.4`` ``GCCcore/9.3.0`` ``13.2`` ``GCCcore/10.2.0`` ``13.3`` ``GCCcore/10.3.0`` +``13.4`` ``GCCcore/11.2.0`` ========= ================== ================================================================ @@ -31834,11 +32327,11 @@ PRANK is a probabilistic multiple alignment program for DNA, codon and amino-a *homepage*: http://wasabiapp.org/software/prank/ -========== ============================== -version toolchain -========== ============================== -``170427`` ``GCC/9.3.0``, ``intel/2018a`` -========== ============================== +========== ============================================== +version toolchain +========== ============================================== +``170427`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``intel/2018a`` +========== ============================================== .. _list_software_PRC_229: @@ -32880,6 +33373,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_pycoQC_591: + +*pycoQC* +++++++++ + +PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. + +*homepage*: https://tleonardi.github.io/pycoQC + +========= ============== +version toolchain +========= ============== +``2.5.2`` ``foss/2021a`` +========= ============== + + .. _list_software_PyCUDA_486: *PyCUDA* @@ -33302,11 +33811,12 @@ PyGraphviz is a Python interface to the Graphviz graph layout and visualization *homepage*: https://pygraphviz.github.io/ -======= ============== -version toolchain -======= ============== -``1.5`` ``foss/2019b`` -======= ============== +======= ============================== +version toolchain +======= ============================== +``1.5`` ``foss/2019b`` +``1.7`` ``foss/2020b``, ``foss/2021a`` +======= ============================== .. _list_software_pygrib_653: @@ -33742,6 +34252,7 @@ version versionsuffix toolchain ``2.4.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``2.6.1.post1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``3.0.1`` ``GCCcore/10.2.0`` +``3.1.0`` ``GCCcore/10.3.0`` =============== ================= ================== @@ -34365,6 +34876,22 @@ version versionsuffix toolchain ========== ================= ================================================================================================================================================================= +.. _list_software_python-docx_1149: + +*python-docx* ++++++++++++++ + +python-docx is a Python library for creating and updating Microsoft Word (.docx) files + +*homepage*: https://python-docx.readthedocs.io/en/latest/ + +========== ================== +version toolchain +========== ================== +``0.8.11`` ``GCCcore/10.2.0`` +========== ================== + + .. _list_software_python-hl7_986: *python-hl7* @@ -34414,6 +34941,7 @@ Faster zlib and gzip compatible compression and decompression by providing pyth version toolchain ========== ================== ``0.11.0`` ``GCCcore/10.3.0`` +``0.11.1`` ``GCCcore/10.2.0`` ========== ================== @@ -34431,6 +34959,7 @@ version versionsuffix toolchain ========== ================= ============== ``0.12.0`` ``-Python-3.6.6`` ``foss/2018b`` ``0.12.0`` ``-Python-3.7.4`` ``foss/2019b`` +``0.12.1`` ``foss/2020b`` ========== ================= ============== @@ -34450,7 +34979,7 @@ version versionsuffix toolchain ``1.1.16`` ``-Python-3.6.6`` ``foss/2018b`` ``1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``1.2.2`` ``-Python-3.8.2`` ``intel/2020a`` -``1.2.4`` ``fosscuda/2020b`` +``1.2.4`` ``foss/2020b``, ``fosscuda/2020b`` ========== ================== =================================================== @@ -34537,6 +35066,7 @@ version versionsuffix toolchain ``1.4.2`` ``-Python-3.7.4-PyTorch-1.4.0`` ``foss/2019b`` ``1.6.3`` ``foss/2020b``, ``fosscuda/2020b`` ``1.6.3`` ``-Python-3.7.4-PyTorch-1.8.1`` ``fosscuda/2019b`` +``2.0.1`` ``-PyTorch-1.9.0`` ``fosscuda/2020b`` ========= =============================== ================================== @@ -34638,7 +35168,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcat_425` - :ref:`list_software_qcint_543` - :ref:`list_software_QCxMS_428` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_Qtconsole_952` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_QtPy_398` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` +:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcat_425` - :ref:`list_software_qcint_543` - :ref:`list_software_QCxMS_428` - :ref:`list_software_QD_149` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_Qtconsole_952` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_QtPy_398` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` .. _list_software_Q6_135: @@ -34723,6 +35253,23 @@ version toolchain ========= ========== +.. _list_software_QD_149: + +*QD* +++++ + +Quad Double computation package + +*homepage*: https://github.com/scibuilder/QD + +========== ============= ============== +version versionsuffix toolchain +========== ============= ============== +``0.8.9`` ``foss/2021a`` +``2.3.17`` ``-20160110`` ``NVHPC/21.2`` +========== ============= ============== + + .. _list_software_QDD_217: *QDD* @@ -34825,6 +35372,7 @@ version toolchain ``2019.7`` ``system`` ``2020.8`` ``system`` ``2020.11`` ``system`` +``2021.8`` ``system`` =========== ========== @@ -34842,6 +35390,7 @@ version versionsuffix toolchain ========== ================= ============== ``0.11.1`` ``-Python-3.7.2`` ``foss/2019a`` ``0.12.0`` ``-Python-3.7.2`` ``foss/2019a`` +``0.31.0`` ``foss/2021a`` ========== ================= ============== @@ -35114,7 +35663,7 @@ version versionsuffix toolchain *QuantumESPRESSO* +++++++++++++++++ -Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). +Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). *homepage*: https://www.quantum-espresso.org @@ -35133,6 +35682,7 @@ version versionsuffix toolchain ``6.5`` ``intel/2019a``, ``intel/2019b`` ``6.6`` ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2019b`` ``6.7`` ``foss/2019b``, ``foss/2020b``, ``foss/2021a``, ``intel/2019b``, ``intel/2021a``, ``iomkl/2019b`` +``6.8`` ``foss/2021a``, ``intel/2021a`` ========= ============= ================================================================================================= @@ -35150,6 +35700,7 @@ version versionsuffix toolchain ========= ================== ============================== ``4.6.0`` ``-Python-3.5.2`` ``foss/2016b`` ``4.6.3`` ``-Python-3.6.4`` ``foss/2018a`` +``5.0.2`` ``foss/2020b`` ``5.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` ``5.0.2`` ``-Python-2.7.18`` ``foss/2020b`` ``5.0.2`` ``-Python-3.7.2`` ``foss/2019a`` @@ -35283,7 +35834,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -35435,9 +35986,26 @@ version toolchain ``1.4.7`` ``GCCcore/8.2.0``, ``gcccuda/2019b`` ``1.4.10`` ``GCC/7.3.0-2.30`` ``1.4.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.4.21`` ``GCCcore/10.2.0`` ========== ==================================== +.. _list_software_radeontop_972: + +*radeontop* ++++++++++++ + +View your GPU utilization, both for the total activity percent and individual blocks. + +*homepage*: https://github.com/clbr/radeontop + +======= ================== +version toolchain +======= ================== +``1.3`` ``GCCcore/10.3.0`` +======= ================== + + .. _list_software_Ragout_626: *Ragout* @@ -35483,6 +36051,7 @@ Read Assignment, Mapping, and Phylogenetic Analysis in Real Time. ============ ================= ============== version versionsuffix toolchain ============ ================= ============== +``1.2.0`` ``foss/2020b`` ``1.2.0rc3`` ``-Python-3.6.6`` ``foss/2018b`` ============ ================= ============== @@ -35528,11 +36097,11 @@ A fast JSON parser/generator for C++ with both SAX/DOM style API *homepage*: https://rapidjson.org -========= ======================================================= -version toolchain -========= ======================================================= -``1.1.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ======================================================= +========= =========================================================================== +version toolchain +========= =========================================================================== +``1.1.0`` ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= =========================================================================== .. _list_software_rapidtide_950: @@ -35755,6 +36324,7 @@ version versionsuffix toolchain ========== ============= ========== ``1.42`` ``-amd64`` ``system`` ``1.54.1`` ``-amd64`` ``system`` +``1.56.0`` ``-amd64`` ``system`` ========== ============= ========== @@ -35840,6 +36410,7 @@ version versionsuffix toolchain ``2019.09.3`` ``-Python-3.7.4`` ``foss/2019b`` ``2020.03.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``2020.09.3`` ``-Python-3.7.4`` ``foss/2019b`` +``2021.03.4`` ``foss/2021a`` ============= ================= =============================== @@ -36289,6 +36860,22 @@ version versionsuffix toolchain ========== ============= =============== +.. _list_software_Rgurobi_730: + +*Rgurobi* ++++++++++ + +Gurobi Optimizer 9.1 interface + +*homepage*: https://www.gurobi.com + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``9.1.2`` ``-R-4.1.0`` ``foss/2021a`` +========= ============= ============== + + .. _list_software_rhdf5_473: *rhdf5* @@ -36323,6 +36910,22 @@ version versionsuffix toolchain ================== ================= =============== +.. _list_software_RInChI_509: + +*RInChI* +++++++++ + +The reaction IUPAC International Chemical Identifier (RInChI TM) is a non-proprietary identifier for chemical reactions that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations. + +*homepage*: https://www.inchi-trust.org/ + +======== ============= ========== +version versionsuffix toolchain +======== ============= ========== +``1.00`` ``-x86_64`` ``system`` +======== ============= ========== + + .. _list_software_rioxarray_993: *rioxarray* @@ -36934,7 +37537,7 @@ version toolchain ``1.35.0`` ``GCCcore/8.2.0`` ``1.37.0`` ``GCCcore/8.3.0`` ``1.42.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.52.1`` ``GCCcore/10.3.0`` +``1.52.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.54.0`` ``GCCcore/11.2.0`` ========== ========================================================================== @@ -36945,7 +37548,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_Snippy_643` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -37169,6 +37772,7 @@ version versionsuffix toolchain ``1.10`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ``1.11`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` ``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` +``1.13`` ``GCC/10.3.0`` ========== ================= ======================================================================================================================================= @@ -37312,9 +37916,9 @@ version versionsuffix toolchain ``2.0.2`` ``-OpenBLAS-0.3.3`` ``gompi/2018.08`` ``2.0.2`` ``-OpenBLAS-0.3.5`` ``gompi/2019a``, ``gompic/2019a`` ``2.1.0`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b`` -``2.1.0`` ``-bf`` ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020b`` +``2.1.0`` ``-bf`` ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2020b`` ``2.1.0`` ``-bl`` ``gompi/2020b`` -``2.1.0`` ``-fb`` ``gompi/2021.07``, ``gompi/2021a`` +``2.1.0`` ``-fb`` ``gompi/2021a``, ``gompi/2021b`` ``2.2`` ``-amd`` ``gompi/2020a`` ========= ================================= ============================================================================================================================================ @@ -37328,13 +37932,13 @@ Scalasca is a software tool that supports the performance optimization of paral *homepage*: https://www.scalasca.org/ -======= ================================ -version toolchain -======= ================================ -``2.3`` ``foss/2016a`` -``2.5`` ``gompi/2019a``, ``gompi/2020a`` -``2.6`` ``gompic/2020b`` -======= ================================ +======= ================================= +version toolchain +======= ================================= +``2.3`` ``foss/2016a`` +``2.5`` ``gompi/2019a``, ``gompi/2020a`` +``2.6`` ``gompi/2021a``, ``gompic/2020b`` +======= ================================= .. _list_software_SCALCE_427: @@ -37362,10 +37966,27 @@ Scanpy is a scalable toolkit for analyzing single-cell gene expression data buil *homepage*: https://scanpy.readthedocs.io/en/stable/ +========= ============================== +version toolchain +========= ============================== +``1.7.2`` ``foss/2020b`` +``1.8.1`` ``foss/2020b``, ``foss/2021a`` +========= ============================== + + +.. _list_software_scGeneFit_888: + +*scGeneFit* ++++++++++++ + +Python code for genetic marker selection using linear programming. + +*homepage*: https://github.com/solevillar/scGeneFit-python + ========= ============== version toolchain ========= ============== -``1.7.2`` ``foss/2020b`` +``1.0.2`` ``foss/2021a`` ========= ============== @@ -37432,6 +38053,7 @@ version versionsuffix toolchain ``1.1.8`` ``-Python-2.7.13`` ``foss/2017a`` ``1.2.1`` ``-Python-3.8.2`` ``foss/2020a`` ``1.3.2`` ``foss/2020b`` +``1.3.3`` ``foss/2021a`` ========= ================== ============== @@ -37663,7 +38285,8 @@ version versionsuffix toolchain ``2020.03`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``2020.11`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``2020.11`` ``-Python-2.7.18`` ``foss/2020b`` -``2021.05`` ``foss/2021a`` +``2021.05`` ``foss/2021a``, ``intel/2021a`` +``2021.10`` ``foss/2021b`` =========== ================== ======================================================================== @@ -37986,6 +38609,7 @@ version versionsuffix toolchain ``0.10.1`` ``intel/2020b`` ``0.10.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``0.11.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``0.11.2`` ``foss/2021a`` ========== ================== ========================================================================================= @@ -38485,6 +39109,7 @@ version toolchain ========= ============================================== ``4.1.3`` ``foss/2019b`` ``4.2.0`` ``foss/2019b``, ``foss/2020a``, ``foss/2020b`` +``4.2.2`` ``foss/2020b``, ``foss/2021a`` ========= ============================================== @@ -38766,9 +39391,9 @@ version versionsuffix toolchain *SimpleITK* +++++++++++ -imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance. +ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. Among them, SimpleITK is a simplified layer built on top of ITK, intended to facilitate its use in rapid prototyping, education, interpreted languages. -*homepage*: https://github.com/scikit-learn-contrib/imbalanced-learn +*homepage*: http://www.simpleitk.org ========= ================== ============== version versionsuffix toolchain @@ -39281,37 +39906,22 @@ version toolchain ========= ============================================================================================================ -.. _list_software_Snippy_643: - -*Snippy* -++++++++ - -Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). Rapid haploid variant calling and core genome alignment. - -*homepage*: https://github.com/tseemann/snippy - -========= ========================= ============= -version versionsuffix toolchain -========= ========================= ============= -``4.6.0`` ``-Java-13-Python-3.8.2`` ``GCC/9.3.0`` -========= ========================= ============= - - .. _list_software_snippy_675: *snippy* ++++++++ -Rapid haploid variant calling and core genome alignment +Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). Rapid haploid variant calling and core genome alignment. *homepage*: https://github.com/tseemann/snippy -========= ================ ============== -version versionsuffix toolchain -========= ================ ============== -``4.4.1`` ``-Perl-5.28.0`` ``foss/2018b`` -``4.6.0`` ``GCC/10.2.0`` -========= ================ ============== +========= ========================= ============== +version versionsuffix toolchain +========= ========================= ============== +``4.4.1`` ``-Perl-5.28.0`` ``foss/2018b`` +``4.6.0`` ``GCC/10.2.0`` +``4.6.0`` ``-Java-13-Python-3.8.2`` ``GCC/9.3.0`` +========= ========================= ============== .. _list_software_snp-sites_934: @@ -39792,6 +40402,7 @@ version toolchain ``1.9.2`` ``intel/2016.02-GCC-4.9`` ``1.9.9`` ``intel/2017b`` ``1.16.1`` ``GCCcore/10.2.0`` +``1.16.2`` ``GCCcore/10.3.0`` ========== ========================= @@ -40558,7 +41169,7 @@ version toolchain ``1.6.4`` ``foss/2018b`` ``2.0.0`` ``GCC/7.3.0-2.30``, ``GCC/8.3.0`` ``2.0.2`` ``GCC/10.2.0`` -``2.0.3`` ``GCC/10.3.0`` +``2.0.3`` ``GCC/10.3.0``, ``GCC/9.3.0`` ============ ================================= @@ -40878,6 +41489,22 @@ version toolchain ========== ======================= +.. _list_software_swifter_772: + +*swifter* ++++++++++ + +A package which efficiently applies any function to a pandas dataframe or series in the fastest available manner. + +*homepage*: https://github.com/jmcarpenter2/swifter + +========= ================================== +version toolchain +========= ================================== +``1.0.9`` ``foss/2020b``, ``fosscuda/2020b`` +========= ================================== + + .. _list_software_SWIG_314: *SWIG* @@ -41041,7 +41668,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` +:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` .. _list_software_tabix_536: @@ -41440,11 +42067,13 @@ version versionsuffix toolchain ``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.2.2`` ``-Python-3.7.4`` ``foss/2019b`` +``2.2.3`` ``foss/2020b`` ``2.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.3.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` ``2.4.1`` ``foss/2020b``, ``fosscuda/2020b`` ``2.4.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``2.5.0`` ``foss/2020b``, ``fosscuda/2020b`` +``2.5.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``2.6.0`` ``foss/2021a`` ``2.6.0`` ``-CUDA-11.3.1`` ``foss/2021a`` ========== ============================= =================================================== @@ -41992,11 +42621,11 @@ A Tcl/Tk widget for OpenGL rendering. *homepage*: https://sourceforge.net/projects/togl/ -======= ================= -version toolchain -======= ================= -``2.0`` ``GCCcore/8.3.0`` -======= ================= +======= ===================================== +version toolchain +======= ===================================== +``2.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +======= ===================================== .. _list_software_Tombo_513: @@ -42015,6 +42644,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_TOML-Fortran_1093: + +*TOML-Fortran* +++++++++++++++ + +TOML parser for Fortran projects + +*homepage*: https://github.com/toml-f/toml-f + +========= ======================================= +version toolchain +========= ======================================= +``0.2.2`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +========= ======================================= + + .. _list_software_TopHat_592: *TopHat* @@ -42546,6 +43191,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_TRUST4_470: + +*TRUST4* +++++++++ + +Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR sequences. + +*homepage*: https://github.com/liulab-dfci/TRUST4 + +=========== ========== +version toolchain +=========== ========== +``1.0.5.1`` ``system`` +=========== ========== + + .. _list_software_Trycycler_961: *Trycycler* @@ -42719,7 +43380,7 @@ version versionsuffix toolchain --- -:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_UCX-CUDA_570` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_unimap_650` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_UShER_423` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` +:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_UCX-CUDA_570` - :ref:`list_software_ucx-py_614` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_unimap_650` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_UShER_423` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` .. _list_software_UCLUST_480: @@ -42759,8 +43420,10 @@ version versionsuffix toolchain ``1.8.0`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` ``1.9.0`` ``GCCcore/10.2.0`` ``1.9.0`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` +``1.9.0`` ``-CUDA-11.2.1`` ``GCCcore/10.2.0`` ``1.10.0`` ``GCCcore/10.3.0`` ``1.11.0`` ``GCCcore/11.2.0`` +``1.11.2`` ``GCCcore/11.2.0`` ============ ================ ======================================================= @@ -42778,9 +43441,26 @@ version versionsuffix toolchain ========== ================ ================== ``1.10.0`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` ``1.11.0`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` +``1.11.2`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` ========== ================ ================== +.. _list_software_ucx-py_614: + +*ucx-py* +++++++++ + +UCX-Py is the Python interface for UCX, a low-level high-performance networking library. UCX and UCX-Py supports several transport methods including InfiniBand and NVLink while still using traditional networking protocols like TCP. + +*homepage*: https://ucx-py.readthedocs.io + +========== ============== +version toolchain +========== ============== +``0.21.0`` ``foss/2020b`` +========== ============== + + .. _list_software_udocker_749: *udocker* @@ -43025,11 +43705,11 @@ UnZip is an extraction utility for archives compressed in .zip format (also call *homepage*: http://www.info-zip.org/UnZip.html -======= ========================================================================================================================================================= -version toolchain -======= ========================================================================================================================================================= -``6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ========================================================================================================================================================= +======= ===================================================================================================================================================================== +version toolchain +======= ===================================================================================================================================================================== +``6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +======= ===================================================================================================================================================================== .. _list_software_UQTk_357: @@ -43155,7 +43835,7 @@ version toolchain --- -:ref:`list_software_V8_142` - :ref:`list_software_Vala_388` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_Vampire_724` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VBZ-Compression_1457` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcflib_630` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VisPy_507` - :ref:`list_software_VMD_231` - :ref:`list_software_voltools_898` - :ref:`list_software_vorbis-tools_1267` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` +:ref:`list_software_V8_142` - :ref:`list_software_Vala_388` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_Vampire_724` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_vawk_441` - :ref:`list_software_VBZ-Compression_1457` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcflib_630` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VisPy_507` - :ref:`list_software_VMD_231` - :ref:`list_software_VMTK_322` - :ref:`list_software_voltools_898` - :ref:`list_software_vorbis-tools_1267` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` .. _list_software_V8_142: @@ -43360,6 +44040,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_vawk_441: + +*vawk* +++++++ + +An awk-like VCF parser + +*homepage*: https://github.com/cc2qe/vawk + +========= ================== ================== +version versionsuffix toolchain +========= ================== ================== +``0.0.1`` ``-Python-2.7.18`` ``GCCcore/10.2.0`` +========= ================== ================== + + .. _list_software_VBZ-Compression_1457: *VBZ-Compression* @@ -43657,6 +44353,22 @@ version versionsuffix toolchain ============ ================== ================================== +.. _list_software_VMTK_322: + +*VMTK* +++++++ + +vmtk is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels. + +*homepage*: https://vmtk.org + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.4.0`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_voltools_898: *voltools* @@ -43843,6 +44555,7 @@ version toolchain ``2.9.1`` ``foss/2018b`` ``2.13.4`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.15.0`` ``GCC/9.3.0`` +``2.18.0`` ``GCC/10.2.0`` ========== ======================================== @@ -44380,7 +45093,7 @@ version versionsuffix toolchain ``4.0.1`` ``-dmpar`` ``intel/2018b`` ``4.0.2`` ``-dmpar`` ``foss/2018b`` ``4.1.3`` ``-dm+sm`` ``intel/2019b`` -``4.1.3`` ``-dmpar`` ``foss/2019b``, ``intel/2019b`` +``4.1.3`` ``-dmpar`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b`` ``4.2.2`` ``-dmpar`` ``foss/2020b`` ``4.3`` ``-dmpar`` ``foss/2021a`` =========== ============= ================================================================ @@ -44501,7 +45214,7 @@ version toolchain --- -:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xTB_270` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_XZ_178` +:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_XZ_178` .. _list_software_X11_186: @@ -44789,12 +45502,12 @@ XCrySDen is a crystalline and molecular structure visualisation program aiming *homepage*: http://www.xcrysden.org/ -========== =============================== -version toolchain -========== =============================== -``1.5.60`` ``intel/2019a`` -``1.6.2`` ``foss/2019b``, ``intel/2019b`` -========== =============================== +========== =============================================== +version toolchain +========== =============================================== +``1.5.60`` ``intel/2019a`` +``1.6.2`` ``foss/2019b``, ``foss/2020b``, ``intel/2019b`` +========== =============================================== .. _list_software_Xerces-C++_816: @@ -44988,6 +45701,7 @@ version versionsuffix toolchain ``2.0201`` ``GCCcore/8.3.0`` ``2.0205`` ``GCCcore/9.3.0`` ``2.0206`` ``GCCcore/10.2.0`` +``2.0207`` ``GCCcore/10.3.0`` ========== ================ =============================== @@ -45023,12 +45737,12 @@ xmlf90 is a basic XML parsing library written in Fortran. *homepage*: https://launchpad.net/xmlf90 -========= ============================== -version toolchain -========= ============================== -``1.5.3`` ``foss/2016b``, ``foss/2017a`` -``1.5.4`` ``iccifort/2019.5.281`` -========= ============================== +========= ================================================================ +version toolchain +========= ================================================================ +``1.5.3`` ``foss/2016b``, ``foss/2017a`` +``1.5.4`` ``GCC/10.2.0``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304`` +========= ================================================================ .. _list_software_XMLSec_524: @@ -45168,28 +45882,12 @@ version toolchain ============== ========================================================== -.. _list_software_xTB_270: - -*xTB* -+++++ - -Semiempirical Extended Tight-Binding Program Package. - -*homepage*: https://xtb-docs.readthedocs.io - -========= =============== -version toolchain -========= =============== -``6.4.1`` ``intel/2021a`` -========= =============== - - .. _list_software_xtb_334: *xtb* +++++ -xtb - An extended tight-binding semi-empirical program package. +Semiempirical Extended Tight-Binding Program Package. *homepage*: https://xtb-docs.readthedocs.io @@ -45198,6 +45896,7 @@ version versionsuffix toolchain ================ ================= =============== ``6.2.2-hotfix`` ``-Python-3.6.3`` ``intel/2017b`` ``6.2.3`` ``foss/2019b`` +``6.4.1`` ``intel/2021a`` ================ ================= =============== @@ -45453,6 +46152,7 @@ version toolchain ``4.8.9`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.8.10`` ``GCCcore/10.2.0`` ``4.8.11`` ``GCCcore/10.3.0`` +``4.8.12`` ``GCCcore/11.2.0`` ========== ==================================== @@ -45465,13 +46165,14 @@ Zarr is a Python package providing an implementation of compressed, chunked, N-d *homepage*: https://zarr.readthedocs.io/en/stable/ -========= ================== ============== -version versionsuffix toolchain -========= ================== ============== -``2.1.4`` ``-Python-2.7.13`` ``foss/2017a`` -``2.4.0`` ``-Python-3.8.2`` ``foss/2020a`` -``2.8.1`` ``foss/2020b`` -========= ================== ============== +========== ================== ============== +version versionsuffix toolchain +========== ================== ============== +``2.1.4`` ``-Python-2.7.13`` ``foss/2017a`` +``2.4.0`` ``-Python-3.8.2`` ``foss/2020a`` +``2.8.1`` ``foss/2020b`` +``2.10.1`` ``foss/2021a`` +========== ================== ============== .. _list_software_ZeroMQ_574: diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index 69d7d6af..861787f1 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -34,6 +34,7 @@ * EB_Java * EB_MATLAB * EB_MCR + * EB_MotionCor2 * EB_NVHPC * EB_ORCA * EB_PGI @@ -230,7 +231,6 @@ * EB_Gctf * EB_libsmm * EB_Modeller - * EB_MotionCor2 * EB_MRtrix * EB_NCL * EB_NEMO @@ -324,6 +324,9 @@ * SystemCompiler * EB_imkl + + * EB_imkl_minus_FFTW + * EB_impi * SystemMPI @@ -357,6 +360,7 @@ * EB_Java * EB_MATLAB * EB_MCR + * EB_MotionCor2 * EB_NVHPC * EB_ORCA * EB_PGI diff --git a/docs/version-specific/easyconfig_constants.rst b/docs/version-specific/easyconfig_constants.rst index ec6d4bf5..99e684ae 100644 --- a/docs/version-specific/easyconfig_constants.rst +++ b/docs/version-specific/easyconfig_constants.rst @@ -20,6 +20,6 @@ Constant name Constant value ``OS_TYPE`` ``Darwin`` System type (e.g. 'Linux' or 'Darwin') ``OS_VERSION`` ``UNKNOWN`` System version ``SYSTEM`` ``{'name': 'system', 'version': 'system'}`` System toolchain -``SYS_PYTHON_VERSION`` ``3.9.5`` System Python version (platform.python_version()) +``SYS_PYTHON_VERSION`` ``3.9.7`` System Python version (platform.python_version()) ====================== ============================================================= ================================================================================ diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index a0398593..82e15abf 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -177,25 +177,26 @@ Support for configuring build with CMake instead of traditional configure script Extra easyconfig parameters specific to ``CMakeMake`` easyblock --------------------------------------------------------------- -======================== ================================================================================================================================================================================================== ================== -easyconfig parameter description default value -======================== ================================================================================================================================================================================================== ================== -``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` -``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` -``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` -``configure_cmd`` Configure command to use ``"cmake"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``generator`` Build file generator to use. None to use CMakes default ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``separate_build_dir`` Perform build in a separate directory ``True`` -``srcdir`` Source directory location to provide to cmake command ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -======================== ================================================================================================================================================================================================== ================== +========================= ================================================================================================================================================================================================== ================== +easyconfig parameter description default value +========================= ================================================================================================================================================================================================== ================== +``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` +``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` +``configure_cmd`` Configure command to use ``"cmake"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``generator`` Build file generator to use. None to use CMakes default ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Build command to use ``"make install"`` +``install_target_subdir`` Subdirectory to use as installation target ``None`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``separate_build_dir`` Perform build in a separate directory ``True`` +``srcdir`` Source directory location to provide to cmake command ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +========================= ================================================================================================================================================================================================== ================== Customised steps in ``CMakeMake`` easyblock ------------------------------------------- @@ -253,27 +254,28 @@ Software configured with CMake but without 'make install' step Extra easyconfig parameters specific to ``CMakeMakeCp`` easyblock ----------------------------------------------------------------- -======================== ================================================================================================================================================================================================== ================== -easyconfig parameter description default value -======================== ================================================================================================================================================================================================== ================== -``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` -``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` -``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` -``configure_cmd`` Configure command to use ``"cmake"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``files_to_copy`` List of files or dirs to copy ``None`` -``generator`` Build file generator to use. None to use CMakes default ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``separate_build_dir`` Perform build in a separate directory ``True`` -``srcdir`` Source directory location to provide to cmake command ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``with_configure`` Run configure script before building ``False`` -======================== ================================================================================================================================================================================================== ================== +========================= ================================================================================================================================================================================================== ================== +easyconfig parameter description default value +========================= ================================================================================================================================================================================================== ================== +``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` +``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` +``configure_cmd`` Configure command to use ``"cmake"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``files_to_copy`` List of files or dirs to copy ``None`` +``generator`` Build file generator to use. None to use CMakes default ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Build command to use ``"make install"`` +``install_target_subdir`` Subdirectory to use as installation target ``None`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``separate_build_dir`` Perform build in a separate directory ``True`` +``srcdir`` Source directory location to provide to cmake command ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``with_configure`` Run configure script before building ``False`` +========================= ================================================================================================================================================================================================== ================== Customised steps in ``CMakeMakeCp`` easyblock --------------------------------------------- @@ -292,25 +294,26 @@ Support for configuring with CMake, building and installing with MesonNinja. Extra easyconfig parameters specific to ``CMakeNinja`` easyblock ---------------------------------------------------------------- -======================== ================================================================================================================================================================================================== ================== -easyconfig parameter description default value -======================== ================================================================================================================================================================================================== ================== -``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` -``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` -``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` -``configure_cmd`` Configure command to use ``"cmake"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``generator`` Build file generator to use. None to use CMakes default ``"Ninja"`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``separate_build_dir`` Perform build in a separate directory ``True`` -``srcdir`` Source directory location to provide to cmake command ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -======================== ================================================================================================================================================================================================== ================== +========================= ================================================================================================================================================================================================== ================== +easyconfig parameter description default value +========================= ================================================================================================================================================================================================== ================== +``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` +``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` +``configure_cmd`` Configure command to use ``"cmake"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``generator`` Build file generator to use. None to use CMakes default ``"Ninja"`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Build command to use ``"make install"`` +``install_target_subdir`` Subdirectory to use as installation target ``None`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``separate_build_dir`` Perform build in a separate directory ``True`` +``srcdir`` Source directory location to provide to cmake command ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +========================= ================================================================================================================================================================================================== ================== Customised steps in ``CMakeNinja`` easyblock -------------------------------------------- @@ -336,46 +339,47 @@ Build a Python package and module with cmake. Extra easyconfig parameters specific to ``CMakePythonPackage`` easyblock ------------------------------------------------------------------------ -======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -easyconfig parameter description default value -======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` -``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` -``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` -``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``configure_cmd`` Configure command to use ``"cmake"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``generator`` Build file generator to use. None to use CMakes default ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` -``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``None`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``separate_build_dir`` Perform build in a separate directory ``True`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``srcdir`` Source directory location to provide to cmake command ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``zipped_egg`` Install as a zipped eggs ``False`` -======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +========================= ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +========================= ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` +``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``configure_cmd`` Configure command to use ``"cmake"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``generator`` Build file generator to use. None to use CMakes default ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Build command to use ``"make install"`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``install_target_subdir`` Subdirectory to use as installation target ``None`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``None`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``separate_build_dir`` Perform build in a separate directory ``True`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``srcdir`` Source directory location to provide to cmake command ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` +========================= ======================================================================================================================================================================================================================================================================================================================== ======================================================================= Customised steps in ``CMakePythonPackage`` easyblock ---------------------------------------------------- @@ -1168,6 +1172,7 @@ easyconfig parameter description ``tar_config_opts`` Override tar settings as determined by configure. ``False`` ``use_gold_linker`` Configure GCC to use GOLD as default linker ``True`` ``usetmppath`` Use temporary path for installation ``False`` +``withamdgcn`` Build GCC with AMD GCN offload support ``False`` ``withcloog`` Build GCC with CLooG support ``False`` ``withisl`` Build GCC with ISL support ``False`` ``withlibiberty`` Enable installing of libiberty ``False`` diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index bbedea28..5234ae99 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -108,7 +108,7 @@ Option flag Option desc ``--packagepath=PACKAGEPATH`` The destination path for the packages built by package-tool (default: /home/example/.local/easybuild/packages) ``--prefix=PREFIX`` Change prefix for buildpath, installpath, sourcepath and repositorypath (used prefix for defaults /home/example/.local/easybuild) ``--recursive-module-unload`` Enable generating of modules that unload recursively. (default: False) -``--repository=REPOSITORY`` Repository type, using repositorypath (type choice; default: FileRepository) (choices: FileRepository, GitRepository) +``--repository=REPOSITORY`` Repository type, using repositorypath (type choice; default: FileRepository) (choices: FileRepository, GitRepository, HgRepository) ``--repositorypath=REPOSITORYPATH`` Repository path, used by repository (is passed as list of arguments to create the repository instance). For more info, use --avail-repositories. (type comma-separated list; default: /home/example/.local/easybuild/ebfiles_repo) ``--sourcepath=SOURCEPATH`` Path(s) to where sources should be downloaded (string, colon-separated) (default: /home/example/.local/easybuild/sources) ``--subdir-modules=SUBDIR-MODULES`` Installpath subdir for modules (default: modules) @@ -184,6 +184,8 @@ Option flag Option description ``--pr-title=PR-TITLE`` Title for new pull request created with --new-pr (type ) ``--preview-pr`` Preview a new pull request (default: False) ``--review-pr=PR#`` Review specified pull request (type ) +``--review-pr-filter=REVIEW-PR-FILTER`` Regex used to filter out easyconfigs to diff against in --review-pr +``--review-pr-max=REVIEW-PR-MAX`` Maximum number of easyconfigs to diff against in --review-pr (type ) ``--sync-branch-with-develop=SYNC-BRANCH-WITH-DEVELOP`` Sync branch with current 'develop' branch (type ) ``--sync-pr-with-develop=PR#`` Sync pull request with current 'develop' branch (type ) ``--test-report-env-filter=TEST-REPORT-ENV-FILTER`` Regex used to filter out variables in environment dump of test report @@ -206,6 +208,7 @@ Option flag Option description ``--avail-hooks`` Show list of known hooks (default: False) ``--avail-toolchain-opts=AVAIL-TOOLCHAIN-OPTS`` Show options for toolchain (type str) ``--check-conflicts`` Check for version conflicts in dependency graphs (default: False) +``--check-eb-deps`` Check presence and version of (required and optional) EasyBuild dependencies (default: False) ``--dep-graph=depgraph.`` Create dependency graph ``--dump-env-script`` Dump source script to set up build environment based on toolchain/dependencies (default: False) ``--easystack=EASYSTACK`` Path to easystack file in YAML format, specifying details of a software stack @@ -295,6 +298,7 @@ Option flag Opt ``--ignore-checksums`` Ignore failing checksum verification (default: False) ``--ignore-osdeps`` Ignore any listed OS dependencies (default: False) ``--ignore-test-failure`` Ignore a failing test step (default: False) +``--insecure-download`` Don't check the server certificate against the available certificate authorities. (default: False) ``--install-latest-eb-release`` Install latest known version of easybuild (default: False) ``--lib-lib64-symlink`` Automatically create symlinks for lib/ pointing to lib64/ if the former is missing (default: True; disable with --disable-lib-lib64-symlink) ``--lib64-fallback-sanity-check`` Fallback in sanity check to lib64/ equivalent for missing libraries (default: True; disable with --disable-lib64-fallback-sanity-check) @@ -308,7 +312,9 @@ Option flag Opt ``--mpi-tests`` Run MPI tests (when relevant) (default: True; disable with --disable-mpi-tests) ``--optarch=OPTARCH`` Set architecture optimization, overriding native architecture optimizations ``--output-format=OUTPUT-FORMAT`` Set output format (type choice; default: txt) (choices: txt, rst) +``--output-style=OUTPUT-STYLE`` Control output style; auto implies using Rich if available to produce rich output, with fallback to basic colored output (type choice; default: auto) (choices: auto, basic, no_color, rich) ``--parallel=PARALLEL`` Specify (maximum) level of parallellism used during build procedure (type int) +``--parallel-extensions-install`` Install list of extensions in parallel (if supported) (default: False) ``--pre-create-installdir`` Create installation directory before submitting build jobs (default: True; disable with --disable-pre-create-installdir) ``-p, --pretend`` Does the build/installation in a test directory located in $HOME/easybuildinstall (default: False) ``--read-only-installdir`` Set read-only permissions on installation directory after installation (default: False) @@ -320,6 +326,7 @@ Option flag Opt ``--sanity-check-only`` Only run sanity check (module is expected to be installed already (default: False) ``--set-default-module`` Set the generated module as default (default: False) ``--set-gid-bit`` Set group ID bit on newly created directories (default: False) +``--show-progress-bar`` Show progress bar in terminal output (default: True; disable with --disable-show-progress-bar) ``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` Silence specified deprecation warnings (type comma-separated list) ``--skip-extensions`` Skip installation of extensions (default: False) ``-t, --skip-test-cases`` Skip running test cases (default: False) @@ -328,6 +335,7 @@ Option flag Opt ``--sysroot=SYSROOT`` Location root directory of system, prefix for standard paths like /usr/lib and /usr/include ``-T, --trace`` Provide more information in output to stdout on progress (default: False) ``--umask=UMASK`` umask to use (e.g. '022'); non-user write permissions on install directories are removed +``--unit-testing-mode`` Run in unit test mode (default: False) ``--update-modules-tool-cache`` Update modules tool cache file(s) after generating module file (default: False) ``--use-ccache=PATH`` Enable use of ccache to speed up compilation, with specified cache dir (type ; default: False) ``--use-existing-modules`` Use existing modules when resolving dependencies with minimal toolchains (default: False) diff --git a/docs/version-specific/toolchain_opts.rst b/docs/version-specific/toolchain_opts.rst index 343ef171..865d4d7a 100644 --- a/docs/version-specific/toolchain_opts.rst +++ b/docs/version-specific/toolchain_opts.rst @@ -5,7 +5,7 @@ Available toolchain options (by toolchain) *(see also* ``eb --avail-toolchain-opts `` *)* -ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iiblf_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - nvompic_ - nvpsmpic_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ +ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - nvompic_ - nvpsmpic_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ .. _ClangGCC: @@ -2543,52 +2543,6 @@ option description ========================= ======================================================================= ========= -.. _iiblf: - -Available options for iiblf toolchain -------------------------------------- - -========================= ======================================================================= ========= -option description default -========================= ======================================================================= ========= -``32bit`` Compile 32bit target ``False`` -``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` -``debug`` Enable debug ``False`` -``defaultopt`` Default compiler optimizations ``False`` -``defaultprec`` Default precision ``False`` -``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` -``i8`` Integers are 8 byte integers ``False`` -``ieee`` Adhere to IEEE-754 rules ``False`` -``intel-static`` Link Intel provided libraries statically ``False`` -``loose`` Loose precision ``False`` -``lowopt`` Low compiler optimizations ``False`` -``no-icc`` Don't set Intel specific macros ``False`` -``noopt`` Disable compiler optimizations ``False`` -``openmp`` Enable OpenMP ``False`` -``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` -``packed-linker-options`` Pack the linker options as comma separated list ``False`` -``pic`` Use PIC ``False`` -``precise`` High precision ``False`` -``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` -``shared`` Build shared library ``False`` -``static`` Build static library ``False`` -``strict`` Strict (highest) precision ``False`` -``unroll`` Unroll loops ``False`` -``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` -``verbose`` Verbose output ``False`` -``veryloose`` Very loose precision ``False`` -========================= ======================================================================= ========= - - .. _iimkl: Available options for iimkl toolchain diff --git a/docs/version-specific/toolchains.rst b/docs/version-specific/toolchains.rst index a990050c..eabb54be 100644 --- a/docs/version-specific/toolchains.rst +++ b/docs/version-specific/toolchains.rst @@ -60,7 +60,6 @@ Name Compiler(s) MPI Linear algebra **iccifortcuda** icc, ifort, CUDA *(none)* *(none)* *(none)* **ictce** icc, ifort impi imkl imkl **iibff** icc, ifort impi BLIS, libFLAME, ScaLAPACK FFTW -**iiblf** icc, ifort impi BLIS, LAPACK, ScaLAPACK FFTW **iimkl** icc, ifort *(none)* imkl imkl **iimklc** icc, ifort, CUDA *(none)* imkl imkl **iimpi** icc, ifort impi *(none)* *(none)* From 3062da92dd3520f0ec2610e607b8257d584636db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Oct 2021 10:47:08 +0200 Subject: [PATCH 170/286] pin to specific Sphinx version and older docutils for building docs --- .readthedocs.yml | 1 + docs/requirements.txt | 2 ++ 2 files changed, 3 insertions(+) create mode 100644 docs/requirements.txt diff --git a/.readthedocs.yml b/.readthedocs.yml index 10836de1..0ddd930f 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -18,3 +18,4 @@ python: install: - method: pip path: . + - requirements: docs/requirements.txt diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 00000000..db0fafbd --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,2 @@ +docutils<0.18 +sphinx==1.8.5 From 9fce0c197f00ad8ae55a512828b73c249ddafaed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Oct 2021 20:45:52 +0200 Subject: [PATCH 171/286] update overview of deprecated toolchains for EasyBuild v4.5.0 --- docs/Deprecated-easyconfigs.rst | 62 +++++++++++++++++++++++---------- 1 file changed, 43 insertions(+), 19 deletions(-) diff --git a/docs/Deprecated-easyconfigs.rst b/docs/Deprecated-easyconfigs.rst index c4706fc0..17e94656 100644 --- a/docs/Deprecated-easyconfigs.rst +++ b/docs/Deprecated-easyconfigs.rst @@ -64,10 +64,12 @@ Deprecated toolchains Overview of deprecated toolchains: * :ref:`deprecated_easyconfigs_toolchains_foss` +* :ref:`deprecated_easyconfigs_toolchains_gcc` * :ref:`deprecated_easyconfigs_toolchains_gompi` * :ref:`deprecated_easyconfigs_toolchains_goolf` * :ref:`deprecated_easyconfigs_toolchains_ictce` * :ref:`deprecated_easyconfigs_toolchains_intel` +* :ref:`deprecated_easyconfigs_toolchains_iomkl` .. _deprecated_easyconfigs_toolchains_foss: @@ -75,11 +77,23 @@ Overview of deprecated toolchains: ``foss`` toolchain ~~~~~~~~~~~~~~~~~~ -* *deprecated since:* EasyBuild v3.9.4 -* *will be archived in:* EasyBuild v4.0.0 +* *deprecated since:* EasyBuild v4.5.0 +* *will be archived in:* EasyBuild v5.0.0 The oldest versions of the ``foss`` toolchain have been deprecated, -which currently includes any version older than ``foss/2016a``. +which currently includes any version older than ``foss/2019a``. + + +.. _deprecated_easyconfigs_toolchains_gcc: + +``GCCcore`` and ``GCC`` toolchains +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +* *deprecated since:* EasyBuild v4.5.0 +* *will be archived in:* EasyBuild v5.0.0 + +The oldest versions of the ``GCCcore`` and ``GCC`` toolchains have been deprecated, +which currently includes any version older than ``8.0``. .. _deprecated_easyconfigs_toolchains_gompi: @@ -87,12 +101,11 @@ which currently includes any version older than ``foss/2016a``. ``gompi`` toolchain ~~~~~~~~~~~~~~~~~~~ -* *deprecated since:* EasyBuild v3.8.0 -* *will be archived in:* EasyBuild v4.0.0 +* *deprecated since:* EasyBuild v4.5.0 +* *will be archived in:* EasyBuild v5.0.0 Versions of the ``gompi`` toolchain that were used as a subtoolchain for a deprecated toolchain -have also been deprecated; this includes ``gompi`` toolchain versions that match ``1.*``, and any version -older than ``gompi/2016a`` (the latter only since EasyBuild v3.9.4). +have also been deprecated; this includes ``gompi`` toolchain versions older than ``gompi/2019a``. .. _deprecated_easyconfigs_toolchains_goolf: @@ -101,7 +114,7 @@ older than ``gompi/2016a`` (the latter only since EasyBuild v3.9.4). ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * *deprecated since:* EasyBuild v3.8.0 -* *will be archived in:* EasyBuild v4.0.0 +* *archived in:* EasyBuild v4.0.0 The ``goolf`` and ``goolfc`` toolchains have been deprecated, since they are superseded by the :ref:`common_toolchains_foss` and ``fosscuda`` toolchains, respectively. @@ -116,7 +129,7 @@ except that ``binutils`` is also included as a companion to ``GCC(core)`` in the ~~~~~~~~~~~~~~~~~~~ * *deprecated since:* EasyBuild v3.8.0 -* *will be archived in:* EasyBuild v4.0.0 +* *archived in:* EasyBuild v4.0.0 The ``ictce`` toolchain has been deprecated, since it is superseded by the :ref:`common_toolchains_intel`. @@ -127,17 +140,28 @@ for the Intel compilers) in the ``intel`` toolchain. .. _deprecated_easyconfigs_toolchains_intel: -Oldest versions of the ``iccifort``, ``iimpi`` and ``intel`` toolchains -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +``iccifort``, ``iimpi`` and ``intel`` toolchains +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -* *deprecated since:* EasyBuild v3.8.0 -* *will be archived in:* EasyBuild v4.0.0 +* *deprecated since:* EasyBuild v4.5.0 +* *will be archived in:* EasyBuild v5.0.0 + +The oldest versions of the ``iccifort``, ``iimpi`` and :ref:`common_toolchains_intel` have been deprecated. + +Deprecated versions include: + +* ``iccifort`` versions older than ``2019.0`` +* ``iimpi`` versions older than ``2019a`` +* ``intel`` versions older than ``2019a`` + + +.. _deprecated_easyconfigs_toolchains_iomkl: -The oldest versions of the ``iccifort``, ``iimpi`` and :ref:`common_toolchains_intel` have been deprecated, -since they are no longer considered relevant for recent systems. +``iompi`` and ``iomkl`` toolchains +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -More specifically, deprecated versions include: +* *deprecated since:* EasyBuild v4.5.0 +* *will be archived in:* EasyBuild v5.0.0 -* ``iccifort`` versions older than ``2016.1.150`` -* ``iimpi`` versions older than ``2016.01``, except version ``8.1.5-*`` -* ``intel`` versions older than ``2016a`` +The oldest versions of the ``iompi`` and ``iomkl`` toolchains have been deprecated, +which currently includes any version older than ``iompi/2019a`` and ``iomkl/2019a``. From dfe4fb39b30f3e76889064e16353ff6bcd6935f7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Oct 2021 21:36:13 +0200 Subject: [PATCH 172/286] another update for overview of deprecated toolchains for EasyBuild v4.5.0 --- docs/Deprecated-easyconfigs.rst | 45 +++++++++++++++++++++------------ 1 file changed, 29 insertions(+), 16 deletions(-) diff --git a/docs/Deprecated-easyconfigs.rst b/docs/Deprecated-easyconfigs.rst index 17e94656..161e1cd0 100644 --- a/docs/Deprecated-easyconfigs.rst +++ b/docs/Deprecated-easyconfigs.rst @@ -65,6 +65,7 @@ Overview of deprecated toolchains: * :ref:`deprecated_easyconfigs_toolchains_foss` * :ref:`deprecated_easyconfigs_toolchains_gcc` +* :ref:`deprecated_easyconfigs_toolchains_gcccuda` * :ref:`deprecated_easyconfigs_toolchains_gompi` * :ref:`deprecated_easyconfigs_toolchains_goolf` * :ref:`deprecated_easyconfigs_toolchains_ictce` @@ -74,14 +75,14 @@ Overview of deprecated toolchains: .. _deprecated_easyconfigs_toolchains_foss: -``foss`` toolchain -~~~~~~~~~~~~~~~~~~ +``foss`` and ``fosscuda`` toolchain +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * *deprecated since:* EasyBuild v4.5.0 * *will be archived in:* EasyBuild v5.0.0 -The oldest versions of the ``foss`` toolchain have been deprecated, -which currently includes any version older than ``foss/2019a``. +The oldest versions of the ``foss`` and ``fosscuda`` toolchains have been deprecated, +which currently includes any version older than ``foss/2019a`` and ``fosscuda/2019a``. .. _deprecated_easyconfigs_toolchains_gcc: @@ -96,16 +97,28 @@ The oldest versions of the ``GCCcore`` and ``GCC`` toolchains have been deprecat which currently includes any version older than ``8.0``. +.. _deprecated_easyconfigs_toolchains_gcccuda: + +``gcccuda`` toolchain +~~~~~~~~~~~~~~~~~~~~~ + +* *deprecated since:* EasyBuild v4.5.0 +* *will be archived in:* EasyBuild v5.0.0 + +The oldest versions of the ``gcccuda`` toolchains have been deprecated, +which currently includes any version older than ``gcccuda/2019a``. + + .. _deprecated_easyconfigs_toolchains_gompi: -``gompi`` toolchain -~~~~~~~~~~~~~~~~~~~ +``gompi`` and ``gompic`` toolchains +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * *deprecated since:* EasyBuild v4.5.0 * *will be archived in:* EasyBuild v5.0.0 -Versions of the ``gompi`` toolchain that were used as a subtoolchain for a deprecated toolchain -have also been deprecated; this includes ``gompi`` toolchain versions older than ``gompi/2019a``. +Versions of the ``gompi`` and ``gompic`` toolchains that were used as a subtoolchain for a deprecated toolchain +have also been deprecated; this includes versions older than ``gompi/2019a`` and ``gompic/2019a``. .. _deprecated_easyconfigs_toolchains_goolf: @@ -140,8 +153,8 @@ for the Intel compilers) in the ``intel`` toolchain. .. _deprecated_easyconfigs_toolchains_intel: -``iccifort``, ``iimpi`` and ``intel`` toolchains -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +``iccifort``, ``iimpi``, ``iimpic``, ``intel``, and ``intelcuda`` toolchains +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * *deprecated since:* EasyBuild v4.5.0 * *will be archived in:* EasyBuild v5.0.0 @@ -151,17 +164,17 @@ The oldest versions of the ``iccifort``, ``iimpi`` and :ref:`common_toolchains_i Deprecated versions include: * ``iccifort`` versions older than ``2019.0`` -* ``iimpi`` versions older than ``2019a`` -* ``intel`` versions older than ``2019a`` +* ``iimpi`` and ``iimpic`` versions older than ``2019a`` +* ``intel`` and ``intelcuda`` versions older than ``2019a`` .. _deprecated_easyconfigs_toolchains_iomkl: -``iompi`` and ``iomkl`` toolchains -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +``iompi``, ``iompic``, ``iomkl``, and ``iomklc`` toolchains +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * *deprecated since:* EasyBuild v4.5.0 * *will be archived in:* EasyBuild v5.0.0 -The oldest versions of the ``iompi`` and ``iomkl`` toolchains have been deprecated, -which currently includes any version older than ``iompi/2019a`` and ``iomkl/2019a``. +The oldest versions of the ``iompi``, ``iompic``, ``iomkl`` and ``iomklc`` toolchains have been deprecated, +which currently includes any version older than ``2019a``. From 2299cd87b238e3ed9578b7c99e956f750e1d5831 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Oct 2021 23:20:50 +0200 Subject: [PATCH 173/286] document dynamic progress bars shown by EasyBuild --- docs/Installation.rst | 2 + docs/Progress_bars.rst | 132 +++++++++++++++++++ docs/img/progress_bar_download.png | Bin 0 -> 48401 bytes docs/img/progress_bar_easyconfig.png | Bin 0 -> 27799 bytes docs/img/progress_bar_extensions.png | Bin 0 -> 21999 bytes docs/img/progress_bar_overall.png | Bin 0 -> 27919 bytes docs/img/progress_bar_overall_easyconfig.png | Bin 0 -> 58827 bytes docs/index.rst | 1 + 8 files changed, 135 insertions(+) create mode 100644 docs/Progress_bars.rst create mode 100644 docs/img/progress_bar_download.png create mode 100644 docs/img/progress_bar_easyconfig.png create mode 100644 docs/img/progress_bar_extensions.png create mode 100644 docs/img/progress_bar_overall.png create mode 100644 docs/img/progress_bar_overall_easyconfig.png diff --git a/docs/Installation.rst b/docs/Installation.rst index a2ed485d..ae25e2f4 100644 --- a/docs/Installation.rst +++ b/docs/Installation.rst @@ -503,6 +503,8 @@ Optional Python packages SVN repository for easyconfig files; * `python-graph-dot `_, only needed for building nice-looking dependency graphs using ``--dep-graph *.dot`` +* `Rich `_, + only needed to let ``eb`` produce rich output, like :ref:`progress_bars`; Sources ------- diff --git a/docs/Progress_bars.rst b/docs/Progress_bars.rst new file mode 100644 index 00000000..9e13d1d2 --- /dev/null +++ b/docs/Progress_bars.rst @@ -0,0 +1,132 @@ +.. _progress_bars: + +Progress bars +============= + +*(supported since: EasyBuild v4.5.0)* + +.. contents:: + :depth: 3 + :backlinks: none + +.. _progress_bar_generic: + +General information on progress bars +------------------------------------ + +EasyBuild will show **progress bars** for various aspects of the installation progress +by default, if the `Rich `_ Python package is available. + +The progress bars shown by EasyBuild are *dynamic*: they are only visible when they are relevant. + +.. _progress_bars_types: + +Types of progress bars +---------------------- + +EasyBuild will show different progress bars to show the progress for different aspects of the installation process. + +Overall progress bar (status bar) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. image:: img/progress_bar_overall.png + :height: 18px + :align: center + +The progress bar at the bottom, also known as the *status bar*, shows the *overall progress* +in installing software for the currently active EasyBuild session. + +From left to right, the following information is included: + +* The total amount of time that this EasyBuild session has spent on installing software. +* The number of easyconfigs that have been processed already, the total number of easyconfigs + being processed, and a count of easyconfigs that failed to installed so far (if there are any). +* The list of already processed easyconfigs, along with the result: + * ``OK`` (in green) for a successful installation; + * ``FAILED`` (in red) a failed installation; + +Processed easyconfigs are shown in reversed order: most recently processed easyconfigs are listed first. +Failing easyconfigs are listed before easyconfigs that were installed successfully, +to highlight failing installations. + +The status bar is not shown if only a single easyconfig file is being installed, +and is hidden automatically as soon as the EasyBuild session finishes. + +Easyconfig progress bar +~~~~~~~~~~~~~~~~~~~~~~~ + +.. image:: img/progress_bar_easyconfig.png + :height: 16px + :align: center + +A dedicated progress bar is shown for every easyconfig file that is installed, +right above the status bar (if present), which shows: + +* The name of the module that is being installed. +* The currently active installation step. +* The number of completed installations steps, as well as the total number of installation steps for this easyconfig. +* A visual progress bar that represents the progress in installing this easyconfig. +* The total amount of time spent on installing this easyconfig so far. + +The progress bar for a specific easyconfig file will be hidden as soon as the installation +finishes (regardless of whether it was successful or not). + +Download progress bars +~~~~~~~~~~~~~~~~~~~~~~ + +.. image:: img/progress_bar_download.png + :height: 56px + :align: center + +When EasyBuild is downloading one or more files, +a dedicated progress bar will be visible: + +* For large downloads: the name of the file being downloaded, + a visual progress bar, the amount of data downloaded so far, + the amount of data to download in total, the download speed, + and the amount of time spent downloading the file so far. +* If there are multiple files being downloaded: an overview of how + many files have been downloaded already, and how many need to be downloaded in total. + +The download progress bars will be hidden as soon as the downloading has been completed (or has failed). + +Extensions progress bar +~~~~~~~~~~~~~~~~~~~~~~~ + +.. image:: img/progress_bar_extensions.png + :height: 22px + :align: center + +When extensions are being installed for a particular easyconfig, +a dedicated progress bar will pop up for the ``extensions`` step, +which shows: + +* The name of the extension that is currently being installed. +* The number of extensions installed so far, and the total number of extensions to install. +* A visual progress bar that represents the progress for installing extensions so far. +* The total amount of time spent installing extensions for this easyconfig. + +.. _progress_bars_configuration: + +Relevant configuration options +------------------------------ + +``output-style`` +~~~~~~~~~~~~~~~~ + +The ``output-style`` configuration option determines the output style of the ``eb`` command. + +Setting ``output-style`` to '``rich``' results in rich output being produced, which includes progress bars. 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17:03:33 +0800 Subject: [PATCH 174/286] update release notes and changelog for EasyBuild v4.5.0 + bump version to 4.5.0 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 196 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 196 insertions(+), 5 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index a38ecb5e..50e95849 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20211029.01** (`Oct 29th 2021`): update release notes for EasyBuild v4.5.0 (see :ref:`release_notes_eb450`) * **release 20210907.01** (`Sep 7th 2021`): update release notes for EasyBuild v4.4.2 (see :ref:`release_notes_eb442`) * **release 20210706.01** (`Jul 6th 2021`): update release notes for EasyBuild v4.4.1 (see :ref:`release_notes_eb441`) * **release 20210602.01** (`Jun 2nd 2021`): update release notes for EasyBuild v4.4.0 (see :ref:`release_notes_eb440`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 80c076d3..de85cda7 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,202 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,467** different software packages, -including 36 different (compiler) toolchains. It contains 241 software-specific easyblocks and 37 generic easyblocks, -alongside 13,265 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,506** different software packages, +including 36 different (compiler) toolchains. It contains 242 software-specific easyblocks and 37 generic easyblocks, +alongside 13,514 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb450: + +EasyBuild v4.5.0 (October 29th 2021) +------------------------------------ + +feature release + +**framework** + +* various enhancements, including: + + * add ``--review-pr-max`` and ``--review-pr-filter`` options to limit easyconfigs used by ``--review-pr`` + retain order of easyconfigs being compared with (`#3754 `_) + * use Rich (if available) to show progress bars when installing easyconfigs (`#3823 `_, `#3826 `_, `#3833 `_, `#3835 `_, `#3844 `_, `#3864 `_, `#3867 `_, `#3882 `_) + + * see also https://docs.easybuild.io/en/latest/Progress_bars.html + + * add support for checking required/optional EasyBuild dependencies via ``eb --check-eb-deps`` (`#3829 `_) + * add support for collecting GPU info (via ``nvidia-smi``), and include it in ``--show-system-info`` and test report (`#3851 `_) + * added support for ``--insecure-download`` configuration option (`#3859 `_) + * make intelfftw toolchain component aware of imkl-FFTW module (`#3861 `_) + * make sure the contrib/hooks tree is included in the source tarball for easybuild-framework (`#3862 `_) + * add ``check_async_cmd`` function to facilitate checking on asynchronously running commands (`#3865 `_, `#3881 `_) + * add initial/experimental support for installing extensions in parallel (`#3667 `_, `#3878 `_) + + * see also https://docs.easybuild.io/en/latest/Installing_extensions_in_parallel.html + + * filter out duplicate paths added to module files, and print warning when they occur (`#3770 `_, `#3874 `_) + +* various bug fixes, including: + + * ensure that path configuration options have absolute path values (`#3832 `_) + * fix broken test by taking into account changed error raised by Python 3.9.7 when copying directory via ``shutil.copyfile`` (`#3840 `_) + * ensure newer location of CUDA stubs is taken into account by RPATH filter (`#3850 `_) + * replace ``which`` by ``command -v`` in ``eb`` wrapper script to avoid dependency on ``which`` command (`#3852 `_) + * refactor EasyBlock to decouple collecting of information on extension source/patch files from downloading them (`#3860 `_) + + * in this context, the ``EasyBlock.fetch_extension_sources`` method was deprecated, and replaced by ``EasyBlock.collect_exts_file_info`` + + * fix library paths to add to ``$LDFLAGS`` for intel-compilers toolchain component (`#3866 `_) + * remove ``--depth 1`` from git clone when ``commit`` specified (`#3871 `_, `#3872 `_) + * make sure correct include directory is used for FlexiBLAS toolchain component (`#3875 `_) + * explicitly disable rebase when pulling develop branch to create a merge commit, since not specifying how to reconcile divergent branches is an error with Git 2.33.1 and newer (`#3879 `_) + * tweak ``test_http_header_fields_urlpat`` to download from ``sources.easybuild.io`` rather than ``https://ftp.gnu.org`` (`#3883 `_) + +* other changes: + + * change ``copy_file`` function to raise an error when trying to copy non-existing file (`#3836 `_, `#3855 `_, `#3877 `_) + * only print the hook messages if EasyBuild is running in debug mode (`#3843 `_) + * deprecate old toolchain versions (pre-2019a common toolchains) (`#3876 `_, `#3884 `_) + + * see also https://docs.easybuild.io/en/latest/Deprecated-easyconfigs.html#deprecated-toolchains + +**easyblocks** + +* new software-specific easyblock for imkl-FFTW (`#2599 `_) + +* minor enhancements and updates, including: + + * add support for installing R extensions in parallel (`#2408 `_) + * update MotionCor2 easyblock to consider to locations for built binary (`#2541 `_, `#2598 `_) + * let GROMACS runtime logs show EasyBuild was used by setting ``-DGMX_VERSION_STRING_OF_FORK`` configuration option (`#2571 `_) + * adjust qa list in WIEN2k easyblock to handle new questions + fix sanity check for v21.1 (`#2572 `_) + * enhance GCC easyblock to add support for AMD GPU offloading (`#2578 `_) + * add support for specifying subdirectory for target installation directory in CMakeMake (`#2579 `_) + * enhance COMSOL easyblock to change permission on build directory during extract step (to allow using patches) (`#2584 `_) + * enhance FlexiBLAS easyblock to support building with Intel MKL (imkl) as backend (`#2588 `_) + * update MATLAB easyblock for 2021b (jre is no longer included) (`#2589 `_) + * update OpenCV easyblock to detect GTK3 and GTK2 dependencies (next to GTK+) (`#2591 `_) + * avoid that path to CUDA install directory is added to ``$PATH`` (`#2593 `_) + * enhance imkl easyblock to add support for installing with NVHPC (`#2595 `_) + * enhance PETSc easyblock to run tests in parallel (`#2601 `_) + * update ELSI easyblock to support two new external dependencies (`#2602 `_) + * add custom custom easyconfig parameter ``backends`` in FlexiBLAS easyblock to specify backends (`#2605 `_) + * detect problem with compiling CPU detection code in configure output in GROMACS easyblock (`#2609 `_) + * use correct include directory for FlexiBLAS (`#2610 `_) + +* various bug fixes, including: + + * unset ``$EASYBUILD_*`` environment variables when running sanity check in EasyBuildMeta easyblock + also unset ``$MODULES_LMCONFLICT`` to avoid conflict when loading EasyBuild module (`#2568 `_) + * ensure that all ABAQUS components get installed for ABAQUS 2021.x (+ add support for enabling/disabling fe-safe) (`#2569 `_) + * fix subdir path in VTune easyblock for 2021.x versions + add sanity check command (`#2576 `_) + * make sure custom easyblock for installing EasyBuild respects requested version of Python (like ``$EB_PYTHON``) (`#2581 `_) + * restore RPATH wrappers for OpenMPI sanity check (`#2582 `_) + * fix installation of libcp2k for recent CP2K versions (`#2585 `_) + * make version regex in OpenSSL wrapper easyblock less strict (version string does not always end with a letter) (`#2597 `_) + * redefine ``collect_exts_file_info`` instead of now deprecated fetch_extension_sources in OCaml easyblock (`#2603 `_) + +* other changes: + + * don't use ``--config=mkl`` for TensorFlow 2.4+ (`#2583 `_) + + * this fixes some performance related issues for TensorFlow, see https://github.com/easybuilders/easybuild-easyblocks/issues/2577 and https://github.com/easybuilders/easybuild-easyconfigs/issues/14120 + + * fix support for recent imkl version in numexpr easyblock (`#2606 `_) + * derive custom easyblock from MotionCor2 from PackedBinary instead of EasyBlock (`#2607 `_) + +**easyconfigs** + +* added easyconfigs for foss/2021b (`#14217 `_) and intel/2021b (`#14218 `_) common toolchains + + * see also https://docs.easybuild.io/en/latest/Common-toolchains.html + +* add easyconfig for gobff/2021a toolchain (`#14019 `_, `#14038 `_) +* added example easyconfig files for 39 new software packages: + + * abTEM (`#13974 `_), ARTS (`#9651 `_), AutoGeneS (`#13903 `_), bashplotlib (`#13942 `_), CIRI-long (`#13985 `_), DFT-D4 (`#12803 `_), + ELSI-RCI (`#14147 `_), ESL-Bundle (`#14179 `_), expecttest (`#14106 `_), fdict (`#14161 `_), flook (`#14161 `_), FreeTDS (`#13952 `_), + HDBSCAN (`#14062 `_), imkl-FFTW (`#14195 `_), isoCirc (`#13982 `_), libfdf (`#14173 `_), libmbd (`#14129 `_), libpspio (`#14173 `_), + libSBML (`#14050 `_), longread_umi (`#13987 `_), Mesa-demos (`#14123 `_), MixMHC2pred (`#14041 `_), NTPoly (`#14183 `_), + OpenSceneGraph (`#14197 `_), panaroo (`#14203 `_), PEPT (`#14077 `_), pycoQC (`#14012 `_), python-docx (`#13930 `_), QD (`#14122 `_), + radeontop (`#14124 `_), Rgurobi (`#14188 `_), RInChI (`#14049 `_), scGeneFit (`#13963 `_), swifter (`#14114 `_), TOML-Fortran (`#13929 `_), + TRUST4 (`#14035 `_), ucx-py (`#14051 `_), vawk (`#14040 `_), VMTK (`#14023 `_) + +* added additional easyconfigs for various supported software packages, including: + + * AlphaFold 2.0.1, artic-ncov2019 2021.06.24, BerkeleyGW 3.0.1, bokeh 2.4.1, Boost.Python 1.76.0, canu 2.2, + Cartopy 0.20.0, CP2K 8.2, CUDA 11.4.2, Dalton 2020.0, dask 2021.9.1, edlib 1.3.9, ELSI 2.7.1, FFTW 3.3.10, + GD 2.73, GDAL 3.3.2, GTDB-Tk 1.7.0, ImageJ 1.52q, jax 0.2.20, Kraken2 2.1.2, leidenalg 0.8.7, libfabric 1.13.2, + libspatialindex 1.9.3, libxc 5.1.6, libxsmm 1.16.2, lifelines 0.26.3, Longshot 0.4.3, LSD2 2.2, MAFFT 7.487, + MEME 5.4.1, MotionCor2 1.4.4, NCCL 2.11.4, netCDF 4.8.1, networkx 2.6.3, Nextflow 21.08.0, OpenBLAS 0.3.18, + OpenCV 4.5.3, OrthoFinder 2.5.4, OSU-Micro-Benchmarks 5.8, PhyML 3.3.20200621, PostgreSQL 13.4, pygraphviz 1.7, + pyproj 3.1.0, python-Levenshtein 0.12.1, PyTorch-Geometric 2.0.1, QIIME2 2021.8.eb, Qiskit 0.31.0, + QuantumESPRESSO 6.8, Racon 1.4.21, rampart 1.2.0, rclone 1.56.0, RDKit 2021.03.4, SAMtools 1.13, scanpy 1.8.1, + scikit-allel 1.3.3, SciPy-bundle 2021.10, Seaborn 0.11.2, SHAPEIT4 4.2.2, spglib 1.16.2, UCX 1.11.2, + UCX-CUDA 1.11.2, VSEARCH 2.18.0, Z3 4.8.12, zarr 2.10.1 + +* minor enhancements, including: + + * add JASPAR2020 to R-bundle-Bioconductor 3.13 (`#13962 `_) + * add Autotools as build dependency for CubeGUI-4.6 (`#14109 `_) + * add compiler/parallel/tcltk R libraries included in base installation to extensions in recent R easyconfigs (`#14189 `_, `#14190 `_, `#14194 `_) + + * required for parallel installation of extensions for these R easyconfigs + + * also add location to MPI startup tests to ``$PATH`` in OSU-Micro-Benchmarks easyconfigs (`#14126 `_) + +* various bug fixes, including: + + * add missing Brotli dependency to freetype (`#13915 `_, `#14002 `_) + * add patch for OpenBLAS 0.3.15 to fix failing numpy tests on aarch64 (`#13923 `_) + * fix source URL + add alternate checksum for ADMIXTURE 1.3.0 (`#13933 `_) + * just use ``cp`` to copy ``stereo_chemical_props.txt`` to AlphaFold installation directory (`#13938 `_) + * add UnZip build dependency to TensorFlow 2.4.1 (`#13958 `_), 2.5.0 (`#13959 `_) and 2.6.0 easyconfigs (`#13960 `_) + * add missing Python dependency for WIEN2k 21.1 + patch to fix build failure for ``lapw0_mpi`` with libxc (`#13961 `_) + * add additional valid checksum for lhs 1.1.1 extension in recent R 4.0.x and 4.1.0 easyconfigs (`#13969 `_) + * fix Fortran system call stdout/err redirection for WIEN2k v21.1 (`#13972 `_) + * add OpenSSL dependency to Kent_tools 418 easyconfig to fix a link error (`#13989 `_) + * make binutils a build-only dependency for Brotli + add sanity check command (`#14004 `_) + * fix installation of Racon v1.4.7 with gcccuda/2019b after move of ClaraGenomicsAnalysis repository (`#14010 `_) + * fix source URL for KEGG.db extension in R-bundle-Bioconductor 3.13 easyconfig (since it's a deprecated library now) (`#14013 `_) + * add patch for BLIS 0.8.1 to fix dgemm FPE signalling on Broadwell (`#14018 `_) + * add patch to fix installation of TensorFlow 2.2.3 on POWER (`#14025 `_) + * fix AmberTools v20 easyconfig using intel/2020a toolchain (`#14028 `_) + * fix download + permissions of binary for USEARCH v11.0.667 (`#14036 `_) + * remove h5py 3.x dependency for Keras with 2020b toolchain, since TensorFlow provides (and requires) h5py 2.x (`#14052 `_) + * correctly specify install prefix for CUDA in OSU-Micro-Benchmarks after renaming CUDAcore to CUDA for 2021a (`#14063 `_) + * add patch to fix failing file system cache test for jax on recent Linux kernels (`#14067 `_), `#14070 `_) + * fix compilation of BWA 0.7.17 with GCC/10.2.0 on POWER (`#14073 `_) + * add missing dependencies for recent LibTIFF versions: XZ, jbigkit, zstd (`#14079 `_) + * add missing header file to existing versions of jbigkit (`#14081 `_) + * fix source URL for SUNDIALS 5.x (`#14092 `_, `#14096 `_) + * add Perl and Python runtime dependencies to Bowtie2 2.4.4 (`#14097 `_) + * fix source URL for SCOTCH 6.1.0 (`#14099 `_) + * drop tcmalloc from SymEngine as it causes crashes with scipy (`#14119 `_) + * fix homepage + description in SimpleITK easyconfigs (`#14125 `_) + * add missing scripts from ``utils`` and ``analysis_scripts`` to ``bin`` for cryoDRGN (`#14137 `_) + * patch ``rsync_from_ncbi.pl`` in Kraken2 v2.1.2 to allow syncing with NCBI servers over HTTPS (`#14148 `_) + * skip ``mkl_fused_batch_norm_op_test`` test (broken on AMD EPYC systems) for TensorFlow 2.5.0 and 2.6.0 (`#14151 `_, `#14153 `_) + * fix incorrect module load message and update morphology plugin of ImageJ 1.51k (`#14152 `_) + * fix XCrySDen v1.6.2 linking to libdl and Togl (`#14160 `_) + * add patch to fix PMIx detection in OpenMPI v4.0.3, v4.0.5, v4.1.0 (`#14177 `_) + * add patch for OpenBLAS 0.3.17 + 0.3.18 to fix segfault triggered by scipy tests (`#14178 `_) + * fix spatstat.* downloads for Seurat v4.0.1 (`#14199 `_) + * add patch for GROMACS 2019.3 easyconfigs using CMake 3.15.3 to fix CPU detection (`#14212 `_) + +* other changes: + + * remove help2man build dependency for flex using system toolchain (because it requires Perl) (`#13922 `_) + * use proper dependency for python-Levenshtein in CIRI-long easyconfig (`#13985 `_) + * in-place updates for foss/2021b and intel/2021b common toolchains + + * update to UCX(-CUDA) 1.11.2 as dependency for OpenMPI v4.1.1 + NCCL v2.10.3 (`#14090 `_) + * update libfabric to 1.13.1 in OpenMPI and add it as a dependency in PMIx for the upcoming foss 2021b toolchain (`#14164 `_) + * update to OpenBLAS 0.3.18 as dependency for FlexiBLAS 3.0.4 with GCCcore/11.2.0 toolchain (`#14167 `_) + * update libfabric to 1.13.2 in OpenMPI v4.1.1 + PMIx 4.1.0 for the upcoming foss/2021b toolchain (`#14176 `_) + + * remove format mapping from homepage of Subread easyconfigs (`#14145 `_) + * add BLIS and imkl (x86_64 only) builddependencies to FlexiBLAS 0.3.4 with GCC/11.2.0 toolchain (`#14225 `_) + + .. _release_notes_eb442: EasyBuild v4.4.2 (September 7th 2021) diff --git a/docs/conf.py b/docs/conf.py index 6d17cf87..acf4eea1 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.4.2' # this is meant to reference the version of EasyBuild +version = '4.5.0' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20210907.0' # this is meant to reference the version of the documentation itself +release = '20211029.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 421a50796c913b4f74ba631dde7268f08f98d9e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Oct 2021 12:24:22 +0200 Subject: [PATCH 175/286] fix suggestions for docs on progress bars --- docs/Progress_bars.rst | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/docs/Progress_bars.rst b/docs/Progress_bars.rst index 9e13d1d2..3df1c7c9 100644 --- a/docs/Progress_bars.rst +++ b/docs/Progress_bars.rst @@ -19,6 +19,12 @@ by default, if the `Rich `_ Python package is av The progress bars shown by EasyBuild are *dynamic*: they are only visible when they are relevant. +Note that for most progress bars the amount of progress made is assumed to be linear across the whole process, +even though it is typically not. Some installation steps take significantly longer than others, +and some easyconfigs may install in a couple minutes while others take much longer, but it is very difficult +to get a good estimate on how much time will be needed. +The download progress bar is an exception here (as long as the size of the file to download could be determined first). + .. _progress_bars_types: Types of progress bars @@ -43,11 +49,13 @@ From left to right, the following information is included: being processed, and a count of easyconfigs that failed to installed so far (if there are any). * The list of already processed easyconfigs, along with the result: * ``OK`` (in green) for a successful installation; - * ``FAILED`` (in red) a failed installation; + * ``FAILED`` (in red) for a failed installation; Processed easyconfigs are shown in reversed order: most recently processed easyconfigs are listed first. -Failing easyconfigs are listed before easyconfigs that were installed successfully, -to highlight failing installations. + +If EasyBuild is configured to continue processing easyconfigs when an installation failed +(for example when using ``--upload-test-report``), failing easyconfigs are listed before easyconfigs +that were installed successfully, to highlight failing installations. The status bar is not shown if only a single easyconfig file is being installed, and is hidden automatically as soon as the EasyBuild session finishes. @@ -83,8 +91,8 @@ a dedicated progress bar will be visible: * For large downloads: the name of the file being downloaded, a visual progress bar, the amount of data downloaded so far, - the amount of data to download in total, the download speed, - and the amount of time spent downloading the file so far. + the amount of data to download in total, the average download speed, + and the estimated time remaining to complete the download (based on average download speed). * If there are multiple files being downloaded: an overview of how many files have been downloaded already, and how many need to be downloaded in total. From 72a319783f1557eb52d9ca541e415100b176c73a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Oct 2021 13:59:05 +0200 Subject: [PATCH 176/286] reword note on progress bar steps being treated equal Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- docs/Progress_bars.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/Progress_bars.rst b/docs/Progress_bars.rst index 3df1c7c9..e14994fd 100644 --- a/docs/Progress_bars.rst +++ b/docs/Progress_bars.rst @@ -19,10 +19,10 @@ by default, if the `Rich `_ Python package is av The progress bars shown by EasyBuild are *dynamic*: they are only visible when they are relevant. -Note that for most progress bars the amount of progress made is assumed to be linear across the whole process, -even though it is typically not. Some installation steps take significantly longer than others, -and some easyconfigs may install in a couple minutes while others take much longer, but it is very difficult -to get a good estimate on how much time will be needed. +Note that for most progress bars each step is treated as being equal even though the time taken for the +various steps varies. There are many factors that impact how long an individual installation step, installing +an easyconfig, or installing an extension may and this makes it very difficult to get a good estimate on how +much time will be needed. The download progress bar is an exception here (as long as the size of the file to download could be determined first). .. _progress_bars_types: From 76ce5e8b4607075b5cafe312f0a620f31707ed6d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Oct 2021 13:56:17 +0200 Subject: [PATCH 177/286] document experimental/initial support for installing extensions in parallel --- docs/Experimental_features.rst | 1 + docs/Installing_extensions_in_parallel.rst | 109 +++++++++++++++++++++ docs/index.rst | 1 + 3 files changed, 111 insertions(+) create mode 100644 docs/Installing_extensions_in_parallel.rst diff --git a/docs/Experimental_features.rst b/docs/Experimental_features.rst index dbca8a87..eb85cdd1 100644 --- a/docs/Experimental_features.rst +++ b/docs/Experimental_features.rst @@ -14,3 +14,4 @@ Currently enabled experimental features include: * support for easyconfig files in YAML syntax (see :ref:`easyconfig_yeb_format`) * support for generating container recipes & images (see :ref:`containers`) * support for using easystack files (see :ref:`easystack`) + * support for installing extensions in parallel (see :ref:`installing_extensions_in_parallel`) diff --git a/docs/Installing_extensions_in_parallel.rst b/docs/Installing_extensions_in_parallel.rst new file mode 100644 index 00000000..e5f085bd --- /dev/null +++ b/docs/Installing_extensions_in_parallel.rst @@ -0,0 +1,109 @@ +.. _installing_extensions_in_parallel: + +Installing extensions in parallel (experimental!) +================================================= + +Since EasyBuild v4.5.0 (initial) support is available for installing extensions in parallel, +that is to run the installation command for multiple extensions that are ready to install at the same time +in the background, to exploit the availability of multiple cores. + +**Note: this is an** :ref:`experimental feature `. +**Some of the mentioned functionality may be subject to change or be prone to errors.** + +.. contents:: + :depth: 3 + :backlinks: none + +.. _installing_extensions_in_parallel_configuration: + +Configuration +------------- + +To let EasyBuild install extensions in parallel, the ``parallel-extensions-install`` configuration option must be +enabled. + +In addition, since the support for installing extensions in parallel is an experimental feature, the ``experimental`` +configuration option must be also be enabled (see also :ref:`experimental_features`). + +How many extension installations should be started (at maximum) at the same time is controlled by +the ``parallel`` configuration option. + + +.. _installing_extensions_in_parallel_requirements: + +Requirements +------------ + +For EasyBuild to be able to install a list of extensions in parallel, two requirements must be met: + +* The easyblock(s) that are used for installing the extensions must have support for determining + which installed extensions are required to fulfill the dependencies for a particular extension. + This is done via the ``required_deps`` property method. +* EasyBuild must be able to start a single shell command (asynchronously, so it runs in the background) + to perform the installation of the extension via the ``run_async`` method, + and check whether the command has completed via the ``async_cmd_check`` method. + +For an example of how ``required_deps``, ``run_async``, and ``async_cmd_check`` can be implemented, +see the `RPackage +`_ easyblock. + +.. _installing_extensions_in_parallel_caveats_known_issues: + +Caveats and Known issues +------------------------ + +*(last update: EasyBuild v4.5.0)* + +There are a couple of caveats and known issues with installing extensions in parallel, +which we hope to resolve in future EasyBuild releases. + +This is also why the support for installing extensions in parallel is currently marked as an experimental feature. + +.. _installing_extensions_in_parallel_caveats_known_issues_only_r: + +Only works for R extensions +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The support for installing extensions in parallel currently only works for R extensions, +since only the ``RPackage`` easyblock (which is used to install R packages as extensions) implements +the necessary methods (see :ref:`installing_extensions_in_parallel_requirements`). + +Supporting other types of extensions (Python, Perl, etc.) requires that the corresponding easyblocks that +are used to install those extensions (like ``PythonPackage``, ``PerlModule``) are enhanced to support determining +required dependencies and starting the installation command asynchronously. + +.. _installing_extensions_in_parallel_caveats_known_issues_exts_list: + +List of extensions must be self-contained +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The EasyBuild framework currently enforces that all required dependencies for a particular extension +are included in the list of extensions that is being installed (specified via the ``exts_list`` easyconfig +parameter). Extensions provided by dependencies are not taken into account (yet). + +As a result, trying to install an +`R-bundle-Bioconductor `_ +easyconfig with ``parallel-extensions-install`` enabled +will result in an error reporting missing required dependencies. + + +.. _installing_extensions_in_parallel_caveats_known_issues_skip: + +Skipping of installed extensions is still done sequentially +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Checking which extensions are already installed for which the installation can be skipped +when ``--skip`` is being used is still done sequentially. + +Additional work is needed to also run these checks in parallel across the cores that are available to EasyBuild. + + +.. _installing_extensions_in_parallel_caveats_known_issues_sanity_check: + +Sanity check for extensions is still run sequentially +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The sanity checks that are done for each extension are still done through a sequential loop over the +list of extensions. + +Additional work is needed to also run these checks in parallel across the cores that are available to EasyBuild. diff --git a/docs/index.rst b/docs/index.rst index 1996ca18..6d6d2097 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -71,6 +71,7 @@ Advanced usage topics Hooks Implementing-easyblocks Including_additional_Python_modules + Installing_extensions_in_parallel Integration_with_GitHub Locks Manipulating_dependencies From d9fb2829b80c1b62dd195b814eb1ceac4af0b1b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Oct 2021 15:22:37 +0200 Subject: [PATCH 178/286] add reference to section on --skip when mentioning that checks for extensions to skip is still being done sequentially --- docs/Installing_extensions_in_parallel.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Installing_extensions_in_parallel.rst b/docs/Installing_extensions_in_parallel.rst index e5f085bd..b9b341b4 100644 --- a/docs/Installing_extensions_in_parallel.rst +++ b/docs/Installing_extensions_in_parallel.rst @@ -93,7 +93,7 @@ Skipping of installed extensions is still done sequentially ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Checking which extensions are already installed for which the installation can be skipped -when ``--skip`` is being used is still done sequentially. +when ``--skip`` (see :ref:`partial_installation_skip`) is being used is still done sequentially. Additional work is needed to also run these checks in parallel across the cores that are available to EasyBuild. From 5580afd4f24d163872e5eaa39a13d115f28486ef Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 29 Oct 2021 21:33:39 +0800 Subject: [PATCH 179/286] bump version to 4.5.0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 1c691a89..775ba896 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.4.2' +VERSION = '4.5.0' # Utility function to read README file From 562ccc32da6730569e7dc8e7ff863699e742ead8 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 1 Dec 2021 16:03:39 +0100 Subject: [PATCH 180/286] Update @ocaisa contact info --- docs/Maintainers.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Maintainers.rst b/docs/Maintainers.rst index 29563b5c..b831e4e7 100644 --- a/docs/Maintainers.rst +++ b/docs/Maintainers.rst @@ -115,9 +115,9 @@ The EasyBuild maintainers all have admin access to the different EasyBuild GitHu * GitHub: `@smoors `_ - e-mail: ``samuel.moors (at) vub.be`` - IRC/Slack: ``smoors`` -* **Alan O'Cais** (`JSC `_) +* **Alan O'Cais** (`CECAM `_) - * GitHub: `@ocaisa `_ - e-mail: ``a.ocais (at) fz-juelich.de`` - IRC/Slack: ``ocaisa`` + * GitHub: `@ocaisa `_ - e-mail: ``alan.ocais (at) epfl.ch`` - IRC/Slack: ``ocaisa`` * **Mikael Öhman** (`Chalmers University of Technology `_) From 41791219c64b9d349cf914844cd89cd2fd29fc88 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Dec 2021 08:54:50 +0100 Subject: [PATCH 181/286] auto-update documentation for EasyBuild v4.5.1 --- docs/version-specific/Supported_software.rst | 2498 +++++++++++++----- docs/version-specific/easyblocks.rst | 1 + 2 files changed, 1863 insertions(+), 636 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index ef0a9c6a..d58ba3e1 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2506 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2575 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow_555` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -115,7 +115,8 @@ version versionsuffix toolchain ``8.10.3`` ``intel/2018b`` ``9.2.1`` ``intel/2020a`` ``9.4.1`` ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` -``9.4.2`` ``intel/2021a`` +``9.4.2`` ``foss/2021a``, ``intel/2021a`` +``9.6.2`` ``intel/2021a``, ``intel/2021b`` ========== ======================== ================================================ @@ -150,6 +151,7 @@ version versionsuffix toolchain ========= ================ =============== ``0.9.9`` ``gompi/2019b`` ``0.9.9`` ``-Perl-5.28.1`` ``gompi/2019a`` +``1.0.0`` ``gompi/2021a`` ========= ================ =============== @@ -162,11 +164,12 @@ abTEM provides a Python API for running simulations of Transmission Electron Mic *homepage*: https://github.com/jacobjma/abTEM -============ =============== ================== -version versionsuffix toolchain -============ =============== ================== -``1.0.0b24`` ``-ASE-3.22.0`` ``fosscuda/2020b`` -============ =============== ================== +============ =============== ================================== +version versionsuffix toolchain +============ =============== ================================== +``1.0.0b24`` ``-ASE-3.22.0`` ``fosscuda/2020b`` +``1.0.0b26`` ``-ASE-3.22.0`` ``foss/2020b``, ``fosscuda/2020b`` +============ =============== ================================== .. _list_software_ABySS_418: @@ -339,6 +342,7 @@ A small library for automatically adjustment of text position in matplotlib plot ========= ================= =============== version versionsuffix toolchain ========= ================= =============== +``0.7.3`` ``foss/2021b`` ``0.7.3`` ``-Python-3.6.6`` ``foss/2018b`` ``0.7.3`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================= =============== @@ -397,6 +401,7 @@ version toolchain ``2019_update3`` ``system`` ``2019_update5`` ``system`` ``2021.2.0`` ``system`` +``2021.4.0`` ``system`` ================ ========== @@ -597,6 +602,7 @@ version toolchain ========= ================================== ``2.0.0`` ``foss/2020b``, ``fosscuda/2020b`` ``2.0.1`` ``foss/2020b``, ``fosscuda/2020b`` +``2.1.1`` ``fosscuda/2020b`` ========= ================================== @@ -964,6 +970,22 @@ version toolchain ========= ====================================== +.. _list_software_ANIcalculator_1282: + +*ANIcalculator* ++++++++++++++++ + +This tool will calculate the bidirectional average nucleotide identity (gANI) and Alignment Fraction (AF) between two genomes. Required input is the full path to the fna file (nucleotide sequence of genes in fasta format) of each query genome. Either the rRNA and tRNA genes can be excluded, or provided in a list with the -ignoreList option. This is necessary as the presence of tRNA and/or rRNA genes in the fna will artificially inflate the ANI. + +*homepage*: https://ani.jgi.doe.gov/html/home.php + +======= ================== +version toolchain +======= ================== +``1.0`` ``GCCcore/10.3.0`` +======= ================== + + .. _list_software_Annif_492: *Annif* @@ -1084,6 +1106,7 @@ antiSMASH allows the rapid genome-wide identification, annotation and analysis o version versionsuffix toolchain ========= ================= ============== ``5.1.2`` ``-Python-3.7.4`` ``foss/2019b`` +``6.0.1`` ``foss/2020b`` ========= ================= ============== @@ -1100,7 +1123,7 @@ ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language to version versionsuffix toolchain ========= ================== ===================================================================================================== ``2.7.7`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b`` -``2.7.7`` ``-Java-11`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.7.7`` ``-Java-11`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.7.7`` ``-Python-2.7.11`` ``foss/2016a`` ``2.7.7`` ``-Python-2.7.13`` ``intel/2017a`` ``2.7.7`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` @@ -1153,12 +1176,12 @@ Convert various sequence formats to FASTA *homepage*: https://github.com/tseemann/any2fasta -========= ================ ======================================================== -version versionsuffix toolchain -========= ================ ======================================================== -``0.4.2`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.4.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -========= ================ ======================================================== +========= ================ ============================================================================ +version versionsuffix toolchain +========= ================ ============================================================================ +``0.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.4.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +========= ================ ============================================================================ .. _list_software_AOCC_278: @@ -1170,13 +1193,13 @@ AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0 *homepage*: https://developer.amd.com/amd-aocc/ -========= ====================================== -version toolchain -========= ====================================== -``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.0.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``3.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========= ====================================== +========= ========================================================== +version toolchain +========= ========================================================== +``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.0.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``3.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ========================================================== .. _list_software_AOMP_301: @@ -1268,12 +1291,13 @@ version toolchain a program to detect tRNA genes and tmRNA genes in nucleotide sequences -*homepage*: http://mbio-serv2.mbioekol.lu.se/ARAGORN/ +*homepage*: http://www.ansikte.se/ARAGORN/ ========== ======================================= version toolchain ========== ======================================= ``1.2.38`` ``foss/2016b``, ``iccifort/2019.5.281`` +``1.2.41`` ``foss/2021b`` ========== ======================================= @@ -1526,7 +1550,7 @@ version toolchain *Arrow* +++++++ -Apache Arrow is a cross-language development platform for in-memory data. +Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data. *homepage*: https://arrow.apache.org @@ -1539,23 +1563,26 @@ version versionsuffix toolchain ``0.16.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``0.17.1`` ``fosscuda/2020b``, ``intel/2020b`` ``0.17.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``6.0.0`` ``foss/2021a``, ``foss/2021b`` ========== ================== =================================== -.. _list_software_arrow_555: +.. _list_software_arrow-R_682: -*arrow* -+++++++ +*arrow-R* ++++++++++ R interface to the Apache Arrow C++ library *homepage*: https://cran.r-project.org/web/packages/arrow -========== ============= ============== -version versionsuffix toolchain -========== ============= ============== -``0.17.1`` ``-R-4.0.0`` ``foss/2020a`` -========== ============= ============== +=========== ============= ============== +version versionsuffix toolchain +=========== ============= ============== +``0.17.1`` ``-R-4.0.0`` ``foss/2020a`` +``6.0.0.2`` ``-R-4.1.0`` ``foss/2021a`` +``6.0.0.2`` ``-R-4.1.2`` ``foss/2021b`` +=========== ============= ============== .. _list_software_ART_231: @@ -1640,6 +1667,22 @@ version toolchain ========= ================= +.. _list_software_ASAP_293: + +*ASAP* +++++++ + +ASAP focuses on fast and fluid image viewing with an easy-to-use interface for making annotations. It consists of two main components: an IO library for reading and writing multi-resolution images and a viewer component for visualizing such images. + +*homepage*: https://computationalpathologygroup.github.io/ASAP/ + +======= ================ ============== +version versionsuffix toolchain +======= ================ ============== +``2.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +======= ================ ============== + + .. _list_software_ASAP3_344: *ASAP3* @@ -1673,35 +1716,35 @@ ASE is a python package providing an open source Atomic Simulation Environment *homepage*: https://wiki.fysik.dtu.dk/ase/ -============== ================== =================================================================== -version versionsuffix toolchain -============== ================== =================================================================== -``3.9.1.4567`` ``-Python-2.7.11`` ``intel/2016a`` -``3.10.0`` ``-Python-2.7.11`` ``intel/2016.02-GCC-4.9`` -``3.11.0`` ``-Python-2.7.12`` ``intel/2016b`` -``3.13.0`` ``-Python-2.7.12`` ``foss/2016b`` -``3.13.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.15.0`` ``-Python-2.7.12`` ``foss/2016b`` -``3.15.0`` ``-Python-2.7.14`` ``intel/2017b`` -``3.15.0`` ``-Python-3.5.2`` ``foss/2016b`` -``3.15.0`` ``-Python-3.6.2`` ``foss/2017b`` -``3.15.0`` ``-Python-3.6.3`` ``foss/2017b`` -``3.16.2`` ``-Python-3.6.4`` ``iomkl/2018.02``, ``iomkl/2018a`` -``3.16.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.17.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.17.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.18.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.18.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``3.19.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``3.20.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``3.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``3.20.1`` ``-Python-3.8.2`` ``intel/2020a`` -``3.21.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``3.21.1`` ``-Python-3.8.2`` ``foss/2020a`` -``3.22.0`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b``, ``intel/2020b`` -============== ================== =================================================================== +============== ================== ==================================================================================== +version versionsuffix toolchain +============== ================== ==================================================================================== +``3.9.1.4567`` ``-Python-2.7.11`` ``intel/2016a`` +``3.10.0`` ``-Python-2.7.11`` ``intel/2016.02-GCC-4.9`` +``3.11.0`` ``-Python-2.7.12`` ``intel/2016b`` +``3.13.0`` ``-Python-2.7.12`` ``foss/2016b`` +``3.13.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.15.0`` ``-Python-2.7.12`` ``foss/2016b`` +``3.15.0`` ``-Python-2.7.14`` ``intel/2017b`` +``3.15.0`` ``-Python-3.5.2`` ``foss/2016b`` +``3.15.0`` ``-Python-3.6.2`` ``foss/2017b`` +``3.15.0`` ``-Python-3.6.3`` ``foss/2017b`` +``3.16.2`` ``-Python-3.6.4`` ``iomkl/2018.02``, ``iomkl/2018a`` +``3.16.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``3.17.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``3.17.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.18.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.18.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``3.19.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``3.20.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``3.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.20.1`` ``-Python-3.8.2`` ``intel/2020a`` +``3.21.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``3.21.1`` ``-Python-3.8.2`` ``foss/2020a`` +``3.22.0`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021a`` +============== ================== ==================================================================================== .. _list_software_ASHS_303: @@ -1820,6 +1863,7 @@ version versionsuffix toolchain ``4.0.1`` ``-Python-3.7.4`` ``foss/2019b`` ``4.0.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``4.2.1`` ``intelcuda/2020b`` +``4.3.1`` ``foss/2021a``, ``intel/2021a`` ========== ================== =============================== @@ -2267,7 +2311,23 @@ version versionsuffix toolchain --- -:ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` +:ref:`list_software_BabelStream_1090` - :ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_bamtofastq_1074` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_bcbio-gff_863` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biom-format_1117` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_Blosc2_549` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_boto3_487` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_Brotli-python_1339` - :ref:`list_software_Brunsli_735` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` + + +.. _list_software_BabelStream_1090: + +*BabelStream* ++++++++++++++ + +STREAM, for lots of devices written in many programming models + +*homepage*: https://uob-hpc.github.io/BabelStream + +======= ============= ============== +version versionsuffix toolchain +======= ============= ============== +``3.4`` ``-omp`` ``GCC/11.2.0`` +======= ============= ============== .. _list_software_babl_401: @@ -2400,6 +2460,22 @@ version versionsuffix toolchain ======= ================== ============= +.. _list_software_bamtofastq_1074: + +*bamtofastq* +++++++++++++ + +Convert 10x BAM files to the original FASTQs compatible with 10x pipelines. + +*homepage*: https://github.com/10XGenomics/bamtofastq + +========= ================== +version toolchain +========= ================== +``1.4.0`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_BamTools_801: *BamTools* @@ -2416,7 +2492,7 @@ version toolchain ``2.4.1`` ``intel/2017a`` ``2.5.0`` ``foss/2016b``, ``intel/2017b`` ``2.5.1`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018b`` -``2.5.2`` ``GCC/10.3.0`` +``2.5.2`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========= ================================================================================================================================================================================================================================================ @@ -2740,6 +2816,23 @@ version toolchain ========= ============== +.. _list_software_bcbio-gff_863: + +*bcbio-gff* ++++++++++++ + +Read and write Generic Feature Format (GFF) with Biopython integration. + +*homepage*: https://github.com/chapmanb/bcbb/tree/master/gff + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.6.6`` ``-Python-3.8.2`` ``foss/2020a`` +``0.6.7`` ``foss/2021a`` +========= ================= ============== + + .. _list_software_BCEL_278: *BCEL* @@ -2777,6 +2870,7 @@ version toolchain ``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ``1.11`` ``GCC/10.2.0`` ``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` +``1.14`` ``GCC/11.2.0`` ========== ========================================================================================= @@ -2905,16 +2999,17 @@ Beautiful Soup is a Python library designed for quick turnaround projects like s *homepage*: https://www.crummy.com/software/BeautifulSoup -========= ================= ================= -version versionsuffix toolchain -========= ================= ================= -``4.6.0`` ``-Python-3.6.3`` ``intel/2017b`` -``4.6.3`` ``-Python-3.6.4`` ``intel/2018a`` -``4.7.1`` ``-Python-3.6.6`` ``intel/2018b`` -``4.8.0`` ``GCCcore/8.2.0`` -``4.9.1`` ``GCCcore/8.3.0`` -``4.9.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -========= ================= ================= +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``4.6.0`` ``-Python-3.6.3`` ``intel/2017b`` +``4.6.3`` ``-Python-3.6.4`` ``intel/2018a`` +``4.7.1`` ``-Python-3.6.6`` ``intel/2018b`` +``4.8.0`` ``GCCcore/8.2.0`` +``4.9.1`` ``GCCcore/8.3.0`` +``4.9.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``4.9.3`` ``GCCcore/10.2.0`` +========= ================= ================== .. _list_software_BEDOPS_445: @@ -2956,7 +3051,7 @@ version toolchain ``2.27.1`` ``GCCcore/6.4.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` ``2.28.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.29.2`` ``GCC/8.3.0``, ``GCC/9.3.0`` -``2.30.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` +``2.30.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304`` ========== ==================================================================================== @@ -3010,7 +3105,7 @@ version versionsuffix toolchain ``1.2.0`` ``intel/2017a``, ``intel/2018a`` ``2.0.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``3.0.1`` ``foss/2021a`` +``3.0.1`` ``foss/2020b``, ``foss/2021a`` ============= ================= ================================================================ @@ -3217,11 +3312,11 @@ Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with *homepage*: https://metacpan.org/pod/Bio::SearchIO::hmmer3 -========= ============== -version toolchain -========= ============== -``1.7.3`` ``GCC/10.2.0`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``1.7.3`` ``GCC/10.2.0``, ``GCC/10.3.0`` +========= ============================== .. _list_software_bioawk_637: @@ -3273,6 +3368,22 @@ version toolchain ========= ============== +.. _list_software_biom-format_1117: + +*biom-format* ++++++++++++++ + +The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project. + +*homepage*: https://biom-format.org + +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``2.1.10`` ``-Python-3.8.2`` ``foss/2020a`` +========== ================= ============== + + .. _list_software_biomart-perl_1230: *biomart-perl* @@ -3363,7 +3474,7 @@ version versionsuffix toolchain ``1.76`` ``-Python-2.7.18`` ``foss/2020b`` ``1.78`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.78`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.79`` ``foss/2021a`` +``1.79`` ``foss/2021a``, ``foss/2021b`` ======== ================== =================================================== @@ -3685,9 +3796,26 @@ version toolchain ``1.17.0`` ``GCCcore/8.2.0`` ``1.17.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.21.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.21.1`` ``GCCcore/11.2.0`` ========== ================================================================== +.. _list_software_Blosc2_549: + +*Blosc2* +++++++++ + +Blosc, an extremely fast, multi-threaded, meta-compressor library + +*homepage*: https://www.blosc.org/ + +========= ================== +version toolchain +========= ================== +``2.0.3`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_bmtagger_841: *bmtagger* @@ -3887,6 +4015,7 @@ version versionsuffix toolchain ``1.72.0`` ``-no_mpi`` ``GCCcore/9.3.0`` ``1.74.0`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` ``1.76.0`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` +``1.77.0`` ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` ========== ================== ==================================================================== @@ -3916,6 +4045,22 @@ version versionsuffix toolchain ========== ================== ==================================================================== +.. _list_software_boto3_487: + +*boto3* ++++++++ + +Boto3 is the Amazon Web Services (AWS) Software Development Kit (SDK) for Python, which allows Python developers to write software that makes use of services like Amazon S3 and Amazon EC2. + +*homepage*: https://github.com/boto/boto3 + +=========== ================== +version toolchain +=========== ================== +``1.20.13`` ``GCCcore/11.2.0`` +=========== ================== + + .. _list_software_Bottleneck_1035: *Bottleneck* @@ -4005,11 +4150,12 @@ The aim of this project is to implement a versatile high-performance version of *homepage*: https://github.com/bpp/bpp -========= ============= -version toolchain -========= ============= -``4.3.8`` ``GCC/8.3.0`` -========= ============= +========= ============== +version toolchain +========= ============== +``4.3.8`` ``GCC/8.3.0`` +``4.4.0`` ``GCC/10.3.0`` +========= ============== .. _list_software_bpytop_670: @@ -4038,11 +4184,12 @@ Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate s *homepage*: https://ccb.jhu.edu/software/bracken/ -========= ================= -version toolchain -========= ================= -``2.6.0`` ``GCCcore/9.3.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``2.6.0`` ``GCCcore/9.3.0`` +``2.6.2`` ``GCCcore/11.2.0`` +========= ================== .. _list_software_BRAKER_439: @@ -4111,6 +4258,38 @@ version toolchain ========= ============================================================================= +.. _list_software_Brotli-python_1339: + +*Brotli-python* ++++++++++++++++ + +Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932. + +*homepage*: https://github.com/google/brotli + +========= ================== +version toolchain +========= ================== +``1.0.9`` ``GCCcore/10.3.0`` +========= ================== + + +.. _list_software_Brunsli_735: + +*Brunsli* ++++++++++ + +Brunsli is a lossless JPEG repacking library. + +*homepage*: https://github.com/google/brunsli/ + +======= ================== +version toolchain +======= ================== +``0.1`` ``GCCcore/10.2.0`` +======= ================== + + .. _list_software_bsddb3_562: *bsddb3* @@ -4289,15 +4468,15 @@ Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively sh *homepage*: http://bio-bwa.sourceforge.net/ -=========== ================================================================================================================================================================================================================================================================= -version toolchain -=========== ================================================================================================================================================================================================================================================================= -``0.7.12`` ``foss/2016b`` -``0.7.13`` ``foss/2016a``, ``intel/2016a`` -``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``0.7.16a`` ``foss/2016b``, ``intel/2017a`` -``0.7.17`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -=========== ================================================================================================================================================================================================================================================================= +=========== ================================================================================================================================================================================================================================================================================= +version toolchain +=========== ================================================================================================================================================================================================================================================================================= +``0.7.12`` ``foss/2016b`` +``0.7.13`` ``foss/2016a``, ``intel/2016a`` +``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``0.7.16a`` ``foss/2016b``, ``intel/2017a`` +``0.7.17`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +=========== ================================================================================================================================================================================================================================================================================= .. _list_software_bwa-meth_789: @@ -4461,7 +4640,7 @@ version toolchain --- -:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_c-ares_571: @@ -4721,12 +4900,14 @@ Cap’n Proto is an insanely fast data interchange format and capability-based R *homepage*: https://capnproto.org -========= ================= -version toolchain -========= ================= -``0.6.1`` ``GCCcore/6.4.0`` -``0.7.0`` ``GCCcore/7.3.0`` -========= ================= +========= ====================================== +version toolchain +========= ====================================== +``0.6.1`` ``GCCcore/6.4.0`` +``0.7.0`` ``GCCcore/7.3.0`` +``0.8.0`` ``GCCcore/9.3.0`` +``0.9.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_Cargo_492: @@ -5210,6 +5391,8 @@ version toolchain ``5.0.1`` ``system`` ``6.0.0`` ``system`` ``6.0.1`` ``system`` +``6.0.2`` ``system`` +``6.1.2`` ``system`` ========= ========== @@ -5347,6 +5530,7 @@ version toolchain ``3.45`` ``GCCcore/7.3.0``, ``intel/2018b`` ``3.47`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.48`` ``GCCcore/9.3.0`` +``3.49`` ``GCCcore/10.2.0`` ======== ===================================================== @@ -5583,6 +5767,7 @@ version versionsuffix toolchain ``1.0.18`` ``-Python-2.7.15`` ``foss/2019a`` ``1.0.18`` ``-Python-2.7.18`` ``foss/2020b`` ``1.1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.1.3`` ``foss/2021a`` ``1.1.3`` ``-Python-3.8.2`` ``intel/2020a`` ========== ================== =============================== @@ -5913,6 +6098,22 @@ version versionsuffix toolchain ========== ================== ====================================== +.. _list_software_Clang-AOMP_831: + +*Clang-AOMP* +++++++++++++ + +AOMP is an open source Clang/LLVM based compiler with added support for the OpenMP® API on Radeon™ GPUs. + +*homepage*: https://github.com/RadeonOpenCompute/llvm-project + +========= ================== +version toolchain +========= ================== +``4.5.0`` ``GCCcore/11.2.0`` +========= ================== + + .. _list_software_Clang-Python-bindings_2063: *Clang-Python-bindings* @@ -5946,6 +6147,22 @@ version toolchain ========= =========================================================================== +.. _list_software_CLEASE_429: + +*CLEASE* +++++++++ + +CLuster Expansion in Atomic Simulation Environment (CLEASE) is a package that automates the cumbersome setup and construction procedure of cluster expansion (CE). It provides a comprehensive list of tools for specifying parameters for CE, generating training structures, fitting effective cluster interaction (ECI) values and running Monte Carlo simulations. + +*homepage*: https://gitlab.com/computationalmaterials/clease + +========== =============== +version toolchain +========== =============== +``0.10.6`` ``intel/2021a`` +========== =============== + + .. _list_software_CLHEP_364: *CLHEP* @@ -6152,6 +6369,22 @@ version toolchain ========== ================================================================================================================================================= +.. _list_software_CMSeq_441: + +*CMSeq* ++++++++ + +CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus. + +*homepage*: https://github.com/SegataLab/cmseq/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.0.3`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_CNT-ILP_503: *CNT-ILP* @@ -6511,7 +6744,7 @@ version toolchain *Coreutils* +++++++++++ -The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system. +The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system. *homepage*: https://www.gnu.org/software/coreutils/ @@ -6522,6 +6755,7 @@ version toolchain ``8.27`` ``GCCcore/5.4.0`` ``8.29`` ``GCCcore/6.4.0`` ``8.32`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``9.0`` ``GCCcore/11.2.0`` ======== ==================================== @@ -6584,20 +6818,20 @@ CP2K is a freely available (GPL) program, written in Fortran 95, to perform atom *homepage*: https://www.cp2k.org/ -======= ============= ================================================================================= -version versionsuffix toolchain -======= ============= ================================================================================= -``3.0`` ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` -``3.0`` ``-psmp`` ``intel/2016b`` -``4.1`` ``intel/2016b`` -``4.1`` ``-psmp`` ``foss/2016b`` -``5.1`` ``foss/2018a``, ``foss/2020a``, ``intel/2017b``, ``intel/2018a``, ``intel/2020a`` -``6.1`` ``foss/2019a``, ``intel/2018a``, ``intel/2020a`` -``7.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` -``7.1`` ``-psmp`` ``foss/2020b`` -``8.1`` ``foss/2020b`` -``8.2`` ``foss/2021a`` -======= ============= ================================================================================= +======= ============= ================================================================================================= +version versionsuffix toolchain +======= ============= ================================================================================================= +``3.0`` ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` +``3.0`` ``-psmp`` ``intel/2016b`` +``4.1`` ``intel/2016b`` +``4.1`` ``-psmp`` ``foss/2016b`` +``5.1`` ``foss/2018a``, ``foss/2020a``, ``foss/2020b``, ``intel/2017b``, ``intel/2018a``, ``intel/2020a`` +``6.1`` ``foss/2019a``, ``intel/2018a``, ``intel/2020a`` +``7.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` +``7.1`` ``-psmp`` ``foss/2020b`` +``8.1`` ``foss/2020b`` +``8.2`` ``foss/2021a`` +======= ============= ================================================================================================= .. _list_software_CPB_213: @@ -6659,10 +6893,26 @@ A small C++ header library which makes it easier to write Python extension modul *homepage*: https://github.com/nucleic/cppy +========= ====================================== +version toolchain +========= ====================================== +``1.1.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== + + +.. _list_software_cpu_features_1286: + +*cpu_features* +++++++++++++++ + +A cross-platform C library to retrieve CPU features (such as available instructions) at runtime. + +*homepage*: https://github.com/google/cpu_features + ========= ================== version toolchain ========= ================== -``1.1.0`` ``GCCcore/10.3.0`` +``0.6.0`` ``GCCcore/10.2.0`` ========= ================== @@ -6846,6 +7096,22 @@ version versionsuffix toolchain ========== ================== ============== +.. _list_software_cromwell_869: + +*cromwell* +++++++++++ + +Cromwell is a Workflow Management System geared towards scientific workflows. + +*homepage*: http://cromwell.readthedocs.io/ + +======= ============= ========== +version versionsuffix toolchain +======= ============= ========== +``56`` ``-Java-11`` ``system`` +======= ============= ========== + + .. _list_software_CrossMap_808: *CrossMap* @@ -7143,6 +7409,7 @@ version toolchain ``11.3.1`` ``system`` ``11.4.1`` ``system`` ``11.4.2`` ``system`` +``11.5.0`` ``system`` ================= ========================================================================== @@ -7367,11 +7634,11 @@ CVS is a version control system, an important component of Source Configuration *homepage*: https://savannah.nongnu.org/projects/cvs -=========== =================================================== -version toolchain -=========== =================================================== -``1.11.23`` ``GCC/4.8.2``, ``GCCcore/4.9.3``, ``GCCcore/6.4.0`` -=========== =================================================== +=========== ======================================================================= +version toolchain +=========== ======================================================================= +``1.11.23`` ``GCC/4.8.2``, ``GCCcore/11.2.0``, ``GCCcore/4.9.3``, ``GCCcore/6.4.0`` +=========== ======================================================================= .. _list_software_CVXOPT_484: @@ -7411,6 +7678,22 @@ version versionsuffix toolchain ========== ================= ============== +.. _list_software_cxxopts_793: + +*cxxopts* ++++++++++ + +cxxopts is a lightweight C++ command line option parser + +*homepage*: https://github.com/jarro2783/cxxopts + +========= ========== +version toolchain +========= ========== +``3.0.0`` ``system`` +========= ========== + + .. _list_software_cysignals_973: *cysignals* @@ -7507,7 +7790,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_dxpy_453` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dRep_395` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_DUBStepR_713` - :ref:`list_software_dxpy_453` .. _list_software_dadi_402: @@ -8049,7 +8332,7 @@ version versionsuffix toolchain ========= ================== ======================================================================== ``4.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2019a`` ``4.4.0`` ``-Python-2.7.15`` ``intel/2018b`` -``4.5.2`` ``GCCcore/10.2.0`` +``4.5.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``4.5.2`` ``-Python-2.7.18`` ``GCCcore/10.2.0`` ========= ================== ======================================================================== @@ -8238,6 +8521,7 @@ Python library for converting dicom files to nifti version versionsuffix toolchain ========== ================= ============== ``2.2.12`` ``-Python-3.8.2`` ``foss/2020a`` +``2.3.0`` ``foss/2020b`` ========== ================= ============== @@ -8619,6 +8903,22 @@ version versionsuffix toolchain ========= ============= ========== +.. _list_software_dRep_395: + +*dRep* +++++++ + +dRep is a python program which performs rapid pair-wise comparison of genome sets. One of it’s major purposes is for genome de-replication, but it can do a lot more. + +*homepage*: https://drep.readthedocs.io/en/latest/ + +========= ============== +version toolchain +========= ============== +``3.0.0`` ``foss/2021a`` +========= ============== + + .. _list_software_DROP_309: *DROP* @@ -8751,6 +9051,22 @@ version versionsuffix toolchain ========== ================== =============== +.. _list_software_DUBStepR_713: + +*DUBStepR* +++++++++++ + +DUBStepR (Determining the Underlying Basis using Step-wise Regression) is a feature selection algorithm for cell type identification in single-cell RNA-sequencing data. + +*homepage*: https://github.com/prabhakarlab/DUBStepR + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``1.2.0`` ``-R-4.1.2`` ``foss/2021b`` +========= ============= ============== + + .. _list_software_dxpy_453: *dxpy* @@ -8773,7 +9089,7 @@ version versionsuffix toolchain --- -:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_ELSI_301` - :ref:`list_software_ELSI-RCI_568` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESL-Bundle_875` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Excel-Writer-XLSX_1559` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_expecttest_1097` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_eht-imaging_1098` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_einops_654` - :ref:`list_software_elastix_762` - :ref:`list_software_ELFIO_367` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_elprep_648` - :ref:`list_software_ELSI_301` - :ref:`list_software_ELSI-RCI_568` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_epiScanpy_940` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESL-Bundle_875` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Excel-Writer-XLSX_1559` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_expecttest_1097` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_E-ANTIC_481: @@ -8921,6 +9237,7 @@ version toolchain ``4.4.0`` ``system`` ``4.4.1`` ``system`` ``4.4.2`` ``system`` +``4.5.0`` ``system`` ========== ========== @@ -9015,7 +9332,7 @@ version versionsuffix toolchain ``1.3.8.post1`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ``1.3.8.post1`` ``-Python-3.8.2`` ``GCC/9.3.0`` ``1.3.8.post2`` ``-Python-3.8.2`` ``iccifort/2020.1.217`` -``1.3.9`` ``GCC/10.2.0`` +``1.3.9`` ``GCC/10.2.0``, ``GCC/10.3.0`` =============== ================= ====================================== @@ -9052,6 +9369,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_eht-imaging_1098: + +*eht-imaging* ++++++++++++++ + +Python modules for simulating and manipulating VLBI data and producing images with regularized maximum likelihood methods. + +*homepage*: https://github.com/achael/eht-imaging + +========= ============== +version toolchain +========= ============== +``1.2.2`` ``foss/2021a`` +========= ============== + + .. _list_software_Eigen_488: *Eigen* @@ -9078,6 +9411,7 @@ version toolchain ``3.3.7`` ``GCCcore/9.3.0``, ``system`` ``3.3.8`` ``GCCcore/10.2.0`` ``3.3.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``3.4.0`` ``GCCcore/10.2.0`` ========== ========================================================== @@ -9100,6 +9434,22 @@ version toolchain ========= =============================================================== +.. _list_software_einops_654: + +*einops* +++++++++ + +Flexible and powerful tensor operations for readable and reliable code. Supports numpy, pytorch, tensorflow, jax, and others. + +*homepage*: https://einops.rocks/ + +========= ================== +version toolchain +========= ================== +``0.3.2`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_elastix_762: *elastix* @@ -9116,6 +9466,22 @@ version toolchain ========= ============== +.. _list_software_ELFIO_367: + +*ELFIO* ++++++++ + +ELFIO is a header-only C++ library intended for reading and generating files in the ELF binary format. + +*homepage*: http://elfio.sourceforge.net + +======= ========== +version toolchain +======= ========== +``3.9`` ``system`` +======= ========== + + .. _list_software_elfutils_872: *elfutils* @@ -9195,6 +9561,22 @@ version toolchain ========= ============== +.. _list_software_elprep_648: + +*elprep* +++++++++ + +elPrep is a high-performance tool for analyzing .sam/.bam files (up to and including variant calling) in sequencing pipelines. + +*homepage*: https://github.com/ExaScience/elprep + +========= ========== +version toolchain +========= ========== +``5.1.1`` ``system`` +========= ========== + + .. _list_software_ELSI_301: *ELSI* @@ -9333,11 +9715,12 @@ enaBrowserTools is a set of scripts that interface with the ENA web services to *homepage*: https://github.com/enasequence/enaBrowserTools/ -========= ================= ================= -version versionsuffix toolchain -========= ================= ================= -``1.5.4`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -========= ================= ================= +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``1.5.4`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``1.6`` ``GCCcore/10.3.0`` +========= ================= ================== .. _list_software_enchant_737: @@ -9423,6 +9806,22 @@ version versionsuffix toolchain ======= ============= ============== +.. _list_software_epiScanpy_940: + +*epiScanpy* ++++++++++++ + +EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq analysis tool Scanpy (Genome Biology, 2018) [Wolf18]. + +*homepage*: https://github.com/colomemaria/episcanpy + +========= ============== +version toolchain +========= ============== +``0.3.1`` ``foss/2021a`` +========= ============== + + .. _list_software_EricScript_1016: *EricScript* @@ -9475,6 +9874,7 @@ version versionsuffix toolchain ``8.0.0`` ``foss/2019b``, ``intel/2019b`` ``8.0.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` ``8.1.1`` ``foss/2021a``, ``intel/2021a`` +``8.2.0`` ``foss/2021b``, ``intel/2021b`` ============ ================ ================================================================================= @@ -9804,7 +10204,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -9946,11 +10346,11 @@ Utilities for indexing and sequence extraction from FASTA files. *homepage*: https://github.com/ekg/fastahack -========= ===================================== -version toolchain -========= ===================================== -``1.0.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========= ===================================== +========= ========================================================= +version toolchain +========= ========================================================= +``1.0.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +========= ========================================================= .. _list_software_FastaIndex_999: @@ -9985,7 +10385,7 @@ version toolchain ``1.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``1.3`` ``iccifort/2019.5.281`` ``1.31`` ``iccifort/2020.1.217`` -``1.33`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``1.33`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` ======== ============================================================== @@ -10794,12 +11194,12 @@ filevercmp function as in sort --version-sort. *homepage*: https://github.com/ekg/filevercmp -============ ================== -version toolchain -============ ================== -``20141119`` ``GCCcore/9.3.0`` -``20191210`` ``GCCcore/10.2.0`` -============ ================== +============ ====================================== +version toolchain +============ ====================================== +``20141119`` ``GCCcore/9.3.0`` +``20191210`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +============ ====================================== .. _list_software_Filtlong_831: @@ -11322,16 +11722,17 @@ Flye is a de novo assembler for long and noisy reads, such as those produced by *homepage*: https://github.com/fenderglass/Flye -========= ================== ======================================= -version versionsuffix toolchain -========= ================== ======================================= -``2.4`` ``-Python-2.7.15`` ``intel/2018b`` -``2.6`` ``-Python-3.7.2`` ``foss/2019a`` -``2.6`` ``-Python-3.7.4`` ``intel/2019b`` -``2.8.1`` ``-Python-3.8.2`` ``intel/2020a`` -``2.8.2`` ``-Python-3.8.2`` ``foss/2020a`` -``2.8.3`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -========= ================== ======================================= +========= ================== ============================================ +version versionsuffix toolchain +========= ================== ============================================ +``2.4`` ``-Python-2.7.15`` ``intel/2018b`` +``2.6`` ``-Python-3.7.2`` ``foss/2019a`` +``2.6`` ``-Python-3.7.4`` ``intel/2019b`` +``2.8.1`` ``-Python-3.8.2`` ``intel/2020a`` +``2.8.2`` ``-Python-3.8.2`` ``foss/2020a`` +``2.8.3`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``2.9`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` +========= ================== ============================================ .. _list_software_FMILibrary_945: @@ -11350,6 +11751,22 @@ version toolchain ========= =============== +.. _list_software_FMM3D_343: + +*FMM3D* ++++++++ + +Flatiron Institute Fast Multipole Libraries: a set of libraries to compute N-body interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a multi-core shared-memory machine. + +*homepage*: https://fmm3d.readthedocs.io + +============ ============== +version toolchain +============ ============== +``20211018`` ``foss/2020b`` +============ ============== + + .. _list_software_FMRIprep_741: *FMRIprep* @@ -11363,6 +11780,7 @@ FMRIprep is a functional magnetic resonance imaging (fMRI) data preprocessing pi version versionsuffix toolchain ========= ================= ============== ``1.1.8`` ``-Python-3.6.6`` ``foss/2018b`` +``1.4.1`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== @@ -11447,6 +11865,22 @@ version toolchain ========= ================================================= +.. _list_software_FORD_299: + +*FORD* +++++++ + +FORD is an automatic documentation generator for modern Fortran programs + +*homepage*: https://github.com/Fortran-FOSS-Programmers/ford/wiki + +========= ================== +version toolchain +========= ================== +``6.1.1`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_foss_443: *foss* @@ -11679,7 +12113,7 @@ version versionsuffix toolchain ========= ================ ====================================================================================================================================================================================== ``3.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` -``3.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``3.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ================ ====================================================================================================================================================================================== @@ -11908,6 +12342,7 @@ version versionsuffix toolchain ``6.0.2`` ``-Python-2.7.15-CUDA-9.2.88`` ``foss/2018b`` ``6.0.2`` ``-Python-3.7.2`` ``foss/2019a`` ``6.0.3`` ``-Python-3.7.4`` ``foss/2019b`` +``6.0.4`` ``-Python-3.7.4`` ``foss/2019b`` ========== ============================== ================================================ @@ -11936,11 +12371,11 @@ A tiny C library for managing SOM (Self-Organizing Maps) neural networks. *homepage*: https://github.com/ekg/fsom -============ ===================================== -version toolchain -============ ===================================== -``20141119`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -============ ===================================== +============ ========================================================= +version toolchain +============ ========================================================= +``20141119`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +============ ========================================================= .. _list_software_FTGL_301: @@ -12148,7 +12583,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPy_272` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -12164,7 +12599,7 @@ Library contains GRIB2 encoder/decoder ('C' version). version toolchain ========= ======================================================================================================================== ``1.6.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``1.6.3`` ``GCCcore/10.3.0`` +``1.6.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ======================================================================================================================== @@ -12422,6 +12857,7 @@ version versionsuffix toolchain ``4.1.8.1`` ``-Java-1.8`` ``GCCcore/9.3.0`` ``4.2.0.0`` ``-Java-1.8`` ``GCCcore/10.2.0`` ``4.2.0.0`` ``-Java-11`` ``GCCcore/10.2.0`` +``4.2.3.0`` ``-Java-11`` ``GCCcore/11.2.0`` ============ =================== ================== @@ -12455,6 +12891,7 @@ The awk utility interprets a special-purpose programming language that makes it version toolchain ========= ============== ``5.1.0`` ``GCC/10.2.0`` +``5.1.1`` ``GCC/10.3.0`` ========= ============== @@ -12511,7 +12948,7 @@ version versionsuffix toolchain *gc* ++++ -The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. +The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. *homepage*: https://hboehm.info/gc/ @@ -12524,6 +12961,7 @@ version toolchain ``7.6.10`` ``GCCcore/8.2.0`` ``7.6.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``8.0.4`` ``GCCcore/10.3.0`` +``8.2.0`` ``GCCcore/11.2.0`` ========== ==================================== @@ -12804,6 +13242,7 @@ version versionsuffix toolchain ``10.1`` ``GCCcore/10.2.0`` ``10.2`` ``GCCcore/10.3.0`` ``10.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``11.1`` ``GCCcore/11.2.0`` ========== ================== =============================== @@ -13797,6 +14236,7 @@ version versionsuffix toolchain ``2.23.0`` ``-nodocs`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.28.0`` ``-nodocs`` ``GCCcore/10.2.0`` ``2.32.0`` ``-nodocs`` ``GCCcore/10.3.0`` +``2.33.1`` ``-nodocs`` ``GCCcore/11.2.0`` =========== ============= ==================================== @@ -13853,6 +14293,7 @@ version versionsuffix toolchain ``3.1.9`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``3.1.14`` ``GCCcore/10.2.0`` ``3.1.18`` ``GCCcore/10.3.0`` +``3.1.24`` ``GCCcore/11.2.0`` ========== ================= =============================== @@ -13903,7 +14344,7 @@ version versionsuffix toolchain ``1.3.9`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.3.9`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` ``1.4.0`` ``GCCcore/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``1.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``1.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ========= ================ ==================================================================================================================================== @@ -14073,7 +14514,7 @@ GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. Alt version toolchain ========== ============================== ``3.0.4`` ``foss/2016b``, ``foss/2018b`` -``3.0.4c`` ``GCC/8.3.0`` +``3.0.4c`` ``GCC/10.2.0``, ``GCC/8.3.0`` ========== ============================== @@ -14086,14 +14527,14 @@ OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics s *homepage*: https://github.com/g-truc/glm -=========== ========================================================= -version toolchain -=========== ========================================================= -``0.9.7.6`` ``intel/2016a`` -``0.9.8.3`` ``GCCcore/5.4.0``, ``GCCcore/7.3.0`` -``0.9.9.0`` ``GCCcore/6.4.0`` -``0.9.9.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0`` -=========== ========================================================= +=========== ============================================================================= +version toolchain +=========== ============================================================================= +``0.9.7.6`` ``intel/2016a`` +``0.9.8.3`` ``GCCcore/5.4.0``, ``GCCcore/7.3.0`` +``0.9.9.0`` ``GCCcore/6.4.0`` +``0.9.9.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` +=========== ============================================================================= .. _list_software_GlobalArrays_1219: @@ -14308,17 +14749,18 @@ GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x *homepage*: https://github.com/aleaxit/gmpy -=========== ================== ====================================================================== -version versionsuffix toolchain -=========== ================== ====================================================================== -``2.0.8`` ``-Python-2.7.13`` ``intel/2017a`` -``2.0.8`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.0.8`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b4`` ``GCC/8.3.0`` -``2.1.0b5`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` -=========== ================== ====================================================================== +============ ================== ====================================================================== +version versionsuffix toolchain +============ ================== ====================================================================== +``2.0.8`` ``-Python-2.7.13`` ``intel/2017a`` +``2.0.8`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2.0.8`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b4`` ``GCC/8.3.0`` +``2.1.0b5`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` +``2.1.0rc1`` ``GCC/11.2.0`` +============ ================== ====================================================================== .. _list_software_gmsh_431: @@ -14483,6 +14925,7 @@ version toolchain ``1.16.3`` ``system`` ``1.16.5`` ``system`` ``1.16.6`` ``system`` +``1.17.3`` ``system`` ========== ================= @@ -14858,6 +15301,22 @@ version versionsuffix toolchain ========= ================== ===================================== +.. _list_software_GPy_272: + +*GPy* ++++++ + +GPy is a Gaussian Process (GP) framework written in Python + +*homepage*: https://sheffieldml.github.io/GPy + +========== ============== +version toolchain +========== ============== +``1.10.0`` ``foss/2021b`` +========== ============== + + .. _list_software_GPyOpt_579: *GPyOpt* @@ -14902,26 +15361,11 @@ Grace is a WYSIWYG tool to make two-dimensional plots of numerical data. ========== ============= ================================================================================================================= version versionsuffix toolchain ========== ============= ================================================================================================================= +``5.1.25`` ``foss/2016a``, ``foss/2021a``, ``intel/2016a`` ``5.1.25`` ``-5build1`` ``foss/2017b``, ``foss/2018a``, ``foss/2019a``, ``foss/2019b``, ``intel/2017b``, ``intel/2019a``, ``intel/2019b`` ========== ============= ================================================================================================================= -.. _list_software_grace_514: - -*grace* -+++++++ - -Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. - -*homepage*: http://freecode.com/projects/grace - -========== =============================== -version toolchain -========== =============================== -``5.1.25`` ``foss/2016a``, ``intel/2016a`` -========== =============================== - - .. _list_software_Gradle_591: *Gradle* @@ -15000,16 +15444,16 @@ GraphicsMagick is the swiss army knife of image processing. *homepage*: https://www.graphicsmagick.org/ -========== ================================ -version toolchain -========== ================================ -``1.3.23`` ``foss/2016a``, ``intel/2016a`` -``1.3.25`` ``intel/2016b``, ``intel/2017a`` -``1.3.28`` ``foss/2018a`` -``1.3.31`` ``foss/2018b`` -``1.3.34`` ``foss/2019a``, ``foss/2019b`` -``1.3.36`` ``foss/2020b`` -========== ================================ +========== ================================== +version toolchain +========== ================================== +``1.3.23`` ``foss/2016a``, ``intel/2016a`` +``1.3.25`` ``intel/2016b``, ``intel/2017a`` +``1.3.28`` ``foss/2018a`` +``1.3.31`` ``foss/2018b`` +``1.3.34`` ``foss/2019a``, ``foss/2019b`` +``1.3.36`` ``GCCcore/11.2.0``, ``foss/2020b`` +========== ================================== .. _list_software_graphite2_902: @@ -15278,42 +15722,43 @@ GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the *homepage*: http://www.gromacs.org -========== ================= ============================================================================================================ -version versionsuffix toolchain -========== ================= ============================================================================================================ -``5.1.2`` ``-hybrid`` ``foss/2016a``, ``intel/2016a`` -``5.1.2`` ``-hybrid-dp`` ``intel/2016a`` -``5.1.2`` ``-mt`` ``foss/2016a`` -``5.1.4`` ``-hybrid`` ``foss/2016b`` -``5.1.4`` ``-mt`` ``foss/2016b`` -``2016`` ``-hybrid`` ``foss/2016b`` -``2016`` ``-mt`` ``foss/2016b`` -``2016.1`` ``-PLUMED`` ``foss/2017a`` -``2016.2`` ``foss/2017a`` -``2016.3`` ``foss/2017a``, ``intel/2017a`` -``2016.3`` ``-GPU-enabled`` ``foss/2016b`` -``2016.4`` ``foss/2017b``, ``fosscuda/2017b``, ``giolf/2017b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` -``2016.5`` ``intel/2018a`` -``2018`` ``foss/2018a`` -``2018.1`` ``-PLUMED`` ``foss/2018b`` -``2018.2`` ``foss/2017b``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018b``, ``intel/2017b``, ``intelcuda/2017b`` -``2018.3`` ``foss/2018b``, ``fosscuda/2018b`` -``2018.4`` ``-PLUMED-2.5.0`` ``foss/2018b``, ``fosscuda/2018b`` -``2019`` ``foss/2018b``, ``fosscuda/2018b`` -``2019.2`` ``fosscuda/2019a`` -``2019.3`` ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019a``, ``fosscuda/2019b`` -``2019.4`` ``foss/2019b`` -``2019.6`` ``fosscuda/2019b`` -``2020`` ``foss/2019b``, ``fosscuda/2019b`` -``2020.1`` ``-Python-3.8.2`` ``foss/2020a`` -``2020.3`` ``fosscuda/2019b`` -``2020.4`` ``-Python-3.8.2`` ``foss/2020a`` -``2020.5`` ``-Python-3.8.2`` ``fosscuda/2020a`` -``2021`` ``foss/2020b``, ``fosscuda/2020b`` -``2021.2`` ``fosscuda/2020b`` -``2021.3`` ``foss/2021a`` -``2021.3`` ``-CUDA-11.3.1`` ``foss/2021a`` -========== ================= ============================================================================================================ +========== ============================= ============================================================================================================ +version versionsuffix toolchain +========== ============================= ============================================================================================================ +``5.1.2`` ``-hybrid`` ``foss/2016a``, ``intel/2016a`` +``5.1.2`` ``-hybrid-dp`` ``intel/2016a`` +``5.1.2`` ``-mt`` ``foss/2016a`` +``5.1.4`` ``-hybrid`` ``foss/2016b`` +``5.1.4`` ``-mt`` ``foss/2016b`` +``2016`` ``-hybrid`` ``foss/2016b`` +``2016`` ``-mt`` ``foss/2016b`` +``2016.1`` ``-PLUMED`` ``foss/2017a`` +``2016.2`` ``foss/2017a`` +``2016.3`` ``foss/2017a``, ``intel/2017a`` +``2016.3`` ``-GPU-enabled`` ``foss/2016b`` +``2016.4`` ``foss/2017b``, ``fosscuda/2017b``, ``giolf/2017b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` +``2016.5`` ``intel/2018a`` +``2018`` ``foss/2018a`` +``2018.1`` ``-PLUMED`` ``foss/2018b`` +``2018.2`` ``foss/2017b``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018b``, ``intel/2017b``, ``intelcuda/2017b`` +``2018.3`` ``foss/2018b``, ``fosscuda/2018b`` +``2018.4`` ``-PLUMED-2.5.0`` ``foss/2018b``, ``fosscuda/2018b`` +``2019`` ``foss/2018b``, ``fosscuda/2018b`` +``2019.2`` ``fosscuda/2019a`` +``2019.3`` ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019a``, ``fosscuda/2019b`` +``2019.4`` ``foss/2019b`` +``2019.6`` ``fosscuda/2019b`` +``2020`` ``foss/2019b``, ``fosscuda/2019b`` +``2020.1`` ``-Python-3.8.2`` ``foss/2020a`` +``2020.3`` ``fosscuda/2019b`` +``2020.4`` ``-Python-3.8.2`` ``foss/2020a`` +``2020.5`` ``-Python-3.8.2`` ``fosscuda/2020a`` +``2021`` ``foss/2020b``, ``fosscuda/2020b`` +``2021.2`` ``fosscuda/2020b`` +``2021.3`` ``foss/2021a`` +``2021.3`` ``-CUDA-11.3.1`` ``foss/2021a`` +``2021.3`` ``-CUDA-11.3.1-PLUMED-2.7.2`` ``foss/2021a`` +========== ============================= ============================================================================================================ .. _list_software_GromacsWrapper_1453: @@ -15415,7 +15860,7 @@ version toolchain ``2.4`` ``GCCcore/6.4.0`` ``2.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.6`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` -``2.7`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``2.7`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` ========= ============================================================================================================================ @@ -15512,7 +15957,7 @@ version versionsuffix toolchain ``1.0.2`` ``-Python-3.7.4`` ``intel/2019b`` ``1.3.0`` ``-Python-3.8.2`` ``intel/2020a`` ``1.5.0`` ``intel/2020b`` -``1.7.0`` ``intel/2020b`` +``1.7.0`` ``foss/2020b``, ``intel/2020b`` ========= ================== =============================== @@ -15615,12 +16060,12 @@ GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free *homepage*: http://gts.sourceforge.net/ -============ =============================================================================================================================================================================================================== -version toolchain -============ =============================================================================================================================================================================================================== -``0.7.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` -``20121130`` ``foss/2017b`` -============ =============================================================================================================================================================================================================== +============ =================================================================================================================================================================================================================================== +version toolchain +============ =================================================================================================================================================================================================================================== +``0.7.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` +``20121130`` ``foss/2017b`` +============ =================================================================================================================================================================================================================================== .. _list_software_gubbins_746: @@ -15713,10 +16158,12 @@ version versionsuffix toolchain ``9.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``9.0.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``9.0.1`` ``system`` +``9.0.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``9.0.3`` ``GCCcore/10.2.0``, ``system`` ``9.1.0`` ``system`` ``9.1.1`` ``GCCcore/10.2.0`` ``9.1.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``system`` +``9.5.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ================= ================================================== @@ -15744,7 +16191,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_HIP_225` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -16005,11 +16452,12 @@ The hdbscan library is a suite of tools to use unsupervised learning to find clu *homepage*: http://hdbscan.readthedocs.io/en/latest/ -========== ============== -version toolchain -========== ============== -``0.8.27`` ``foss/2021a`` -========== ============== +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``0.8.24`` ``-Python-3.7.4`` ``foss/2019b`` +``0.8.27`` ``foss/2021a`` +========== ================= ============== .. _list_software_HDDM_285: @@ -16115,7 +16563,7 @@ version versionsuffix toolchain ``1.10.6`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpic/2020a`` ``1.10.7`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpic/2020b`` ``1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` -``1.12.1`` ``gompi/2021a``, ``gompi/2021b`` +``1.12.1`` ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021b`` ================= ============= ================================================================================================================================================================================================================== @@ -16333,11 +16781,27 @@ Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. appl *homepage*: https://github.com/google/highway -========== ================== -version toolchain -========== ================== -``0.12.2`` ``GCCcore/10.3.0`` -========== ================== +========== ====================================== +version toolchain +========== ====================================== +``0.12.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========== ====================================== + + +.. _list_software_HIP_225: + +*HIP* ++++++ + +HIP is a C++ Runtime API and Kernel Language that allows developers to create portable applications for AMD and NVIDIA GPUs from single source code. + +*homepage*: https://github.com/ROCm-Developer-Tools/HIP + +========= ============= ================== +version versionsuffix toolchain +========= ============= ================== +``4.5.0`` ``-amd`` ``GCCcore/11.2.0`` +========= ============= ================== .. _list_software_hipify-clang_1211: @@ -16469,11 +16933,11 @@ HMMER is used for searching sequence databases for sequence homologs, and for m *homepage*: http://hmmer.org -========= ============================= -version toolchain -========= ============================= -``2.3.2`` ``GCC/10.3.0``, ``GCC/8.3.0`` -========= ============================= +========= ============================================= +version toolchain +========= ============================================= +``2.3.2`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0`` +========= ============================================= .. _list_software_hmmlearn_852: @@ -16538,6 +17002,7 @@ version versionsuffix toolchain ``0.22.1`` ``-CUDA-11.3.1-TensorFlow-2.6.0`` ``foss/2021a`` ``0.22.1`` ``-TensorFlow-2.5.0`` ``fosscuda/2020b`` ``0.22.1`` ``-TensorFlow-2.5.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.23.0`` ``-CUDA-11.3.1-PyTorch-1.10.0`` ``foss/2021a`` ========== =================================== ================================== @@ -16695,6 +17160,7 @@ version versionsuffix toolchain ``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` ``1.11`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` ``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` +``1.14`` ``GCC/11.2.0`` ``20160107`` ``-PacBio`` ``intel/2017a`` ============ ============= =========================================================================================================================================================== @@ -16834,6 +17300,7 @@ version toolchain ========== =============== ``2.3.13`` ``foss/2016b`` ``2.5.1`` ``gompi/2019a`` +``2.5.33`` ``gompi/2021a`` ========== =============== @@ -16906,7 +17373,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -17168,6 +17635,22 @@ version toolchain ========= ================================================================================================== +.. _list_software_idemux_652: + +*idemux* +++++++++ + +idemux - inline barcode demultiplexing Idemux is a command line tool designed to demultiplex paired-end FASTQ files from QuantSeq-Pool. + +*homepage*: https://github.com/Lexogen-Tools/idemux + +========= ================== +version toolchain +========= ================== +``0.1.6`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_ieeg-cli_767: *ieeg-cli* @@ -17485,6 +17968,22 @@ version toolchain ============ =============== +.. _list_software_imagecodecs_1140: + +*imagecodecs* ++++++++++++++ + +Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in the tifffile, czifile, zarr, and other scientific image input/output modules. + +*homepage*: https://github.com/cgohlke/imagecodecs + +============= ============== +version toolchain +============= ============== +``2021.8.26`` ``foss/2020b`` +============= ============== + + .. _list_software_imageio_731: *imageio* @@ -17494,14 +17993,14 @@ Imageio is a Python library that provides an easy interface to read and write a *homepage*: https://imageio.github.io -========= ================= =============================== -version versionsuffix toolchain -========= ================= =============================== -``2.3.0`` ``-Python-3.6.4`` ``intel/2018a`` -``2.5.0`` ``foss/2019a`` -``2.9.0`` ``fosscuda/2020b`` -``2.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -========= ================= =============================== +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``2.3.0`` ``-Python-3.6.4`` ``intel/2018a`` +``2.5.0`` ``foss/2019a`` +``2.9.0`` ``foss/2020b``, ``fosscuda/2020b`` +``2.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +========= ================= ================================== .. _list_software_ImageJ_557: @@ -17811,6 +18310,22 @@ version versionsuffix toolchain ========= =================== ========== +.. _list_software_InChI_427: + +*InChI* ++++++++ + +The IUPAC International Chemical Identifier (InChI TM) is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations. + +*homepage*: https://www.inchi-trust.org/ + +======== ============== +version toolchain +======== ============== +``1.06`` ``GCC/10.3.0`` +======== ============== + + .. _list_software_Inelastica_1021: *Inelastica* @@ -17859,6 +18374,7 @@ Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases version toolchain ========= ================================================================ ``1.1.2`` ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018b`` +``1.1.4`` ``foss/2021b`` ========= ================================================================ @@ -17916,9 +18432,9 @@ version toolchain *Inspector* +++++++++++ -Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications +Intel Inspector is a dynamic memory and threading error checking tool for users developing serial and parallel applications -*homepage*: https://software.intel.com/en-us/intel-inspector-xe +*homepage*: https://software.intel.com/en-us/inspector ================ ========== version toolchain @@ -17933,6 +18449,7 @@ version toolchain ``2018_update3`` ``system`` ``2019_update2`` ``system`` ``2019_update5`` ``system`` +``2021.4.0`` ``system`` ================ ========== @@ -18149,11 +18666,11 @@ An interval tree can be used to efficiently find a set of numeric intervals ove *homepage*: https://github.com/ekg/intervaltree -======= ===================================== -version toolchain -======= ===================================== -``0.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -======= ===================================== +======= ========================================================= +version toolchain +======= ========================================================= +``0.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +======= ========================================================= .. _list_software_intltool_885: @@ -18616,6 +19133,7 @@ version versionsuffix toolchain ``5.0b01`` ``-Python-3.6.6`` ``foss/2018b`` ``5.1.2`` ``foss/2020a``, ``fosscuda/2020a`` ``5.1.2`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``5.2.1`` ``foss/2020b`` ========== ================== ================================== @@ -18692,7 +19210,7 @@ version toolchain --- -:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_jax_323` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_JSON-GLib_709` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` +:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_jax_323` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_JSON-GLib_709` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyter-matlab-proxy_2080` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` - :ref:`list_software_jxrlib_651` .. _list_software_JAGS_293: @@ -18825,16 +19343,18 @@ version versionsuffix toolchain *jax* +++++ -Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more +Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more *homepage*: https://pypi.python.org/pypi/jax -========== ================================== -version toolchain -========== ================================== -``0.2.19`` ``foss/2020b``, ``fosscuda/2020b`` -``0.2.20`` ``foss/2021a`` -========== ================================== +========== ================ ================================== +version versionsuffix toolchain +========== ================ ================================== +``0.2.19`` ``foss/2020b``, ``fosscuda/2020b`` +``0.2.20`` ``foss/2021a`` +``0.2.24`` ``foss/2021a`` +``0.2.24`` ``-CUDA-11.3.1`` ``foss/2021a`` +========== ================ ================================== .. _list_software_JAXFrontCE_884: @@ -19073,11 +19593,11 @@ A C library that implements a dynamic array. *homepage*: http://judy.sourceforge.net/ -========= ============================================================================ -version toolchain -========= ============================================================================ -``1.0.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= ============================================================================ +========= ================================================================================================ +version toolchain +========= ================================================================================================ +``1.0.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ================================================================================================ .. _list_software_Julia_501: @@ -19102,6 +19622,8 @@ version versionsuffix toolchain ``1.5.3`` ``-linux-x86_64`` ``system`` ``1.6.1`` ``-linux-x86_64`` ``system`` ``1.6.2`` ``-linux-x86_64`` ``system`` +``1.6.4`` ``-linux-x86_64`` ``system`` +``1.7.0`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -19138,6 +19660,22 @@ version versionsuffix toolchain ======== =================== ========== +.. _list_software_jupyter-matlab-proxy_2080: + +*jupyter-matlab-proxy* +++++++++++++++++++++++ + +MATLAB Integration for Jupyter + +*homepage*: https://github.com/mathworks/jupyter-matlab-proxy + +========= ================== +version toolchain +========= ================== +``0.3.4`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_JupyterHub_1042: *JupyterHub* @@ -19192,6 +19730,22 @@ version toolchain ========= =============== +.. _list_software_jxrlib_651: + +*jxrlib* +++++++++ + +Open source implementation of jpegxr + +*homepage*: https://github.com/4creators/jxrlib + +======= ================== +version toolchain +======= ================== +``1.1`` ``GCCcore/10.2.0`` +======= ================== + + .. _list_software_letter_k: *K* @@ -19340,6 +19894,7 @@ version versionsuffix toolchain ``401`` ``gompi/2019b`` ``411`` ``GCC/10.2.0`` ``418`` ``GCC/10.3.0`` +``422`` ``GCC/11.2.0`` ``20130806`` ``-linux.x86_64`` ``system`` ``20171107`` ``-linux.x86_64`` ``system`` ``20180716`` ``-linux.x86_64`` ``system`` @@ -19425,12 +19980,13 @@ version toolchain KING is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequencing project. Applications of KING include family relationship inference and pedigree error checking, quality control, population substructure identification, forensics, gene mapping, etc. -*homepage*: https://people.virginia.edu/~wc9c/KING/ +*homepage*: https://kingrelatedness.com/ ========= ========== version toolchain ========= ========== ``2.2.4`` ``system`` +``2.2.7`` ``system`` ========= ========== @@ -19664,7 +20220,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libfdf_615` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libmbd_618` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpspio_866` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libSBML_613` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_longread_umi_1270` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LBFGS++_452` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_LERC_294` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaec_608` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libavif_733` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libfdf_615` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_LibLZF_515` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libmbd_618` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libnsl_644` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpspio_866` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libSBML_613` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libtree_743` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_longread_umi_1270` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPeg_360` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -19822,6 +20378,22 @@ version versionsuffix toolchain ============== ============= =============== +.. _list_software_LBFGS++_452: + +*LBFGS++* ++++++++++ + +A header-only C++ library for L-BFGS and L-BFGS-B algorithms + +*homepage*: https://lbfgspp.statr.me + +========= ========== +version toolchain +========= ========== +``0.1.0`` ``system`` +========= ========== + + .. _list_software_LCov_372: *LCov* @@ -19939,6 +20511,22 @@ version toolchain ========== ================= +.. _list_software_LERC_294: + +*LERC* +++++++ + +LERC is an open-source image or raster format which supports rapid encoding and decoding for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, so the precision of the original input image is preserved (within user defined error bounds). + +*homepage*: https://github.com/Esri/lerc + +======= ================== +version toolchain +======= ================== +``3.0`` ``GCCcore/10.2.0`` +======= ================== + + .. _list_software_less_439: *less* @@ -19990,6 +20578,22 @@ version toolchain ========= ================== +.. _list_software_libaec_608: + +*libaec* +++++++++ + +Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa. + +*homepage*: https://gitlab.dkrz.de/k202009/libaec + +========= ================== +version toolchain +========= ================== +``1.0.6`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_libaio_624: *libaio* @@ -19999,12 +20603,12 @@ Asynchronous input/output library that uses the kernels native interface. *homepage*: https://pagure.io/libaio -=========== ====================================== -version toolchain -=========== ====================================== -``0.3.111`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.3.112`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -=========== ====================================== +=========== ========================================================== +version toolchain +=========== ========================================================== +``0.3.111`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.3.112`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +=========== ========================================================== .. _list_software_libarchive_1049: @@ -20042,6 +20646,22 @@ version toolchain ========= ================= +.. _list_software_libavif_733: + +*libavif* ++++++++++ + +This library aims to be a friendly, portable C implementation of the AV1 Image File Format, as described here: https://aomediacodec.github.io/av1-avif/ + +*homepage*: https://github.com/AOMediaCodec/libavif + +========= ============== +version toolchain +========= ============== +``0.9.0`` ``foss/2020b`` +========= ============== + + .. _list_software_libBigWig_880: *libBigWig* @@ -20109,7 +20729,7 @@ version toolchain ``1.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.14`` ``GCCcore/10.2.0`` ``1.15`` ``GCCcore/10.3.0`` -``1.17`` ``GCCcore/10.3.0`` +``1.17`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ======== ========================================================================================================= @@ -20250,6 +20870,7 @@ version versionsuffix toolchain ``3.20.4`` ``GCCcore/8.2.0`` ``3.20.6`` ``GCCcore/8.3.0`` ``3.20.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``3.20.8`` ``GCCcore/11.2.0`` ========== ================== ========================================================= @@ -20346,6 +20967,7 @@ version toolchain ``20150310`` ``GCC/4.9.2``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0`` ``20190529`` ``GCCcore/8.2.0`` ``20201201`` ``GCCcore/10.2.0`` +``20210528`` ``GCCcore/11.2.0`` ============ =================================================== @@ -20376,11 +20998,11 @@ libelf is a free ELF object file access library *homepage*: https://directory.fsf.org/wiki/Libelf -========== ============================================================================================================================ -version toolchain -========== ============================================================================================================================ -``0.8.13`` ``GCC/4.8.3``, ``GCC/4.9.2``, ``GCCcore/10.2.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` -========== ============================================================================================================================ +========== ================================================================================================================================================ +version toolchain +========== ================================================================================================================================================ +``0.8.13`` ``GCC/4.8.3``, ``GCC/4.9.2``, ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +========== ================================================================================================================================================ .. _list_software_libepoxy_876: @@ -20878,17 +21500,17 @@ Libint library is used to evaluate the traditional (electron repulsion) and cert *homepage*: https://github.com/evaleev/libint -========= ================ =================================================================================================================================================================================================== -version versionsuffix toolchain -========= ================ =================================================================================================================================================================================================== -``1.1.4`` ``intel/2016a`` -``1.1.6`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018a``, ``foss/2020a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` -``2.0.3`` ``foss/2018b``, ``gompi/2019a``, ``intel/2018b`` -``2.1.0`` ``intel/2016b`` -``2.4.2`` ``intel/2018a`` -``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` -``2.6.0`` ``-lmax-6-cp2k`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a`` -========= ================ =================================================================================================================================================================================================== +========= ================ =================================================================================================================================================================================================================== +version versionsuffix toolchain +========= ================ =================================================================================================================================================================================================================== +``1.1.4`` ``intel/2016a`` +``1.1.6`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018a``, ``foss/2020a``, ``foss/2020b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` +``2.0.3`` ``foss/2018b``, ``gompi/2019a``, ``intel/2018b`` +``2.1.0`` ``intel/2016b`` +``2.4.2`` ``intel/2018a`` +``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` +``2.6.0`` ``-lmax-6-cp2k`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a`` +========= ================ =================================================================================================================================================================================================================== .. _list_software_LiBis_467: @@ -20943,10 +21565,27 @@ JPEG XL image format reference implementation *homepage*: https://github.com/libjxl/libjxl +========= ================== +version toolchain +========= ================== +``0.5`` ``GCCcore/10.3.0`` +``0.6.1`` ``GCCcore/10.2.0`` +========= ================== + + +.. _list_software_LibLZF_515: + +*LibLZF* +++++++++ + +LibLZF is a very small data compression library. It consists of only two .c and two .h files and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still written in portable C. + +*homepage*: http://oldhome.schmorp.de/marc/liblzf.html + ======= ================== version toolchain ======= ================== -``0.5`` ``GCCcore/10.3.0`` +``3.4`` ``GCCcore/10.2.0`` ======= ================== @@ -21063,6 +21702,22 @@ version toolchain ========= ================== +.. _list_software_libnsl_644: + +*libnsl* +++++++++ + +The libnsl package contains the public client interface for NIS(YP). + +*homepage*: https://github.com/thkukuk/libnsl + +========= ================== +version toolchain +========= ================== +``1.3.0`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_libobjcryst_1191: *libobjcryst* @@ -21722,6 +22377,22 @@ version toolchain ========= ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +.. _list_software_libtree_743: + +*libtree* ++++++++++ + +libtree is a tool that turns ldd into a tree, explains why shared libraries are found and why not and optionally deploys executables and dependencies into a single directory + +*homepage*: https://github.com/haampie/libtree + +========= ================== +version toolchain +========= ================== +``2.0.0`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_libunistring_1306: *libunistring* @@ -21908,7 +22579,7 @@ version toolchain ``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` ``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` ``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` +``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``foss/2020b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` ``4.0.1`` ``foss/2017b``, ``intel/2017b`` ``4.0.3`` ``foss/2016b``, ``foss/2017a`` ``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` @@ -21916,7 +22587,7 @@ version toolchain ``5.1.2`` ``GCC/10.2.0`` ``5.1.3`` ``GCC/10.2.0`` ``5.1.5`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` -``5.1.6`` ``GCC/11.2.0`` +``5.1.6`` ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` ========= ===================================================================================================================================================================================================================================== @@ -22443,7 +23114,7 @@ version toolchain *likwid* ++++++++ -Likwid stands for Like I knew what I am doing. This project contributes easy to use command line tools for Linux to support programmers in developing high performance multi threaded programs. +Likwid stands for Like I knew what I am doing. This project contributes easy to use command line tools for Linux to support programmers in developing high performance multi threaded programs. *homepage*: https://github.com/RRZE-HPC/likwid @@ -22456,7 +23127,7 @@ version toolchain ``4.3.2`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``5.0.1`` ``GCCcore/8.3.0`` ``5.1.0`` ``GCCcore/9.3.0`` -``5.2.0`` ``GCCcore/10.2.0`` +``5.2.0`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` ========= ===================================================================== @@ -22846,6 +23517,22 @@ version toolchain ========= =============== +.. _list_software_LPeg_360: + +*LPeg* +++++++ + +LPeg is a new pattern-matching library for Lua, based on Parsing Expression Grammars (PEGs). + +*homepage*: http://www.inf.puc-rio.br/~roberto/lpeg/ + +========= ================== +version toolchain +========= ================== +``1.0.2`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_LPJmL_415: *LPJmL* @@ -22990,18 +23677,18 @@ Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combin *homepage*: https://www.lua.org/ -=========== =================================================================== -version toolchain -=========== =================================================================== -``5.1.4-5`` ``GCC/4.8.2`` -``5.1.4-8`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``system`` -``5.1.5`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` -``5.2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``5.3.4`` ``GCCcore/7.2.0``, ``system`` -``5.3.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` -``5.4.2`` ``GCCcore/10.2.0`` -``5.4.3`` ``GCCcore/10.3.0`` -=========== =================================================================== +=========== ======================================================================================= +version toolchain +=========== ======================================================================================= +``5.1.4-5`` ``GCC/4.8.2`` +``5.1.4-8`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``system`` +``5.1.5`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +``5.2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``5.3.4`` ``GCCcore/7.2.0``, ``system`` +``5.3.5`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +``5.4.2`` ``GCCcore/10.2.0`` +``5.4.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +=========== ======================================================================================= .. _list_software_LuaJIT_521: @@ -23174,7 +23861,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -23268,6 +23955,7 @@ version versionsuffix toolchain ``7.471`` ``-with-extensions`` ``iimpi/2020a`` ``7.475`` ``-with-extensions`` ``GCC/10.2.0``, ``gompi/2020b`` ``7.487`` ``-with-extensions`` ``gompi/2021a`` +``7.490`` ``-with-extensions`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``gompi/2021b`` ========= ==================== ======================================================================================= @@ -23440,6 +24128,7 @@ version versionsuffix toolchain ======= ============= =========================================================================================== ``6.7`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``6.7`` ``-minimal`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``6.8`` ``GCCcore/11.2.0`` ======= ============= =========================================================================================== @@ -23577,7 +24266,7 @@ version toolchain ``10.3.14`` ``foss/2019a`` ``10.4.13`` ``gompi/2019b`` ``10.5.8`` ``GCC/10.2.0`` -``10.6.4`` ``GCC/10.3.0`` +``10.6.4`` ``GCC/10.3.0``, ``GCC/11.2.0`` =========== =============================== @@ -23632,6 +24321,8 @@ version toolchain ======= ============== ``2.0`` ``foss/2018a`` ``2.1`` ``foss/2018b`` +``2.2`` ``GCC/9.3.0`` +``2.3`` ``GCC/10.3.0`` ======= ============== @@ -23810,6 +24501,7 @@ version versionsuffix toolchain ``3.2.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``3.3.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``3.4.2`` ``foss/2021a``, ``intel/2021a`` +``3.4.3`` ``foss/2021b``, ``intel/2021b`` ========= ================================= ======================================================================== @@ -24080,6 +24772,7 @@ version versionsuffix toolchain ``R2020b`` ``.5`` ``system`` ``R2021a`` ``.0`` ``system`` ``R2021a`` ``.3`` ``system`` +``R2021b`` ``system`` ========== ============= ========== @@ -24253,6 +24946,7 @@ MedPy is a library and script collection for medical image processing in Python, ========= ================= ============== version versionsuffix toolchain ========= ================= ============== +``0.4.0`` ``foss/2020b`` ``0.4.0`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -24331,6 +25025,22 @@ version versionsuffix toolchain ========= ================== ================================= +.. _list_software_Megalodon_918: + +*Megalodon* ++++++++++++ + +Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome. + +*homepage*: https://github.com/nanoporetech/megalodon + +========= ================================== +version toolchain +========= ================================== +``2.3.5`` ``foss/2020b``, ``fosscuda/2020b`` +========= ================================== + + .. _list_software_Meld_386: *Meld* @@ -24833,13 +25543,13 @@ METIS is a set of serial programs for partitioning graphs, partitioning finite e *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview -========= ============= ========================================================================================================================================================================================================================================================================== -version versionsuffix toolchain -========= ============= ========================================================================================================================================================================================================================================================================== -``5.0.2`` ``gimkl/2.11.5`` -``5.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``5.1.0`` ``-32bitIDX`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -========= ============= ========================================================================================================================================================================================================================================================================== +========= ============= ============================================================================================================================================================================================================================================================================================== +version versionsuffix toolchain +========= ============= ============================================================================================================================================================================================================================================================================================== +``5.0.2`` ``gimkl/2.11.5`` +``5.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``5.1.0`` ``-32bitIDX`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +========= ============= ============================================================================================================================================================================================================================================================================================== .. _list_software_mhcflurry_988: @@ -25117,6 +25827,7 @@ version toolchain ``2.17`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/9.3.0`` ``2.18`` ``GCCcore/10.2.0`` ``2.20`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.22`` ``GCCcore/11.2.0`` ========== ====================================================== @@ -25438,8 +26149,9 @@ version toolchain ``8-fac81`` ``intel/2018b`` ``10-6d92c`` ``gompi/2019b``, ``iimpi/2019b`` ``11-e1a1c`` ``iimpi/2019b`` -``13-45111`` ``gompi/2020b`` +``13-45111`` ``gompi/2020b``, ``gompi/2021b`` ``13-45111-20211006`` ``gompi/2020b`` +``13-45111-20211019`` ``gompi/2020b`` ===================== ================================ @@ -25741,13 +26453,13 @@ Motif refers to both a graphical user interface (GUI) specification and the widg *homepage*: https://motif.ics.com/ -========= ======================================================================================================================================================= -version toolchain -========= ======================================================================================================================================================= -``2.3.5`` ``foss/2016a``, ``intel/2016a`` -``2.3.7`` ``intel/2017a`` -``2.3.8`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` -========= ======================================================================================================================================================= +========= =========================================================================================================================================================================== +version toolchain +========= =========================================================================================================================================================================== +``2.3.5`` ``foss/2016a``, ``intel/2016a`` +``2.3.7`` ``intel/2017a`` +``2.3.8`` ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` +========= =========================================================================================================================================================================== .. _list_software_MotionCor2_972: @@ -26181,11 +26893,11 @@ generate multiset combinations (n multichoose k). *homepage*: https://github.com/ekg/multichoose -========= ===================================== -version toolchain -========= ===================================== -``1.0.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========= ===================================== +========= ========================================================= +version toolchain +========= ========================================================= +``1.0.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +========= ========================================================= .. _list_software_MultiNest_933: @@ -26259,7 +26971,7 @@ MUMmer is a system for rapidly aligning entire genomes, whether in complete or ============== ===================================================== version toolchain ============== ===================================================== -``3.23`` ``GCCcore/9.3.0``, ``foss/2016b`` +``3.23`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``foss/2016b`` ``4.0.0beta2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0``, ``foss/2018b`` ============== ===================================================== @@ -26310,11 +27022,11 @@ A C++ Library for Parsing Expressions with Strings, Complex Numbers, Vectors, Ma *homepage*: https://beltoforion.de/en/muparserx/ -========= ================== -version toolchain -========= ================== -``4.0.8`` ``GCCcore/10.3.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``4.0.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== .. _list_software_MuPeXI_536: @@ -26376,12 +27088,13 @@ MUST detects usage errors of the Message Passing Interface (MPI) and reports the *homepage*: https://hpc.rwth-aachen.de/must/ -======= ================= ============== -version versionsuffix toolchain -======= ================= ============== -``1.6`` ``-Python-3.6.6`` ``foss/2018b`` -``1.6`` ``-Python-3.7.4`` ``foss/2019b`` -======= ================= ============== +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``1.6`` ``-Python-3.6.6`` ``foss/2018b`` +``1.6`` ``-Python-3.7.4`` ``foss/2019b`` +``1.7.2`` ``foss/2021a`` +========= ================= ============== .. _list_software_MuTect_594: @@ -26642,7 +27355,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -27141,6 +27854,7 @@ version toolchain ``4.9.3`` ``foss/2019b`` ``4.9.7`` ``foss/2020a``, ``foss/2020b`` ``5.0.1`` ``foss/2021a`` +``5.0.3`` ``foss/2021b``, ``intel/2021b`` ========= =============================== @@ -27353,7 +28067,7 @@ version versionsuffix toolchain ``4.7.1`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` ``4.7.4`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2020b`` ``4.8.0`` ``gompi/2021a``, ``iimpi/2021a`` -``4.8.1`` ``gompi/2021b`` +``4.8.1`` ``gompi/2021b``, ``iimpi/2021b`` =========== ================ ========================================================================================================================== @@ -27382,14 +28096,14 @@ NetCDF (network Common Data Form) is a set of software libraries and machine-in *homepage*: https://www.unidata.ucar.edu/software/netcdf/ -========= ================ ====================================================================================================================================================== -version versionsuffix toolchain -========= ================ ====================================================================================================================================================== -``4.3.0`` ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``4.3.0`` ``-HDF5-1.8.18`` ``intel/2017a`` -``4.3.0`` ``-HDF5-1.8.19`` ``intel/2017b`` -``4.3.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a`` -========= ================ ====================================================================================================================================================== +========= ================ ======================================================================================================================================================================== +version versionsuffix toolchain +========= ================ ======================================================================================================================================================================== +``4.3.0`` ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +``4.3.0`` ``-HDF5-1.8.18`` ``intel/2017a`` +``4.3.0`` ``-HDF5-1.8.19`` ``intel/2017b`` +``4.3.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b`` +========= ================ ======================================================================================================================================================================== .. _list_software_netCDF-Fortran_1309: @@ -27412,7 +28126,7 @@ version versionsuffix toolchain ``4.4.4`` ``-HDF5-1.8.19`` ``foss/2017b``, ``intel/2017b`` ``4.4.5`` ``gompi/2019a``, ``iimpi/2019a`` ``4.5.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` -``4.5.3`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a`` +``4.5.3`` ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b`` ========= ================ ==================================================================================================================================================================================================================================================================================================================================== @@ -27613,7 +28327,7 @@ version versionsuffix toolchain ``2.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``2.5.1`` ``foss/2021a`` ``2.6.2`` ``foss/2020b`` -``2.6.3`` ``foss/2021a`` +``2.6.3`` ``foss/2021a``, ``foss/2021b`` ========= ================== ======================================================================== @@ -27719,7 +28433,7 @@ version toolchain ========= ================================== ``3.1.3`` ``foss/2020b``, ``fosscuda/2020b`` ``3.5.1`` ``foss/2018b``, ``foss/2019a`` -``3.5.2`` ``foss/2020a`` +``3.5.2`` ``foss/2020a``, ``foss/2021a`` ========= ================================== @@ -28028,6 +28742,7 @@ JSON for Modern C++ version toolchain ========== ================== ``3.10.0`` ``GCCcore/10.3.0`` +``3.10.4`` ``GCCcore/11.2.0`` ========== ================== @@ -28069,6 +28784,22 @@ version versionsuffix toolchain ========= ================== ================================== +.. _list_software_nnU-Net_645: + +*nnU-Net* ++++++++++ + +nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found in the domain It condenses and automates the keys decisions for designing a successful segmentation pipeline for any given dataset. + +*homepage*: https://github.com/MIC-DKFZ/nnUNet + +========= ============== +version toolchain +========= ============== +``1.7.0`` ``foss/2020b`` +========= ============== + + .. _list_software_Node-RED_654: *Node-RED* @@ -28506,6 +29237,7 @@ version toolchain ``21.3`` ``system`` ``21.5`` ``system`` ``21.7`` ``system`` +``21.9`` ``system`` ========= ========== @@ -29022,6 +29754,7 @@ version versionsuffix toolchain ``7`` ``foss/2019b`` ``7`` ``-20200508`` ``foss/2019b`` ``8`` ``foss/2020a``, ``foss/2020b`` +``8`` ``-20210316`` ``foss/2020b`` ``9`` ``foss/2021a`` ``v1606+`` ``foss/2018b`` ``v1612+`` ``foss/2018b`` @@ -29265,8 +29998,10 @@ version versionsuffix toolchain ``4.0.5`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` ``4.0.5`` ``-CUDA-11.2.1`` ``NVHPC/21.2`` ``4.0.6`` ``GCC/10.3.0`` +``4.0.7`` ``GCC/10.3.0`` ``4.1.0`` ``GCC/10.2.0`` ``4.1.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0`` +``4.1.2`` ``GCC/11.2.0`` ``system`` ``GCC/system-2.29`` ========== ================ ==================================================================================================================== @@ -29413,12 +30148,12 @@ OpenSlide is a C library that provides a simple interface to read whole-slide im *homepage*: https://openslide.org/ -========= =============== ================= -version versionsuffix toolchain -========= =============== ================= -``3.4.1`` ``GCCcore/8.2.0`` -``3.4.1`` ``-largefiles`` ``GCCcore/8.2.0`` -========= =============== ================= +========= =============== ===================================== +version versionsuffix toolchain +========= =============== ===================================== +``3.4.1`` ``GCCcore/8.2.0`` +``3.4.1`` ``-largefiles`` ``GCCcore/10.3.0``, ``GCCcore/8.2.0`` +========= =============== ===================================== .. _list_software_openslide-python_1682: @@ -29775,7 +30510,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -29899,6 +30634,22 @@ version toolchain ========== ============== +.. _list_software_PAL2NAL_490: + +*PAL2NAL* ++++++++++ + +PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. The program automatically assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the input alignment, which is suitable for the analysis of pseudogenes. The resulting codon alignment can further be subjected to the calculation of synonymous (d_S) and non-synonymous (d_N) subs- titution rates. + +*homepage*: http://www.bork.embl.de/pal2nal/ + +======= ====================================== +version toolchain +======= ====================================== +``14`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +======= ====================================== + + .. _list_software_PAML_298: *PAML* @@ -29912,7 +30663,7 @@ PAML is a package of programs for phylogenetic analyses of DNA or protein sequ version toolchain ======== ========================================================== ``4.9i`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` -``4.9j`` ``GCCcore/9.3.0`` +``4.9j`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ======== ========================================================== @@ -29929,6 +30680,7 @@ A pangenome analysis pipeline. version toolchain ========= ============== ``1.2.8`` ``foss/2020b`` +``1.2.9`` ``foss/2021a`` ========= ============== @@ -30065,11 +30817,13 @@ Software package for assigning SARS-CoV-2 genome sequences to global lineages. T *homepage*: https://cov-lineages.org/pangolin.html -========== ============== -version toolchain -========== ============== -``3.1.11`` ``foss/2020b`` -========== ============== +========== ========================== ============== +version versionsuffix toolchain +========== ========================== ============== +``3.1.11`` ``foss/2020b`` +``3.1.16`` ``-pangoLEARN-2021-10-18`` ``foss/2021b`` +``3.1.16`` ``-pangoLEARN-2021-11-25`` ``foss/2021b`` +========== ========================== ============== .. _list_software_PAPI_298: @@ -30089,7 +30843,7 @@ version toolchain ``5.6.0`` ``GCCcore/6.4.0`` ``5.7.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``6.0.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``6.0.0.1`` ``GCCcore/10.3.0`` +``6.0.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` =========== ======================================================== @@ -30167,15 +30921,15 @@ parasail is a SIMD C (C99) library containing implementations of the Smith-Wate *homepage*: https://github.com/jeffdaily/parasail -========= ============================== -version toolchain -========= ============================== -``2.2`` ``intel/2018a`` -``2.4`` ``foss/2018b`` -``2.4.1`` ``GCC/8.3.0``, ``intel/2019b`` -``2.4.2`` ``iccifort/2020.1.217`` -``2.4.3`` ``GCC/10.2.0`` -========= ============================== +========= ====================================== +version toolchain +========= ====================================== +``2.2`` ``intel/2018a`` +``2.4`` ``foss/2018b`` +``2.4.1`` ``GCC/8.3.0``, ``intel/2019b`` +``2.4.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` +``2.4.3`` ``GCC/10.2.0`` +========= ====================================== .. _list_software_Paraver_721: @@ -31094,6 +31848,22 @@ version versionsuffix toolchain ============= ================== =============================== +.. _list_software_photontorch_1208: + +*photontorch* ++++++++++++++ + +Photontorch is a photonic simulator for highly parallel simulation and optimization of photonic circuits in time and frequency domain. Photontorch features CUDA enabled simulation and optimization of photonic circuits. It leverages the deep learning framework PyTorch to view the photonic circuit as essentially a recurrent neural network. This enables the use of native PyTorch optimizers to optimize the (physical) parameters of the circuit. + +*homepage*: https://docs.photontorch.com/ + +========= ================================== +version toolchain +========= ================================== +``0.4.1`` ``foss/2020b``, ``fosscuda/2020b`` +========= ================================== + + .. _list_software_phototonic_1095: *phototonic* @@ -31335,6 +32105,7 @@ version versionsuffix toolchain ``5.3.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``6.0.0`` ``GCCcore/8.2.0`` ``6.2.1`` ``GCCcore/8.3.0`` +``6.2.2`` ``-Python-2.7.18`` ``foss/2020b`` ``7.0.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``8.0.1`` ``GCCcore/10.2.0`` ``8.2.0`` ``GCCcore/10.3.0`` @@ -31600,6 +32371,22 @@ version toolchain ========== ============================================================================================================================================================================================================================ +.. _list_software_pkgconf_744: + +*pkgconf* ++++++++++ + +pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org. + +*homepage*: https://github.com/pkgconf/pkgconf + +========= ================== +version toolchain +========= ================== +``1.8.0`` ``GCCcore/11.2.0`` +========= ================== + + .. _list_software_pkgconfig_952: *pkgconfig* @@ -31628,6 +32415,7 @@ version versionsuffix toolchain ``1.5.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``1.5.1`` ``-python`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0`` ``1.5.4`` ``-python`` ``GCCcore/10.3.0`` +``1.5.5`` ``-python`` ``GCCcore/11.2.0`` ========= ================== =================================================== @@ -31869,6 +32657,7 @@ version toolchain ``4.8.1`` ``GCCcore/9.3.0`` ``4.14.3`` ``GCCcore/10.2.0`` ``5.1.0`` ``GCCcore/10.3.0`` +``5.4.0`` ``GCCcore/11.2.0`` ========== ================== @@ -31966,6 +32755,22 @@ version toolchain ========= ======================================================= +.. _list_software_pmx_341: + +*pmx* ++++++ + +pmx (formerly pymacs) is a small bunch of classes to read structure files such as pdb or gro and trajectory data in gromacs xtc format. Over the years it has been extended towards a versatile (bio-) molecular structure manipulation package with some additional functionalities, e.g. gromacs file parsers and scripts for setup and analysis of free energy calculations. + +*homepage*: https://github.com/deGrootLab/pmx + +======= ================== ============== +version versionsuffix toolchain +======= ================== ============== +``2.0`` ``-Python-2.7.18`` ``foss/2020b`` +======= ================== ============== + + .. _list_software_PnetCDF_612: *PnetCDF* @@ -32253,6 +33058,22 @@ version toolchain =========== ================================================================================= +.. _list_software_PPanGGOLiN_847: + +*PPanGGOLiN* +++++++++++++ + +PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species. + +*homepage*: https://github.com/labgem/PPanGGOLiN + +=========== ============== +version toolchain +=========== ============== +``1.1.136`` ``foss/2021b`` +=========== ============== + + .. _list_software_PPfold_581: *PPfold* @@ -32327,11 +33148,11 @@ PRANK is a probabilistic multiple alignment program for DNA, codon and amino-a *homepage*: http://wasabiapp.org/software/prank/ -========== ============================================== -version toolchain -========== ============================================== -``170427`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``intel/2018a`` -========== ============================================== +========== ============================================================== +version toolchain +========== ============================================================== +``170427`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0``, ``intel/2018a`` +========== ============================================================== .. _list_software_PRC_229: @@ -32494,12 +33315,28 @@ Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbi *homepage*: https://github.com/hyattpd/Prodigal/ -========= ================================================================================================================= -version toolchain -========= ================================================================================================================= -``2.6.2`` ``GCC/4.9.3-binutils-2.25`` -``2.6.3`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ================================================================================================================= +========= ========================================================================================================================================================= +version toolchain +========= ========================================================================================================================================================= +``2.6.2`` ``GCC/4.9.3-binutils-2.25`` +``2.6.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ========================================================================================================================================================= + + +.. _list_software_ProFit_596: + +*ProFit* +++++++++ + +ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate program for performing least squares fits of two or more protein structures. It performs a very simple and basic function, but allows as much flexibility as possible in performing this procedure. Thus one can specify subsets of atoms to be considered, specify zones to be fitted by number, sequence, or by sequence alignment. + +*homepage*: http://www.bioinf.org.uk/software/profit + +======= ============== +version toolchain +======= ============== +``3.3`` ``GCC/10.3.0`` +======= ============== .. _list_software_PROJ_315: @@ -32551,15 +33388,15 @@ Prokka is a software tool for the rapid annotation of prokaryotic genomes. *homepage*: https://www.vicbioinformatics.com/software.prokka.shtml -========== ================== ================================================= -version versionsuffix toolchain -========== ================== ================================================= -``1.11`` ``-BioPerl-1.7.0`` ``foss/2016b`` -``1.13`` ``-BioPerl-1.7.2`` ``intel/2018a`` -``1.13.4`` ``foss/2018b`` -``1.13.7`` ``gompi/2019a`` -``1.14.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020b`` -========== ================== ================================================= +========== ================== ================================================================== +version versionsuffix toolchain +========== ================== ================================================================== +``1.11`` ``-BioPerl-1.7.0`` ``foss/2016b`` +``1.13`` ``-BioPerl-1.7.2`` ``intel/2018a`` +``1.13.4`` ``foss/2018b`` +``1.13.7`` ``gompi/2019a`` +``1.14.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020b``, ``gompi/2021a`` +========== ================== ================================================================== .. _list_software_prompt-toolkit_1493: @@ -33022,6 +33859,22 @@ version toolchain ============ =============== +.. _list_software_pugixml_774: + +*pugixml* ++++++++++ + +pugixml is a light-weight C++ XML processing library + +*homepage*: https://pugixml.org/ + +========== ================== +version toolchain +========== ================== +``1.11.4`` ``GCCcore/10.3.0`` +========== ================== + + .. _list_software_pullseq_774: *pullseq* @@ -33162,16 +34015,16 @@ pybedtools wraps and extends BEDTools and offers feature-level manipulations fro *homepage*: https://daler.github.io/pybedtools -========== ================== ======================================= -version versionsuffix toolchain -========== ================== ======================================= -``0.7.10`` ``-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` -``0.7.10`` ``-Python-3.6.6`` ``foss/2018b`` -``0.8.0`` ``foss/2019a``, ``intel/2019a`` -``0.8.1`` ``foss/2019b`` -``0.8.2`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -``0.8.2`` ``-Python-2.7.18`` ``GCC/10.2.0`` -========== ================== ======================================= +========== ================== ======================================================= +version versionsuffix toolchain +========== ================== ======================================================= +``0.7.10`` ``-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` +``0.7.10`` ``-Python-3.6.6`` ``foss/2018b`` +``0.8.0`` ``foss/2019a``, ``intel/2019a`` +``0.8.1`` ``foss/2019b`` +``0.8.2`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304`` +``0.8.2`` ``-Python-2.7.18`` ``GCC/10.2.0`` +========== ================== ======================================================= .. _list_software_PyBerny_713: @@ -33199,13 +34052,13 @@ A python extension, written in C, for quick access to bigBed files and access t *homepage*: https://github.com/deeptools/pyBigWig -========== ================= ==================================== -version versionsuffix toolchain -========== ================= ==================================== -``0.3.13`` ``-Python-3.6.6`` ``foss/2018b`` -``0.3.17`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` -``0.3.18`` ``GCCcore/10.2.0``, ``foss/2021a`` -========== ================= ==================================== +========== ================= ================================================== +version versionsuffix toolchain +========== ================= ================================================== +``0.3.13`` ``-Python-3.6.6`` ``foss/2018b`` +``0.3.17`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +``0.3.18`` ``GCCcore/10.2.0``, ``foss/2021a``, ``foss/2021b`` +========== ================= ================================================== .. _list_software_pybind11_744: @@ -33576,6 +34429,7 @@ version versionsuffix toolchain =========== ================= ================== ``0.5.9.5`` ``GCCcore/10.2.0`` ``0.5.9.5`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.6.3.1`` ``GCCcore/10.3.0`` =========== ================= ================== @@ -33621,13 +34475,13 @@ A pythonic wrapper around FFTW, the FFT library, presenting a unified interface *homepage*: https://github.com/pyFFTW/pyFFTW -========== ================= ================== -version versionsuffix toolchain -========== ================= ================== -``0.11.1`` ``intel/2019a`` -``0.11.1`` ``-Python-3.6.6`` ``foss/2018b`` -``0.12.0`` ``fosscuda/2020b`` -========== ================= ================== +========== ================= ================================== +version versionsuffix toolchain +========== ================= ================================== +``0.11.1`` ``intel/2019a`` +``0.11.1`` ``-Python-3.6.6`` ``foss/2018b`` +``0.12.0`` ``foss/2020b``, ``fosscuda/2020b`` +========== ================= ================================== .. _list_software_pyfits_671: @@ -34318,22 +35172,22 @@ PyQt5 is a set of Python bindings for v5 of the Qt application framework from Th *homepage*: http://www.riverbankcomputing.co.uk/software/pyqt -========== ================== =============================== -version versionsuffix toolchain -========== ================== =============================== -``5.7`` ``-Python-2.7.11`` ``foss/2016a`` -``5.7.1`` ``-Python-2.7.12`` ``intel/2016b`` -``5.8.2`` ``-Python-2.7.13`` ``intel/2017a`` -``5.9.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``5.9.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``5.11.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` -``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``5.13.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``5.15.1`` ``GCCcore/10.2.0`` -``5.15.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``5.15.4`` ``GCCcore/10.3.0`` -========== ================== =============================== +========== ================== ====================================== +version versionsuffix toolchain +========== ================== ====================================== +``5.7`` ``-Python-2.7.11`` ``foss/2016a`` +``5.7.1`` ``-Python-2.7.12`` ``intel/2016b`` +``5.8.2`` ``-Python-2.7.13`` ``intel/2017a`` +``5.9.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``5.9.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``5.11.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``5.13.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``5.15.1`` ``GCCcore/10.2.0`` +``5.15.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``5.15.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========== ================== ====================================== .. _list_software_PyQtGraph_896: @@ -34501,6 +35355,7 @@ version versionsuffix toolchain ``0.15.3`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ``0.16.0.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` ``0.16.0.1`` ``-Python-2.7.18`` ``GCC/10.2.0`` +``0.17.0`` ``GCC/11.2.0`` ============ ================== ============================================================================================================== @@ -34619,6 +35474,22 @@ version versionsuffix toolchain ========== ================= ================== +.. _list_software_PySide2_640: + +*PySide2* ++++++++++ + +PySide2 is the official Python module from the Qt for Python project, which provides access to the complete Qt 5.12+ framework. + +*homepage*: https://pypi.python.org/pypi/PySide2 + +============ ================== +version toolchain +============ ================== +``5.14.2.3`` ``GCCcore/10.2.0`` +============ ================== + + .. _list_software_pysndfx_780: *pysndfx* @@ -34729,27 +35600,28 @@ PyTables is a package for managing hierarchical datasets and designed to efficie *homepage*: https://www.pytables.org -=========== ================== =================================================================== -version versionsuffix toolchain -=========== ================== =================================================================== -``3.2.2`` ``-Python-2.7.12`` ``foss/2016b`` -``3.2.3.1`` ``-Python-2.7.12`` ``intel/2016b`` -``3.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.3.0`` ``-Python-3.5.2`` ``intel/2016b`` -``3.4.2`` ``-Python-2.7.13`` ``foss/2017a`` -``3.4.2`` ``-Python-3.6.1`` ``intel/2017a`` -``3.4.2`` ``-Python-3.6.3`` ``intel/2017b`` -``3.4.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``3.4.4`` ``-Python-2.7.15`` ``foss/2018b`` -``3.4.4`` ``-Python-3.5.1`` ``foss/2016a`` -``3.4.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``3.5.2`` ``intel/2019a`` -``3.5.2`` ``-Python-2.7.14`` ``intel/2018a`` -``3.5.2`` ``-Python-2.7.16`` ``intel/2019b`` -``3.6.1`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b``, ``intel/2020b`` -``3.6.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``3.6.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -=========== ================== =================================================================== +=========== ================== =================================================================================== +version versionsuffix toolchain +=========== ================== =================================================================================== +``3.2.2`` ``-Python-2.7.12`` ``foss/2016b`` +``3.2.3.1`` ``-Python-2.7.12`` ``intel/2016b`` +``3.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.3.0`` ``-Python-3.5.2`` ``intel/2016b`` +``3.4.2`` ``-Python-2.7.13`` ``foss/2017a`` +``3.4.2`` ``-Python-3.6.1`` ``intel/2017a`` +``3.4.2`` ``-Python-3.6.3`` ``intel/2017b`` +``3.4.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``3.4.4`` ``-Python-2.7.15`` ``foss/2018b`` +``3.4.4`` ``-Python-3.5.1`` ``foss/2016a`` +``3.4.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``3.5.2`` ``intel/2019a`` +``3.5.2`` ``-Python-2.7.14`` ``intel/2018a`` +``3.5.2`` ``-Python-2.7.16`` ``intel/2019b`` +``3.5.2`` ``-Python-2.7.18`` ``foss/2020b`` +``3.6.1`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2020b``, ``intel/2020b`` +``3.6.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``3.6.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +=========== ================== =================================================================================== .. _list_software_pytest_681: @@ -34855,7 +35727,7 @@ version versionsuffix toolchain ``2.7.15`` ``-bare`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``2.7.16`` ``GCCcore/8.3.0`` ``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``2.7.18`` ``-bare`` ``GCCcore/10.3.0`` +``2.7.18`` ``-bare`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.5.1`` ``foss/2016a``, ``intel/2016a`` ``3.5.2`` ``foss/2016.04``, ``foss/2016b``, ``intel/2016b`` ``3.5.2`` ``-bare`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` @@ -34979,6 +35851,7 @@ version versionsuffix toolchain ``1.1.16`` ``-Python-3.6.6`` ``foss/2018b`` ``1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``1.2.2`` ``-Python-3.8.2`` ``intel/2020a`` +``1.2.3`` ``-Python-3.8.2`` ``foss/2020a`` ``1.2.4`` ``foss/2020b``, ``fosscuda/2020b`` ========== ================== =================================================== @@ -35024,30 +35897,32 @@ Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTo *homepage*: https://pytorch.org/ -========= ============================= ================================== -version versionsuffix toolchain -========= ============================= ================================== -``0.3.1`` ``-Python-2.7.14`` ``fosscuda/2017b`` -``0.3.1`` ``-Python-3.6.3`` ``fosscuda/2017b`` -``0.3.1`` ``-Python-3.6.4`` ``intel/2018a`` -``0.3.1`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` -``0.4.1`` ``-Python-3.6.4`` ``intel/2018a`` -``1.0.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``1.1.0`` ``-Python-3.7.2`` ``foss/2019a`` -``1.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` -``1.3.1`` ``fosscuda/2020b`` -``1.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``1.6.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``1.6.0`` ``-Python-3.7.4-imkl`` ``fosscuda/2019b`` -``1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` -``1.7.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``1.7.1`` ``-Python-3.8.2`` ``fosscuda/2020a`` -``1.8.1`` ``foss/2020b``, ``fosscuda/2020b`` -``1.8.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``1.9.0`` ``foss/2020b``, ``fosscuda/2020b`` -``1.9.0`` ``-imkl`` ``fosscuda/2020b`` -========= ============================= ================================== +========== ============================= ================================== +version versionsuffix toolchain +========== ============================= ================================== +``0.3.1`` ``-Python-2.7.14`` ``fosscuda/2017b`` +``0.3.1`` ``-Python-3.6.3`` ``fosscuda/2017b`` +``0.3.1`` ``-Python-3.6.4`` ``intel/2018a`` +``0.3.1`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` +``0.4.1`` ``-Python-3.6.4`` ``intel/2018a`` +``1.0.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``1.1.0`` ``-Python-3.7.2`` ``foss/2019a`` +``1.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` +``1.3.1`` ``fosscuda/2020b`` +``1.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.6.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.6.0`` ``-Python-3.7.4-imkl`` ``fosscuda/2019b`` +``1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` +``1.7.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.7.1`` ``-Python-3.8.2`` ``fosscuda/2020a`` +``1.8.1`` ``foss/2020b``, ``fosscuda/2020b`` +``1.8.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.9.0`` ``foss/2020b``, ``fosscuda/2020b`` +``1.9.0`` ``-imkl`` ``fosscuda/2020b`` +``1.10.0`` ``foss/2021a`` +``1.10.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +========== ============================= ================================== .. _list_software_PyTorch-Geometric_1685: @@ -35682,7 +36557,7 @@ version versionsuffix toolchain ``6.5`` ``intel/2019a``, ``intel/2019b`` ``6.6`` ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2019b`` ``6.7`` ``foss/2019b``, ``foss/2020b``, ``foss/2021a``, ``intel/2019b``, ``intel/2021a``, ``iomkl/2019b`` -``6.8`` ``foss/2021a``, ``intel/2021a`` +``6.8`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` ========= ============= ================================================================================================= @@ -35700,7 +36575,7 @@ version versionsuffix toolchain ========= ================== ============================== ``4.6.0`` ``-Python-3.5.2`` ``foss/2016b`` ``4.6.3`` ``-Python-3.6.4`` ``foss/2018a`` -``5.0.2`` ``foss/2020b`` +``5.0.2`` ``foss/2020b``, ``foss/2021a`` ``5.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` ``5.0.2`` ``-Python-2.7.18`` ``foss/2020b`` ``5.0.2`` ``-Python-3.7.2`` ``foss/2019a`` @@ -35834,7 +36709,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -35872,6 +36747,7 @@ version versionsuffix toolchain ``4.0.4`` ``foss/2020b``, ``fosscuda/2020b`` ``4.0.5`` ``foss/2020b``, ``fosscuda/2020b`` ``4.1.0`` ``foss/2021a`` +``4.1.2`` ``foss/2021b`` ========= ============================= =================================================== @@ -35900,6 +36776,7 @@ version versionsuffix toolchain ``3.11`` ``-R-4.0.0`` ``foss/2020a`` ``3.12`` ``-R-4.0.3`` ``foss/2020b`` ``3.13`` ``-R-4.1.0`` ``foss/2021a`` +``3.14`` ``-R-4.1.2`` ``foss/2021b`` ======== ============= =============================== @@ -35979,15 +36856,15 @@ Ultrafast consensus module for raw de novo genome assembly of long uncorrected r *homepage*: https://github.com/clara-genomics/racon-gpu -========== ==================================== -version toolchain -========== ==================================== -``1.3.2`` ``GCCcore/8.2.0`` -``1.4.7`` ``GCCcore/8.2.0``, ``gcccuda/2019b`` -``1.4.10`` ``GCC/7.3.0-2.30`` -``1.4.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.4.21`` ``GCCcore/10.2.0`` -========== ==================================== +========== ====================================== +version toolchain +========== ====================================== +``1.3.2`` ``GCCcore/8.2.0`` +``1.4.7`` ``GCCcore/8.2.0``, ``gcccuda/2019b`` +``1.4.10`` ``GCC/7.3.0-2.30`` +``1.4.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.4.21`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========== ====================================== .. _list_software_radeontop_972: @@ -36317,7 +37194,7 @@ version versionsuffix toolchain Rclone is a command line program to sync files and directories to and from a variety of online storage services -*homepage*: https://rclone.org/ +*homepage*: https://rclone.org ========== ============= ========== version versionsuffix toolchain @@ -36325,6 +37202,7 @@ version versionsuffix toolchain ``1.42`` ``-amd64`` ``system`` ``1.54.1`` ``-amd64`` ``system`` ``1.56.0`` ``-amd64`` ``system`` +``1.57.0`` ``system`` ========== ============= ========== @@ -36577,6 +37455,8 @@ version toolchain ``3.6.3`` ``system`` ``3.7.3`` ``system`` ``3.8.0`` ``system`` +``3.9.0`` ``system`` +``3.9.1`` ``system`` ========= ========== @@ -36597,6 +37477,22 @@ version toolchain ========= ============== +.. _list_software_Relate_605: + +*Relate* +++++++++ + +Software for estimating genome-wide genealogies for thousands of samples + +*homepage*: https://myersgroup.github.io/relate/ + +============ ============= ============== +version versionsuffix toolchain +============ ============= ============== +``20211123`` ``-R-4.0.3`` ``foss/2020b`` +============ ============= ============== + + .. _list_software_RELION_457: *RELION* @@ -37187,6 +38083,118 @@ version versionsuffix toolchain ========== ================ =============== +.. _list_software_ROCm_337: + +*ROCm* +++++++ + +AMD ROCm is the first open-source software development platform for HPC/Hyperscale-class GPU computing. AMD ROCm brings the UNIX philosophy of choice, minimalism and modular software development to GPU computing. + +*homepage*: https://rocmdocs.amd.com/en/latest/ + +========= ================== +version toolchain +========= ================== +``4.5.0`` ``GCCcore/11.2.0`` +========= ================== + + +.. _list_software_rocm-cmake_991: + +*rocm-cmake* +++++++++++++ + +ROCM cmake modules provides cmake modules for common build tasks needed for the ROCM software stack + +*homepage*: https://github.com/RadeonOpenCompute/rocm-cmake + +========= ================== +version toolchain +========= ================== +``4.5.0`` ``GCCcore/11.2.0`` +========= ================== + + +.. _list_software_ROCm-CompilerSupport_1974: + +*ROCm-CompilerSupport* +++++++++++++++++++++++ + +The compiler support repository provides various Lightning Compiler related services + +*homepage*: https://github.com/RadeonOpenCompute/ROCm-CompilerSupport + +========= ================== +version toolchain +========= ================== +``4.5.0`` ``GCCcore/11.2.0`` +========= ================== + + +.. _list_software_rocm-smi_807: + +*rocm-smi* +++++++++++ + +The ROCm System Management Interface Library, or ROCm SMI library, is part of the Radeon Open Compute ROCm software stack. It is a C library for Linux that provides a user space interface for applications to monitor and control GPU applications. + +*homepage*: https://github.com/RadeonOpenCompute/rocm_smi_lib + +========= ================== +version toolchain +========= ================== +``4.5.0`` ``GCCcore/11.2.0`` +========= ================== + + +.. _list_software_rocminfo_861: + +*rocminfo* +++++++++++ + +ROCm Application for Reporting System Info + +*homepage*: https://github.com/RadeonOpenCompute/rocminfo + +========= ================== +version toolchain +========= ================== +``4.5.0`` ``GCCcore/11.2.0`` +========= ================== + + +.. _list_software_ROCR-Runtime_1095: + +*ROCR-Runtime* +++++++++++++++ + +The user-mode API interfaces and libraries necessary for host applications to launch compute kernels to available HSA ROCm kernel agents + +*homepage*: https://github.com/RadeonOpenCompute/ROCR-Runtime + +========= ================== +version toolchain +========= ================== +``4.5.0`` ``GCCcore/11.2.0`` +========= ================== + + +.. _list_software_ROCT-Thunk-Interface_1837: + +*ROCT-Thunk-Interface* +++++++++++++++++++++++ + +The user-mode API interfaces used to interact with the ROCk driver + +*homepage*: https://github.com/RadeonOpenCompute/ROCT-Thunk-Interface + +========= ================== +version toolchain +========= ================== +``4.5.0`` ``GCCcore/11.2.0`` +========= ================== + + .. _list_software_ROI_PAC_541: *ROI_PAC* @@ -37326,6 +38334,7 @@ version versionsuffix toolchain ``2.7.9`` ``-Python-2.7.12`` ``foss/2016b`` ``2.8.2`` ``-Python-2.7.13`` ``intel/2017a`` ``3.2.6`` ``-Python-3.7.4`` ``foss/2019b`` +``3.4.5`` ``foss/2021b`` ========= ================== =============== @@ -37548,7 +38557,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -37773,6 +38782,7 @@ version versionsuffix toolchain ``1.11`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` ``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` ``1.13`` ``GCC/10.3.0`` +``1.14`` ``GCC/11.2.0`` ========== ================= ======================================================================================================================================= @@ -37974,6 +38984,22 @@ version toolchain ========= ============================== +.. _list_software_SCENIC_437: + +*SCENIC* +++++++++ + +SCENIC Suite is a set of tools to study and decipher gene regulation. + +*homepage*: https://scenic.aertslab.org + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``1.2.4`` ``-R-4.1.0`` ``foss/2021a`` +========= ============= ============== + + .. _list_software_scGeneFit_888: *scGeneFit* @@ -38134,6 +39160,7 @@ version versionsuffix toolchain ``0.16.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``0.17.1`` ``-Python-3.8.2`` ``foss/2020a`` ``0.18.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``0.18.3`` ``foss/2021a`` ========== ================== =================================================== @@ -38176,7 +39203,8 @@ version versionsuffix toolchain ``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``0.23.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``0.23.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -``0.24.2`` ``foss/2021a`` +``0.24.2`` ``foss/2021a``, ``intel/2021a`` +``1.0.1`` ``foss/2021b`` ========== ================================= ======================================================================== @@ -38286,7 +39314,7 @@ version versionsuffix toolchain ``2020.11`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``2020.11`` ``-Python-2.7.18`` ``foss/2020b`` ``2021.05`` ``foss/2021a``, ``intel/2021a`` -``2021.10`` ``foss/2021b`` +``2021.10`` ``foss/2021b``, ``intel/2021b`` =========== ================== ======================================================================== @@ -38609,7 +39637,7 @@ version versionsuffix toolchain ``0.10.1`` ``intel/2020b`` ``0.10.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``0.11.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``0.11.2`` ``foss/2021a`` +``0.11.2`` ``foss/2021a``, ``foss/2021b`` ========== ================== ========================================================================================= @@ -39148,6 +40176,22 @@ version toolchain ======== ================= +.. _list_software_Shasta_612: + +*Shasta* +++++++++ + +The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input. Computational methods used by the Shasta assembler include: Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads. Using in some phases of the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10). + +*homepage*: https://github.com/chanzuckerberg/shasta + +========= ============== +version toolchain +========= ============== +``0.8.0`` ``foss/2020b`` +========= ============== + + .. _list_software_shift_542: *shift* @@ -39334,6 +40378,22 @@ version versionsuffix toolchain ========== ================= ================================== +.. _list_software_SimNIBS_597: + +*SimNIBS* ++++++++++ + +SimNIBS is a free and open source software package for the Simulation of Non-invasive Brain Stimulation. + +*homepage*: https://simnibs.github.io/simnibs + +========= ============== +version toolchain +========= ============== +``3.2.4`` ``foss/2020b`` +========= ============== + + .. _list_software_SimPEG_517: *SimPEG* @@ -39391,7 +40451,7 @@ version versionsuffix toolchain *SimpleITK* +++++++++++ -ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. Among them, SimpleITK is a simplified layer built on top of ITK, intended to facilitate its use in rapid prototyping, education, interpreted languages. +SimpleITK is a simplified programming interface to the algorithms and data structures of the Insight Toolkit (ITK). *homepage*: http://www.simpleitk.org @@ -39402,6 +40462,7 @@ version versionsuffix toolchain ``1.1.0`` ``-Python-3.6.4`` ``foss/2018a`` ``1.1.0`` ``-Python-3.6.6`` ``foss/2018b`` ``1.2.4`` ``-Python-3.7.4`` ``foss/2019b`` +``2.1.0`` ``foss/2020b`` ========= ================== ============== @@ -39759,11 +40820,11 @@ smith-waterman-gotoh alignment algorithm. *homepage*: https://github.com/ekg/smithwaterman -============ ===================================== -version toolchain -============ ===================================== -``20160702`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -============ ===================================== +============ ========================================================= +version toolchain +============ ========================================================= +``20160702`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +============ ========================================================= .. _list_software_Smoldyn_742: @@ -39799,6 +40860,22 @@ version versionsuffix toolchain =============== =================== ========== +.. _list_software_SMV_246: + +*SMV* ++++++ + +Smokeview is a visualization program that displays output of FDS and CFAST simulations. + +*homepage*: https://github.com/firemodels/smv + +========== ======================= +version toolchain +========== ======================= +``6.7.17`` ``iccifort/2020.4.304`` +========== ======================= + + .. _list_software_snakemake_944: *snakemake* @@ -39817,6 +40894,7 @@ version versionsuffix toolchain ``5.26.1`` ``-Python-3.8.2`` ``intel/2020a`` ``6.1.0`` ``foss/2020b`` ``6.6.1`` ``foss/2021a`` +``6.10.0`` ``foss/2021b`` ========== ================= =============================== @@ -39933,11 +41011,11 @@ Finds SNP sites from a multi-FASTA alignment file. *homepage*: https://sanger-pathogens.github.io/snp-sites/ -========= ===================================== -version toolchain -========= ===================================== -``2.5.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========= ===================================== +========= ========================================================= +version toolchain +========= ========================================================= +``2.5.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +========= ========================================================= .. _list_software_snpEff_610: @@ -40233,6 +41311,7 @@ version versionsuffix toolchain ``3.14.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` ``3.15.2`` ``GCC/10.2.0`` ``3.15.2`` ``-Python-2.7.18`` ``GCC/10.2.0`` +``3.15.3`` ``GCC/10.3.0`` ========== ================== ============================================== @@ -40427,7 +41506,7 @@ version versionsuffix toolchain ``1.16.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.16.0`` ``-Python-3.7.4`` ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` ``1.16.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.16.1`` ``foss/2021a`` +``1.16.1`` ``foss/2021a``, ``intel/2021a`` ================ ================== ======================================================== @@ -40583,6 +41662,7 @@ Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) alg version toolchain ========= ================== ``3.0.1`` ``GCC/7.3.0-2.30`` +``3.4.0`` ``GCC/10.2.0`` ``4.0.0`` ``GCC/8.3.0`` ``4.0.7`` ``GCC/10.2.0`` ========= ================== @@ -40717,6 +41797,22 @@ version versionsuffix toolchain ========= ============= ================== +.. _list_software_SRST2_382: + +*SRST2* ++++++++ + +Short Read Sequence Typing for Bacterial Pathogens + +*homepage*: https://katholt.github.io/srst2 + +================== ================== ============== +version versionsuffix toolchain +================== ================== ============== +``0.2.0-20210620`` ``-Python-2.7.18`` ``foss/2020b`` +================== ================== ============== + + .. _list_software_SSAHA2_418: *SSAHA2* @@ -40759,12 +41855,13 @@ SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension *homepage*: https://github.com/nsoranzo/sspace_basic -========= ================ =============== -version versionsuffix toolchain -========= ================ =============== -``2.1.1`` ``-Perl-5.24.1`` ``intel/2017a`` -``2.1.1`` ``-Perl-5.26.0`` ``intel/2017b`` -========= ================ =============== +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``2.1.1`` ``-Perl-5.24.1`` ``intel/2017a`` +``2.1.1`` ``-Perl-5.26.0`` ``intel/2017b`` +``2.1.1`` ``-Python-2.7.18`` ``GCC/10.2.0`` +========= ================== =============== .. _list_software_SSW_253: @@ -40783,6 +41880,22 @@ version toolchain ======= ===================================== +.. _list_software_STACEY_457: + +*STACEY* +++++++++ + +The BEAST2 package STACEY can be used for species delimitation and species tree estimation, based on the multispecies coalescent model. + +*homepage*: http://www.indriid.com/software.html + +========= ============== +version toolchain +========= ============== +``1.2.5`` ``GCC/10.2.0`` +========= ============== + + .. _list_software_Stack_502: *Stack* @@ -41023,6 +42136,7 @@ Detects integrations of any sort in high-throughput sequencing (HTS) data. STEA ============== ================== ============== version versionsuffix toolchain ============== ================== ============== +``2019.09.12`` ``foss/2021b`` ``2019.09.12`` ``-Python-2.7.16`` ``foss/2019b`` ============== ================== ============== @@ -41235,7 +42349,7 @@ version versionsuffix toolchain ``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b``, ``intel/2019b`` ``5.7.1`` ``-METIS-5.1.0`` ``foss/2020a``, ``intel/2020a`` ``5.8.1`` ``-METIS-5.1.0`` ``foss/2020b``, ``intel/2020b`` -``5.10.1`` ``-METIS-5.1.0`` ``foss/2021a`` +``5.10.1`` ``-METIS-5.1.0`` ``foss/2021a``, ``foss/2021b`` ========== =================== ================================================================================================= @@ -41668,7 +42782,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` +:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_termcolor_983` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_ThemisPy_819` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmux_462` - :ref:`list_software_TOBIAS_450` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` .. _list_software_tabix_536: @@ -41696,11 +42810,11 @@ C++ wrapper to tabix indexer *homepage*: https://github.com/ekg/tabixpp -========= ============================= -version toolchain -========= ============================= -``1.1.0`` ``GCC/10.2.0``, ``GCC/9.3.0`` -========= ============================= +========= ============================================= +version toolchain +========= ============================================= +``1.1.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` +========= ============================================= .. _list_software_taco_423: @@ -41827,28 +42941,29 @@ Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ *homepage*: https://software.intel.com/en-us/articles/intel-tbb/ -============== ================================================== -version toolchain -============== ================================================== -``4.0.0.233`` ``system`` -``4.0.5.339`` ``system`` -``4.3.6.211`` ``system`` -``4.4.2.152`` ``system`` -``2017.2.132`` ``system`` -``2017.4.174`` ``system`` -``2017.6.196`` ``system`` -``2017_U5`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2017a`` -``2017_U6`` ``GCCcore/6.3.0``, ``intel/2017a`` -``2018_U1`` ``GCCcore/6.4.0`` -``2018_U2`` ``GCCcore/6.4.0`` -``2018_U3`` ``GCCcore/6.4.0`` -``2018_U5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2019_U4`` ``GCCcore/8.2.0`` -``2019_U9`` ``GCCcore/8.3.0`` -``2020.1`` ``GCCcore/9.3.0`` -``2020.2`` ``GCCcore/8.3.0`` -``2020.3`` ``GCCcore/10.2.0`` -============== ================================================== +============== ========================================================== +version toolchain +============== ========================================================== +``4.0.0.233`` ``system`` +``4.0.5.339`` ``system`` +``4.3.6.211`` ``system`` +``4.4.2.152`` ``system`` +``2017.2.132`` ``system`` +``2017.4.174`` ``system`` +``2017.6.196`` ``system`` +``2017_U5`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2017a`` +``2017_U6`` ``GCCcore/6.3.0``, ``intel/2017a`` +``2018_U1`` ``GCCcore/6.4.0`` +``2018_U2`` ``GCCcore/6.4.0`` +``2018_U3`` ``GCCcore/6.4.0`` +``2018_U5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2019_U4`` ``GCCcore/8.2.0`` +``2019_U9`` ``GCCcore/8.3.0`` +``2020.1`` ``GCCcore/9.3.0`` +``2020.2`` ``GCCcore/8.3.0`` +``2020.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2021.4.0`` ``GCCcore/11.2.0`` +============== ========================================================== .. _list_software_tbl2asn_694: @@ -42128,6 +43243,22 @@ version toolchain ======= ============= +.. _list_software_termcolor_983: + +*termcolor* ++++++++++++ + +Termcolor is a header-only C++ library for printing colored messages to the terminal. + +*homepage*: https://termcolor.readthedocs.io/ + +========= ========== +version toolchain +========= ========== +``2.0.0`` ``system`` +========= ========== + + .. _list_software_Tesla-Deployment-Kit_1948: *Tesla-Deployment-Kit* @@ -42316,6 +43447,22 @@ version versionsuffix toolchain ========= ================== =================================================== +.. _list_software_ThemisPy_819: + +*ThemisPy* +++++++++++ + +A header-only C++ library for L-BFGS and L-BFGS-B algorithms + +*homepage*: https://github.com/aeb/ThemisPy + +========= ============== +version toolchain +========= ============== +``0.3.0`` ``foss/2021a`` +========= ============== + + .. _list_software_THetA_438: *THetA* @@ -42592,6 +43739,22 @@ version toolchain ======== ====================================== +.. _list_software_TOBIAS_450: + +*TOBIAS* +++++++++ + +TOBIAS is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data, and includes: Correction of Tn5 insertion bias; Calculation of footprint scores within regulatory regions; Estimation of bound/unbound transcription factor binding sites; and Visualization of footprints within and across different conditions + +*homepage*: https://github.com/loosolab/TOBIAS + +=========== ============== +version toolchain +=========== ============== +``0.12.12`` ``foss/2021b`` +=========== ============== + + .. _list_software_ToFu_382: *ToFu* @@ -42720,14 +43883,15 @@ Data loaders and abstractions for text and NLP *homepage*: https://github.com/pytorch/text -========= =============================== ================================== -version versionsuffix toolchain -========= =============================== ================================== -``0.5.0`` ``-PyTorch-1.4.0-Python-3.7.4`` ``fosscuda/2019b`` -``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` -``0.8.1`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` -``0.9.1`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` -========= =============================== ================================== +========== =============================== ================================== +version versionsuffix toolchain +========== =============================== ================================== +``0.5.0`` ``-PyTorch-1.4.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` +``0.8.1`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` +``0.9.1`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` +``0.10.0`` ``-PyTorch-1.9.0`` ``fosscuda/2020b`` +========== =============================== ================================== .. _list_software_torchvision_1208: @@ -42739,23 +43903,26 @@ Datasets, Transforms and Models specific to Computer Vision *homepage*: https://github.com/pytorch/vision -========= ==================================== ================================== -version versionsuffix toolchain -========= ==================================== ================================== -``0.2.0`` ``-Python-3.6.4`` ``intel/2018a`` -``0.2.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` -``0.2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` -``0.4.2`` ``-PyTorch-1.3.1`` ``fosscuda/2020b`` -``0.4.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``0.5.0`` ``-Python-3.7.4-PyTorch-1.4.0`` ``fosscuda/2019b`` -``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` -``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0-imkl`` ``fosscuda/2019b`` -``0.8.2`` ``-PyTorch-1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` -``0.8.2`` ``-Python-3.7.4-PyTorch-1.7.1`` ``fosscuda/2019b`` -``0.9.1`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` -``0.9.1`` ``-Python-3.7.4-PyTorch-1.8.1`` ``fosscuda/2019b`` -========= ==================================== ================================== +========== ==================================== ================================== +version versionsuffix toolchain +========== ==================================== ================================== +``0.2.0`` ``-Python-3.6.4`` ``intel/2018a`` +``0.2.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` +``0.2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` +``0.4.2`` ``-PyTorch-1.3.1`` ``fosscuda/2020b`` +``0.4.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``0.5.0`` ``-Python-3.7.4-PyTorch-1.4.0`` ``fosscuda/2019b`` +``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` +``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0-imkl`` ``fosscuda/2019b`` +``0.8.2`` ``-PyTorch-1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` +``0.8.2`` ``-Python-3.7.4-PyTorch-1.7.1`` ``fosscuda/2019b`` +``0.9.1`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` +``0.9.1`` ``-Python-3.7.4-PyTorch-1.8.1`` ``fosscuda/2019b`` +``0.10.0`` ``-PyTorch-1.9.0`` ``fosscuda/2020b`` +``0.11.1`` ``foss/2021a`` +``0.11.1`` ``-CUDA-11.3.1`` ``foss/2021a`` +========== ==================================== ================================== .. _list_software_TotalView_927: @@ -42800,6 +43967,7 @@ version versionsuffix toolchain ``4.60.0`` ``GCCcore/10.2.0`` ``4.61.1`` ``GCCcore/10.3.0`` ``4.61.2`` ``GCCcore/10.3.0`` +``4.62.3`` ``GCCcore/11.2.0`` ========== ================== =============================== @@ -43196,15 +44364,16 @@ version versionsuffix toolchain *TRUST4* ++++++++ -Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR sequences. +Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to report the corresponding information. TRUST4 supports both single-end and paired-end sequencing data with any read length. *homepage*: https://github.com/liulab-dfci/TRUST4 -=========== ========== -version toolchain -=========== ========== -``1.0.5.1`` ``system`` -=========== ========== +=========== ============== +version toolchain +=========== ============== +``1.0.5.1`` ``system`` +``1.0.6`` ``GCC/11.2.0`` +=========== ============== .. _list_software_Trycycler_961: @@ -43220,6 +44389,7 @@ Trycycler is a tool for generating consensus long-read assemblies for bacterial version versionsuffix toolchain ========= ================= ============== ``0.3.3`` ``-Python-3.8.2`` ``foss/2020a`` +``0.5.2`` ``foss/2021a`` ========= ================= ============== @@ -43611,6 +44781,7 @@ version versionsuffix toolchain ========= ================= =============== ``0.4.7`` ``-Python-3.7.2`` ``foss/2019a`` ``0.4.8`` ``-Python-3.8.2`` ``gompi/2020a`` +``0.4.9`` ``gompi/2021a`` ========= ================= =============== @@ -43760,6 +44931,7 @@ UShER is now a package consisting of a family of programs for rapid phylogeneti version toolchain ========= =============== ``0.4.1`` ``gompi/2020b`` +``0.5.0`` ``gompi/2021b`` ========= =============== @@ -44097,12 +45269,12 @@ vcflib provides methods to manipulate and interpret sequence variation as it can *homepage*: https://github.com/vcflib/vcflib -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``1.0.2`` ``GCC/10.2.0`` -``1.0.2`` ``-Python-3.8.2`` ``GCC/9.3.0`` -========= ================= ============== +========= ================= ============================== +version versionsuffix toolchain +========= ================= ============================== +``1.0.2`` ``GCC/10.2.0``, ``GCC/10.3.0`` +``1.0.2`` ``-Python-3.8.2`` ``GCC/9.3.0`` +========= ================= ============================== .. _list_software_vcfnp_541: @@ -44504,6 +45676,7 @@ version versionsuffix toolchain ``5.2.4`` ``system`` ``5.2.5`` ``system`` ``5.2.6`` ``system`` +``5.2.7`` ``system`` =========== ================================== =============== @@ -44637,6 +45810,7 @@ version toolchain ``2019_update5`` ``system`` ``2020_update3`` ``system`` ``2021.6.0`` ``system`` +``2021.9.0`` ``system`` ================= ========== @@ -44706,16 +45880,16 @@ A tool for obtaining maximally-localised Wannier functions *homepage*: http://www.wannier.org -=========== ============= ================================================================================= -version versionsuffix toolchain -=========== ============= ================================================================================= -``1.2`` ``intel/2016.02-GCC-4.9`` -``2.0.1`` ``intel/2016.02-GCC-4.9``, ``intel/2016a`` -``2.0.1.1`` ``-abinit`` ``intel/2018b`` -``2.1.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``3.0.0`` ``intel/2018b`` -``3.1.0`` ``foss/2020b``, ``foss/2021a``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a`` -=========== ============= ================================================================================= +=========== ============= ================================================================================================================== +version versionsuffix toolchain +=========== ============= ================================================================================================================== +``1.2`` ``intel/2016.02-GCC-4.9`` +``2.0.1`` ``intel/2016.02-GCC-4.9``, ``intel/2016a`` +``2.0.1.1`` ``-abinit`` ``intel/2018b`` +``2.1.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``3.0.0`` ``intel/2018b`` +``3.1.0`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` +=========== ============= ================================================================================================================== .. _list_software_WannierTools_1253: @@ -45073,6 +46247,7 @@ version versionsuffix toolchain ``4.0.2`` ``-dmpar`` ``foss/2018b`` ``4.1`` ``-dmpar`` ``intel/2019b`` ``4.2`` ``-dmpar`` ``foss/2020b`` +``4.3.1`` ``-dmpar`` ``foss/2021a`` ========= ============= =============== @@ -45341,6 +46516,7 @@ version versionsuffix toolchain ``0.16.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``0.16.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``0.19.0`` ``foss/2021a`` +``0.20.1`` ``foss/2021b``, ``intel/2021b`` ========== ================== =================================================== @@ -45645,6 +46821,7 @@ version toolchain ========= ================== ``1.4.0`` ``GCCcore/10.2.0`` ``1.4.4`` ``GCCcore/10.3.0`` +``3.0.2`` ``GCCcore/11.2.0`` ========= ================== @@ -46040,6 +47217,7 @@ Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecula version toolchain ========= ========================= ``3.4.2`` ``intel/2016.02-GCC-4.9`` +``5.0.4`` ``intel/2021a`` ========= ========================= @@ -46134,7 +47312,7 @@ version toolchain --- -:ref:`list_software_Z3_141` - :ref:`list_software_zarr_447` - :ref:`list_software_ZeroMQ_574` - :ref:`list_software_zingeR_623` - :ref:`list_software_Zip_307` - :ref:`list_software_zlib_433` - :ref:`list_software_zlibbioc_846` - :ref:`list_software_ZPAQ_316` - :ref:`list_software_zsh_341` - :ref:`list_software_zstd_453` +:ref:`list_software_Z3_141` - :ref:`list_software_zarr_447` - :ref:`list_software_ZeroMQ_574` - :ref:`list_software_zfp_336` - :ref:`list_software_zingeR_623` - :ref:`list_software_Zip_307` - :ref:`list_software_zlib_433` - :ref:`list_software_zlib-ng_691` - :ref:`list_software_zlibbioc_846` - :ref:`list_software_Zopfli_628` - :ref:`list_software_ZPAQ_316` - :ref:`list_software_zsh_341` - :ref:`list_software_zstd_453` .. _list_software_Z3_141: @@ -46198,6 +47376,22 @@ version toolchain ========= ========================================================================================================= +.. _list_software_zfp_336: + +*zfp* ++++++ + +zfp is a compressed format for representing multidimensional floating-point and integer arrays. zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications that read and write large data sets to and from disk. + +*homepage*: https://github.com/LLNL/zfp + +========= ================== +version toolchain +========= ================== +``0.5.5`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_zingeR_623: *zingeR* @@ -46249,6 +47443,22 @@ version toolchain ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +.. _list_software_zlib-ng_691: + +*zlib-ng* ++++++++++ + +zlib data compression library for the next generation systems + +*homepage*: https://github.com/zlib-ng/zlib-ng + +========= ================== +version toolchain +========= ================== +``2.0.5`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_zlibbioc_846: *zlibbioc* @@ -46266,6 +47476,22 @@ version versionsuffix toolchain ========== ============= =============== +.. _list_software_Zopfli_628: + +*Zopfli* +++++++++ + +Zopfli Compression Algorithm is a compression library programmed in C to perform very good, but slow, deflate or zlib compression. + +*homepage*: https://github.com/google/zopfli + +========= ================== +version toolchain +========= ================== +``1.0.3`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_ZPAQ_316: *ZPAQ* diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index 861787f1..cd9d12fe 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -52,6 +52,7 @@ * BuildEnv * CrayToolchain + * EB_Clang_minus_AOMP * EB_OpenSSL_wrapper * PythonBundle * SystemCompiler From 17b6cd5a85cab4cd5fea4bd7c74366fdf1af86be Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Dec 2021 20:03:18 +0800 Subject: [PATCH 182/286] update release notes and changelog for EasyBuild v4.5.1 + bump version to 4.5.1 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 127 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 128 insertions(+), 4 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 50e95849..2fb0cd62 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20211213.01** (`Dec 13th 2021`): update release notes for EasyBuild v4.5.1 (see :ref:`release_notes_eb451`) * **release 20211029.01** (`Oct 29th 2021`): update release notes for EasyBuild v4.5.0 (see :ref:`release_notes_eb450`) * **release 20210907.01** (`Sep 7th 2021`): update release notes for EasyBuild v4.4.2 (see :ref:`release_notes_eb442`) * **release 20210706.01** (`Jul 6th 2021`): update release notes for EasyBuild v4.4.1 (see :ref:`release_notes_eb441`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index de85cda7..858d85ce 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,135 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,506** different software packages, +The latest version of EasyBuild provides support for building and installing **2,575** different software packages, including 36 different (compiler) toolchains. It contains 242 software-specific easyblocks and 37 generic easyblocks, -alongside 13,514 easyconfig files. +alongside 13,812 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb451: + +EasyBuild v4.5.1 (December 13th 2021) +------------------------------------- + +bugfix/update release + +**framework** + +* various enhancements, including: + + * also dump environment to reprod directory (`#3374 `_) + * determine which extensions can be skipped in parallel (if ``--parallel-extensions-install`` is enabled) (`#3890 `_) + * fall back to sequential installation for extensions with unknown dependencies when using ``--parallel-extensions-install`` (`#3906 `_) + * allow oversubscription in sanity check for OpenMPI-based toolchains (`#3909 `_) + +* various bug fixes, including: + + * don't try to ensure absolute path for path part of ``repositorypath`` (`#3893 `_, `#3899 `_) + * fix typo in EULA agreement error message (`#3894 `_) + * only remove lock if it was created in the same EasyBuild session (not if it existed already) (`#3889 `_) + * introduce ``EasyBlock.post_init`` method to correctly define ``builddir`` variable when ``build-in-installdir`` mode is enabled in easyconfig or easyblock (`#3900 `_) + * also show download progress bar when using ``--inject-checksums`` (`#3905 `_) + * pick up custom ``extract_cmd`` specified for extension (`#3907 `_) + * make ``test_run_cmd_async`` more robust against fluke failures (`#3908 `_) + +**easyblocks** + +* new software-specific easyblock for Clang-AOMP (`#2617 `_) +* minor enhancements and updates, including: + + * enhance Rpm generic easyblock to support installing tarball of RPMs (by unpacking it first) + take into account ``(pre)installopts`` (`#2580 `_) + * add option to control use of MKL-DNN in jaxlib easyblock (`#2619 `_) + * update SAMtools easyblock to support installation of SAMtools 1.14 (`#2620 `_) + * add option to ignore PLUMED version check for GROMACS (`#2621 `_) + * update Inspector easyblock for recent versions (>= 2021, oneAPI versions) (`#2624 `_) + * enhance tbb easyblock by adding option to build Python bindings (`#2626 `_) + * fix patching of ``CMakeLists.txt`` for Eigen v3.4 (`#2633 `_) + +* various bug fixes, including: + + * update CP2K easyblock to use ``-D__MKL`` for CP2K versions newer than 2.3 (`#2586 `_) + * set OpenMPI configuration for ORCA sanity check (`#2596 `_) + * allow oversubscription in OpenMPI sanity check (`#2611 `_) + * set ``wm_*`` class variables in OpenFOAM easyblock constructor (to fix ``--sanity-check-only``) (`#2616 `_) + * remove newline from easybuild-easyblocks package description (required to avoid installation error with setuptools>=59.0.0) (`#2623 `_) + * avoid patching binary files + other enhancements for MUMmer easyblock (`#2630 `_) + * enable ``build-in-installdir`` mode in constructor of PETSc and SLEPc easyblocks (`#2631 `_) + * skip netcdf4-python tests that require network connectivity (`#2634 `_) + + +**easyconfigs** + +* added example easyconfig files for 71 new software packages: + + * ANIcalculator (`#14478 `_, `#14494 `_, `#14510 `_), arrow-R (`#14267 `_), ASAP (`#14367 `_), BabelStream (`#14503 `_), bamtofastq (`#14391 `_), + bcbio-gff (`#14322 `_), biom-format (`#13205 `_), Blosc2 (`#14247 `_), boto3 (`#14452 `_), Brotli-python (`#14528 `_), Brunsli (`#14247 `_), + Clang-AOMP (`#14327 `_), CLEASE (`#14413 `_), CMSeq (`#14326 `_), cpu_features (`#14385 `_), cromwell (`#12125 `_), + cxxopts (`#14487 `_, `#14504 `_), dRep (`#14479 `_), DUBStepR (`#14495 `_), eht-imaging (`#14239 `_), einops (`#14373 `_), + ELFIO (`#14488 `_, `#14504 `_), elprep (`#14422 `_), epiScanpy (`#14447 `_), FMM3D (`#14257 `_), FORD (`#13653 `_), GPy (`#14380 `_), + HIP (`#14339 `_), idemux (`#14499 `_), imagecodecs (`#14247 `_), InChI (`#13902 `_), jupyter-matlab-proxy (`#14270 `_), jxrlib (`#14247 `_), + LBFGS++ (`#14230 `_), LERC (`#14247 `_), libaec (`#14247 `_), libavif (`#14246 `_), LibLZF (`#14246 `_), libnsl (`#14494 `_), + libtree (`#14501 `_), LPeg (`#14157 `_), Megalodon (`#14256 `_), nnU-Net (`#14249 `_), PAL2NAL (`#14430 `_), photontorch (`#14410 `_), + pkgconf (`#14426 `_), pmx (`#14319 `_), PPanGGOLiN (`#14449 `_), ProFit (`#14340 `_), pugixml (`#14367 `_, `#14492 `_), PySide2 (`#13460 `_), + Relate (`#14443 `_), ROCm (`#14355 `_), rocm-cmake (`#14327 `_), ROCm-CompilerSupport (`#14327 `_), rocminfo (`#14327 `_), + rocm-smi (`#14354 `_), ROCR-Runtime (`#14327 `_), ROCT-Thunk-Interface (`#14327 `_), SCENIC (`#14260 `_), Shasta (`#14385 `_), + SimNIBS (`#14257 `_), SMV (`#14157 `_), SRST2 (`#14253 `_), STACEY (`#14293 `_), termcolor (`#14489 `_, `#14504 `_), ThemisPy (`#14231 `_), + TOBIAS (`#14452 `_, `#14458 `_), zfp (`#14246 `_), zlib-ng (`#14246 `_), Zopfli (`#14246 `_) + +* added additional easyconfigs for various supported software packages, including: + + * ABINIT 9.6.2, ABRicate 1.0.0, AlphaFold 2.1.1, antiSMASH 6.0.1, Arrow 6.0.0, astropy 4.3.1, BCFtools 1.14, + BeautifulSoup 4.9.3, Boost 1.77.0, bpp 4.4.0, Bracken 2.6.2, CapnProto 0.9.1, CellRanger 6.1.2, Eigen 3.4.0, + enaBrowserTool 1.6, ESMF 8.2.0, Flye 2.9, FMRIprep 1.4.1, FSL 6.0.4, GATK 4.2.3.0, gc 8.2.0, GDB 11.1, git 2.33.1, + Go 1.17.3, Gurobi 9.5.0, Horovod 0.23.0, HTSlib 1.14, HyPhy 2.5.33, Infernal 1.1.4, Inspector 2021.4.0 ITK 5.2.1, + jax 0.2.24, Julia 1.7.0, Kent_tools 422, king 2.2.7, libdwarf 20210528, MAFFT 7.490, makeinfo 6.8, Mash 2.3, + matplotlib 3.4.3, MCR R2021b, minimap2 2.22, MUST 1.7.2, NCO 5.0.3, NCO 5.0.3, nlohmann_json 3.10.4, NVHPC 21.9, + OpenMPI 4.0.7 + 4.1.2, panaroo 1.2.9, pangolin 3.1.16, pkgconfig 1.5.5, plotly.py 5.4.0, pyfaidx 0.6.3.1, + Pysam 0.17.0, PyTorch 1.10.0, R 4.1.2, R-bundle-Bioconductor 3.14, ReFrame 3.9.1, rpy2 3.4.5, scikit-image 0.18.3, + scikit-learn 1.0.1 SimpleITK 2.1.0, snakemake 6.10.0, SPAdes 3.15.3, tbb 2021.4.0, torchtext 0.10.0, + torchvision 0.11.1, tqdm 4.62.3, TRUST4 1.0.6, Trycycler 0.5.2, Unicycler 0.4.9, UShER 0.5.0, WPS 4.3.1, + xarray 0.20.1, XlsxWriter 3.0.2, Yambo 5.0.4 + +* minor enhancements, including: + + * add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 (`#14259 `_) + * add extensions for R v4.1.x: + + * geex + momentfit (`#14299 `_); StatMatch, leaflet, tmap + collapse (`#14328 `_), genoPlotR + penfa (`#14433 `_), adcovsim (`#14484 `_) + + * add M3Drop extension to R-bundle-Bioconductor 3.14 (`#14436 `_) + +* various bug fixes, including: + + * specify to use Python provided as dependency, remove ``separate_build_dir``, and fix URL in comment for Arrow 0.17.1 (`#14263 `_) + * fix ``gettid`` nameclash with glibc 2.30 in Bazel 0.25.2, 0.26.1, 0.29.1, and 1.1.0 (`#14269 `_) + * restore and fix sanity check commands in RStudio-Server 1.4 (`#14275 `_) + * add pkg-config build dependency to Python easyconfigs, to ensure OpenSSL wrapper is detected (`#14316 `_) + * add patch for UCX v1.11.2 to fix missing include statement for ``string.h`` (`#14317 `_) + * set ``$DALTON_TMPDIR`` to build directory to run Dalton tests (`#14341 `_) + * add patch for libfabric v1.12.1 to fix ``unknown link width 0x10`` warning (`#14387 `_) + * add missing Automake dependency to PhyML 3.3.20200621 (`#14397 `_) + * add git as build dependency to Python 3.8.x and 3.9.x easyconfigs (required for pbr extension) (`#14421 `_) + * add missing XZ dependency to recent PROJ easyconfigs (`#14429 `_) + * fix homepage/source URL for king v2.2.4 (`#14444 `_) + * add patch for GCCcore 9.1-9.3 to fix compatibility with recent kernel headers (`#14453 `_) + * add patch for GCCcore 10.1-11.1 to fix compatibility with recent kernel headers (`#14454 `_) + * add patch to fix CVE-2021-43527 in NSS (`#14497 `_) + * pass tests on A* GPUs by setting ``NVIDIA_TF32_OVERRIDE=0`` in jax 0.2.19 (`#14502 `_) + * add patch to fix broken (hanging) Mash binaries (`#14511 `_) + * add missing Perl build dependency for Longshot (`#14535 `_) + * add googletest build dependency for Highway (`#14536 `_) + * seed in PCRE2 sources to fix broken MariaDB 10.5.8 + 10.6.4 easyconfigs (`#14537 `_) + +* other changes: + + * rename R bindings for Arrow to arrow-R, so it can be used in a lowercase module naming scheme (`#14262 `_) + * comment out imkl build dependency for FlexiBLAS 3.0.4 with GCC/11.2.0 (`#14335 `_) + * don't add ``bin`` subdir to ``$PATH`` via ``modextrapaths`` in ReFrame easyconfigs (`#14415 `_) + * consistently use 'Grace' software name + sync ``homepage``/``source_urls`` (`#14493 `_) + * move cxxopts, termcolor and ELFIO header only libraries to ``SYSTEM`` toolchain (`#14504 `_) + + .. _release_notes_eb450: EasyBuild v4.5.0 (October 29th 2021) diff --git a/docs/conf.py b/docs/conf.py index acf4eea1..63f342a8 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.5.0' # this is meant to reference the version of EasyBuild +version = '4.5.1' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20211029.0' # this is meant to reference the version of the documentation itself +release = '20211213.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From d204e99b43fdbb268de99609141b960cadbe2422 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Dec 2021 22:02:07 +0800 Subject: [PATCH 183/286] bump version to 4.5.1 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 775ba896..37bf3d96 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.5.0' +VERSION = '4.5.1' # Utility function to read README file From 03ffa3ce229ea70714a7b1ce1a08571947e811d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Dec 2021 15:20:03 +0100 Subject: [PATCH 184/286] bump count for software-specific easyblocks (due to Clang-AOMP easyblock) --- docs/Release_notes.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 858d85ce..9bd0f683 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -4,7 +4,7 @@ EasyBuild release notes ======================= The latest version of EasyBuild provides support for building and installing **2,575** different software packages, -including 36 different (compiler) toolchains. It contains 242 software-specific easyblocks and 37 generic easyblocks, +including 36 different (compiler) toolchains. It contains 243 software-specific easyblocks and 37 generic easyblocks, alongside 13,812 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. From a3f392cf9db57b99b4a2443ee6c16e000d40a4e3 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 11 Jan 2022 15:12:08 +0100 Subject: [PATCH 185/286] Update ocaisa email address (again) --- docs/Maintainers.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Maintainers.rst b/docs/Maintainers.rst index b831e4e7..560acb82 100644 --- a/docs/Maintainers.rst +++ b/docs/Maintainers.rst @@ -117,7 +117,7 @@ The EasyBuild maintainers all have admin access to the different EasyBuild GitHu * **Alan O'Cais** (`CECAM `_) - * GitHub: `@ocaisa `_ - e-mail: ``alan.ocais (at) epfl.ch`` - IRC/Slack: ``ocaisa`` + * GitHub: `@ocaisa `_ - e-mail: ``alan.ocais (at) cecam.org`` - IRC/Slack: ``ocaisa`` * **Mikael Öhman** (`Chalmers University of Technology `_) From 43f5c61bae9236e63124fa08c97306e51fd939f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Jan 2022 21:29:26 +0100 Subject: [PATCH 186/286] auto-update docs for EasyBuild v4.5.2 --- docs/version-specific/Supported_software.rst | 2135 ++++++++++++------ docs/version-specific/easyblocks.rst | 2 +- docs/version-specific/generic_easyblocks.rst | 226 +- 3 files changed, 1624 insertions(+), 739 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index d58ba3e1..6fddd098 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2575 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2622 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_alevin-fry_1021` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMD-uProf_779` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_ANGEL_359` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_atropos_776` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Austin_628` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock-GPU_1075` - :ref:`list_software_AutoDock-Vina_1237` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -268,14 +268,14 @@ AdapterRemoval searches for and removes remnant adapter sequences from High-Thr *homepage*: https://github.com/MikkelSchubert/adapterremoval -========= ============================== -version toolchain -========= ============================== -``2.2.0`` ``foss/2016b`` -``2.2.2`` ``foss/2018b`` -``2.3.1`` ``foss/2018b`` -``2.3.2`` ``GCC/10.2.0``, ``GCC/10.3.0`` -========= ============================== +========= ============================================== +version toolchain +========= ============================================== +``2.2.0`` ``foss/2016b`` +``2.2.2`` ``foss/2018b`` +``2.3.1`` ``foss/2018b`` +``2.3.2`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0`` +========= ============================================== .. _list_software_ADDA_266: @@ -488,6 +488,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_alevin-fry_1021: + +*alevin-fry* +++++++++++++ + +alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding. + +*homepage*: https://github.com/COMBINE-lab/alevin-fry + +========= ================== +version toolchain +========= ================== +``0.4.3`` ``GCCcore/11.2.0`` +========= ================== + + .. _list_software_ALFA_276: *ALFA* @@ -784,6 +800,22 @@ version toolchain ========= ================== +.. _list_software_AMD-uProf_779: + +*AMD-uProf* ++++++++++++ + +AMD uProf is a performance analysis tool for applications running on Windows, Linux & FreeBSD operating systems. It allows developers to better understand the runtime performance of their application and to identify ways to improve its performance. + +*homepage*: https://developer.amd.com/amd-uprof/ + +=========== ========== +version toolchain +=========== ========== +``3.4.502`` ``system`` +=========== ========== + + .. _list_software_AMOS_304: *AMOS* @@ -793,11 +825,11 @@ The AMOS consortium is committed to the development of open-source whole genome *homepage*: http://amos.sourceforge.net -========= ============== -version toolchain -========= ============== -``3.1.0`` ``foss/2018b`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``3.1.0`` ``foss/2018b``, ``foss/2021b`` +========= ============================== .. _list_software_AMPHORA2_570: @@ -915,6 +947,7 @@ version toolchain ``2020.07`` ``system`` ``2020.11`` ``system`` ``2021.05`` ``system`` +``2021.11`` ``system`` =========== ========== @@ -950,6 +983,22 @@ version toolchain ======== ============== +.. _list_software_ANGEL_359: + +*ANGEL* ++++++++ + +ANGEL: Robust Open Reading Frame prediction + +*homepage*: https://github.com/PacificBiosciences/ANGEL + +======= ================= ============== +version versionsuffix toolchain +======= ================= ============== +``3.0`` ``-Python-3.7.2`` ``foss/2019a`` +======= ================= ============== + + .. _list_software_angsd_525: *angsd* @@ -1011,12 +1060,13 @@ ANNOVAR is an efficient software tool to utilize update-to-date information to *homepage*: http://annovar.openbioinformatics.org/en/latest/ -============= ================ ================= -version versionsuffix toolchain -============= ================ ================= -``2016Feb01`` ``-Perl-5.22.1`` ``foss/2016a`` -``20191024`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -============= ================ ================= +============= ================ ================== +version versionsuffix toolchain +============= ================ ================== +``2016Feb01`` ``-Perl-5.22.1`` ``foss/2016a`` +``20191024`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``20200607`` ``-Perl-5.34.0`` ``GCCcore/11.2.0`` +============= ================ ================== .. _list_software_ANSYS_398: @@ -1106,6 +1156,7 @@ antiSMASH allows the rapid genome-wide identification, annotation and analysis o version versionsuffix toolchain ========= ================= ============== ``5.1.2`` ``-Python-3.7.4`` ``foss/2019b`` +``5.2.0`` ``foss/2020b`` ``6.0.1`` ``foss/2020b`` ========= ================= ============== @@ -1471,6 +1522,7 @@ version versionsuffix toolchain ``9.880.1`` ``foss/2020a`` ``9.900.1`` ``foss/2019b``, ``foss/2020a`` ``10.5.3`` ``foss/2020b`` +``10.7.5`` ``foss/2021a`` =========== ================== =============================== @@ -1507,7 +1559,7 @@ version toolchain ``3.5.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b`` ``3.6.2`` ``intel/2018a`` ``3.7.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` -``3.8.0`` ``foss/2020b``, ``foss/2021a`` +``3.8.0`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` ========= ================================================================================ @@ -1554,17 +1606,18 @@ Apache Arrow (incl. PyArrow Python bindings), a cross-language development platf *homepage*: https://arrow.apache.org -========== ================== =================================== -version versionsuffix toolchain -========== ================== =================================== -``0.7.1`` ``-Python-3.6.3`` ``intel/2017b`` -``0.12.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``0.12.0`` ``-Python-3.6.6`` ``intel/2018b`` -``0.16.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``0.17.1`` ``fosscuda/2020b``, ``intel/2020b`` -``0.17.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``6.0.0`` ``foss/2021a``, ``foss/2021b`` -========== ================== =================================== +========== ================== =================================================== +version versionsuffix toolchain +========== ================== =================================================== +``0.7.1`` ``-Python-3.6.3`` ``intel/2017b`` +``0.12.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.12.0`` ``-Python-3.6.6`` ``intel/2018b`` +``0.16.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.17.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``0.17.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``6.0.0`` ``foss/2021a``, ``foss/2021b`` +``6.0.1`` ``foss/2021a`` +========== ================== =================================================== .. _list_software_arrow-R_682: @@ -2000,6 +2053,22 @@ version versionsuffix toolchain ========= ================== ================= +.. _list_software_atropos_776: + +*atropos* ++++++++++ + +Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. + +*homepage*: https://atropos.readthedocs.io + +========== ================= =============== +version versionsuffix toolchain +========== ================= =============== +``1.1.21`` ``-Python-3.6.6`` ``intel/2018b`` +========== ================= =============== + + .. _list_software_ATSAS_380: *ATSAS* @@ -2091,6 +2160,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_Austin_628: + +*Austin* +++++++++ + +Austin is a Python frame stack sampler for CPython written in pure C. + +*homepage*: https://github.com/P403n1x87/austin + +========= ============================== +version toolchain +========= ============================== +``3.2.0`` ``GCCcore/11.2.0``, ``system`` +========= ============================== + + .. _list_software_AUTO-07p_573: *AUTO-07p* @@ -2147,31 +2232,49 @@ version toolchain *AutoDock* ++++++++++ -AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. +AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. *homepage*: http://autodock.scripps.edu/ -=========== ============= -version toolchain -=========== ============= -``4.2.5.1`` ``GCC/5.2.0`` -=========== ============= +=========== ============== +version toolchain +=========== ============== +``4.2.5.1`` ``GCC/5.2.0`` +``4.2.6`` ``GCC/10.3.0`` +=========== ============== + + +.. _list_software_AutoDock-GPU_1075: + +*AutoDock-GPU* +++++++++++++++ + +OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly parallelizable LGA by processing ligand-receptor poses in parallel over multiple compute units. AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. + +*homepage*: https://github.com/ccsb-scripps/AutoDock-GPU +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``1.5.3`` ``-CUDA-11.3.1`` ``GCC/10.3.0`` +========= ================ ============== -.. _list_software_AutoDock_Vina_1287: -*AutoDock_Vina* +.. _list_software_AutoDock-Vina_1237: + +*AutoDock-Vina* +++++++++++++++ -AutoDock Vina is an open-source program for doing molecular docking. +AutoDock Vina is an open-source program for doing molecular docking. -*homepage*: http://vina.scripps.edu/index.html +*homepage*: https://vina.scripps.edu/ -========= ============== ========== -version versionsuffix toolchain -========= ============== ========== -``1.1.2`` ``_linux_x86`` ``system`` -========= ============== ========== +========= ============== ============== +version versionsuffix toolchain +========= ============== ============== +``1.1.2`` ``-linux_x86`` ``system`` +``1.2.3`` ``foss/2021a`` +========= ============== ============== .. _list_software_AutoGeneS_875: @@ -2311,7 +2414,7 @@ version versionsuffix toolchain --- -:ref:`list_software_BabelStream_1090` - :ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_bamtofastq_1074` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_bcbio-gff_863` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biom-format_1117` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_Blosc2_549` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_boto3_487` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_Brotli-python_1339` - :ref:`list_software_Brunsli_735` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` +:ref:`list_software_BabelStream_1090` - :ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_bamtofastq_1074` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_bcbio-gff_863` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biom-format_1117` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_Blosc2_549` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_boost_histogram_1620` - :ref:`list_software_boto3_487` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_Brotli-python_1339` - :ref:`list_software_Brunsli_735` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` .. _list_software_BabelStream_1090: @@ -2704,29 +2807,29 @@ Bazel is a build tool that builds code quickly and reliably. It is used to build *homepage*: https://bazel.io/ -========== ============= ========================================================= -version versionsuffix toolchain -========== ============= ========================================================= -``0.4.4`` ``system`` -``0.7.0`` ``GCCcore/6.4.0`` -``0.10.0`` ``GCCcore/6.4.0`` -``0.11.0`` ``GCCcore/6.4.0`` -``0.11.1`` ``GCCcore/6.4.0`` -``0.12.0`` ``GCCcore/6.4.0`` -``0.16.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``0.18.0`` ``GCCcore/7.3.0`` -``0.20.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``0.25.2`` ``GCCcore/8.2.0`` -``0.26.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.29.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.29.1`` ``-Java-1.8`` ``GCCcore/9.3.0`` -``1.1.0`` ``GCCcore/8.3.0`` -``2.0.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` -``3.4.1`` ``GCCcore/8.3.0`` -``3.6.0`` ``GCCcore/9.3.0`` -``3.7.1`` ``GCCcore/8.3.0`` -``3.7.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0`` -========== ============= ========================================================= +========== ============= ============================================================================= +version versionsuffix toolchain +========== ============= ============================================================================= +``0.4.4`` ``system`` +``0.7.0`` ``GCCcore/6.4.0`` +``0.10.0`` ``GCCcore/6.4.0`` +``0.11.0`` ``GCCcore/6.4.0`` +``0.11.1`` ``GCCcore/6.4.0`` +``0.12.0`` ``GCCcore/6.4.0`` +``0.16.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``0.18.0`` ``GCCcore/7.3.0`` +``0.20.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``0.25.2`` ``GCCcore/8.2.0`` +``0.26.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.29.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.29.1`` ``-Java-1.8`` ``GCCcore/9.3.0`` +``1.1.0`` ``GCCcore/8.3.0`` +``2.0.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +``3.4.1`` ``GCCcore/8.3.0`` +``3.6.0`` ``GCCcore/9.3.0`` +``3.7.1`` ``GCCcore/8.3.0`` +``3.7.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` +========== ============= ============================================================================= .. _list_software_bbcp_407: @@ -2900,14 +3003,14 @@ bcl2fastq Conversion Software both demultiplexes data and converts BCL files gen *homepage*: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html -========== ================== ============================================================================================= -version versionsuffix toolchain -========== ================== ============================================================================================= -``2.19.1`` ``-Python-2.7.12`` ``foss/2016b`` -``2.20.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``intel/2019a`` -``2.20.0`` ``-Python-2.7.12`` ``foss/2016b`` -``2.20.0`` ``-Python-2.7.14`` ``intel/2017b`` -========== ================== ============================================================================================= +========== ================== ============================================================================================================= +version versionsuffix toolchain +========== ================== ============================================================================================================= +``2.19.1`` ``-Python-2.7.12`` ``foss/2016b`` +``2.20.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``intel/2019a`` +``2.20.0`` ``-Python-2.7.12`` ``foss/2016b`` +``2.20.0`` ``-Python-2.7.14`` ``intel/2017b`` +========== ================== ============================================================================================================= .. _list_software_bcolz_538: @@ -3533,13 +3636,14 @@ version toolchain A tool to map bisulfite converted sequence reads and determine cytosine methylation states -*homepage*: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ +*homepage*: https://www.bioinformatics.babraham.ac.uk/projects/bismark/ ========== =============================== version toolchain ========== =============================== ``0.19.0`` ``intel/2017b`` ``0.20.1`` ``foss/2018b``, ``intel/2018b`` +``0.23.1`` ``foss/2021b`` ========== =============================== @@ -3567,6 +3671,7 @@ version toolchain ``3.6.1`` ``GCCcore/10.1.0`` ``3.7.1`` ``GCCcore/10.2.0``, ``system`` ``3.7.6`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0``, ``system`` +``3.8.2`` ``system`` ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -3682,6 +3787,7 @@ version versionsuffix toolchain ``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a``, ``iimpi/2019b`` ``2.10.1`` ``gompi/2020a``, ``iimpi/2020a`` ``2.11.0`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a`` +``2.12.0`` ``gompi/2021b`` ========== ================== ================================================================== @@ -3706,9 +3812,9 @@ version toolchain *Blender* +++++++++ -Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. +Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline, modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. -*homepage*: https://www.blender.org/ +*homepage*: https://www.blender.org ========= ============================= =============================== version versionsuffix toolchain @@ -3718,6 +3824,7 @@ version versionsuffix toolchain ``2.79b`` ``-Python-3.6.6`` ``intel/2018b`` ``2.79b`` ``-Python-3.6.6-CUDA-9.2.88`` ``foss/2018b`` ``2.81`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.0.0`` ``-linux-x64`` ``system`` ========= ============================= =============================== @@ -4045,6 +4152,22 @@ version versionsuffix toolchain ========== ================== ==================================================================== +.. _list_software_boost_histogram_1620: + +*boost_histogram* ++++++++++++++++++ + +Boost-histogram is a Python package providing Python bindings for Boost.Histogram. + +*homepage*: https://boost-histogram.readthedocs.io + +========= ============== +version toolchain +========= ============== +``1.2.1`` ``foss/2021a`` +========= ============== + + .. _list_software_boto3_487: *boto3* @@ -4121,7 +4244,7 @@ version toolchain ``2.3.5.1`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` ``2.4.1`` ``GCC/9.3.0`` ``2.4.2`` ``GCC/10.2.0``, ``GCC/9.3.0`` -``2.4.4`` ``GCC/10.3.0`` +``2.4.4`` ``GCC/10.3.0``, ``GCC/11.2.0`` =========== ====================================================================================================== @@ -4468,15 +4591,15 @@ Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively sh *homepage*: http://bio-bwa.sourceforge.net/ -=========== ================================================================================================================================================================================================================================================================================= -version toolchain -=========== ================================================================================================================================================================================================================================================================================= -``0.7.12`` ``foss/2016b`` -``0.7.13`` ``foss/2016a``, ``intel/2016a`` -``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``0.7.16a`` ``foss/2016b``, ``intel/2017a`` -``0.7.17`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -=========== ================================================================================================================================================================================================================================================================================= +=========== ===================================================================================================================================================================================================================================================================================================== +version toolchain +=========== ===================================================================================================================================================================================================================================================================================================== +``0.7.12`` ``foss/2016b`` +``0.7.13`` ``foss/2016a``, ``intel/2016a`` +``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``0.7.16a`` ``foss/2016b``, ``intel/2017a`` +``0.7.17`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/11.2.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +=========== ===================================================================================================================================================================================================================================================================================================== .. _list_software_bwa-meth_789: @@ -4640,7 +4763,7 @@ version toolchain --- -:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_c-ares_571: @@ -4707,6 +4830,22 @@ version toolchain ========= ============= +.. _list_software_CAFE5_324: + +*CAFE5* ++++++++ + +Software for Computational Analysis of gene Family Evolution The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa. + +*homepage*: https://github.com/hahnlab/CAFE5 + +========= ============== +version toolchain +========= ============== +``5.0.0`` ``GCC/10.2.0`` +========= ============== + + .. _list_software_Caffe_469: *Caffe* @@ -4763,6 +4902,23 @@ version toolchain ========== ==================================== +.. _list_software_Calcam_577: + +*Calcam* +++++++++ + +Calcam is a Python package providing tools for spatial calibration of cameras, i.e. determining the mapping between pixel coordinates in an image and real-world 3D sight lines & coordinates. + +*homepage*: https://euratom-software.github.io/calcam + +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``2.1.0`` ``-Python-2.7.14`` ``intel/2018a`` +``2.1.0`` ``-Python-3.6.4`` ``intel/2018a`` +========= ================== =============== + + .. _list_software_Calendrical_1106: *Calendrical* @@ -4842,19 +4998,19 @@ Canu is a fork of the Celera Assembler designed for high-noise single-molecule s *homepage*: https://canu.readthedocs.io -========= ================ =============================== -version versionsuffix toolchain -========= ================ =============================== -``1.4`` ``foss/2016b`` -``1.7`` ``intel/2018a`` -``1.8`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``1.8`` ``-Perl-5.28.0`` ``foss/2018b`` -``1.8`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -``1.9`` ``-Java-11`` ``GCCcore/8.3.0`` -``2.1.1`` ``GCCcore/10.2.0`` -``2.1.1`` ``-Java-11`` ``GCCcore/9.3.0`` -``2.2`` ``GCCcore/10.3.0`` -========= ================ =============================== +========= ================ ====================================== +version versionsuffix toolchain +========= ================ ====================================== +``1.4`` ``foss/2016b`` +``1.7`` ``intel/2018a`` +``1.8`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``1.8`` ``-Perl-5.28.0`` ``foss/2018b`` +``1.8`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``1.9`` ``-Java-11`` ``GCCcore/8.3.0`` +``2.1.1`` ``GCCcore/10.2.0`` +``2.1.1`` ``-Java-11`` ``GCCcore/9.3.0`` +``2.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ================ ====================================== .. _list_software_Canvas_604: @@ -4926,6 +5082,22 @@ version toolchain ========== ============== +.. _list_software_Carma_484: + +*Carma* ++++++++ + +Carma - A molecular dynamics analysis program + +*homepage*: http://utopia.duth.gr/~glykos/Carma.html + +======== ============== +version toolchain +======== ============== +``2.01`` ``foss/2019b`` +======== ============== + + .. _list_software_carputils_983: *carputils* @@ -5224,14 +5396,14 @@ CD-HIT is a very widely used program for clustering and comparing protein or nu *homepage*: https://github.com/weizhongli/cdhit -========= ============== ===================================================================================================== -version versionsuffix toolchain -========= ============== ===================================================================================================== -``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` -``4.6.6`` ``foss/2016b`` -``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` -``4.8.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` -========= ============== ===================================================================================================== +========= ============== ===================================================================================================================== +version versionsuffix toolchain +========= ============== ===================================================================================================================== +``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` +``4.6.6`` ``foss/2016b`` +``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` +``4.8.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` +========= ============== ===================================================================================================================== .. _list_software_CDAT_284: @@ -5292,11 +5464,13 @@ cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for anal *homepage*: https://github.com/Magdoll/cDNA_Cupcake -======= ================== =============== -version versionsuffix toolchain -======= ================== =============== -``5.8`` ``-Python-2.7.14`` ``intel/2018a`` -======= ================== =============== +========== ================== =============== +version versionsuffix toolchain +========== ================== =============== +``5.8`` ``-Python-2.7.14`` ``intel/2018a`` +``24.2.0`` ``-Python-3.8.2`` ``foss/2020a`` +``26.0.0`` ``foss/2021a`` +========== ================== =============== .. _list_software_CDO_214: @@ -5317,7 +5491,7 @@ version toolchain ``1.9.2`` ``intel/2017b`` ``1.9.5`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``1.9.8`` ``intel/2019b`` -``1.9.10`` ``gompi/2020b``, ``gompi/2021a`` +``1.9.10`` ``gompi/2019b``, ``gompi/2020b``, ``gompi/2021a`` ========== ================================================= @@ -5579,7 +5753,7 @@ version versionsuffix toolchain ``4.11.1`` ``-Python-3.6.6`` ``foss/2018b`` ``4.14`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``4.14.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``4.14.3`` ``gompi/2021a`` +``4.14.3`` ``gompi/2021a``, ``gompi/2021b`` ``4.14.3`` ``-Python-3.8.2`` ``gompi/2020a``, ``iimpi/2020a`` ``5.2`` ``gompi/2020b`` ========== ================== ================================ @@ -5767,7 +5941,7 @@ version versionsuffix toolchain ``1.0.18`` ``-Python-2.7.15`` ``foss/2019a`` ``1.0.18`` ``-Python-2.7.18`` ``foss/2020b`` ``1.1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.1.3`` ``foss/2021a`` +``1.1.3`` ``foss/2021a``, ``foss/2021b`` ``1.1.3`` ``-Python-3.8.2`` ``intel/2020a`` ========== ================== =============================== @@ -5819,11 +5993,12 @@ CHERAB is a python library for forward modelling diagnostics based on spectrosc *homepage*: https://cherab.github.io/documentation/index.html -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``1.2.0`` ``-Python-3.6.6`` ``intel/2018b`` -========= ================= =============== +========= ================= =============================== +version versionsuffix toolchain +========= ================= =============================== +``1.2.0`` ``-Python-3.6.6`` ``intel/2018b`` +``1.3.0`` ``foss/2020b``, ``intel/2020b`` +========= ================= =============================== .. _list_software_chewBBACA_752: @@ -6364,8 +6539,9 @@ version toolchain ``3.15.3`` ``GCCcore/8.3.0`` ``3.16.4`` ``GCCcore/9.3.0`` ``3.18.4`` ``GCCcore/10.2.0``, ``system`` -``3.20.1`` ``GCCcore/10.3.0`` +``3.20.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.21.1`` ``GCCcore/11.2.0`` +``3.22.1`` ``GCCcore/11.2.0`` ========== ================================================================================================================================================= @@ -6501,6 +6677,22 @@ version versionsuffix toolchain ============ ============= =============== +.. _list_software_Cogent_608: + +*Cogent* +++++++++ + +Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on Iso-Seq data and in cases where there is no reference genome or the ref genome is highly incomplete. + +*homepage*: https://github.com/Magdoll/Cogent + +========= ============== +version toolchain +========= ============== +``8.0.0`` ``foss/2021a`` +========= ============== + + .. _list_software_Coin_393: *Coin* @@ -6563,6 +6755,7 @@ A toolbox for comparative genomics. version versionsuffix toolchain ========== ================== ============== ``0.0.23`` ``-Python-2.7.15`` ``foss/2018b`` +``0.1.2`` ``foss/2021b`` ========== ================== ============== @@ -6830,7 +7023,7 @@ version versionsuffix toolchain ``7.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` ``7.1`` ``-psmp`` ``foss/2020b`` ``8.1`` ``foss/2020b`` -``8.2`` ``foss/2021a`` +``8.2`` ``foss/2021a``, ``intel/2021a`` ======= ============= ================================================================================================= @@ -7430,6 +7623,7 @@ version toolchain ``11.2.1`` ``system`` ``11.2.2`` ``system`` ``11.3.0`` ``system`` +``11.4.0`` ``system`` ========== ========== @@ -7656,6 +7850,7 @@ version versionsuffix toolchain ``1.1.9`` ``-Python-2.7.13`` ``intel/2017a`` ``1.2.1`` ``-Python-3.6.4`` ``intel/2018a`` ``1.2.3`` ``foss/2019a`` +``1.2.3`` ``-Python-3.6.6`` ``intel/2018b`` ``1.2.4`` ``-Python-3.7.4`` ``intel/2019b`` ``1.2.6`` ``foss/2020b``, ``foss/2021a`` ========= ================== ============================== @@ -7731,6 +7926,7 @@ version versionsuffix toolchain ``0.29.10`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``0.29.10`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``0.29.22`` ``GCCcore/10.2.0`` +``3.0a5`` ``GCCcore/10.2.0`` =========== ================== =============================== @@ -7790,7 +7986,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dRep_395` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_DUBStepR_713` - :ref:`list_software_dxpy_453` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dlib_411` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dRep_395` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_DualSPHysics_1180` - :ref:`list_software_DUBStepR_713` - :ref:`list_software_dune-core_898` - :ref:`list_software_dune-fem_785` - :ref:`list_software_dxpy_453` - :ref:`list_software_DyMat_479` .. _list_software_dadi_402: @@ -7903,6 +8099,7 @@ DAS Tool is an automated method that integrates the results of a flexible number version versionsuffix toolchain ========= ========================== ============== ``1.1.1`` ``-R-3.5.1-Python-2.7.15`` ``foss/2018b`` +``1.1.1`` ``-R-4.1.2`` ``foss/2021b`` ========= ========================== ============== @@ -8325,14 +8522,14 @@ version versionsuffix toolchain A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. -*homepage*: https://pypi.python.org/pypi/DendroPy/ +*homepage*: https://dendropy.org/ ========= ================== ======================================================================== version versionsuffix toolchain ========= ================== ======================================================================== ``4.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2019a`` ``4.4.0`` ``-Python-2.7.15`` ``intel/2018b`` -``4.5.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``4.5.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``4.5.2`` ``-Python-2.7.18`` ``GCCcore/10.2.0`` ========= ================== ======================================================================== @@ -8505,6 +8702,7 @@ version toolchain ``2.0.6`` ``GCC/7.3.0-2.30`` ``2.0.7`` ``GCC/10.2.0`` ``2.0.11`` ``GCC/10.3.0`` +``2.0.13`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========== ================================================================ @@ -8582,13 +8780,13 @@ dill extends python's pickle module for serializing and de-serializing python ob *homepage*: https://pypi.org/project/dill/ -========= ===================================== -version toolchain -========= ===================================== -``0.3.0`` ``GCCcore/8.2.0`` -``0.3.3`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` -``0.3.4`` ``GCCcore/10.3.0`` -========= ===================================== +========= ====================================== +version toolchain +========= ====================================== +``0.3.0`` ``GCCcore/8.2.0`` +``0.3.3`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +``0.3.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== .. _list_software_DIRAC_355: @@ -8676,6 +8874,23 @@ version versionsuffix toolchain ======== ================= =============================== +.. _list_software_dlib_411: + +*dlib* +++++++ + +Dlib is a modern C++ toolkit containing machine learning algorithms and tools for creating complex software in C++ to solve real world problems. It is used in both industry and academia in a wide range of domains including robotics, embedded devices, mobile phones, and large high performance computing environments. + +*homepage*: https://github.com/davisking/dlib + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``19.22`` ``foss/2021a`` +``19.22`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== + + .. _list_software_dm-reverb_900: *dm-reverb* @@ -8805,11 +9020,12 @@ version toolchain *homepage*: https://www.microsoft.com/net/ -========= ================= -version toolchain -========= ================= -``2.0.7`` ``GCCcore/6.4.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``2.0.7`` ``GCCcore/6.4.0`` +``6.0.1`` ``GCCcore/11.2.0`` +========= ================== .. _list_software_dotNET-SDK_829: @@ -8825,6 +9041,7 @@ version toolchain version versionsuffix toolchain =========== ============== ========== ``3.1.300`` ``-linux-x64`` ``system`` +``6.0.101`` ``-linux-x64`` ``system`` =========== ============== ========== @@ -9051,6 +9268,23 @@ version versionsuffix toolchain ========== ================== =============== +.. _list_software_DualSPHysics_1180: + +*DualSPHysics* +++++++++++++++ + +DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. The code is developed to study free-surface flow phenomena where Eulerian methods can be difficult to apply, such as waves or impact of dam-breaks on off-shore structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal with real-life engineering problems. + +*homepage*: https://dual.sphysics.org/ + +=========== ===================== ============== +version versionsuffix toolchain +=========== ===================== ============== +``5.0.175`` ``GCC/11.2.0`` +``5.0.175`` ``-CUDA-%(cudaver)s`` ``GCC/11.2.0`` +=========== ===================== ============== + + .. _list_software_DUBStepR_713: *DUBStepR* @@ -9067,6 +9301,38 @@ version versionsuffix toolchain ========= ============= ============== +.. _list_software_dune-core_898: + +*dune-core* ++++++++++++ + +The Dune core modules build the stable basis of Dune. They follow a consistent release cycle and have high requirements regarding stability and backwards compatibility. These modules build the foundation for higher-level components. + +*homepage*: https://www.dune-project.org/groups/core/ + +=============== ============== +version toolchain +=============== ============== +``2.8.0.post1`` ``foss/2020b`` +=============== ============== + + +.. _list_software_dune-fem_785: + +*dune-fem* +++++++++++ + +DUNE-FEM is a discretization module based on DUNE containing all the building blocks required to implement efficient solvers for a wide range of (systems of non linear) partial differential equations. DUNE-FEM can also be used through an extensive Python interface which brings all components of DUNE-FEM and the DUNE core modules to Python. + +*homepage*: https://www.dune-project.org/modules/dune-fem/ + +=========== ============== +version toolchain +=========== ============== +``2.8.0.6`` ``foss/2020b`` +=========== ============== + + .. _list_software_dxpy_453: *dxpy* @@ -9083,13 +9349,29 @@ version versionsuffix toolchain =========== ================== =============== +.. _list_software_DyMat_479: + +*DyMat* ++++++++ + +Read and process result files from Dymola and OpenModelica with Python. + +*homepage*: https://www.j-raedler.de/projects/DyMat + +======= =============== ============== +version versionsuffix toolchain +======= =============== ============== +``0.7`` ``-2020-12-12`` ``foss/2021b`` +======= =============== ============== + + .. _list_software_letter_e: *E* --- -:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_eht-imaging_1098` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_einops_654` - :ref:`list_software_elastix_762` - :ref:`list_software_ELFIO_367` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_elprep_648` - :ref:`list_software_ELSI_301` - :ref:`list_software_ELSI-RCI_568` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_epiScanpy_940` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESL-Bundle_875` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Excel-Writer-XLSX_1559` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_expecttest_1097` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_eht-imaging_1098` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_einops_654` - :ref:`list_software_elastix_762` - :ref:`list_software_elbencho_832` - :ref:`list_software_ELFIO_367` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_elprep_648` - :ref:`list_software_ELSI_301` - :ref:`list_software_ELSI-RCI_568` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_Embree_592` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_epiScanpy_940` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESL-Bundle_875` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExaML_439` - :ref:`list_software_Excel-Writer-XLSX_1559` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_expecttest_1097` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_E-ANTIC_481: @@ -9238,6 +9520,7 @@ version toolchain ``4.4.1`` ``system`` ``4.4.2`` ``system`` ``4.5.0`` ``system`` +``4.5.1`` ``system`` ========== ========== @@ -9411,7 +9694,7 @@ version toolchain ``3.3.7`` ``GCCcore/9.3.0``, ``system`` ``3.3.8`` ``GCCcore/10.2.0`` ``3.3.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``3.4.0`` ``GCCcore/10.2.0`` +``3.4.0`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` ========== ========================================================== @@ -9424,14 +9707,14 @@ The EIGENSOFT package combines functionality from our population genetics method *homepage*: http://www.hsph.harvard.edu/alkes-price/software/ -========= =============================================================== -version toolchain -========= =============================================================== -``6.0.1`` ``foss/2016a`` -``6.1.1`` ``foss/2016a`` -``6.1.4`` ``foss/2016b`` -``7.2.1`` ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``intel/2019a`` -========= =============================================================== +========= =============================================================================== +version toolchain +========= =============================================================================== +``6.0.1`` ``foss/2016a`` +``6.1.1`` ``foss/2016a`` +``6.1.4`` ``foss/2016b`` +``7.2.1`` ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2021a``, ``intel/2019a`` +========= =============================================================================== .. _list_software_einops_654: @@ -9466,6 +9749,22 @@ version toolchain ========= ============== +.. _list_software_elbencho_832: + +*elbencho* +++++++++++ + +A distributed storage benchmark for files, objects & blocks with support for GPUs + +*homepage*: https://github.com/breuner/elbencho + +========= ============== +version toolchain +========= ============== +``2.0-3`` ``GCC/10.3.0`` +========= ============== + + .. _list_software_ELFIO_367: *ELFIO* @@ -9605,11 +9904,11 @@ ELSI-RCI provides and enhances open-source software packages which iteratively s *homepage*: https://wordpress.elsi-interchange.org/ -========= =============================== -version toolchain -========= =============================== -``0.1.0`` ``foss/2020b``, ``intel/2020b`` -========= =============================== +========= =========================================================================================================================== +version toolchain +========= =========================================================================================================================== +``0.1.0`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``foss/2020b``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0``, ``intel/2020b`` +========= =========================================================================================================================== .. _list_software_Emacs_489: @@ -9672,6 +9971,22 @@ version versionsuffix toolchain ========= ================= ================================================================================================================================================ +.. _list_software_Embree_592: + +*Embree* +++++++++ + +Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel® Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license. + +*homepage*: https://embree.github.io/ + +========= ====================================== +version toolchain +========= ====================================== +``3.4.0`` ``iccifort/2018.1.163-GCC-6.4.0-2.28`` +========= ====================================== + + .. _list_software_emcee_511: *emcee* @@ -10044,6 +10359,22 @@ version toolchain ======= ============== +.. _list_software_ExaML_439: + +*ExaML* ++++++++ + +Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI + +*homepage*: https://github.com/stamatak/ExaML/ + +========== =============== =============== +version versionsuffix toolchain +========== =============== =============== +``3.0.22`` ``-hybrid-avx`` ``gompi/2021a`` +========== =============== =============== + + .. _list_software_Excel-Writer-XLSX_1559: *Excel-Writer-XLSX* @@ -10157,11 +10488,11 @@ This library implements expect tests (also known as "golden" tests). Expect test *homepage*: https://github.com/ezyang/expecttest -========= ================== -version toolchain -========= ================== -``0.1.3`` ``GCCcore/10.3.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``0.1.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_eXpress_746: @@ -10195,6 +10526,7 @@ version toolchain ``3.4.1`` ``foss/2017a`` ``3.7.1`` ``intel/2019a`` ``3.8.0`` ``gompi/2020b`` +``3.8.3`` ``gompi/2021a`` ========= =============== @@ -10204,7 +10536,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMPy_348` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -10420,6 +10752,7 @@ version toolchain ========== ============================================================ ``0.19.7`` ``foss/2018b`` ``0.20.0`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``0.23.2`` ``GCC/11.2.0`` ========== ============================================================ @@ -10611,12 +10944,12 @@ FastTree infers approximately-maximum-likelihood phylogenetic trees from alignme *homepage*: http://www.microbesonline.org/fasttree/ -========== =========================================================================== -version toolchain -========== =========================================================================== -``2.1.10`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``2.1.11`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== =========================================================================== +========== =============================================================================================== +version toolchain +========== =============================================================================================== +``2.1.10`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``2.1.11`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== =============================================================================================== .. _list_software_FastViromeExplorer_1873: @@ -11767,6 +12100,22 @@ version toolchain ============ ============== +.. _list_software_FMPy_348: + +*FMPy* +++++++ + +FMPy is a free Python library to simulate Functional Mock-up Units (FMUs). + +*homepage*: https://github.com/CATIA-Systems/FMPy + +========= ============== +version toolchain +========= ============== +``0.3.2`` ``foss/2021a`` +========= ============== + + .. _list_software_FMRIprep_741: *FMRIprep* @@ -12025,11 +12374,11 @@ FragGeneScan is an application for finding (fragmented) genes in short reads. *homepage*: http://omics.informatics.indiana.edu/FragGeneScan/ -======== ===================================================== -version toolchain -======== ===================================================== -``1.31`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``foss/2018b`` -======== ===================================================== +======== ========================================================================= +version toolchain +======== ========================================================================= +``1.31`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``foss/2018b`` +======== ========================================================================= .. _list_software_FRANz_417: @@ -12126,11 +12475,11 @@ FreeImage is an Open Source library project for developers who would like to sup *homepage*: http://freeimage.sourceforge.net -========== =========================================================================== -version toolchain -========== =========================================================================== -``3.18.0`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== =========================================================================== +========== =============================================================================================== +version toolchain +========== =============================================================================================== +``3.18.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== =============================================================================================== .. _list_software_FreeSASA_682: @@ -12154,7 +12503,7 @@ version toolchain *FreeSurfer* ++++++++++++ -FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data. +FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data. *homepage*: https://surfer.nmr.mgh.harvard.edu/ @@ -12168,6 +12517,9 @@ version versionsuffix toolchain ``7.1.1`` ``-centos6_x86_64`` ``system`` ``7.1.1`` ``-centos7_x86_64`` ``system`` ``7.1.1`` ``-centos8_x86_64`` ``system`` +``7.2.0`` ``-centos7_x86_64`` ``system`` +``7.2.0`` ``-centos8_x86_64`` ``system`` +``7.2.0`` ``-ubuntu18_amd64`` ``system`` ========= =================== ========== @@ -12387,11 +12739,11 @@ FTGL is a free open source library to enable developers to use arbitrary fonts i *homepage*: http://ftgl.sourceforge.net/docs/html/ -============= ====================================================================================== -version toolchain -============= ====================================================================================== -``2.1.3-rc5`` ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2018b``, ``intel/2017b`` -============= ====================================================================================== +============= ========================================================================================================== +version toolchain +============= ========================================================================================================== +``2.1.3-rc5`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2018b``, ``intel/2017b`` +============= ========================================================================================================== .. _list_software_Fujitsu_746: @@ -12535,11 +12887,11 @@ The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Ex *homepage*: https://launchpad.net/futile -========= =============================== -version toolchain -========= =============================== -``1.8.3`` ``foss/2020b``, ``intel/2020b`` -========= =============================== +========= ================================================================================================= +version toolchain +========= ================================================================================================= +``1.8.3`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` +========= ================================================================================================= .. _list_software_future_667: @@ -12583,7 +12935,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPy_272` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_genozip_764` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPy_272` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -13578,11 +13930,11 @@ Gengetopt is a tool to write command line option parsing code for C programs. *homepage*: https://www.gnu.org/software/gengetopt/gengetopt.html -======== ===================================== -version toolchain -======== ===================================== -``2.23`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -======== ===================================== +======== ========================================================= +version toolchain +======== ========================================================= +``2.23`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +======== ========================================================= .. _list_software_Genome_Profiler_1533: @@ -13702,6 +14054,22 @@ version versionsuffix toolchain ========== ================== ========== +.. _list_software_genozip_764: + +*genozip* ++++++++++ + +Genozip is a compressor for genomic files - it compresses FASTQ, SAM/BAM/CRAM, VCF, FASTA and others. + +*homepage*: https://genozip.com + +========== ================== +version toolchain +========== ================== +``13.0.5`` ``GCCcore/11.2.0`` +========== ================== + + .. _list_software_gensim_643: *gensim* @@ -13783,6 +14151,7 @@ Georges the lemur opinionated particle accelerator modeling Python package. Also ========== ================= ============== version versionsuffix toolchain ========== ================= ============== +``2019.2`` ``foss/2021a`` ``2019.2`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================= ============== @@ -13923,6 +14292,7 @@ version toolchain ``0.10.6`` ``GCCcore/7.3.0`` ``0.11.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.12.2`` ``GCC/10.3.0`` +``0.12.6`` ``GCC/11.2.0`` ========== ==================================== @@ -13935,14 +14305,14 @@ GFF/GTF parsing utility providing format conversions, region filtering, FASTA se *homepage*: https://github.com/gpertea/gffread -========== ==================================== -version toolchain -========== ==================================== -``0.9.12`` ``foss/2016b`` -``0.10.6`` ``GCCcore/7.3.0`` -``0.11.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.12.7`` ``GCC/10.3.0`` -========== ==================================== +========== ====================================== +version toolchain +========== ====================================== +``0.9.12`` ``foss/2016b`` +``0.10.6`` ``GCCcore/7.3.0`` +``0.11.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.12.7`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ====================================== .. _list_software_gflags_628: @@ -14492,7 +14862,7 @@ version toolchain Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. -*homepage*: http://www.cbcb.umd.edu/software/glimmer/ +*homepage*: http://ccb.jhu.edu/software/glimmer/index.shtml ========= ============================== version toolchain @@ -14782,6 +15152,7 @@ version versionsuffix toolchain ``4.5.6`` ``-Python-3.7.4`` ``foss/2019b`` ``4.7.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``4.8.4`` ``-Python-3.6.4`` ``foss/2018a`` +``4.9.0`` ``foss/2021a`` ========= ================== =============================== @@ -14864,7 +15235,7 @@ version toolchain Portable interactive, function plotting utility -*homepage*: http://gnuplot.sourceforge.net/ +*homepage*: http://gnuplot.sourceforge.net ========= ================================================================ version toolchain @@ -14877,7 +15248,7 @@ version toolchain ``5.2.6`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b`` ``5.2.8`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``5.4.1`` ``GCCcore/10.2.0`` -``5.4.2`` ``GCCcore/10.3.0`` +``5.4.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ================================================================ @@ -15465,11 +15836,11 @@ Graphite is a "smart font" system developed specifically to handle the complexi *homepage*: https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home -========== ================= -version toolchain -========== ================= -``1.3.14`` ``GCCcore/8.3.0`` -========== ================= +========== ===================================== +version toolchain +========== ===================================== +``1.3.14`` ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` +========== ===================================== .. _list_software_GraPhlAn_749: @@ -15860,7 +16231,7 @@ version toolchain ``2.4`` ``GCCcore/6.4.0`` ``2.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.6`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` -``2.7`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` +``2.7`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ========= ============================================================================================================================ @@ -15949,16 +16320,16 @@ A toolkit for assigning objective taxonomic classifications to bacterial and arc *homepage*: https://github.com/Ecogenomics/GTDBTk -========= ================== =============================== -version versionsuffix toolchain -========= ================== =============================== -``0.2.2`` ``-Python-2.7.15`` ``intel/2018b`` -``0.3.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` -``1.0.2`` ``-Python-3.7.4`` ``intel/2019b`` -``1.3.0`` ``-Python-3.8.2`` ``intel/2020a`` -``1.5.0`` ``intel/2020b`` -``1.7.0`` ``foss/2020b``, ``intel/2020b`` -========= ================== =============================== +========= ================== =============================================== +version versionsuffix toolchain +========= ================== =============================================== +``0.2.2`` ``-Python-2.7.15`` ``intel/2018b`` +``0.3.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` +``1.0.2`` ``-Python-3.7.4`` ``intel/2019b`` +``1.3.0`` ``-Python-3.8.2`` ``intel/2020a`` +``1.5.0`` ``intel/2020b`` +``1.7.0`` ``foss/2020b``, ``foss/2021a``, ``intel/2020b`` +========= ================== =============================================== .. _list_software_GTK+_273: @@ -16015,6 +16386,7 @@ GTK+ is the primary library used to construct user interfaces in GNOME. It prov version toolchain =========== ================== ``3.24.29`` ``GCCcore/10.3.0`` +``3.24.31`` ``GCCcore/11.2.0`` =========== ================== @@ -16191,7 +16563,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_HIP_225` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_HIP_225` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hivtrace_854` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -16273,6 +16645,7 @@ version versionsuffix toolchain ``2.10.0`` ``-serial-Python-3.7.4`` ``foss/2019b`` ``3.1.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``3.2.1`` ``foss/2021a`` +``3.6.0`` ``foss/2021b``, ``intel/2021b`` ========== ===================================== ==================================================================================== @@ -16873,6 +17246,22 @@ version toolchain ============== ================================================================================= +.. _list_software_hivtrace_854: + +*hivtrace* +++++++++++ + +HIV-TRACE is an application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. + +*homepage*: https://github.com/veg/hivtrace + +========= ============== +version toolchain +========= ============== +``0.6.2`` ``foss/2021a`` +========= ============== + + .. _list_software_hl7apy_597: *hl7apy* @@ -16920,7 +17309,7 @@ version toolchain ``3.1b2`` ``GCC/6.4.0-2.28``, ``foss/2016a``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a``, ``intel/2018a`` ``3.2.1`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iimpi/2019b``, ``intel/2018b`` ``3.3.1`` ``gompi/2020a``, ``iimpi/2020a`` -``3.3.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2020b`` +``3.3.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b``, ``iimpi/2020b`` ========= ============================================================================================================================================ @@ -17003,6 +17392,7 @@ version versionsuffix toolchain ``0.22.1`` ``-TensorFlow-2.5.0`` ``fosscuda/2020b`` ``0.22.1`` ``-TensorFlow-2.5.0-Python-3.7.4`` ``fosscuda/2019b`` ``0.23.0`` ``-CUDA-11.3.1-PyTorch-1.10.0`` ``foss/2021a`` +``0.23.0`` ``-TensorFlow-2.5.0`` ``fosscuda/2020b`` ========== =================================== ================================== @@ -17087,7 +17477,7 @@ version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -17329,21 +17719,22 @@ Hypothesis is an advanced testing library for Python. It lets you write tests wh *homepage*: https://github.com/HypothesisWorks/hypothesis -========== ================= ================================== -version versionsuffix toolchain -========== ================= ================================== -``4.5.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``4.23.4`` ``GCCcore/8.2.0`` -``4.39.3`` ``-Python-3.6.4`` ``intel/2018a`` -``4.44.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``4.53.1`` ``GCCcore/10.2.0`` -``5.6.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``5.41.2`` ``GCCcore/10.2.0`` -``5.41.5`` ``GCCcore/10.2.0`` -``6.7.0`` ``GCCcore/10.2.0`` -``6.13.1`` ``GCCcore/10.3.0`` -``6.14.6`` ``GCCcore/11.2.0`` -========== ================= ================================== +========== ================== ================================== +version versionsuffix toolchain +========== ================== ================================== +``4.5.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``4.23.4`` ``GCCcore/8.2.0`` +``4.39.3`` ``-Python-3.6.4`` ``intel/2018a`` +``4.44.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``4.53.1`` ``GCCcore/10.2.0`` +``4.57.1`` ``-Python-2.7.18`` ``GCCcore/11.2.0`` +``5.6.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``5.41.2`` ``GCCcore/10.2.0`` +``5.41.5`` ``GCCcore/10.2.0`` +``6.7.0`` ``GCCcore/10.2.0`` +``6.13.1`` ``GCCcore/10.3.0`` +``6.14.6`` ``GCCcore/11.2.0`` +========== ================== ================================== .. _list_software_Hypre_520: @@ -17373,7 +17764,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intervaltree-python_2020` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_IsoNet_594` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -17628,11 +18019,11 @@ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequen *homepage*: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/ -========= ================================================================================================== -version toolchain -========= ================================================================================================== -``1.1.3`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` -========= ================================================================================================== +========= ================================================================================================================== +version toolchain +========= ================================================================================================================== +``1.1.3`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` +========= ================================================================================================================== .. _list_software_idemux_652: @@ -17758,6 +18149,7 @@ version toolchain ``0.8.5`` ``foss/2020b`` ``0.9.1`` ``foss/2020b``, ``fosscuda/2020b`` ``0.9.4`` ``foss/2021a`` +``0.9.5`` ``foss/2021b`` ========= ================================================ @@ -17894,6 +18286,7 @@ version versionsuffix toolchain ``2020b`` ``system`` ``2021a`` ``system`` ``2021b`` ``system`` +``2022.00`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ===================== ==================== ========== @@ -18170,6 +18563,7 @@ version versionsuffix toolchain ``2021.2.0`` ``gompi/2021a``, ``iimpi/2021a``, ``iompi/2021a`` ``2021.3.0`` ``gompi/2021a`` ``2021.4.0`` ``system`` +``2022.0.1`` ``system`` ============== ============= ====================================================================================================================================================================================================================================================================== @@ -18186,6 +18580,7 @@ FFTW interfaces using Intel oneAPI Math Kernel Library version toolchain ============ ================================ ``2021.4.0`` ``gompi/2021b``, ``iimpi/2021b`` +``2022.0.1`` ``iimpi/2022.00`` ============ ================================ @@ -18287,6 +18682,7 @@ version versionsuffix toolchain ``2021.2.0`` ``intel-compilers/2021.2.0`` ``2021.3.0`` ``intel-compilers/2021.3.0`` ``2021.4.0`` ``intel-compilers/2021.4.0`` +``2021.5.0`` ``intel-compilers/2022.0.1`` ``system`` ``iccifort/system-GCC-system-2.29`` =============== ============= ================================================================================================================================================================================================================================ @@ -18450,6 +18846,7 @@ version toolchain ``2019_update2`` ``system`` ``2019_update5`` ``system`` ``2021.4.0`` ``system`` +``2022.0.0`` ``system`` ================ ========== @@ -18547,6 +18944,7 @@ version versionsuffix toolchain ``2020b`` ``system`` ``2021a`` ``system`` ``2021b`` ``system`` +``2022.00`` ``system`` ===================== ============= ========== @@ -18566,6 +18964,7 @@ version toolchain ``2021.2.0`` ``system`` ``2021.3.0`` ``system`` ``2021.4.0`` ``system`` +``2022.0.1`` ``system`` ============ ========== @@ -18673,6 +19072,22 @@ version toolchain ======= ========================================================= +.. _list_software_intervaltree-python_2020: + +*intervaltree-python* ++++++++++++++++++++++ + +A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment + +*homepage*: https://github.com/chaimleib/intervaltree + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` +========= ================= ============== + + .. _list_software_intltool_885: *intltool* @@ -18944,6 +19359,7 @@ version versionsuffix toolchain ``5.8.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``5.8.0`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``fosscuda/2018b``, ``fosscuda/2019a``, ``intel/2018b`` ``5.8.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``5.10.0`` ``-Python-2.7.18`` ``foss/2021b`` ``6.2.1`` ``-Python-3.6.4`` ``foss/2017a`` ``6.3.1`` ``-Python-3.6.4`` ``intel/2018a`` ``6.4.0`` ``-Python-3.6.4`` ``foss/2018a`` @@ -18974,6 +19390,7 @@ version versionsuffix toolchain ``1.6.6`` ``intel/2018a`` ``1.6.12`` ``foss/2018b``, ``foss/2020a``, ``intel/2019b`` ``2.1.2`` ``foss/2020a``, ``gompi/2020b`` +``2.1.3`` ``gompi/2021a`` ========== ============= =============================================== @@ -19022,11 +19439,11 @@ Intelligent Storage Acceleration Library *homepage*: https://github.com/intel/isa-l -========== ====================================== -version toolchain -========== ====================================== -``2.30.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========== ====================================== +========== ========================================================== +version toolchain +========== ========================================================== +``2.30.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ========================================================== .. _list_software_ISL_232: @@ -19066,6 +19483,22 @@ version toolchain ========= ============== +.. _list_software_IsoNet_594: + +*IsoNet* +++++++++ + +IsoNet stands for for ISOtropic reconstructioN of Electron Tomography. It trains deep convolutional neural networks to reconstruct meaningful contents in the mis sing wedge for electron tomography, and to increase signal-to-noise ratio, using the information learned from the original tomogram. The software requires tomograms as input. Observing at about 30A resolution, the IsoNet generated tomograms are largely isotropic. + +*homepage*: https://github.com/Heng-Z/IsoNet + +=========================== ================== +version toolchain +=========================== ================== +``0.1_20210822_04_674f67f`` ``fosscuda/2020b`` +=========================== ================== + + .. _list_software_ispc_431: *ispc* @@ -19105,6 +19538,8 @@ version toolchain ``2018.3.022`` ``system`` ``2019.2.026`` ``system`` ``2019.4.036`` ``system`` +``2021.2.0`` ``system`` +``2021.5.0`` ``system`` ============== ========== @@ -19275,7 +19710,7 @@ version toolchain *Java* ++++++ -Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. +Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. *homepage*: https://java.com/ @@ -19324,6 +19759,7 @@ version versionsuffix toolchain ``1.8.0_271`` ``system`` ``1.8.0_281`` ``system`` ``1.8.0_292`` ``-OpenJDK`` ``system`` +``1.8.0_311`` ``system`` ``1.8_191`` ``-b26-OpenJDK`` ``system`` ``1.8_265`` ``-b01-OpenJDK-aarch64`` ``system`` ``1.9.0.4`` ``system`` @@ -19333,8 +19769,12 @@ version versionsuffix toolchain ``11.0.8`` ``-aarch64`` ``system`` ``13`` ``system`` ``13.0.2`` ``system`` +``15`` ``system`` +``15.0.1`` ``system`` ``16`` ``system`` ``16.0.1`` ``system`` +``17`` ``system`` +``17.0.1`` ``system`` ============= ======================== ========== @@ -19581,6 +20021,7 @@ version toolchain ``2.0.5`` ``system`` ``2.4.0`` ``system`` ``2.4.1`` ``system`` +``2.4.2`` ``system`` ========= ========== @@ -19623,7 +20064,9 @@ version versionsuffix toolchain ``1.6.1`` ``-linux-x86_64`` ``system`` ``1.6.2`` ``-linux-x86_64`` ``system`` ``1.6.4`` ``-linux-x86_64`` ``system`` +``1.6.5`` ``-linux-x86_64`` ``system`` ``1.7.0`` ``-linux-x86_64`` ``system`` +``1.7.1`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -19786,6 +20229,7 @@ Fast static image export for web-based visualization libraries with zero depende version toolchain ========= ================== ``0.1.0`` ``GCCcore/10.2.0`` +``0.2.1`` ``GCCcore/10.3.0`` ========= ================== @@ -20147,6 +20591,7 @@ version toolchain ``2.7`` ``GCCcore/7.3.0`` ``2.7.1`` ``GCCcore/8.2.0`` ``2.8`` ``GCC/10.3.0``, ``GCCcore/10.2.0`` +``2.8.1`` ``GCCcore/11.2.0`` ========= ================================== @@ -20475,6 +20920,7 @@ version versionsuffix toolchain ``0.8.2`` ``-Python-3.8.2`` ``foss/2020a`` ``0.8.3`` ``foss/2020b``, ``fosscuda/2020b`` ``0.8.7`` ``foss/2021a`` +``0.8.8`` ``foss/2021b`` ========= ================= ================================== @@ -20888,6 +21334,7 @@ version toolchain ======= ===================================== ``1.5`` ``GCCcore/7.3.0`` ``1.7`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.8`` ``GCCcore/11.2.0`` ======= ===================================== @@ -20967,6 +21414,7 @@ version toolchain ``20150310`` ``GCC/4.9.2``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0`` ``20190529`` ``GCCcore/8.2.0`` ``20201201`` ``GCCcore/10.2.0`` +``20210305`` ``GCCcore/10.3.0`` ``20210528`` ``GCCcore/11.2.0`` ============ =================================================== @@ -20998,11 +21446,11 @@ libelf is a free ELF object file access library *homepage*: https://directory.fsf.org/wiki/Libelf -========== ================================================================================================================================================ -version toolchain -========== ================================================================================================================================================ -``0.8.13`` ``GCC/4.8.3``, ``GCC/4.9.2``, ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` -========== ================================================================================================================================================ +========== ==================================================================================================================================================================== +version toolchain +========== ==================================================================================================================================================================== +``0.8.13`` ``GCC/4.8.3``, ``GCC/4.9.2``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +========== ==================================================================================================================================================================== .. _list_software_libepoxy_876: @@ -21178,7 +21626,7 @@ version toolchain GD is an open source code library for the dynamic creation of images by programmers. -*homepage*: https://libgd.github.io/ +*homepage*: https://libgd.github.io ========= ============================================================================================================ version toolchain @@ -21189,6 +21637,7 @@ version toolchain ``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b``, ``intel/2018a`` ``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``2.3.1`` ``GCCcore/10.3.0`` +``2.3.3`` ``GCCcore/11.2.0`` ========= ============================================================================================================ @@ -21509,7 +21958,7 @@ version versionsuffix toolchain ``2.1.0`` ``intel/2016b`` ``2.4.2`` ``intel/2018a`` ``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` -``2.6.0`` ``-lmax-6-cp2k`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a`` +``2.6.0`` ``-lmax-6-cp2k`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a``, ``iimpi/2021a`` ========= ================ =================================================================================================================================================================================================================== @@ -22955,6 +23404,7 @@ version toolchain ``1.10`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.16.1`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` ``1.16.2`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` +``1.17`` ``GCC/11.2.0`` ========== =============================================================================================== @@ -23305,6 +23755,7 @@ version versionsuffix toolchain ``1.0.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``1.0.1`` ``-Python-3.8.2`` ``foss/2020a`` ``1.0.2`` ``foss/2020b``, ``intel/2020b`` +``1.0.3`` ``foss/2021a`` ========== ================== =============================== @@ -23617,6 +24068,7 @@ version toolchain ========= ================== ``1.9.7`` ``GCCcore/9.3.0`` ``2.2`` ``GCCcore/10.2.0`` +``2.3`` ``GCCcore/10.3.0`` ========= ================== @@ -23861,7 +24313,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -23918,6 +24370,22 @@ version versionsuffix toolchain ================== ================== =============================== +.. _list_software_MACSE_361: + +*MACSE* ++++++++ + +MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. + +*homepage*: https://bioweb.supagro.inra.fr/macse/index.php + +======== ============= ========== +version versionsuffix toolchain +======== ============= ========== +``2.06`` ``-Java-15`` ``system`` +======== ============= ========== + + .. _list_software_maeparser_960: *maeparser* @@ -23989,6 +24457,7 @@ version toolchain ========== ============== ``1.07b`` ``foss/2018b`` ``1.07bb`` ``GCC/8.3.0`` +``1.09b`` ``GCC/11.2.0`` ========== ============== @@ -24189,6 +24658,7 @@ mapDamage2 is a computational framework written in Python and R, which track ========= ============= ============== version versionsuffix toolchain ========= ============= ============== +``2.2.1`` ``foss/2021b`` ``2.2.1`` ``-R-4.0.4`` ``foss/2020b`` ========= ============= ============== @@ -24430,6 +24900,7 @@ version toolchain ``2020a`` ``system`` ``2020b`` ``system`` ``2021a`` ``system`` +``2021b`` ``system`` ========= ========== @@ -24460,49 +24931,49 @@ matplotlib is a python 2D plotting library which produces publication quality fi *homepage*: https://matplotlib.org -========= ================================= ======================================================================== -version versionsuffix toolchain -========= ================================= ======================================================================== -``1.4.3`` ``-Python-2.7.12`` ``intel/2016b`` -``1.5.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``1.5.1`` ``-Python-2.7.11-freetype-2.6.3`` ``foss/2016a``, ``intel/2016a`` -``1.5.1`` ``-Python-2.7.12`` ``intel/2016b`` -``1.5.1`` ``-Python-3.5.1`` ``foss/2016a``, ``intel/2016a`` -``1.5.1`` ``-Python-3.5.2`` ``intel/2016b`` -``1.5.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.5.2`` ``-Python-3.5.2`` ``intel/2016b`` -``1.5.3`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.5.3`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``2.0.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.0.0`` ``-Python-2.7.13`` ``intel/2017a`` -``2.0.1`` ``-Python-3.6.1`` ``intel/2017a`` -``2.0.2`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` -``2.0.2`` ``-Python-2.7.13-Qt-4.8.7`` ``intel/2017a`` -``2.0.2`` ``-Python-2.7.13-libpng-1.6.29`` ``intel/2017a`` -``2.0.2`` ``-Python-3.6.1`` ``foss/2017a`` -``2.0.2`` ``-Python-3.6.1-libpng-1.6.29`` ``intel/2017a`` -``2.1.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``2.1.0`` ``-Python-3.6.2`` ``foss/2017b`` -``2.1.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``2.1.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.1.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.2`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``2.1.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018.02``, ``iomkl/2018a`` -``2.2.3`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``2.2.3`` ``-Python-3.6.6`` ``intel/2018b`` -``2.2.4`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``2.2.4`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``2.2.5`` ``-Python-2.7.16`` ``foss/2019b`` -``2.2.5`` ``-Python-2.7.18`` ``foss/2020a``, ``foss/2020b``, ``fosscuda/2020a``, ``intel/2020a`` -``3.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` -``3.0.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` -``3.2.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` -``3.3.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -``3.4.2`` ``foss/2021a``, ``intel/2021a`` -``3.4.3`` ``foss/2021b``, ``intel/2021b`` -========= ================================= ======================================================================== +========= ================================= =================================================================================== +version versionsuffix toolchain +========= ================================= =================================================================================== +``1.4.3`` ``-Python-2.7.12`` ``intel/2016b`` +``1.5.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``1.5.1`` ``-Python-2.7.11-freetype-2.6.3`` ``foss/2016a``, ``intel/2016a`` +``1.5.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.5.1`` ``-Python-3.5.1`` ``foss/2016a``, ``intel/2016a`` +``1.5.1`` ``-Python-3.5.2`` ``intel/2016b`` +``1.5.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``1.5.2`` ``-Python-3.5.2`` ``intel/2016b`` +``1.5.3`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``1.5.3`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``2.0.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``2.0.0`` ``-Python-2.7.13`` ``intel/2017a`` +``2.0.1`` ``-Python-3.6.1`` ``intel/2017a`` +``2.0.2`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``2.0.2`` ``-Python-2.7.13-Qt-4.8.7`` ``intel/2017a`` +``2.0.2`` ``-Python-2.7.13-libpng-1.6.29`` ``intel/2017a`` +``2.0.2`` ``-Python-3.6.1`` ``foss/2017a`` +``2.0.2`` ``-Python-3.6.1-libpng-1.6.29`` ``intel/2017a`` +``2.1.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``2.1.0`` ``-Python-3.6.2`` ``foss/2017b`` +``2.1.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``2.1.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.1.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.2`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``2.1.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018.02``, ``iomkl/2018a`` +``2.2.3`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``2.2.3`` ``-Python-3.6.6`` ``intel/2018b`` +``2.2.4`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` +``2.2.4`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2.2.5`` ``-Python-2.7.16`` ``foss/2019b`` +``2.2.5`` ``-Python-2.7.18`` ``foss/2020a``, ``foss/2020b``, ``foss/2021b``, ``fosscuda/2020a``, ``intel/2020a`` +``3.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` +``3.0.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` +``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` +``3.2.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` +``3.3.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +``3.4.2`` ``foss/2021a``, ``intel/2021a`` +``3.4.3`` ``foss/2021b``, ``intel/2021b`` +========= ================================= =================================================================================== .. _list_software_MATSim_523: @@ -24601,13 +25072,13 @@ MaxBin is software for binning assembled metagenomic sequences based on an Expec *homepage*: https://sourceforge.net/projects/maxbin/ -========= ================ ==================== -version versionsuffix toolchain -========= ================ ==================== -``2.2.6`` ``-Perl-5.28.0`` ``foss/2018b`` -``2.2.7`` ``gompi/2020b`` -``2.2.7`` ``-Perl-5.28.1`` ``GCC/8.2.0-2.31.1`` -========= ================ ==================== +========= ================ ================================ +version versionsuffix toolchain +========= ================ ================================ +``2.2.6`` ``-Perl-5.28.0`` ``foss/2018b`` +``2.2.7`` ``gompi/2020b``, ``gompi/2021b`` +``2.2.7`` ``-Perl-5.28.1`` ``GCC/8.2.0-2.31.1`` +========= ================ ================================ .. _list_software_MaxQuant_815: @@ -25011,18 +25482,18 @@ An ultra-fast single-node solution for large and complex metagenomics assembly *homepage*: https://github.com/voutcn/megahit -========= ================== ================================= -version versionsuffix toolchain -========= ================== ================================= -``1.1.2`` ``-Python-2.7.14`` ``foss/2018a`` -``1.1.3`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a`` -``1.1.3`` ``-Python-3.6.3`` ``foss/2017b`` -``1.1.4`` ``-Python-2.7.15`` ``foss/2018b`` -``1.1.4`` ``-Python-3.6.6`` ``foss/2018b`` -``1.2.8`` ``GCCcore/8.2.0`` -``1.2.9`` ``GCCcore/9.3.0``, ``foss/2018b`` -``1.2.9`` ``-Python-2.7.18`` ``GCCcore/10.2.0`` -========= ================== ================================= +========= ================== ===================================================== +version versionsuffix toolchain +========= ================== ===================================================== +``1.1.2`` ``-Python-2.7.14`` ``foss/2018a`` +``1.1.3`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a`` +``1.1.3`` ``-Python-3.6.3`` ``foss/2017b`` +``1.1.4`` ``-Python-2.7.15`` ``foss/2018b`` +``1.1.4`` ``-Python-3.6.6`` ``foss/2018b`` +``1.2.8`` ``GCCcore/8.2.0`` +``1.2.9`` ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``foss/2018b`` +``1.2.9`` ``-Python-2.7.18`` ``GCCcore/10.2.0`` +========= ================== ===================================================== .. _list_software_Megalodon_918: @@ -25348,6 +25819,7 @@ version versionsuffix toolchain ========== ================== =============== ``2.12.1`` ``-Python-2.7.15`` ``foss/2018b`` ``2.14`` ``gompi/2019a`` +``2.15`` ``gompi/2021b`` ``2.15`` ``-Python-2.7.18`` ``gompi/2020b`` ========== ================== =============== @@ -25449,6 +25921,22 @@ version toolchain ============== ============== +.. _list_software_MetaPhlAn_858: + +*MetaPhlAn* ++++++++++++ + +MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data + +*homepage*: https://github.com/biobakery/MetaPhlAn + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``3.0.9`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_MetaPhlAn2_908: *MetaPhlAn2* @@ -25585,6 +26073,22 @@ version versionsuffix toolchain ======= ================= ================================== +.. _list_software_MicrobeAnnotator_1655: + +*MicrobeAnnotator* +++++++++++++++++++ + +Easy-to-use pipeline for the comprehensive metabolic annotation of microbial genomes. + +*homepage*: https://github.com/cruizperez/MicrobeAnnotator + +========= ============== +version toolchain +========= ============== +``2.0.5`` ``foss/2021a`` +========= ============== + + .. _list_software_microctools_1198: *microctools* @@ -25878,6 +26382,7 @@ version versionsuffix toolchain ======= ================== =============================== ``1.4`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``1.4`` ``-Python-2.7.16`` ``intel/2019b`` +``1.6`` ``intel/2021b`` ======= ================== =============================== @@ -26221,6 +26726,23 @@ version versionsuffix toolchain ================ ====================== ========== +.. _list_software_mold_428: + +*mold* +++++++ + +mold is a high-performance drop-in replacement for existing Unix linkers. + +*homepage*: https://github.com/rui314/mold + +========= ================== +version toolchain +========= ================== +``0.9.6`` ``GCCcore/11.2.0`` +``1.0.0`` ``GCCcore/11.2.0`` +========= ================== + + .. _list_software_Molden_607: *Molden* @@ -26279,7 +26801,7 @@ version versionsuffix toolchain ``1.4.4`` ``-Python-3.7.2`` ``intel/2019a`` ``1.4.5`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``1.4.5`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.4.8`` ``foss/2021a`` +``1.4.8`` ``foss/2020b``, ``foss/2021a`` ========= ================== =============================== @@ -26925,21 +27447,23 @@ Aggregate results from bioinformatics analyses across many samples into a single *homepage*: https://multiqc.info -======= ================== =============================== -version versionsuffix toolchain -======= ================== =============================== -``0.9`` ``-Python-2.7.12`` ``foss/2016b`` -``1.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``1.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.6`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``1.6`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.7`` ``-Python-2.7.15`` ``intel/2018b`` -``1.7`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.8`` ``-Python-2.7.16`` ``intel/2019b`` -``1.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.9`` ``-Python-3.7.4`` ``foss/2019b`` -``1.9`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -======= ================== =============================== +========== ================== =============================== +version versionsuffix toolchain +========== ================== =============================== +``0.9`` ``-Python-2.7.12`` ``foss/2016b`` +``1.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``1.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``1.6`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``1.6`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``1.7`` ``-Python-2.7.15`` ``intel/2018b`` +``1.7`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.8`` ``-Python-2.7.16`` ``intel/2019b`` +``1.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.9`` ``-Python-3.7.4`` ``foss/2019b`` +``1.9`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.10.1`` ``foss/2020b`` +``1.11`` ``foss/2021a`` +========== ================== =============================== .. _list_software_Multiwfn_854: @@ -26968,12 +27492,12 @@ MUMmer is a system for rapidly aligning entire genomes, whether in complete or *homepage*: http://mummer.sourceforge.net/ -============== ===================================================== -version toolchain -============== ===================================================== -``3.23`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``foss/2016b`` -``4.0.0beta2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0``, ``foss/2018b`` -============== ===================================================== +============== ========================================================================= +version toolchain +============== ========================================================================= +``3.23`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``foss/2016b`` +``4.0.0beta2`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``foss/2018b`` +============== ========================================================================= .. _list_software_MUMPS_402: @@ -27050,17 +27574,18 @@ version versionsuffix toolchain *MUSCLE* ++++++++ -MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks. +MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks. *homepage*: https://drive5.com/muscle/ -============ =============== ========================================================================================================================================================== -version versionsuffix toolchain -============ =============== ========================================================================================================================================================== -``3.8.31`` ``GCC/7.3.0-2.30``, ``GCCcore/10.2.0``, ``foss/2016a``, ``foss/2017b``, ``foss/2018a``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``3.8.31`` ``-i86linux64`` ``system`` -``3.8.1551`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` -============ =============== ========================================================================================================================================================== +============ =============== ================================================================================================================================================================================================= +version versionsuffix toolchain +============ =============== ================================================================================================================================================================================================= +``3.8.31`` ``GCC/7.3.0-2.30``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2017b``, ``foss/2018a``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``3.8.31`` ``-i86linux64`` ``system`` +``3.8.1551`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` +``5.0.1428`` ``GCCcore/10.3.0`` +============ =============== ================================================================================================================================================================================================= .. _list_software_MuSiC_449: @@ -27355,7 +27880,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numdiff_745` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -27906,7 +28431,7 @@ Ncview is a visual browser for netCDF format files. Typically you would use ncv version toolchain ========= ====================================================================================================================================================================================== ``2.1.7`` ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``gompi/2019a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b``, ``iomkl/2018b`` -``2.1.8`` ``gompi/2020a`` +``2.1.8`` ``gompi/2020a``, ``gompi/2021a`` ========= ====================================================================================================================================================================================== @@ -28500,7 +29025,7 @@ version versionsuffix toolchain *NGS-Python* ++++++++++++ -NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. +NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. *homepage*: https://github.com/ncbi/ngs @@ -28508,6 +29033,7 @@ NGS is a new, domain-specific API for accessing reads, alignments and pileups pr version versionsuffix toolchain ========== ================== =============== ``1.2.3`` ``-Python-2.7.11`` ``intel/2016a`` +``2.9.3`` ``-Python-3.6.6`` ``intel/2018b`` ``2.10.4`` ``-Python-2.7.16`` ``gompi/2019b`` ========== ================== =============== @@ -29160,12 +29686,30 @@ version versionsuffix toolchain ``0.46.0`` ``foss/2019a`` ``0.47.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``0.50.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.50.1`` ``-Python-3.8.2`` ``foss/2020a`` ``0.52.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``0.52.0`` ``-Python-3.8.2`` ``foss/2020a`` ``0.53.1`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` +``0.54.1`` ``foss/2021b`` ========== ================== =================================================== +.. _list_software_numdiff_745: + +*numdiff* ++++++++++ + +Numdiff (which I will also write numdiff) is a little program that can be used to compare putatively similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats. Equivalently, Numdiff is a program with the capability to appropriately compare files containing numerical fields (and not only). + +*homepage*: https://www.nongnu.org/numdiff/ + +========= ================== +version toolchain +========= ================== +``5.9.0`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_numexpr_783: *numexpr* @@ -29238,6 +29782,7 @@ version toolchain ``21.5`` ``system`` ``21.7`` ``system`` ``21.9`` ``system`` +``21.11`` ``system`` ========= ========== @@ -29302,7 +29847,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSceneGraph_1394` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFace_769` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSceneGraph_1394` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -29331,11 +29876,12 @@ The OBITools programs aims to help you to manipulate various data and sequence f *homepage*: http://www.grenoble.prabi.fr/trac/OBITools -========= ================== ============== -version versionsuffix toolchain -========= ================== ============== -``1.2.9`` ``-Python-2.7.11`` ``foss/2016a`` -========= ================== ============== +========== ================== ============== +version versionsuffix toolchain +========== ================== ============== +``1.2.9`` ``-Python-2.7.11`` ``foss/2016a`` +``1.2.13`` ``-Python-2.7.15`` ``foss/2019a`` +========== ================== ============== .. _list_software_OBITools3_798: @@ -29384,6 +29930,7 @@ Open CASCADE Technology (OCCT) is an object-oriented C++ class library designed version toolchain =========== ============== ``7.3.0p4`` ``foss/2019b`` +``7.5.0p1`` ``foss/2021a`` =========== ============== @@ -29576,6 +30123,7 @@ version versionsuffix toolchain ``2.4.1`` ``-Python-3.6.6`` ``intel/2018b`` ``2.4.1`` ``-Python-3.7.2`` ``intel/2019a`` ``3.0.0`` ``-Python-3.7.4`` ``gompi/2019b`` +``3.1.1`` ``gompi/2021a`` ``3.1.1`` ``-Python-3.7.4`` ``gompi/2019b`` ========= ================== =============== @@ -29632,6 +30180,7 @@ version versionsuffix toolchain ======= ================= ============== ``3.2`` ``-Python-3.8.2`` ``foss/2020a`` ``6.0`` ``foss/2020b`` +``8.2`` ``foss/2021a`` ======= ================= ============== @@ -29688,7 +30237,7 @@ version versionsuffix toolchain ``3.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``3.3.0`` ``-Python-3.6.1`` ``intel/2017a`` ``3.3.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``3.4.1`` ``-Python-2.7.14`` ``foss/2018a`` +``3.4.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``3.4.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``3.4.1`` ``-Python-3.6.4-contrib`` ``foss/2018a`` ``3.4.5`` ``-Python-2.7.15`` ``foss/2018b`` @@ -29727,6 +30276,23 @@ version toolchain ========= ================================ +.. _list_software_OpenFace_769: + +*OpenFace* +++++++++++ + +OpenFace – a state-of-the art tool intended for facial landmark detection, head pose estimation, facial action unit recognition, and eye-gaze estimation. + +*homepage*: https://github.com/TadasBaltrusaitis/OpenFace + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``2.2.0`` ``foss/2021a`` +``2.2.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== + + .. _list_software_OpenFOAM_693: *OpenFOAM* @@ -29766,6 +30332,7 @@ version versionsuffix toolchain ``v2006`` ``foss/2020a``, ``intel/2020a`` ``v2012`` ``foss/2020a`` ``v2106`` ``foss/2021a`` +``v2112`` ``foss/2021b`` ================ ============= ================================================= @@ -30311,20 +30878,22 @@ ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum c *homepage*: https://orcaforum.kofo.mpg.de -====================== ================== =============== -version versionsuffix toolchain -====================== ================== =============== -``3_0_2-linux_x86-64`` ``-OpenMPI-1.8.1`` ``system`` -``4.0.0.2`` ``-OpenMPI-2.0.2`` ``system`` -``4.0.1`` ``-OpenMPI-2.0.2`` ``system`` -``4.1.0`` ``-OpenMPI-3.1.3`` ``system`` -``4.2.0`` ``gompi/2019b`` -``4.2.1`` ``gompi/2019b`` -``5.0.0`` ``gompi/2021a`` -``5.0.0`` ``-static`` ``gompi/2021a`` -``5.0.1`` ``gompi/2021a`` -``5.0.1`` ``-static`` ``gompi/2021a`` -====================== ================== =============== +====================== ================== ================================ +version versionsuffix toolchain +====================== ================== ================================ +``3_0_2-linux_x86-64`` ``-OpenMPI-1.8.1`` ``system`` +``4.0.0.2`` ``-OpenMPI-2.0.2`` ``system`` +``4.0.1`` ``-OpenMPI-2.0.2`` ``system`` +``4.1.0`` ``-OpenMPI-3.1.3`` ``system`` +``4.2.0`` ``gompi/2019b`` +``4.2.1`` ``gompi/2019b`` +``5.0.0`` ``gompi/2021a`` +``5.0.0`` ``-static`` ``gompi/2021a`` +``5.0.1`` ``gompi/2021a`` +``5.0.1`` ``-static`` ``gompi/2021a`` +``5.0.2`` ``gompi/2021a``, ``gompi/2021b`` +``5.0.2`` ``-static`` ``gompi/2021a``, ``gompi/2021b`` +====================== ================== ================================ .. _list_software_ORFfinder_863: @@ -30510,7 +31079,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -30659,12 +31228,12 @@ PAML is a package of programs for phylogenetic analyses of DNA or protein sequ *homepage*: http://abacus.gene.ucl.ac.uk/software/paml.html -======== ========================================================== -version toolchain -======== ========================================================== -``4.9i`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` -``4.9j`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -======== ========================================================== +======== ============================================================================= +version toolchain +======== ============================================================================= +``4.9i`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +``4.9j`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +======== ============================================================================= .. _list_software_panaroo_752: @@ -30928,7 +31497,7 @@ version toolchain ``2.4`` ``foss/2018b`` ``2.4.1`` ``GCC/8.3.0``, ``intel/2019b`` ``2.4.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` -``2.4.3`` ``GCC/10.2.0`` +``2.4.3`` ``GCC/10.2.0``, ``GCC/10.3.0`` ========= ====================================== @@ -30971,7 +31540,7 @@ version versionsuffix toolchain ``5.6.2`` ``-Python-3.7.4-mpi`` ``foss/2019b``, ``intel/2019b`` ``5.8.0`` ``-Python-3.8.2-mpi`` ``foss/2020a``, ``intel/2020a`` ``5.8.1`` ``-mpi`` ``foss/2020b`` -``5.9.1`` ``-mpi`` ``foss/2021a`` +``5.9.1`` ``-mpi`` ``foss/2021a``, ``foss/2021b`` ========= ====================== ================================================================================================= @@ -31018,11 +31587,11 @@ ParMETIS is an MPI-based parallel library that implements a variety of algorithm *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview -========= ============================================================================================================================================================================================================================================================================================================================================= -version toolchain -========= ============================================================================================================================================================================================================================================================================================================================================= -``4.0.3`` ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -========= ============================================================================================================================================================================================================================================================================================================================================= +========= ================================================================================================================================================================================================================================================================================================================================================================================================================================== +version toolchain +========= ================================================================================================================================================================================================================================================================================================================================================================================================================================== +``4.0.3`` ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +========= ================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_ParMGridGen_1040: @@ -31420,13 +31989,13 @@ PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. *homepage*: http://sco.h-its.org/exelixis/web/software/pear/ -========== ==================================================================== -version toolchain -========== ==================================================================== -``0.9.8`` ``foss/2016b``, ``intel/2016b`` -``0.9.10`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` -``0.9.11`` ``GCC/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` -========== ==================================================================== +========== ==================================================================================== +version toolchain +========== ==================================================================================== +``0.9.8`` ``foss/2016b``, ``intel/2016b`` +``0.9.10`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +``0.9.11`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` +========== ==================================================================================== .. _list_software_PennCNV_632: @@ -31845,6 +32414,7 @@ version versionsuffix toolchain ``2.2.0`` ``-Python-3.7.2`` ``intel/2019a`` ``2.7.1`` ``-Python-3.7.4`` ``intel/2019b`` ``2.7.1`` ``-Python-3.8.2`` ``intel/2020a`` +``2.12.0`` ``foss/2020b`` ============= ================== =============================== @@ -31945,6 +32515,23 @@ version toolchain ============ =============== +.. _list_software_PhyloPhlAn_991: + +*PhyloPhlAn* +++++++++++++ + +PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. + +*homepage*: https://github.com/biobakery/phylophlan + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``3.0`` ``-Python-3.8.2`` ``foss/2020a`` +``3.0.2`` ``foss/2021a`` +========= ================= ============== + + .. _list_software_PhyML_458: *PhyML* @@ -32110,6 +32697,7 @@ version versionsuffix toolchain ``8.0.1`` ``GCCcore/10.2.0`` ``8.2.0`` ``GCCcore/10.3.0`` ``8.3.1`` ``GCCcore/11.2.0`` +``8.3.2`` ``GCCcore/11.2.0`` ========= ================================= =================================================== @@ -32132,6 +32720,7 @@ version versionsuffix toolchain ``7.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``8.2.0`` ``GCCcore/10.3.0`` ``8.3.1`` ``GCCcore/11.2.0`` +``8.3.2`` ``GCCcore/11.2.0`` =============== ================= =================================================== @@ -32649,16 +33238,16 @@ An open-source, interactive graphing library for Python *homepage*: https://plot.ly/python -========== ================== -version toolchain -========== ================== -``4.1.0`` ``intel/2019a`` -``4.4.1`` ``intel/2019b`` -``4.8.1`` ``GCCcore/9.3.0`` -``4.14.3`` ``GCCcore/10.2.0`` -``5.1.0`` ``GCCcore/10.3.0`` -``5.4.0`` ``GCCcore/11.2.0`` -========== ================== +========== ====================================== +version toolchain +========== ====================================== +``4.1.0`` ``intel/2019a`` +``4.4.1`` ``intel/2019b`` +``4.8.1`` ``GCCcore/9.3.0`` +``4.14.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``5.1.0`` ``GCCcore/10.3.0`` +``5.4.0`` ``GCCcore/11.2.0`` +========== ====================================== .. _list_software_PLplot_603: @@ -32708,7 +33297,8 @@ version versionsuffix toolchain ``2.6.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``2.6.2`` ``foss/2020b``, ``intel/2020b`` ``2.7.0`` ``foss/2020b`` -``2.7.2`` ``foss/2021a`` +``2.7.2`` ``foss/2021a``, ``intel/2021a`` +``2.7.3`` ``foss/2021b`` ========= ================== ================================================ @@ -32894,6 +33484,7 @@ version toolchain ``0.70.1`` ``foss/2018b`` ``0.90.1`` ``GCCcore/8.3.0`` ``21.06.1`` ``GCC/10.3.0`` +``22.01.0`` ``GCC/11.2.0`` =========== ================= @@ -33188,6 +33779,22 @@ version versionsuffix toolchain ========= ================= =============================== +.. _list_software_PREQUAL_538: + +*PREQUAL* ++++++++++ + +A program to identify and mask regions with non-homologous adjacent characters in FASTA files. + +*homepage*: https://github.com/simonwhelan/prequal + +======== ================== +version toolchain +======== ================== +``1.02`` ``GCCcore/11.2.0`` +======== ================== + + .. _list_software_preseq_656: *preseq* @@ -33255,6 +33862,7 @@ version versionsuffix toolchain ========== ================ ============== ``0.20.4`` ``-Perl-5.28.0`` ``foss/2018b`` ``0.20.4`` ``-Perl-5.32.0`` ``foss/2020b`` +``0.20.4`` ``-Perl-5.34.0`` ``foss/2021b`` ========== ================ ============== @@ -33716,7 +34324,7 @@ Interpolating scaling function Poisson Solver Library version toolchain ========= ================================================================================================= ``1.7.6`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``1.8.3`` ``foss/2020b``, ``intel/2020b`` +``1.8.3`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` ========= ================================================================================================= @@ -33884,11 +34492,27 @@ Utility program for extracting sequences from a fasta/fastq file *homepage*: https://github.com/bcthomas/pullseq -========= ================= -version toolchain -========= ================= -``1.0.2`` ``GCCcore/7.3.0`` -========= ================= +========= ===================================== +version toolchain +========= ===================================== +``1.0.2`` ``GCCcore/11.2.0``, ``GCCcore/7.3.0`` +========= ===================================== + + +.. _list_software_PuLP_353: + +*PuLP* +++++++ + +PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to solve linear problems. + +*homepage*: https://github.com/coin-or/pulp + +========= ============== +version toolchain +========= ============== +``2.5.1`` ``foss/2021a`` +========= ============== .. _list_software_py_233: @@ -34070,17 +34694,18 @@ pybind11 is a lightweight header-only library that exposes C++ types in Python a *homepage*: https://pybind11.readthedocs.io -========= ================= ================== -version versionsuffix toolchain -========= ================= ================== -``2.2.4`` ``-Python-3.6.4`` ``foss/2018a`` -``2.2.4`` ``-Python-3.6.6`` ``intel/2018b`` -``2.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``2.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``2.6.0`` ``GCCcore/10.2.0`` -``2.6.2`` ``GCCcore/10.3.0`` -``2.7.1`` ``GCCcore/11.2.0`` -========= ================= ================== +========= ================== ================== +version versionsuffix toolchain +========= ================== ================== +``2.2.4`` ``-Python-3.6.4`` ``foss/2018a`` +``2.2.4`` ``-Python-3.6.6`` ``intel/2018b`` +``2.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``2.6.0`` ``GCCcore/10.2.0`` +``2.6.2`` ``GCCcore/10.3.0`` +``2.7.1`` ``GCCcore/11.2.0`` +``2.7.1`` ``-Python-2.7.18`` ``GCCcore/11.2.0`` +========= ================== ================== .. _list_software_PyCairo_695: @@ -34092,20 +34717,36 @@ Python bindings for the cairo library *homepage*: https://pycairo.readthedocs.io/ -========== ================== ==================================== -version versionsuffix toolchain -========== ================== ==================================== -``1.10.0`` ``-Python-2.7.11`` ``intel/2016a`` -``1.16.1`` ``-Python-3.6.3`` ``foss/2017b`` -``1.16.2`` ``-Python-2.7.14`` ``intel/2017b`` -``1.18.0`` ``-Python-2.7.14`` ``intel/2018a`` -``1.18.0`` ``-Python-2.7.15`` ``foss/2018b`` -``1.18.0`` ``-Python-3.6.6`` ``foss/2018b`` -``1.18.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``1.18.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.20.0`` ``GCCcore/10.2.0`` -``1.20.1`` ``GCCcore/10.3.0`` -========== ================== ==================================== +========== ================== ====================================== +version versionsuffix toolchain +========== ================== ====================================== +``1.10.0`` ``-Python-2.7.11`` ``intel/2016a`` +``1.16.1`` ``-Python-3.6.3`` ``foss/2017b`` +``1.16.2`` ``-Python-2.7.14`` ``intel/2017b`` +``1.18.0`` ``-Python-2.7.14`` ``intel/2018a`` +``1.18.0`` ``-Python-2.7.15`` ``foss/2018b`` +``1.18.0`` ``-Python-3.6.6`` ``foss/2018b`` +``1.18.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``1.18.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.20.0`` ``GCCcore/10.2.0`` +``1.20.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ================== ====================================== + + +.. _list_software_PyCalib_676: + +*PyCalib* ++++++++++ + +Python library for classifier calibration + +*homepage*: https://github.com/classifier-calibration/PyCalib + +============== ============== +version toolchain +============== ============== +``0.1.0.dev0`` ``foss/2021b`` +============== ============== .. _list_software_PyCharm_692: @@ -35011,12 +35652,12 @@ PyOpenCL lets you access GPUs and other massively parallel compute devices from *homepage*: https://mathema.tician.de/software/pyopencl/ -============ ================= =============================== -version versionsuffix toolchain -============ ================= =============================== -``2020.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``2021.1.2`` ``foss/2020b``, ``intel/2020b`` -============ ================= =============================== +============ ================= =================================================== +version versionsuffix toolchain +============ ================= =================================================== +``2020.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2021.1.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +============ ================= =================================================== .. _list_software_PyOpenGL_750: @@ -35028,17 +35669,17 @@ PyOpenGL is the most common cross platform Python binding to OpenGL and related *homepage*: http://pyopengl.sourceforge.net -=========== ================== ===================================== -version versionsuffix toolchain -=========== ================== ===================================== -``3.1.1a1`` ``GCCcore/8.2.0`` -``3.1.1a1`` ``-Python-2.7.11`` ``intel/2016a`` -``3.1.1a1`` ``-Python-2.7.12`` ``foss/2016b`` -``3.1.1a1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` -``3.1.3b2`` ``-Python-2.7.14`` ``intel/2018a`` -``3.1.3b2`` ``-Python-2.7.15`` ``foss/2018b`` -``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` -=========== ================== ===================================== +=========== ================== ========================================================= +version versionsuffix toolchain +=========== ================== ========================================================= +``3.1.1a1`` ``GCCcore/8.2.0`` +``3.1.1a1`` ``-Python-2.7.11`` ``intel/2016a`` +``3.1.1a1`` ``-Python-2.7.12`` ``foss/2016b`` +``3.1.1a1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` +``3.1.3b2`` ``-Python-2.7.14`` ``intel/2018a`` +``3.1.3b2`` ``-Python-2.7.15`` ``foss/2018b`` +``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0`` +=========== ================== ========================================================= .. _list_software_pyparsing_989: @@ -35172,22 +35813,22 @@ PyQt5 is a set of Python bindings for v5 of the Qt application framework from Th *homepage*: http://www.riverbankcomputing.co.uk/software/pyqt -========== ================== ====================================== -version versionsuffix toolchain -========== ================== ====================================== -``5.7`` ``-Python-2.7.11`` ``foss/2016a`` -``5.7.1`` ``-Python-2.7.12`` ``intel/2016b`` -``5.8.2`` ``-Python-2.7.13`` ``intel/2017a`` -``5.9.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``5.9.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``5.11.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` -``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``5.13.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``5.15.1`` ``GCCcore/10.2.0`` -``5.15.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``5.15.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========== ================== ====================================== +========== ================== ================================================ +version versionsuffix toolchain +========== ================== ================================================ +``5.7`` ``-Python-2.7.11`` ``foss/2016a`` +``5.7.1`` ``-Python-2.7.12`` ``intel/2016b`` +``5.8.2`` ``-Python-2.7.13`` ``intel/2017a`` +``5.9.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``5.9.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``5.11.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``5.13.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``5.15.1`` ``GCCcore/10.2.0`` +``5.15.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``5.15.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========== ================== ================================================ .. _list_software_PyQtGraph_896: @@ -35207,6 +35848,7 @@ version versionsuffix toolchain ``0.10.0`` ``-Python-3.7.2`` ``intel/2019a`` ``0.11.0`` ``-Python-3.7.4`` ``foss/2019b`` ``0.11.1`` ``foss/2020b``, ``fosscuda/2020b`` +``0.12.3`` ``foss/2021a`` ========== ================= ================================== @@ -35726,7 +36368,7 @@ version versionsuffix toolchain ``2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``2.7.15`` ``-bare`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``2.7.16`` ``GCCcore/8.3.0`` -``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ``2.7.18`` ``-bare`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.5.1`` ``foss/2016a``, ``intel/2016a`` ``3.5.2`` ``foss/2016.04``, ``foss/2016b``, ``intel/2016b`` @@ -35797,6 +36439,7 @@ version versionsuffix toolchain ``0.8.0`` ``foss/2019b``, ``foss/2020a`` ``0.9.0`` ``foss/2020b``, ``fosscuda/2020b`` ``0.9.6`` ``foss/2021a`` +``0.9.8`` ``foss/2021b`` =============== ================== ================================== @@ -35852,7 +36495,7 @@ version versionsuffix toolchain ``1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``1.2.2`` ``-Python-3.8.2`` ``intel/2020a`` ``1.2.3`` ``-Python-3.8.2`` ``foss/2020a`` -``1.2.4`` ``foss/2020b``, ``fosscuda/2020b`` +``1.2.4`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` ========== ================== =================================================== @@ -35920,7 +36563,7 @@ version versionsuffix toolchain ``1.8.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``1.9.0`` ``foss/2020b``, ``fosscuda/2020b`` ``1.9.0`` ``-imkl`` ``fosscuda/2020b`` -``1.10.0`` ``foss/2021a`` +``1.10.0`` ``foss/2021a``, ``fosscuda/2020b`` ``1.10.0`` ``-CUDA-11.3.1`` ``foss/2021a`` ========== ============================= ================================== @@ -35945,6 +36588,22 @@ version versionsuffix toolchain ========= =============================== ================================== +.. _list_software_PyTorch3D_832: + +*PyTorch3D* ++++++++++++ + +PyTorch3D is FAIR's library of reusable components for deep learning with 3D data. + +*homepage*: https://pytorch3d.org/ + +========= ================== ================== +version versionsuffix toolchain +========= ================== ================== +``0.4.0`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` +========= ================== ================== + + .. _list_software_PyVCF_424: *PyVCF* @@ -36034,6 +36693,7 @@ version versionsuffix toolchain ``17.0.0`` ``-Python-2.7.14-zmq4`` ``foss/2018a`` ``17.0.0`` ``-Python-3.6.4-zmq4`` ``foss/2018a`` ``18.1.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``22.3.0`` ``GCCcore/10.3.0`` ========== ======================= =============================== @@ -36043,7 +36703,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcat_425` - :ref:`list_software_qcint_543` - :ref:`list_software_QCxMS_428` - :ref:`list_software_QD_149` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_Qtconsole_952` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_QtPy_398` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` +:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcat_425` - :ref:`list_software_QCG-PilotJob_1067` - :ref:`list_software_qcint_543` - :ref:`list_software_QCxMS_428` - :ref:`list_software_QD_149` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_Qtconsole_952` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_QtPy_398` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` .. _list_software_Q6_135: @@ -36096,6 +36756,22 @@ version versionsuffix toolchain ========= ================= =============================== +.. _list_software_QCG-PilotJob_1067: + +*QCG-PilotJob* +++++++++++++++ + +A python service for easy execution of many tasks inside a single allocation. + +*homepage*: https://qcg-pilotjob.readthedocs.org + +========== ============== +version toolchain +========== ============== +``0.12.3`` ``foss/2021a`` +========== ============== + + .. _list_software_qcint_543: *qcint* @@ -36394,7 +37070,7 @@ version toolchain ``5.13.1`` ``GCCcore/8.3.0`` ``5.14.1`` ``GCCcore/9.3.0`` ``5.14.2`` ``GCCcore/10.2.0`` -``5.15.2`` ``GCCcore/10.3.0`` +``5.15.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ==================================================================================== @@ -36709,7 +37385,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_RaGOO_408` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_RAPSearch2_875` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -36883,6 +37559,22 @@ version toolchain ======= ================== +.. _list_software_RaGOO_408: + +*RaGOO* ++++++++ + +A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome + +*homepage*: https://github.com/malonge/RaGOO + +======== ================= ============== +version versionsuffix toolchain +======== ================= ============== +``1.11`` ``-Python-3.6.6`` ``foss/2018b`` +======== ================= ============== + + .. _list_software_Ragout_626: *Ragout* @@ -36997,6 +37689,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_RAPSearch2_875: + +*RAPSearch2* +++++++++++++ + +RAPSearch stands for Reduced Alphabet based Protein similarity Search + +*homepage*: https://omics.informatics.indiana.edu/mg/RAPSearch2 + +======== ============= +version toolchain +======== ============= +``2.24`` ``GCC/9.3.0`` +======== ============= + + .. _list_software_Rascaf_592: *Rascaf* @@ -37088,18 +37796,18 @@ RAxML search algorithm for maximum likelihood based inference of phylogenetic tr *homepage*: https://github.com/stamatak/standard-RAxML -========== ================== =================================================================================== -version versionsuffix toolchain -========== ================== =================================================================================== -``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` -``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` -``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` -``8.2.12`` ``-hybrid-avx2`` ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2019b``, ``intel/2018b``, ``intel/2019a`` -``8.2.12`` ``-pthreads-avx2`` ``GCC/10.2.0`` -========== ================== =================================================================================== +========== ================== ==================================================================================================== +version versionsuffix toolchain +========== ================== ==================================================================================================== +``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` +``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` +``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` +``8.2.12`` ``-hybrid-avx2`` ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2019b``, ``intel/2018b``, ``intel/2019a`` +``8.2.12`` ``-pthreads-avx2`` ``GCC/10.2.0`` +========== ================== ==================================================================================================== .. _list_software_RAxML-NG_614: @@ -37163,11 +37871,12 @@ Raysect is an OOP ray-tracing framework for Python *homepage*: https://raysect.org -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``0.6.0`` ``-Python-3.6.6`` ``intel/2018b`` -========= ================= =============== +========= ================= =============================== +version versionsuffix toolchain +========= ================= =============================== +``0.6.0`` ``-Python-3.6.6`` ``intel/2018b`` +``0.7.1`` ``foss/2020b``, ``intel/2020b`` +========= ================= =============================== .. _list_software_RBFOpt_525: @@ -37307,6 +38016,7 @@ version versionsuffix toolchain ``2.7`` ``-Java-1.7.0_60`` ``system`` ``2.12`` ``-Java-1.8`` ``system`` ``2.13`` ``-Java-11`` ``system`` +``2.13`` ``-Java-17`` ``system`` ======== ================== ========== @@ -37761,7 +38471,7 @@ version versionsuffix toolchain *Rgurobi* +++++++++ -Gurobi Optimizer 9.1 interface +Gurobi Optimizer 9.5 interface *homepage*: https://www.gurobi.com @@ -37769,6 +38479,7 @@ Gurobi Optimizer 9.1 interface version versionsuffix toolchain ========= ============= ============== ``9.1.2`` ``-R-4.1.0`` ``foss/2021a`` +``9.5.0`` ``-R-4.1.0`` ``foss/2021a`` ========= ============= ============== @@ -38503,7 +39214,7 @@ version toolchain ``2.6.3`` ``GCCcore/8.2.0`` ``2.7.1`` ``GCCcore/8.3.0`` ``2.7.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.0.1`` ``GCCcore/10.3.0`` +``3.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ================================================ @@ -38557,7 +39268,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_SCopeLoomR_963` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_ShengBTE_720` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_SHTns_464` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_STRUMPACK_698` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -38981,6 +39692,7 @@ version toolchain ========= ============================== ``1.7.2`` ``foss/2020b`` ``1.8.1`` ``foss/2020b``, ``foss/2021a`` +``1.8.2`` ``foss/2021b`` ========= ============================== @@ -39029,6 +39741,7 @@ Schrodinger aims to provide integrated software solutions and services that tr version toolchain ========== ========== ``2020-4`` ``system`` +``2021-4`` ``system`` ========== ========== @@ -39315,6 +40028,7 @@ version versionsuffix toolchain ``2020.11`` ``-Python-2.7.18`` ``foss/2020b`` ``2021.05`` ``foss/2021a``, ``intel/2021a`` ``2021.10`` ``foss/2021b``, ``intel/2021b`` +``2021.10`` ``-Python-2.7.18`` ``foss/2021b`` =========== ================== ======================================================================== @@ -39404,6 +40118,22 @@ version versionsuffix toolchain =========== ================== ================= +.. _list_software_SCopeLoomR_963: + +*SCopeLoomR* +++++++++++++ + +An R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ... + +*homepage*: https://github.com/aertslab/SCopeLoomR + +========== ============= ============== +version versionsuffix toolchain +========== ============= ============== +``0.13.0`` ``-R-4.1.2`` ``foss/2021b`` +========== ============= ============== + + .. _list_software_Score-P_633: *Score-P* @@ -39440,6 +40170,7 @@ version versionsuffix toolchain ``6.0.6`` ``foss/2018a``, ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2018a`` ``6.0.9`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` ``6.1.0`` ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2020b`` +``6.1.2`` ``gompi/2021b`` =================== ============= ===================================================================================================================================================== @@ -39801,7 +40532,10 @@ SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic plac version versionsuffix toolchain ========== ================= ============== ``4.3.10`` ``-Python-3.7.4`` ``foss/2019b`` +``4.3.10`` ``-Python-3.8.2`` ``foss/2020a`` ``4.4.0`` ``foss/2020b`` +``4.5.0`` ``foss/2021a`` +``4.5.1`` ``foss/2021b`` ========== ================= ============== @@ -39947,12 +40681,12 @@ Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FA *homepage*: https://github.com/lh3/seqtk/ -======= ================================================================================================== -version toolchain -======= ================================================================================================== -``1.2`` ``foss/2016b``, ``intel/2017a`` -``1.3`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` -======= ================================================================================================== +======= ================================================================================================================== +version toolchain +======= ================================================================================================================== +``1.2`` ``foss/2016b``, ``intel/2017a`` +``1.3`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` +======= ================================================================================================================== .. _list_software_Serf_400: @@ -40192,6 +40926,22 @@ version toolchain ========= ============== +.. _list_software_ShengBTE_720: + +*ShengBTE* +++++++++++ + +A solver for the Boltzmann transport equation for phonons. + +*homepage*: https://bitbucket.org/sousaw/shengbte + +========= ============== +version toolchain +========= ============== +``1.1.1`` ``foss/2021a`` +========= ============== + + .. _list_software_shift_542: *shift* @@ -40236,6 +40986,7 @@ Sensitive Short Read Homology Search for Paired-End Reads ============ ================== ============== version versionsuffix toolchain ============ ================== ============== +``20170125`` ``foss/2021b`` ``20170125`` ``-Python-2.7.15`` ``foss/2018b`` ============ ================== ============== @@ -40274,6 +41025,23 @@ version toolchain ============== ================== +.. _list_software_SHTns_464: + +*SHTns* ++++++++ + +Spherical Harmonic Transform library aimed at high performance numerical simulations in spherical geometries. + +*homepage*: https://bitbucket.org/nschaeff/shtns + +========= ============== +version toolchain +========= ============== +``2.7`` ``foss/2021b`` +``3.5.1`` ``foss/2021b`` +========= ============== + + .. _list_software_Sibelia_697: *Sibelia* @@ -40577,18 +41345,18 @@ SIP is a tool that makes it very easy to create Python bindings for C and C++ li *homepage*: http://www.riverbankcomputing.com/software/sip/ -=========== ================== =============================================== -version versionsuffix toolchain -=========== ================== =============================================== -``4.18`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``4.18.1`` ``-Python-2.7.11`` ``foss/2016a`` -``4.18.1`` ``-Python-2.7.12`` ``intel/2016b`` -``4.19`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``4.19.2`` ``-Python-2.7.13`` ``intel/2017a`` -``4.19.8`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` -``4.19.8`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``4.19.13`` ``-Python-2.7.15`` ``fosscuda/2018b`` -=========== ================== =============================================== +=========== ================== ================================================================ +version versionsuffix toolchain +=========== ================== ================================================================ +``4.18`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``4.18.1`` ``-Python-2.7.11`` ``foss/2016a`` +``4.18.1`` ``-Python-2.7.12`` ``intel/2016b`` +``4.19`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``4.19.2`` ``-Python-2.7.13`` ``intel/2017a`` +``4.19.8`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``4.19.8`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``4.19.13`` ``-Python-2.7.15`` ``fosscuda/2018b`` +=========== ================== ================================================================ .. _list_software_SKESA_375: @@ -41285,6 +42053,7 @@ version toolchain ``0.11.2`` ``system`` ``0.12.1`` ``system`` ``0.16.2`` ``system`` +``0.17.0`` ``system`` ========== ========== @@ -41311,7 +42080,7 @@ version versionsuffix toolchain ``3.14.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` ``3.15.2`` ``GCC/10.2.0`` ``3.15.2`` ``-Python-2.7.18`` ``GCC/10.2.0`` -``3.15.3`` ``GCC/10.3.0`` +``3.15.3`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========== ================== ============================================== @@ -41341,29 +42110,29 @@ Spark is Hadoop MapReduce done in memory *homepage*: https://spark.apache.org -========= =========================================== =============================== -version versionsuffix toolchain -========= =========================================== =============================== -``1.3.0`` ``system`` -``1.4.1`` ``system`` -``1.5.0`` ``system`` -``1.6.0`` ``system`` -``1.6.1`` ``system`` -``2.0.0`` ``system`` -``2.0.2`` ``system`` -``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_144`` ``system`` -``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_152`` ``system`` -``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3`` ``intel/2017b`` -``2.3.0`` ``-Hadoop-2.7-Java-1.8.0_162`` ``system`` -``2.4.0`` ``-Hadoop-2.7-Java-1.8`` ``system`` -``2.4.0`` ``-Hadoop-2.7-Java-1.8-Python-3.6.6`` ``intel/2018b`` -``2.4.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``2.4.0`` ``-Python-3.6.6`` ``intel/2018b`` -``2.4.5`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` -``3.0.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``3.1.1`` ``fosscuda/2020b`` -``3.1.1`` ``-Python-3.8.2`` ``foss/2020a`` -========= =========================================== =============================== +========= =========================================== ================================== +version versionsuffix toolchain +========= =========================================== ================================== +``1.3.0`` ``system`` +``1.4.1`` ``system`` +``1.5.0`` ``system`` +``1.6.0`` ``system`` +``1.6.1`` ``system`` +``2.0.0`` ``system`` +``2.0.2`` ``system`` +``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_144`` ``system`` +``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_152`` ``system`` +``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3`` ``intel/2017b`` +``2.3.0`` ``-Hadoop-2.7-Java-1.8.0_162`` ``system`` +``2.4.0`` ``-Hadoop-2.7-Java-1.8`` ``system`` +``2.4.0`` ``-Hadoop-2.7-Java-1.8-Python-3.6.6`` ``intel/2018b`` +``2.4.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``2.4.0`` ``-Python-3.6.6`` ``intel/2018b`` +``2.4.5`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` +``3.0.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``3.1.1`` ``foss/2020b``, ``fosscuda/2020b`` +``3.1.1`` ``-Python-3.8.2`` ``foss/2020a`` +========= =========================================== ================================== .. _list_software_sparsehash_1074: @@ -41749,6 +42518,7 @@ SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, version versionsuffix toolchain ========= ================== ============== ``0.4.3`` ``-Python-2.7.15`` ``foss/2018b`` +``1.0.0`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== ============== @@ -42026,7 +42796,7 @@ version toolchain ``2.7.6a`` ``GCC/10.2.0``, ``GCC/9.3.0`` ``2.7.7a`` ``GCC/10.2.0``, ``GCC/9.3.0`` ``2.7.8a`` ``GCC/10.2.0`` -``2.7.9a`` ``GCC/10.3.0`` +``2.7.9a`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========== ============================================================== @@ -42121,6 +42891,7 @@ version versionsuffix toolchain ``0.11.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``0.12.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``0.12.2`` ``foss/2021a`` +``0.13.1`` ``foss/2021b``, ``intel/2021b`` ========== ================== =================================================== @@ -42250,6 +43021,22 @@ version toolchain ========= ===================================================================================== +.. _list_software_STRUMPACK_698: + +*STRUMPACK* ++++++++++++ + +STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner for both dense and sparse systems using low-rank structured factorization with randomized sampling. + +*homepage*: https://fastmath-scidac.llnl.gov/software/strumpack.html + +========= =============================== +version toolchain +========= =============================== +``6.1.0`` ``foss/2020b``, ``intel/2020b`` +========= =============================== + + .. _list_software_suave_548: *suave* @@ -42275,16 +43062,16 @@ High performance read alignment, quantification and mutation discovery *homepage*: http://subread.sourceforge.net/ -============ ================================= -version toolchain -============ ================================= -``1.5.0-p1`` ``foss/2016a``, ``foss/2016b`` -``1.6.3`` ``foss/2018b`` -``1.6.4`` ``foss/2018b`` -``2.0.0`` ``GCC/7.3.0-2.30``, ``GCC/8.3.0`` -``2.0.2`` ``GCC/10.2.0`` -``2.0.3`` ``GCC/10.3.0``, ``GCC/9.3.0`` -============ ================================= +============ ============================================= +version toolchain +============ ============================================= +``1.5.0-p1`` ``foss/2016a``, ``foss/2016b`` +``1.6.3`` ``foss/2018b`` +``1.6.4`` ``foss/2018b`` +``2.0.0`` ``GCC/7.3.0-2.30``, ``GCC/8.3.0`` +``2.0.2`` ``GCC/10.2.0`` +``2.0.3`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` +============ ============================================= .. _list_software_Subversion_1072: @@ -42333,24 +43120,25 @@ SuiteSparse is a collection of libraries manipulate sparse matrices. *homepage*: https://faculty.cse.tamu.edu/davis/suitesparse.html -========== =================== ================================================================================================= -version versionsuffix toolchain -========== =================== ================================================================================================= -``4.5.1`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` -``4.5.2`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` -``4.5.3`` ``-METIS-5.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``4.5.3`` ``-ParMETIS-4.0.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``4.5.5`` ``-METIS-5.1.0`` ``foss/2017a``, ``intel/2017a`` -``4.5.5`` ``-ParMETIS-4.0.3`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``4.5.6`` ``-METIS-5.1.0`` ``foss/2017b`` -``5.1.2`` ``-METIS-5.1.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``5.1.2`` ``-ParMETIS-4.0.3`` ``foss/2017b``, ``intel/2017b`` -``5.4.0`` ``-METIS-5.1.0`` ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` -``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b``, ``intel/2019b`` -``5.7.1`` ``-METIS-5.1.0`` ``foss/2020a``, ``intel/2020a`` -``5.8.1`` ``-METIS-5.1.0`` ``foss/2020b``, ``intel/2020b`` -``5.10.1`` ``-METIS-5.1.0`` ``foss/2021a``, ``foss/2021b`` -========== =================== ================================================================================================= +========== ============================ ================================================================================================= +version versionsuffix toolchain +========== ============================ ================================================================================================= +``4.5.1`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` +``4.5.2`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` +``4.5.3`` ``-METIS-5.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` +``4.5.3`` ``-ParMETIS-4.0.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``4.5.5`` ``-METIS-5.1.0`` ``foss/2017a``, ``intel/2017a`` +``4.5.5`` ``-ParMETIS-4.0.3`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``4.5.6`` ``-METIS-5.1.0`` ``foss/2017b`` +``5.1.2`` ``-METIS-5.1.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``5.1.2`` ``-ParMETIS-4.0.3`` ``foss/2017b``, ``intel/2017b`` +``5.4.0`` ``-METIS-5.1.0`` ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` +``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b``, ``intel/2019b`` +``5.7.1`` ``-METIS-5.1.0`` ``foss/2020a``, ``intel/2020a`` +``5.8.1`` ``-METIS-5.1.0`` ``foss/2020b``, ``intel/2020b`` +``5.10.1`` ``-METIS-5.1.0`` ``foss/2021a``, ``foss/2021b`` +``5.10.1`` ``-METIS-5.1.0-CUDA-11.3.1`` ``foss/2021a`` +========== ============================ ================================================================================================= .. _list_software_SUMACLUST_705: @@ -42782,7 +43570,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_termcolor_983` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_ThemisPy_819` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmux_462` - :ref:`list_software_TOBIAS_450` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` +:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TALYS_397` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_termcolor_983` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_ThemisPy_819` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmux_462` - :ref:`list_software_TN93_270` - :ref:`list_software_TOBIAS_450` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` .. _list_software_tabix_536: @@ -42897,6 +43685,22 @@ version toolchain ======= ============== +.. _list_software_TALYS_397: + +*TALYS* ++++++++ + +TALYS is a nuclear reaction program. + +*homepage*: https://tendl.web.psi.ch/tendl_2019/talys.html + +======== ===================================== +version toolchain +======== ===================================== +``1.95`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +======== ===================================== + + .. _list_software_TAMkin_548: *TAMkin* @@ -43394,6 +44198,7 @@ TeX is a typesetting language. Instead of visually formatting your text, you ent version toolchain ============ ================= ``20200406`` ``GCCcore/8.3.0`` +``20210324`` ``GCC/11.2.0`` ============ ================= @@ -43671,7 +44476,7 @@ version versionsuffix toolchain ``2.7.15`` ``GCCcore/8.2.0`` ``2.7.15`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.7.16`` ``GCCcore/8.3.0`` -``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ``3.6.1`` ``-Python-3.6.1`` ``foss/2017a``, ``intel/2017a`` ``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` ``3.6.3`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` @@ -43739,6 +44544,22 @@ version toolchain ======== ====================================== +.. _list_software_TN93_270: + +*TN93* +++++++ + +This is a simple program meant to compute pairwise distances between aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance. + +*homepage*: https://github.com/veg/tn93 + +========= ================== +version toolchain +========= ================== +``1.0.7`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_TOBIAS_450: *TOBIAS* @@ -44109,11 +44930,11 @@ TreeMix is a method for inferring the patterns of population splits and mixtures *homepage*: http://bitbucket.org/nygcresearch/treemix -======== =============== -version toolchain -======== =============== -``1.13`` ``intel/2018a`` -======== =============== +======== =============================== +version toolchain +======== =============================== +``1.13`` ``GCC/10.3.0``, ``intel/2018a`` +======== =============================== .. _list_software_TreeShrink_1023: @@ -44221,11 +45042,11 @@ A tool for automated alignment trimming in large-scale phylogenetic analyses *homepage*: http://trimal.cgenomics.org/ -========= ======================================================== -version toolchain -========= ======================================================== -``1.4.1`` ``GCC/8.2.0-2.31.1``, ``GCCcore/9.3.0``, ``intel/2018a`` -========= ======================================================== +========= ============================================================================ +version toolchain +========= ============================================================================ +``1.4.1`` ``GCC/8.2.0-2.31.1``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``intel/2018a`` +========= ============================================================================ .. _list_software_Trimmomatic_1158: @@ -45302,16 +46123,16 @@ The aim of VCFtools is to provide easily accessible methods for working with c *homepage*: https://vcftools.github.io -========== ================ ===================================================================================== -version versionsuffix toolchain -========== ================ ===================================================================================== -``0.1.14`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` -``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` -``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` -``0.1.16`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` -``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` -========== ================ ===================================================================================== +========== ================ ===================================================================================================== +version versionsuffix toolchain +========== ================ ===================================================================================================== +``0.1.14`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` +``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` +``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` +``0.1.16`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` +``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` +========== ================ ===================================================================================================== .. _list_software_VEGAS_374: @@ -45811,6 +46632,7 @@ version toolchain ``2020_update3`` ``system`` ``2021.6.0`` ``system`` ``2021.9.0`` ``system`` +``2022.0.0`` ``system`` ================= ========== @@ -46214,20 +47036,20 @@ The Worker framework has been developed to help deal with parameter exploration *homepage*: https://github.com/gjbex/worker -========== ================ =============== -version versionsuffix toolchain -========== ================ =============== -``1.6.4`` ``intel/2016a`` -``1.6.5`` ``intel/2016a`` -``1.6.6`` ``intel/2016b`` -``1.6.7`` ``-intel-2016b`` ``system`` -``1.6.7`` ``-intel-2017a`` ``system`` -``1.6.7`` ``-intel-2017b`` ``system`` -``1.6.8`` ``-intel-2018a`` ``system`` -``1.6.8`` ``-intel-2018b`` ``system`` -``1.6.11`` ``intel/2019b`` -``1.6.12`` ``-foss-2019a`` ``system`` -========== ================ =============== +========== ================ ============================== +version versionsuffix toolchain +========== ================ ============================== +``1.6.4`` ``intel/2016a`` +``1.6.5`` ``intel/2016a`` +``1.6.6`` ``intel/2016b`` +``1.6.7`` ``-intel-2016b`` ``system`` +``1.6.7`` ``-intel-2017a`` ``system`` +``1.6.7`` ``-intel-2017b`` ``system`` +``1.6.8`` ``-intel-2018a`` ``system`` +``1.6.8`` ``-intel-2018b`` ``system`` +``1.6.11`` ``intel/2019b`` +``1.6.12`` ``foss/2019a``, ``foss/2021b`` +========== ================ ============================== .. _list_software_WPS_250: @@ -46316,12 +47138,12 @@ Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio *homepage*: https://github.com/ruanjue/wtdbg2 -======= ================== -version toolchain -======= ================== -``2.3`` ``GCC/7.3.0-2.30`` -``2.5`` ``GCCcore/9.3.0`` -======= ================== +======= ===================================== +version toolchain +======= ===================================== +``2.3`` ``GCC/7.3.0-2.30`` +``2.5`` ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +======= ===================================== .. _list_software_wxPropertyGrid_1498: @@ -46389,7 +47211,7 @@ version toolchain --- -:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_XZ_178` +:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_xxHash_628` - :ref:`list_software_XZ_178` .. _list_software_X11_186: @@ -46866,20 +47688,20 @@ Perl binding for libxml2 *homepage*: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod -========== ================ =============================== -version versionsuffix toolchain -========== ================ =============================== -``2.0132`` ``-Perl-5.24.0`` ``foss/2016b``, ``intel/2016b`` -``2.0132`` ``-Perl-5.24.1`` ``intel/2017a`` -``2.0132`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``2.0132`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``2.0132`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -``2.0200`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -``2.0201`` ``GCCcore/8.3.0`` -``2.0205`` ``GCCcore/9.3.0`` -``2.0206`` ``GCCcore/10.2.0`` -``2.0207`` ``GCCcore/10.3.0`` -========== ================ =============================== +========== ================ ====================================== +version versionsuffix toolchain +========== ================ ====================================== +``2.0132`` ``-Perl-5.24.0`` ``foss/2016b``, ``intel/2016b`` +``2.0132`` ``-Perl-5.24.1`` ``intel/2017a`` +``2.0132`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``2.0132`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``2.0132`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``2.0200`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``2.0201`` ``GCCcore/8.3.0`` +``2.0205`` ``GCCcore/9.3.0`` +``2.0206`` ``GCCcore/10.2.0`` +``2.0207`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ================ ====================================== .. _list_software_XML-Parser_907: @@ -47112,6 +47934,22 @@ version toolchain =========== ===================================== +.. _list_software_xxHash_628: + +*xxHash* +++++++++ + +xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit. + +*homepage*: https://cyan4973.github.io/xxHash + +========= ================== +version toolchain +========= ================== +``0.8.0`` ``GCCcore/11.2.0`` +========= ================== + + .. _list_software_XZ_178: *XZ* @@ -47140,7 +47978,7 @@ version versionsuffix toolchain --- -:ref:`list_software_YACS_304` - :ref:`list_software_Yade_387` - :ref:`list_software_yaff_422` - :ref:`list_software_Yambo_504` - :ref:`list_software_YANK_307` - :ref:`list_software_YAPS_317` - :ref:`list_software_Yasm_410` - :ref:`list_software_YAXT_326` - :ref:`list_software_Yices_509` +:ref:`list_software_YACS_304` - :ref:`list_software_Yade_387` - :ref:`list_software_yaff_422` - :ref:`list_software_Yambo_504` - :ref:`list_software_yaml-cpp_803` - :ref:`list_software_YANK_307` - :ref:`list_software_YAPS_317` - :ref:`list_software_Yasm_410` - :ref:`list_software_YAXT_326` - :ref:`list_software_Yices_509` .. _list_software_YACS_304: @@ -47198,6 +48036,7 @@ version versionsuffix toolchain ``1.4.5`` ``-Python-2.7.15`` ``intel/2018b`` ``1.5.0`` ``-Python-2.7.15`` ``intel/2018b`` ``1.5.0`` ``-Python-3.7.2`` ``intel/2019a`` +``1.6.0`` ``foss/2020b`` ``1.6.0`` ``-Python-3.7.2`` ``intel/2019a`` ``1.6.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``1.6.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` @@ -47221,6 +48060,22 @@ version toolchain ========= ========================= +.. _list_software_yaml-cpp_803: + +*yaml-cpp* +++++++++++ + +yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec + +*homepage*: https://github.com/jbeder/yaml-cpp + +========= ================= +version toolchain +========= ================= +``0.6.3`` ``GCCcore/8.3.0`` +========= ================= + + .. _list_software_YANK_307: *YANK* @@ -47312,7 +48167,7 @@ version toolchain --- -:ref:`list_software_Z3_141` - :ref:`list_software_zarr_447` - :ref:`list_software_ZeroMQ_574` - :ref:`list_software_zfp_336` - :ref:`list_software_zingeR_623` - :ref:`list_software_Zip_307` - :ref:`list_software_zlib_433` - :ref:`list_software_zlib-ng_691` - :ref:`list_software_zlibbioc_846` - :ref:`list_software_Zopfli_628` - :ref:`list_software_ZPAQ_316` - :ref:`list_software_zsh_341` - :ref:`list_software_zstd_453` +:ref:`list_software_Z3_141` - :ref:`list_software_zarr_447` - :ref:`list_software_ZeroMQ_574` - :ref:`list_software_zfp_336` - :ref:`list_software_Zgoubi_624` - :ref:`list_software_zingeR_623` - :ref:`list_software_Zip_307` - :ref:`list_software_zlib_433` - :ref:`list_software_zlib-ng_691` - :ref:`list_software_zlibbioc_846` - :ref:`list_software_Zopfli_628` - :ref:`list_software_ZPAQ_316` - :ref:`list_software_zsh_341` - :ref:`list_software_zstd_453` .. _list_software_Z3_141: @@ -47392,6 +48247,22 @@ version toolchain ========= ================== +.. _list_software_Zgoubi_624: + +*Zgoubi* +++++++++ + +Zgoubi is a ray-tracing code in use for charged particle beam dynamics simulations. It can simulate beam dynamics in a large variety of machines and optical systems. + +*homepage*: https://zgoubi.sourceforge.io + +========= ================== +version toolchain +========= ================== +``6.0.2`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_zingeR_623: *zingeR* diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index cd9d12fe..f4170b2b 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -85,6 +85,7 @@ * EB_Geant4 * EB_GROMACS * EB_LAMMPS + * EB_Libint * EB_LLVM * EB_netCDF * EB_OpenBabel @@ -137,7 +138,6 @@ * EB_Hypre * EB_LAPACK * EB_libdrm - * EB_Libint * EB_libQGLViewer * EB_libxml2 * EB_Lua diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index 82e15abf..f4598106 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -103,15 +103,17 @@ Build environment of toolchain: only generate module file Extra easyconfig parameters specific to ``BuildEnv`` easyblock -------------------------------------------------------------- -=========================== =========================================================================== ============= -easyconfig parameter description default value -=========================== =========================================================================== ============= -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -=========================== =========================================================================== ============= +=============================== =========================================================================== ============= +easyconfig parameter description default value +=============================== =========================================================================== ============= +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` +=============================== =========================================================================== ============= .. _Bundle: @@ -125,15 +127,17 @@ Bundle of modules: only generate module files, nothing to build/install Extra easyconfig parameters specific to ``Bundle`` easyblock ------------------------------------------------------------ -=========================== =========================================================================== ============= -easyconfig parameter description default value -=========================== =========================================================================== ============= -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -=========================== =========================================================================== ============= +=============================== =========================================================================== ============= +easyconfig parameter description default value +=============================== =========================================================================== ============= +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` +=============================== =========================================================================== ============= Customised steps in ``Bundle`` easyblock ---------------------------------------- @@ -630,15 +634,17 @@ Compiler toolchain: generate module file only, nothing to build/install Extra easyconfig parameters specific to ``CrayToolchain`` easyblock ------------------------------------------------------------------- -=========================== =========================================================================== ============= -easyconfig parameter description default value -=========================== =========================================================================== ============= -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -=========================== =========================================================================== ============= +=============================== =========================================================================== ============= +easyconfig parameter description default value +=============================== =========================================================================== ============= +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` +=============================== =========================================================================== ============= .. _FortranPythonPackage: @@ -942,36 +948,38 @@ Bundle of modules: only generate module files, nothing to build/install Extra easyconfig parameters specific to ``PythonBundle`` easyblock ------------------------------------------------------------------ -=========================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -easyconfig parameter description default value -=========================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``zipped_egg`` Install as a zipped eggs ``False`` -=========================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +=============================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +=============================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` +``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` +=============================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= .. _PythonPackage: @@ -1141,45 +1149,47 @@ Support for generating a module file for the system compiler with specified name Extra easyconfig parameters specific to ``SystemCompiler`` easyblock -------------------------------------------------------------------- -============================== =================================================================================================================================================================================================== ==================== -easyconfig parameter description default value -============================== =================================================================================================================================================================================================== ==================== -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``clooguseisl`` Use ISL with CLooG or not ``False`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``configure_cmd`` Configure command to use ``"./configure"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -``generate_standalone_module`` Add known path/library extensions and environment variables for the compiler to the final module ``False`` -``generic`` Build GCC and support libraries such that it runs on all processors of the target architecture (use False to enforce non-generic regardless of configuration) ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` -``languages`` List of languages to build GCC for (--enable-languages) ``[]`` -``license_activation`` License activation type ``"license_server"`` -``m32`` Enable 32-bit toolchain ``False`` -``multilib`` Build multilib gcc (both i386 and x86_64) ``False`` -``pplwatchdog`` Enable PPL watchdog ``False`` -``prefer_lib_subdir`` Configure GCC to prefer 'lib' subdirs over 'lib64' when linking ``False`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``profiled`` Bootstrap GCC with profile-guided optimizations ``False`` -``requires_runtime_license`` Boolean indicating whether or not a runtime license is required ``True`` -``serial_number`` Serial number for the product ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``use_gold_linker`` Configure GCC to use GOLD as default linker ``True`` -``usetmppath`` Use temporary path for installation ``False`` -``withamdgcn`` Build GCC with AMD GCN offload support ``False`` -``withcloog`` Build GCC with CLooG support ``False`` -``withisl`` Build GCC with ISL support ``False`` -``withlibiberty`` Enable installing of libiberty ``False`` -``withlto`` Enable LTO support ``True`` -``withnvptx`` Build GCC with NVPTX offload support ``False`` -``withppl`` Build GCC with PPL support ``False`` -============================== =================================================================================================================================================================================================== ==================== +=============================== =================================================================================================================================================================================================== ==================== +easyconfig parameter description default value +=============================== =================================================================================================================================================================================================== ==================== +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``clooguseisl`` Use ISL with CLooG or not ``False`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``configure_cmd`` Configure command to use ``"./configure"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``generate_standalone_module`` Add known path/library extensions and environment variables for the compiler to the final module ``False`` +``generic`` Build GCC and support libraries such that it runs on all processors of the target architecture (use False to enforce non-generic regardless of configuration) ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Build command to use ``"make install"`` +``languages`` List of languages to build GCC for (--enable-languages) ``[]`` +``license_activation`` License activation type ``"license_server"`` +``m32`` Enable 32-bit toolchain ``False`` +``multilib`` Build multilib gcc (both i386 and x86_64) ``False`` +``pplwatchdog`` Enable PPL watchdog ``False`` +``prefer_lib_subdir`` Configure GCC to prefer 'lib' subdirs over 'lib64' when linking ``False`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``profiled`` Bootstrap GCC with profile-guided optimizations ``False`` +``requires_runtime_license`` Boolean indicating whether or not a runtime license is required ``True`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` +``serial_number`` Serial number for the product ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``use_gold_linker`` Configure GCC to use GOLD as default linker ``True`` +``usetmppath`` Use temporary path for installation ``False`` +``withamdgcn`` Build GCC with AMD GCN offload support ``False`` +``withcloog`` Build GCC with CLooG support ``False`` +``withisl`` Build GCC with ISL support ``False`` +``withlibiberty`` Enable installing of libiberty ``False`` +``withlto`` Enable LTO support ``True`` +``withnvptx`` Build GCC with NVPTX offload support ``False`` +``withppl`` Build GCC with PPL support ``False`` +=============================== =================================================================================================================================================================================================== ==================== .. _SystemMPI: @@ -1221,6 +1231,8 @@ easyconfig parameter description ``ofi_internal`` Use internal shipped libfabric instead of external libfabric ``True`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` ``requires_runtime_license`` Boolean indicating whether or not a runtime license is required ``True`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` ``serial_number`` Serial number for the product ``None`` ``set_mpi_wrapper_aliases_gcc`` Set compiler for mpigcc/mpigxx via aliases ``False`` ``set_mpi_wrapper_aliases_intel`` Set compiler for mpiicc/mpiicpc/mpiifort via aliases ``False`` @@ -1268,16 +1280,18 @@ Compiler toolchain easyblock: nothing to install, just generate module file. Extra easyconfig parameters specific to ``Toolchain`` easyblock --------------------------------------------------------------- -============================ =========================================================================================================== ============= -easyconfig parameter description default value -============================ =========================================================================================================== ============= -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -``set_env_external_modules`` Include setenv statements for toolchain components that use an external module, based on available metadata ``False`` -============================ =========================================================================================================== ============= +=============================== =========================================================================================================== ============= +easyconfig parameter description default value +=============================== =========================================================================================================== ============= +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` +``set_env_external_modules`` Include setenv statements for toolchain components that use an external module, based on available metadata ``False`` +=============================== =========================================================================================================== ============= .. _VSCPythonPackage: From bd2c8754dae2dfa3651fff9764ef644f98e5711d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 24 Jan 2022 07:36:39 +0800 Subject: [PATCH 187/286] update release notes and changelog for EasyBuild v4.5.2 + bump version to 4.5.2 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 132 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 133 insertions(+), 4 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 2fb0cd62..bf546db3 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20220124.01** (`Jan 24th 2022`): update release notes for EasyBuild v4.5.2 (see :ref:`release_notes_eb452`) * **release 20211213.01** (`Dec 13th 2021`): update release notes for EasyBuild v4.5.1 (see :ref:`release_notes_eb451`) * **release 20211029.01** (`Oct 29th 2021`): update release notes for EasyBuild v4.5.0 (see :ref:`release_notes_eb450`) * **release 20210907.01** (`Sep 7th 2021`): update release notes for EasyBuild v4.4.2 (see :ref:`release_notes_eb442`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 9bd0f683..fbe269d5 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,140 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,575** different software packages, +The latest version of EasyBuild provides support for building and installing **2,622** different software packages, including 36 different (compiler) toolchains. It contains 243 software-specific easyblocks and 37 generic easyblocks, -alongside 13,812 easyconfig files. +alongside 14,080 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb452: + +EasyBuild v4.5.2 (January 24th 2022) +------------------------------------ + +bugfix/update release + +**framework** + +* various enhancements, including: + + * automatically prepend value for ``env-for-shebang`` configuration setting with sysroot (`#3919 `_) + * enhance ``update_build_option`` to return original value + add support for ``update_build_options`` (`#3923 `_) + * fix compatibility with Python 3.10 (`#3926 `_, `#3933 `_) + * also take ``/etc/os-release`` into account in ``get_os_name`` and ``get_os_version`` (`#3930 `_) + * enhance ``get_cpu_architecture`` and ``get_cpu_family`` to be aware of RISC-V (`#3931 `_) + +* various bug fixes, including: + + * relax pattern checks in ``test_toy_exts_parallel`` (`#3921 `_) + * use ``sources.easybuild.io`` as backup URL for downloading Environment Modules sources to run test suite (`#3928 `_) + * make intelfftw toolchain component aware of GCCcore (`#3929 `_) + +* other changes: + + * deprecate use of (actual) patch files that don't have a filename ending with ``.patch`` (`#3920 `_) + * remove version restriction for keyring in ``requirements.txt`` to test with latest version (`#3925 `_) + * simplify ``requirements.txt`` by removing Python 2.6 support (`#3927 `_) + * only run GitHub tests when testing with Lua module syntax, to avoid hitting GitHub rate limit when running tests (`#3938 `_) + +**easyblocks** + +* minor enhancements and updates, including: + + * remove necessity for license for oneAPI versions (>= 2021.x) in itac easyblock (`#2492 `_) + * add CUDA support in SuiteSparse easyblock (`#2627 `_) + * use all available cores for running Perl test suite (`#2637 `_) + * add option to not copy the license file for Gurobi (`#2639 `_, `#2641 `_) + * update AOCC easyblock to support version 3.2.0 (`#2643 `_) + * don't grep for specific version in ``--version`` output of Intel compiler commands for versions 2022.x (`#2644 `_) + * add support for enabling sanity checks for specific components in the Bundle easyblock (`#2649 `_) + * update Libint easyblock for LibInt v2.7.0 which requires configuring via CMake (`#2650 `_) + * update Mathematica easyblock for version 13 (`#2652 `_) + * add sanity check command for Bazel (`#2653 `_) + * update NAMD easyblock to allow non-system csh (`#2654 `_) + * enhance CUDA easyblock to create version independent pkgconfig files (`#2656 `_) + * add ``util`` subdirectory to ``$PATH`` for WPS (`#2658 `_) + +* various bug fixes, including: + + * convert version numbers to strictly numerical in Siesta easyblock (`#2553 `_) + * fix shebang of scripts in Perl installation if installation prefix is too long (`#2640 `_) + * enhance IntelBase easyblock to avoid crash when ``$USER`` is not set (`#2642 `_) + * fix quotes in definition of default platform macro and enhance sanity check in GATE easyblock (`#2645 `_) + * avoid excessively long shebang line in compile script for WRF (`#2648 `_) + * fix checking of Intel Fortran compiler version in CP2K easyblock for recent toolchains (`#2651 `_) + +**easyconfigs** + +* added easyconfig for intel/2022.00 toolchain (`#14620 `_) + +* added example easyconfig files for 48 new software packages: + + * alevin-fry (`#14617 `_), AMD-uProf (`#14626 `_), ANGEL (`#11857 `_), atropos (`#7580 `_), Austin (`#14596 `_), AutoDock-GPU (`#14671 `_), + AutoDock-Vina (`#14675 `_), boost_histogram (`#14516 `_), CAFE5 (`#14603 `_), Calcam (`#7488 `_), Carma (`#14527 `_), Cogent (`#14278 `_), + dlib (`#14556 `_), DualSPHysics (`#14632 `_), dune-core (`#14693 `_), dune-fem (`#14693 `_), DyMat (`#14615 `_), elbencho (`#14548 `_), + Embree (`#7471 `_), ExaML (`#14530 `_), FMPy (`#14481 `_), genozip (`#14583 `_), hivtrace (`#14691 `_), intervaltree-python (`#8995 `_), + IsoNet (`#14075 `_), MACSE (`#14709 `_), MetaPhlAn (`#12917 `_), MicrobeAnnotator (`#14549 `_), mold (`#14595 `_), numdiff (`#14609 `_), + OpenFace (`#14556 `_), PhyloPhlAn (`#14564 `_), PREQUAL (`#14722 `_), PuLP (`#14581 `_), PyCalib (`#14616 `_), PyTorch3D (`#13240 `_), + QCG-PilotJob (`#14337 `_), RaGOO (`#8995 `_), RAPSearch2 (`#13199 `_), SCopeLoomR (`#14518 `_), ShengBTE (`#14557 `_), SHTns (`#14682 `_), + STRUMPACK (`#14560 `_), TALYS (`#14716 `_), TN93 (`#14691 `_), xxHash (`#14251 `_), yaml-cpp (`#14547 `_), Zgoubi (`#14516 `_) + +* added additional easyconfigs for various supported software packages, including: + + * annovar 20200607, antiSMASH 5.2.0, Armadillo 10.7.5, Arrow 6.0.1, Bismark 0.23.1, BLAST+ 2.12.0, + cDNA_Cupcake 26.0.0, CHERAB 1.3.0, CMake 3.22.1, CP2K 8.2, DIAMOND 2.0.13, dotNET-Core-Runtime 6.0.1, + dotNET-SDK 6.0.101, Extrae 3.8.3, fastp 0.23.2, FreeSurfer 7.2.0, GffCompare 0.12.6, gmsh 4.9.0, GTK3 3.24.31, + h5py 3.6.0, igraph 0.9.5, Inspector 2022.0.0, IQ-TREE 2.1.3, itac 2021.5.0.eb, Java/15 + Java/17, JUBE 2.4.2, + libdeflate 1.8, libxsmm 1.17, LSD2 2.3, MAGMA 1.09b, MATLAB 2021b, MinPath 1.6, MultiQC 1.11, MUSCLE 5.0.1428, + numba 0.54.1, NVHPC 21.11, OBITools 1.2.13, occt 7.5.0p1, openCARP 8.2, OpenCV 3.4.1, OpenFOAM v2112, ORCA 5.0.2, + phonopy 2.12.0, Pillow 8.3.2, Pillow-SIMD 8.3.2, PLUMED 2.7.3, poppler 22.01.0, PyQtGraph 0.12.3, + python-igraph 0.9.8, PyZMQ 22.3.0, Raysect 0.7.1, Rgurobi 9.5.0, scanpy 1.8.2, Schrodinger 2021, SqueezeMeta 1.0.0, + statsmodels 0.13.1, texlive 20210324, VTune 2022.0.0 + +* minor enhancements, including: + + * add yaml-cpp dependency to Trilinos 12.12.1 with foss/2019b (`#14547 `_) + * include output of failing code style check in message produced by failing easyconfigs style test (`#14578 `_) + * bundle LAPACKE with FlexiBLAS 3.0.4 (`#14591 `_), `#14769 `_) + * add extensions to R v4.1.2 easyconfig: semTools, mirt, OpenMX (`#14634 `_), FactorCopula (`#14648 `_), rpact, ldbounds (`#14750 `_) + * add extensions to R-bundle-Bioconductor 3.14: ExomeDepth (`#14684 `_), DSS (`#14748 `_), pathview (`#14806 `_) + +* various bug fixes, including: + + * fix ``homepage`` and ``source_urls`` for GLIMMER 3.02b (`#7945 `_) + * fix source URL for Trilinos 12.12.1 with foss/2019b (`#14547 `_) + * use proper Perl dependency for worker 1.6.12 with foss/2019a (fixes installation on RHEL8 OS) (`#14565 `_) + * fix checksum and versions of annovar v20191024 (`#14579 `_) + * add patch for Rust 1.52.2 and 1.54.0 to fix build when using alternate sysroot (`#14584 `_) + * retain version in filename for cromwell sources (`#14586 `_) + * specify compiler to use in WildMagic easyconfig (`#14594 `_) + * avoid need for git build dependency for recent x265 easyconfigs (`#14605 `_) + * fix broken patch file for recent GPAW versions (`#14619 `_) + * add alternative checksum for Siesta-4.1-MaX-1.0 (`#14643 `_) + * add missing PCRE dependency for pullseq + add sanity check commands (`#14650 `_) + * use ``%(arch)s`` template to avoid hardcoding ``x86_64`` in recent XML-LibXML easyconfigs (`#14655 `_) + * fix name for (binary) AutoDock-Vina v1.1.2 (`#14675 `_) + * add patch to fix memory leak in OpenMPI that heavily affects CP2K, SIESTA, QuantumESPRESSO, VASP, ... (`#14726 `_) + * set ``$GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS`` for installing grcpio extension included with: + + * TensorFlow 2.2.3-2.4.1 with 2020* toolchain (`#14729 `_) and 2.5.0+ (`#14728 `_) + * Ray-project (`#14730 `_) + + * enforce using internal boost for bcl2fastq2 with a GCC 10.x toolchain (`#14741 `_) + * add patch for hard-coded checksum value of downloaded source file in the source code of RDKit 2021.03.4 (`#14743 `_) + * also install ``libaio.so.1`` symlink in easyconfigs for libaio v0.3.112 (`#14745 `_) + * do not use external libgcrypt or python for libxslt with recent toolchains (`#14756 `_) + * add patches to fix CVE-2021-23437 for Pillow (`#14765 `_) and Pillow-SIMD (`#14792 `_) + * add libXfont2 patch to fix build when libbsd is present (`#14821 `_) + +* other changes: + + * update Java 1.8 wrapper to 1.8.0_311 for x86_64 (`#14644 `_) + * bring gffread back down to GCCcore level for toolchain version 10.3.0 (`#14660 `_) + * update build dependencies for recent binutils + GCCcore easyconfigs to avoid depending on M4 1.4.18 with system toolchain (`#14731 `_), `#14755 `_) + * bump nbconvert extension in recent IPython easyconfigs to version 6.4.0 (`#14738 `_) + + .. _release_notes_eb451: EasyBuild v4.5.1 (December 13th 2021) diff --git a/docs/conf.py b/docs/conf.py index 63f342a8..a7cbc823 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.5.1' # this is meant to reference the version of EasyBuild +version = '4.5.2' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20211213.0' # this is meant to reference the version of the documentation itself +release = '20220124.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 2a24ead93f3f14746589d31cbe5504d4dc250fb7 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 24 Jan 2022 14:15:49 +0800 Subject: [PATCH 188/286] bump version to 4.5.2 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 37bf3d96..86a7110d 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.5.1' +VERSION = '4.5.2' # Utility function to read README file From c9975e66149751bb66041d9b9f29b358a8db0474 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 29 Jan 2022 19:35:57 +0100 Subject: [PATCH 189/286] specify easybuild.io as EasyBuild homepage in setup.py + docs landing page --- docs/index.rst | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/index.rst b/docs/index.rst index 27c1c638..3aafbf41 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -5,7 +5,7 @@ EasyBuild documentation -Welcome to the documentation of `EasyBuild `_, a software build and installation framework +Welcome to the documentation of `EasyBuild `_, a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. This documentation is intended for EasyBuild version |version|, and was last rebuilt on |today|. diff --git a/setup.py b/setup.py index 37bf3d96..fae2766a 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ def read(fname): on High Performance Computing (HPC) systems in an efficient way.""", license="GPLv2", keywords="software build building installation installing compilation HPC scientific", - url="https://easybuilders.github.io/easybuild", + url="https://easybuild.io", long_description=read("README.rst"), classifiers=[ "Development Status :: 5 - Production/Stable", From b302b27e2695d9cab807d894870819c4ca1141cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Feb 2022 20:38:52 +0100 Subject: [PATCH 190/286] add Jasper Grimm as EasyBuild maintainer --- docs/Maintainers.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/Maintainers.rst b/docs/Maintainers.rst index 560acb82..b66351db 100644 --- a/docs/Maintainers.rst +++ b/docs/Maintainers.rst @@ -99,6 +99,10 @@ The EasyBuild maintainers all have admin access to the different EasyBuild GitHu * GitHub: `@fgeorgatos `_ - e-mail: ``kefalonia (at) gmail.com`` - IRC/Slack: ``fotis`` +* **Jasper Grimm** (`University or York `_) + + * GitHub: `@jfgrimm `_ - e-mail: ``jasper.grimm (at) york.ac.uk`` - IRC/Slack: ``Jasper`` + * **Balázs Hajgató** (`HPC-UGent `_) * GitHub: `@hajgato `_ - e-mail: ``balazs.hajgato (at) ugent.be`` - IRC/Slack: ``hajgato`` From e009ffa1e57c8dc1d9b460c20f5b710b4435b70b Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 4 Feb 2022 10:43:24 +0100 Subject: [PATCH 191/286] Create Installing-Lmod-without-root-permissions.rst --- docs/Installing-Lmod-without-root-permissions.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/Installing-Lmod-without-root-permissions.rst b/docs/Installing-Lmod-without-root-permissions.rst index c67f60f7..66c6562f 100644 --- a/docs/Installing-Lmod-without-root-permissions.rst +++ b/docs/Installing-Lmod-without-root-permissions.rst @@ -6,11 +6,12 @@ Installing Lmod without root permissions This short guide will show how to install Lmod (and Lua, on which it depends) on Linux, without requiring root permissions. -Installing lua using the steps below does require rsync, make and gcc Lua ~~~ +Dependencies: Installing Lua using the steps below requires rsync, make and gcc + Build and install Lua using the source tarball available in the Lmod SourceForge repository (`http://sourceforge.net/projects/lmod/files/`_). This version is a lot easier to build, and already includes the required From 4f921247cd8e33d331b3a00a9e1a662e867a4c12 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 4 Feb 2022 10:56:07 +0100 Subject: [PATCH 192/286] Tweak new text --- docs/Writing_easyconfig_files.rst | 32 ++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index 93d54544..ce6fa823 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -160,28 +160,30 @@ Example: Patches ^^^^^^^ -Patches can be provided via the ``patches`` easyconfig parameter (list). And patch could be defined as: +Patches can be provided via the ``patches`` easyconfig parameter (list). A patch can be defined as: -* string -* tuple -* dict +* a ``string``, +* a ``tuple``, or +* a ``dict`` The most straight-forward use-case is ``string``, which contains the name of the patch file -and has to have ``.patch`` extension. +(and must have ``.patch`` extension). -``Tuple`` adds possibility to specify patch level, which is used in patch command. -This is mostly needed, if patch file just adds new files and generally is not possible to determine starting directory. +A ``tuple`` adds the possibility to specify the patch level which is used in patch command. +This is mostly needed if patch file adds new files or generally itis not possible to determine +starting directory. -.. note:: ``Tuple`` also have special usage, if the patch file have any other extension than ``.patch`` - In this case, first tuple argument is file which should be copied to unpacked source dir and second tuple argument - is target path, where the files should be copied relative to unpacked source dir. See more in example below. +.. note:: ``tuple`` also has special usage if the patch file has any other extension than ``.patch``. + In this case, first tuple argument is file which should be copied to unpacked source dir and + second tuple argument is target path, where the files should be copied relative to unpacked + source dir. See more in example below. -``Dict`` adds ability to pass ``patch`` command additional arguments. For example ``--binary`` flag is needed to patch -files with CRLF endings. -The ``dict`` has required ``filename`` key, and ``level`` and ``opts`` optional ones. +A ``dict`` adds the ability to pass the ``patch`` command additional arguments. For example, the +``--binary`` flag is needed to patchfiles with CRLF endings. +The ``dict`` has a required ``filename`` key, with ``level`` and ``opts`` being optional ones. -.. note:: Filling just ``filename`` in ``dict`` is same as using plain ``string`` definition. - Filling ``filename`` and ``level`` is same as using ``tuple`` definition. +.. note:: Specifying only ``filename`` in ``dict`` is the same as using a plain ``string`` definition. + Specifying ``filename`` and ``level`` is same as using a ``tuple`` definition. Example: ``` From bf33cdc1be2dd3b4004d4f51b679419d247b85aa Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 4 Feb 2022 10:57:28 +0100 Subject: [PATCH 193/286] Typo --- docs/Writing_easyconfig_files.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index ce6fa823..b4f027e2 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -170,7 +170,7 @@ The most straight-forward use-case is ``string``, which contains the name of the (and must have ``.patch`` extension). A ``tuple`` adds the possibility to specify the patch level which is used in patch command. -This is mostly needed if patch file adds new files or generally itis not possible to determine +This is mostly needed if patch file adds new files or generally it is not possible to determine starting directory. .. note:: ``tuple`` also has special usage if the patch file has any other extension than ``.patch``. From 9f9cafb887945f930bce9dd3cf11fa82f55927ba Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 4 Feb 2022 10:58:20 +0100 Subject: [PATCH 194/286] Argh, another typo --- docs/Writing_easyconfig_files.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index b4f027e2..acf6aac1 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -179,7 +179,7 @@ starting directory. source dir. See more in example below. A ``dict`` adds the ability to pass the ``patch`` command additional arguments. For example, the -``--binary`` flag is needed to patchfiles with CRLF endings. +``--binary`` flag is needed to patch files with CRLF endings. The ``dict`` has a required ``filename`` key, with ``level`` and ``opts`` being optional ones. .. note:: Specifying only ``filename`` in ``dict`` is the same as using a plain ``string`` definition. From b24c21d8d04f30f9e8d2fe842ee805772da56102 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 4 Feb 2022 11:02:52 +0100 Subject: [PATCH 195/286] Tweak formatting --- docs/Writing_easyconfig_files.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index acf6aac1..073a3bb5 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -174,16 +174,16 @@ This is mostly needed if patch file adds new files or generally it is not possib starting directory. .. note:: ``tuple`` also has special usage if the patch file has any other extension than ``.patch``. - In this case, first tuple argument is file which should be copied to unpacked source dir and - second tuple argument is target path, where the files should be copied relative to unpacked - source dir. See more in example below. + In this case, the first tuple argument is a file which should be copied to unpacked source + dir and the second tuple argument is the target path, where the files should be copied + relative to the unpacked source dir. See below for an example of this use case. A ``dict`` adds the ability to pass the ``patch`` command additional arguments. For example, the ``--binary`` flag is needed to patch files with CRLF endings. The ``dict`` has a required ``filename`` key, with ``level`` and ``opts`` being optional ones. .. note:: Specifying only ``filename`` in ``dict`` is the same as using a plain ``string`` definition. - Specifying ``filename`` and ``level`` is same as using a ``tuple`` definition. + Specifying ``filename`` and ``level`` is same as using a ``tuple`` definition. Example: ``` From 1ee13d440c34f2816756c64eadf3246937fd7d48 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 4 Feb 2022 11:05:36 +0100 Subject: [PATCH 196/286] Update Writing_easyconfig_files.rst --- docs/Writing_easyconfig_files.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index 073a3bb5..e4abe1d2 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -171,12 +171,12 @@ The most straight-forward use-case is ``string``, which contains the name of the A ``tuple`` adds the possibility to specify the patch level which is used in patch command. This is mostly needed if patch file adds new files or generally it is not possible to determine -starting directory. +the starting directory. -.. note:: ``tuple`` also has special usage if the patch file has any other extension than ``.patch``. +.. note:: ``tuple`` also has a special use case if the patch file has any other extension than ``.patch``. In this case, the first tuple argument is a file which should be copied to unpacked source - dir and the second tuple argument is the target path, where the files should be copied - relative to the unpacked source dir. See below for an example of this use case. + dir and the second tuple argument is the target path, where the files should be copied to + (relative to the unpacked source dir). See below for an example of this use case. A ``dict`` adds the ability to pass the ``patch`` command additional arguments. For example, the ``--binary`` flag is needed to patch files with CRLF endings. From e22f16a967a53a5a4ab3eb9b146c059778406283 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 4 Feb 2022 16:20:38 +0100 Subject: [PATCH 197/286] Add Docker command examples --- docs/Containers.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/Containers.rst b/docs/Containers.rst index aceebce6..16fb9581 100644 --- a/docs/Containers.rst +++ b/docs/Containers.rst @@ -330,6 +330,11 @@ which will be stored in ``$HOME/.local/easybuild/containers``:: == Temporary log file(s) /tmp/eb-dLZTNF/easybuild-LPLeG0.log* have been removed. == Temporary directory /tmp/eb-dLZTNF has been removed. +Docker supports a limited set of the container options. Example of commands that can be used with to generate +Docker containers are:: + + eb --containerize --container-type=docker --experimental --container-config=ubuntu:20.04 zlib-1.2.11.eb + eb --containerize --container-type=docker --experimental --container-config=centos:7 zlib-1.2.11.eb .. _containers_example_recipe: From b565d891375abe675f8e613d54b12e04b5b04c96 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 4 Feb 2022 17:11:22 +0100 Subject: [PATCH 198/286] Update Containers.rst --- docs/Containers.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Containers.rst b/docs/Containers.rst index 16fb9581..67fe69d0 100644 --- a/docs/Containers.rst +++ b/docs/Containers.rst @@ -330,7 +330,7 @@ which will be stored in ``$HOME/.local/easybuild/containers``:: == Temporary log file(s) /tmp/eb-dLZTNF/easybuild-LPLeG0.log* have been removed. == Temporary directory /tmp/eb-dLZTNF has been removed. -Docker supports a limited set of the container options. Example of commands that can be used with to generate +Docker supports a limited set of the container options. Example of commands that can be used to generate Docker containers are:: eb --containerize --container-type=docker --experimental --container-config=ubuntu:20.04 zlib-1.2.11.eb From 1e0b814022db5825af3829b03516bed074c2ed16 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Feb 2022 17:27:18 +0100 Subject: [PATCH 199/286] fix typo in 'Consistency' in section title --- docs/Configuration.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Configuration.rst b/docs/Configuration.rst index 7756667e..a971b821 100644 --- a/docs/Configuration.rst +++ b/docs/Configuration.rst @@ -35,8 +35,8 @@ The order of preference for the different configuration types is as listed above .. _configuration_consistency: -Consistentency across supported configuration types -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Consistency across supported configuration types +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Note that the various available configuration options are handled **consistently** across the supported configuration types. From b612c51e8c42d7cfa1a6e13b7a544bfd79674777 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Feb 2022 22:11:55 +0100 Subject: [PATCH 200/286] auto-update docs for EasyBuild v4.5.3 --- docs/version-specific/Supported_software.rst | 1304 ++++++++++++------ docs/version-specific/easyblocks.rst | 2 + 2 files changed, 904 insertions(+), 402 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 6fddd098..0f2cf7ab 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2622 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2647 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_alevin-fry_1021` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMD-uProf_779` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_ANGEL_359` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_atropos_776` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Austin_628` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock-GPU_1075` - :ref:`list_software_AutoDock-Vina_1237` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_alevin-fry_1021` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMD-uProf_779` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_ANGEL_359` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_Arcade-Learning-Environment_2655` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_atropos_776` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Austin_628` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock-GPU_1075` - :ref:`list_software_AutoDock-Vina_1237` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -445,15 +445,16 @@ version versionsuffix toolchain *aiohttp* +++++++++ -" Async http client/server framework +Asynchronous HTTP client/server framework for asyncio and Python. *homepage*: https://github.com/aio-libs/aiohttp -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``3.5.4`` ``-Python-3.6.6`` ``foss/2018b`` -========= ================= ============== +========= ================= ====================================== +version versionsuffix toolchain +========= ================= ====================================== +``3.5.4`` ``-Python-3.6.6`` ``foss/2018b`` +``3.8.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ================= ====================================== .. _list_software_ALADIN_425: @@ -1240,7 +1241,7 @@ version versionsuffix toolchain *AOCC* ++++++ -AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0 +AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0 *homepage*: https://developer.amd.com/amd-aocc/ @@ -1250,6 +1251,7 @@ version toolchain ``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``3.0.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``3.2.0`` ``GCCcore/11.2.0`` ========= ========================================================== @@ -1370,6 +1372,22 @@ version toolchain ========== ================================================================================ +.. _list_software_Arcade-Learning-Environment_2655: + +*Arcade-Learning-Environment* ++++++++++++++++++++++++++++++ + +The Arcade Learning Environment (ALE) is a simple framework that allows researchers and hobbyists to develop AI agents for Atari 2600 games. It is built on top of the Atari 2600 emulator Stella and separates the details of emulation from agent design. This video depicts over 50 games currently supported in the ALE. + +*homepage*: https://github.com/mgbellemare/Arcade-Learning-Environment + +========= ============== +version toolchain +========= ============== +``0.7.3`` ``foss/2021b`` +========= ============== + + .. _list_software_arcasHLA_735: *arcasHLA* @@ -1701,6 +1719,7 @@ version versionsuffix toolchain ========== ================= =============================== ``0.7.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``0.11.1`` ``intel/2020b`` +``0.11.4`` ``intel/2021b`` ========== ================= =============================== @@ -1908,16 +1927,16 @@ The Astropy Project is a community effort to develop a single core package for *homepage*: https://www.astropy.org/ -========== ================== =============================== -version versionsuffix toolchain -========== ================== =============================== -``2.0.12`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``2.0.14`` ``foss/2019a`` -``4.0.1`` ``-Python-3.7.4`` ``foss/2019b`` -``4.0.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``4.2.1`` ``intelcuda/2020b`` -``4.3.1`` ``foss/2021a``, ``intel/2021a`` -========== ================== =============================== +========== ================== =============================================== +version versionsuffix toolchain +========== ================== =============================================== +``2.0.12`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``2.0.14`` ``foss/2019a`` +``4.0.1`` ``-Python-3.7.4`` ``foss/2019b`` +``4.0.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``4.2.1`` ``intelcuda/2020b`` +``4.3.1`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` +========== ================== =============================================== .. _list_software_at-spi2-atk_1005: @@ -2045,12 +2064,13 @@ Tools to make using job arrays a lot more convenient. *homepage*: https://github.com/gjbex/atools -========= ================== ================= -version versionsuffix toolchain -========= ================== ================= -``1.4.2`` ``-Python-2.7.12`` ``intel/2016b`` -``1.4.6`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` -========= ================== ================= +========= ================== ====================================== +version versionsuffix toolchain +========= ================== ====================================== +``1.4.2`` ``-Python-2.7.12`` ``intel/2016b`` +``1.4.6`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +``1.4.8`` ``-Python-2.7.18`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ================== ====================================== .. _list_software_atropos_776: @@ -2414,7 +2434,7 @@ version versionsuffix toolchain --- -:ref:`list_software_BabelStream_1090` - :ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_bamtofastq_1074` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_bcbio-gff_863` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biom-format_1117` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_Blosc2_549` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_boost_histogram_1620` - :ref:`list_software_boto3_487` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_Brotli-python_1339` - :ref:`list_software_Brunsli_735` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` +:ref:`list_software_BabelStream_1090` - :ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_Bambi_475` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_bamtofastq_1074` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_bcbio-gff_863` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biom-format_1117` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_Blosc2_549` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_boost_histogram_1620` - :ref:`list_software_boto3_487` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_Brotli-python_1339` - :ref:`list_software_Brunsli_735` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` .. _list_software_BabelStream_1090: @@ -2514,6 +2534,22 @@ version toolchain ========= ============================= +.. _list_software_Bambi_475: + +*Bambi* ++++++++ + +Bambi is a high-level Bayesian model-building interface written in Python. It works with the probabilistic programming frameworks PyMC3 and is designed to make it extremely easy to fit Bayesian mixed-effects models common in biology, social sciences and other disciplines. + +*homepage*: https://bambinos.github.io/bambi + +========= =============== +version toolchain +========= =============== +``0.7.1`` ``intel/2021b`` +========= =============== + + .. _list_software_BAMM_285: *BAMM* @@ -3102,17 +3138,18 @@ Beautiful Soup is a Python library designed for quick turnaround projects like s *homepage*: https://www.crummy.com/software/BeautifulSoup -========= ================= ================== -version versionsuffix toolchain -========= ================= ================== -``4.6.0`` ``-Python-3.6.3`` ``intel/2017b`` -``4.6.3`` ``-Python-3.6.4`` ``intel/2018a`` -``4.7.1`` ``-Python-3.6.6`` ``intel/2018b`` -``4.8.0`` ``GCCcore/8.2.0`` -``4.9.1`` ``GCCcore/8.3.0`` -``4.9.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``4.9.3`` ``GCCcore/10.2.0`` -========= ================= ================== +========== ================= ====================================== +version versionsuffix toolchain +========== ================= ====================================== +``4.6.0`` ``-Python-3.6.3`` ``intel/2017b`` +``4.6.3`` ``-Python-3.6.4`` ``intel/2018a`` +``4.7.1`` ``-Python-3.6.6`` ``intel/2018b`` +``4.8.0`` ``GCCcore/8.2.0`` +``4.9.1`` ``GCCcore/8.3.0`` +``4.9.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``4.9.3`` ``GCCcore/10.2.0`` +``4.10.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ================= ====================================== .. _list_software_BEDOPS_445: @@ -3577,7 +3614,7 @@ version versionsuffix toolchain ``1.76`` ``-Python-2.7.18`` ``foss/2020b`` ``1.78`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.78`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.79`` ``foss/2021a``, ``foss/2021b`` +``1.79`` ``foss/2021a``, ``foss/2021b``, ``intel/2021b`` ======== ================== =================================================== @@ -3773,22 +3810,22 @@ Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing prim *homepage*: https://blast.ncbi.nlm.nih.gov/ -========== ================== ================================================================== -version versionsuffix toolchain -========== ================== ================================================================== -``2.2.31`` ``system`` -``2.3.0`` ``-Python-2.7.11`` ``foss/2016a`` -``2.6.0`` ``-Python-2.7.12`` ``foss/2016b`` -``2.6.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` -``2.6.0`` ``-Python-2.7.14`` ``intel/2017b`` -``2.7.1`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -``2.7.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.8.1`` ``foss/2018b`` -``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a``, ``iimpi/2019b`` -``2.10.1`` ``gompi/2020a``, ``iimpi/2020a`` -``2.11.0`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a`` -``2.12.0`` ``gompi/2021b`` -========== ================== ================================================================== +========== ================== =================================================================================== +version versionsuffix toolchain +========== ================== =================================================================================== +``2.2.31`` ``system`` +``2.3.0`` ``-Python-2.7.11`` ``foss/2016a`` +``2.6.0`` ``-Python-2.7.12`` ``foss/2016b`` +``2.6.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``2.6.0`` ``-Python-2.7.14`` ``intel/2017b`` +``2.7.1`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +``2.7.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.8.1`` ``foss/2018b`` +``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``gompi/2021b``, ``iimpi/2019a``, ``iimpi/2019b`` +``2.10.1`` ``gompi/2020a``, ``iimpi/2020a`` +``2.11.0`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a`` +``2.12.0`` ``gompi/2021b`` +========== ================== =================================================================================== .. _list_software_BLAT_291: @@ -3992,6 +4029,7 @@ version versionsuffix toolchain ``2.0.2`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``2.2.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``2.4.1`` ``foss/2021a`` +``2.4.2`` ``foss/2021b`` =========== ================== =================================================== @@ -4149,6 +4187,7 @@ version versionsuffix toolchain ``1.72.0`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a`` ``1.74.0`` ``GCC/10.2.0`` ``1.76.0`` ``GCC/10.3.0`` +``1.77.0`` ``GCC/11.2.0`` ========== ================== ==================================================================== @@ -4218,6 +4257,7 @@ version toolchain ``1.2.2`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ``1.2.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` ``1.3.0`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``1.3.1`` ``GCC/11.2.0`` =========== ===================================================================================================================================== @@ -4763,7 +4803,7 @@ version toolchain --- -:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CASTEP_448` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_Crumble_714` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_c-ares_571: @@ -5150,6 +5190,22 @@ version toolchain ======= ============== +.. _list_software_CASTEP_448: + +*CASTEP* +++++++++ + +CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more. + +*homepage*: http://www.castep.org + +========== ====================================================================================== +version toolchain +========== ====================================================================================== +``21.1.1`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``foss/2019b``, ``intel/2019b``, ``iomkl/2019b`` +========== ====================================================================================== + + .. _list_software_CastXML_636: *CastXML* @@ -5482,17 +5538,17 @@ CDO is a collection of command line Operators to manipulate and analyse Climate *homepage*: https://code.zmaw.de/projects/cdo -========== ================================================= -version toolchain -========== ================================================= -``1.7.2`` ``intel/2016b`` -``1.8.1`` ``intel/2017a`` -``1.9.1`` ``intel/2017b`` -``1.9.2`` ``intel/2017b`` -``1.9.5`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``1.9.8`` ``intel/2019b`` -``1.9.10`` ``gompi/2019b``, ``gompi/2020b``, ``gompi/2021a`` -========== ================================================= +========== ================================================================== +version toolchain +========== ================================================================== +``1.7.2`` ``intel/2016b`` +``1.8.1`` ``intel/2017a`` +``1.9.1`` ``intel/2017b`` +``1.9.2`` ``intel/2017b`` +``1.9.5`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +``1.9.8`` ``intel/2019b`` +``1.9.10`` ``gompi/2019b``, ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2021b`` +========== ================================================================== .. _list_software_cdsapi_628: @@ -5704,7 +5760,7 @@ version toolchain ``3.45`` ``GCCcore/7.3.0``, ``intel/2018b`` ``3.47`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.48`` ``GCCcore/9.3.0`` -``3.49`` ``GCCcore/10.2.0`` +``3.49`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` ======== ===================================================== @@ -5981,6 +6037,7 @@ version toolchain ``1.8`` ``intel/2016b`` ``1.8.8`` ``intel/2018b`` ``1.8.9`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b`` +``1.8.11`` ``foss/2021b`` =========== ================================================================================= @@ -6270,6 +6327,7 @@ version versionsuffix toolchain ``11.0.0`` ``GCCcore/9.3.0`` ``11.0.1`` ``GCCcore/10.2.0``, ``gcccuda/2020b`` ``12.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``13.0.1`` ``GCCcore/11.2.0`` ========== ================== ====================================== @@ -6358,7 +6416,8 @@ version toolchain ``2.4.0.0`` ``intel/2017b`` ``2.4.1.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018b`` ``2.4.1.3`` ``foss/2019b``, ``foss/2020a`` -``2.4.4.0`` ``GCC/10.2.0`` +``2.4.4.0`` ``GCC/10.2.0``, ``GCC/11.2.0`` +``2.4.5.1`` ``GCC/11.2.0`` =========== ================================================================ @@ -6453,11 +6512,11 @@ ClustalW2 is a general purpose multiple sequence alignment program for DNA or pr *homepage*: https://www.ebi.ac.uk/Tools/msa/clustalw2/ -======= =========================================================================================================================================================== -version toolchain -======= =========================================================================================================================================================== -``2.1`` ``GCC/10.3.0``, ``foss/2016b``, ``foss/2018b``, ``foss/2021a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b``, ``intel/2020a`` -======= =========================================================================================================================================================== +======= =========================================================================================================================================================================== +version toolchain +======= =========================================================================================================================================================================== +``2.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``foss/2016b``, ``foss/2018b``, ``foss/2021a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b``, ``intel/2020a`` +======= =========================================================================================================================================================================== .. _list_software_Cluster-Buster_1412: @@ -6702,11 +6761,11 @@ Coin is an OpenGL-based, 3D graphics library that has its roots in the Open Inve *homepage*: https://coin3d.github.io -========= ============== -version toolchain -========= ============== -``4.0.0`` ``GCC/10.3.0`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``4.0.0`` ``GCC/10.3.0``, ``GCC/11.2.0`` +========= ============================== .. _list_software_CoinUtils_922: @@ -6854,7 +6913,7 @@ version versionsuffix toolchain *ConnectomeWorkbench* +++++++++++++++++++++ -Connectome Workbench is an open-source visualization and discovery tool used to explore data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualization platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data. +Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. *homepage*: https://www.humanconnectome.org/software/connectome-workbench @@ -6864,6 +6923,7 @@ version versionsuffix toolchain ``1.2.2`` ``system`` ``1.3.2`` ``GCCcore/8.2.0``, ``foss/2017b``, ``intel/2017b`` ``1.4.2`` ``-rh_linux64`` ``system`` +``1.5.0`` ``GCCcore/10.3.0`` ========= =============== ================================================== @@ -7354,6 +7414,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_Crumble_714: + +*Crumble* ++++++++++ + +Exploration of controlled loss of quality values for compressing CRAM files + +*homepage*: https://github.com/jkbonfield/crumble + +========= ============== +version toolchain +========= ============== +``0.8.3`` ``GCC/11.2.0`` +========= ============== + + .. _list_software_cryoDRGN_744: *cryoDRGN* @@ -7492,13 +7568,13 @@ Program for finding CTFs of electron micrographs. *homepage*: https://grigoriefflab.umassmed.edu/ctffind4 -========== ================ ====================================================== -version versionsuffix toolchain -========== ================ ====================================================== -``4.1.13`` ``foss/2019a``, ``fosscuda/2019a``, ``fosscuda/2019b`` -``4.1.14`` ``foss/2019b``, ``fosscuda/2019b``, ``fosscuda/2020b`` -``4.1.14`` ``-CUDA-11.3.1`` ``foss/2021a`` -========== ================ ====================================================== +========== ================ ====================================================================== +version versionsuffix toolchain +========== ================ ====================================================================== +``4.1.13`` ``foss/2019a``, ``fosscuda/2019a``, ``fosscuda/2019b`` +``4.1.14`` ``foss/2019b``, ``foss/2021b``, ``fosscuda/2019b``, ``fosscuda/2020b`` +``4.1.14`` ``-CUDA-11.3.1`` ``foss/2021a`` +========== ================ ====================================================================== .. _list_software_Cube_383: @@ -7603,6 +7679,8 @@ version toolchain ``11.4.1`` ``system`` ``11.4.2`` ``system`` ``11.5.0`` ``system`` +``11.5.1`` ``system`` +``11.6.0`` ``system`` ================= ========================================================================== @@ -7624,6 +7702,7 @@ version toolchain ``11.2.2`` ``system`` ``11.3.0`` ``system`` ``11.4.0`` ``system`` +``11.5.1`` ``system`` ========== ========== @@ -7799,6 +7878,7 @@ version versionsuffix toolchain ``2.10`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``2.10`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``3.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``3.5`` ``GCCcore/11.2.0`` ========= ================== ================================================ @@ -7986,7 +8066,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dlib_411` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dRep_395` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_DualSPHysics_1180` - :ref:`list_software_DUBStepR_713` - :ref:`list_software_dune-core_898` - :ref:`list_software_dune-fem_785` - :ref:`list_software_dxpy_453` - :ref:`list_software_DyMat_479` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_deepmedic_928` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dlib_411` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dRep_395` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_DualSPHysics_1180` - :ref:`list_software_DUBStepR_713` - :ref:`list_software_dune-core_898` - :ref:`list_software_dune-fem_785` - :ref:`list_software_dxpy_453` - :ref:`list_software_DyMat_479` .. _list_software_dadi_402: @@ -8135,6 +8215,7 @@ version versionsuffix toolchain ``2.18.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``2021.2.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``2021.9.1`` ``foss/2021a`` +``2022.1.0`` ``foss/2021b`` ============ ================== =================================================== @@ -8435,7 +8516,7 @@ version versionsuffix toolchain DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively. -*homepage*: https://deepdiff.readthedocs.io/en/latest/ +*homepage*: https://zepworks.com/deepdiff/current/ ========= ================== =============================== version versionsuffix toolchain @@ -8444,9 +8525,27 @@ version versionsuffix toolchain ``3.3.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``4.0.6`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``5.0.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``5.7.0`` ``GCCcore/11.2.0`` ========= ================== =============================== +.. _list_software_deepmedic_928: + +*deepmedic* ++++++++++++ + +Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans. + +*homepage*: https://biomedia.doc.ic.ac.uk/software/deepmedic/ + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``0.8.2`` ``foss/2021a`` +``0.8.2`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== + + .. _list_software_DeepSurv_814: *DeepSurv* @@ -8479,6 +8578,7 @@ version versionsuffix toolchain ``3.3.1`` ``-Python-3.6.6`` ``foss/2018b`` ``3.3.1`` ``-Python-3.7.4`` ``intel/2019b`` ``3.3.1`` ``-Python-3.8.2`` ``foss/2020a`` +``3.5.0`` ``foss/2021a`` ========= ================= =============== @@ -8916,12 +9016,13 @@ dm-tree provides tree, a library for working with nested data structures. In a w *homepage*: https://github.com/deepmind/tree -========= ================== -version toolchain -========= ================== -``0.1.1`` ``GCCcore/8.3.0`` -``0.1.5`` ``GCCcore/10.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``0.1.1`` ``GCCcore/8.3.0`` +``0.1.5`` ``GCCcore/10.2.0`` +``0.1.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== .. _list_software_DMCfun_541: @@ -9150,6 +9251,7 @@ version versionsuffix toolchain ========= ============= ============== ``1.0.3`` ``-R-4.0.3`` ``foss/2020b`` ``1.1.0`` ``-R-4.0.3`` ``foss/2020b`` +``1.1.1`` ``-R-4.1.2`` ``foss/2021b`` ========= ============= ============== @@ -9521,6 +9623,7 @@ version toolchain ``4.4.2`` ``system`` ``4.5.0`` ``system`` ``4.5.1`` ``system`` +``4.5.2`` ``system`` ========== ========== @@ -9562,6 +9665,7 @@ version versionsuffix toolchain ``2.18.0`` ``gompi/2020a`` ``2.20.0`` ``gompi/2020b`` ``2.22.1`` ``gompi/2021a`` +``2.24.2`` ``iimpi/2021b`` ========== ================== ================================ @@ -9931,6 +10035,7 @@ version versionsuffix toolchain ``25.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``26.3`` ``GCCcore/8.3.0`` ``27.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``27.2`` ``GCCcore/11.2.0`` ======== ============= ======================================================= @@ -10536,7 +10641,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMPy_348` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMPy_348` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoBiS_435` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -10584,7 +10689,7 @@ FabIO is an I/O library for images produced by 2D X-ray detectors and written in version versionsuffix toolchain ========== ================= ================================== ``0.10.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``0.11.0`` ``foss/2020b`` +``0.11.0`` ``foss/2020b``, ``fosscuda/2020b`` ========== ================= ================================== @@ -10678,11 +10783,11 @@ Utilities for indexing and sequence extraction from FASTA files. *homepage*: https://github.com/ekg/fastahack -========= ========================================================= -version toolchain -========= ========================================================= -``1.0.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -========= ========================================================= +========= ============================================================================= +version toolchain +========= ============================================================================= +``1.0.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========= ============================================================================= .. _list_software_FastaIndex_999: @@ -10752,7 +10857,7 @@ version toolchain ========== ============================================================ ``0.19.7`` ``foss/2018b`` ``0.20.0`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``0.23.2`` ``GCC/11.2.0`` +``0.23.2`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========== ============================================================ @@ -10877,11 +10982,11 @@ FastQTL is a QTL mapper *homepage*: http://fastqtl.sourceforge.net/ -========= ============== -version toolchain -========= ============== -``2.184`` ``foss/2018b`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``2.184`` ``GCC/11.2.0``, ``foss/2018b`` +========= ============================== .. _list_software_fastqz_665: @@ -11100,6 +11205,7 @@ version versionsuffix toolchain ``6.7.4`` ``intel/2020a`` ``6.7.5`` ``intel/2020a`` ``6.7.6`` ``intel/2020b`` +``6.7.7`` ``intel/2021b`` ========= ============= ================================ @@ -11515,6 +11621,7 @@ version toolchain ``5.38`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``5.39`` ``GCCcore/10.2.0`` ``5.40`` ``GCCcore/10.3.0`` +``5.41`` ``GCCcore/11.2.0`` ======== ==================================== @@ -11527,12 +11634,12 @@ filevercmp function as in sort --version-sort. *homepage*: https://github.com/ekg/filevercmp -============ ====================================== -version toolchain -============ ====================================== -``20141119`` ``GCCcore/9.3.0`` -``20191210`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -============ ====================================== +============ ========================================================== +version toolchain +============ ========================================================== +``20141119`` ``GCCcore/9.3.0`` +``20191210`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +============ ========================================================== .. _list_software_Filtlong_831: @@ -11830,6 +11937,7 @@ version versionsuffix toolchain ``1.1.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``1.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``1.1.4`` ``GCCcore/10.3.0`` +``2.0.2`` ``GCCcore/11.2.0`` ========= ================= ================== @@ -12153,6 +12261,22 @@ version toolchain ========= ==================================== +.. _list_software_FoBiS_435: + +*FoBiS* ++++++++ + +A Fortran Building System for automatic building modern Fortran projects + +*homepage*: https://github.com/szaghi/FoBiS + +========= ================== +version toolchain +========= ================== +``3.0.5`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_FoldX_477: *FoldX* @@ -12227,6 +12351,7 @@ FORD is an automatic documentation generator for modern Fortran programs version toolchain ========= ================== ``6.1.1`` ``GCCcore/10.2.0`` +``6.1.6`` ``GCCcore/10.3.0`` ========= ================== @@ -12723,11 +12848,11 @@ A tiny C library for managing SOM (Self-Organizing Maps) neural networks. *homepage*: https://github.com/ekg/fsom -============ ========================================================= -version toolchain -============ ========================================================= -``20141119`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -============ ========================================================= +============ ============================================================================= +version toolchain +============ ============================================================================= +``20141119`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +============ ============================================================================= .. _list_software_FTGL_301: @@ -13159,6 +13284,7 @@ version versionsuffix toolchain ``8.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``8.2`` ``-Python-2.7.15`` ``foss/2018b`` ``9.0`` ``-Python-3.7.4`` ``foss/2019b`` +``9.1`` ``foss/2021b`` =========== =============================== =============================== @@ -13785,7 +13911,8 @@ version toolchain ``10.5`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018b`` ``10.6`` ``foss/2019b`` ``10.6.2`` ``foss/2020a`` -``10.7.1`` ``GCC/10.2.0`` +``10.7.1`` ``GCC/10.2.0``, ``GCC/11.2.0`` +``11.0.0`` ``GCC/11.2.0`` ============= ================================================================ @@ -13868,6 +13995,7 @@ version toolchain ========== ============================== ``0.97`` ``foss/2016b``, ``foss/2017a`` ``0.98.1`` ``foss/2018b`` +``0.98.5`` ``foss/2021b`` ========== ============================== @@ -14765,14 +14893,14 @@ GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan *homepage*: https://www.glfw.org -========= ================== -version toolchain -========= ================== -``3.2.1`` ``intel/2018a`` -``3.3.2`` ``GCCcore/9.3.0`` -``3.3.3`` ``GCCcore/10.2.0`` -``3.3.4`` ``GCCcore/10.3.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``3.2.1`` ``intel/2018a`` +``3.3.2`` ``GCCcore/9.3.0`` +``3.3.3`` ``GCCcore/10.2.0`` +``3.3.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== .. _list_software_GLib_350: @@ -15268,6 +15396,7 @@ version toolchain ``3.4.7`` ``GNU/4.9.3-2.25`` ``3.4.11`` ``foss/2016a`` ``3.7.2`` ``GCCcore/10.3.0`` +``3.7.3`` ``GCCcore/11.2.0`` ========== ================== @@ -15297,6 +15426,7 @@ version toolchain ``1.16.5`` ``system`` ``1.16.6`` ``system`` ``1.17.3`` ``system`` +``1.17.6`` ``system`` ========== ================= @@ -15659,17 +15789,18 @@ version toolchain *gpustat* +++++++++ -dstat-like utilization monitor for NVIDIA GPUs +A simple command-line utility for querying and monitoring GPU status *homepage*: https://github.com/wookayin/gpustat -========= ================== ===================================== -version versionsuffix toolchain -========= ================== ===================================== -``0.5.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``0.6.0`` ``GCCcore/10.3.0``, ``gcccuda/2020b`` -``0.6.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` -========= ================== ===================================== +=========== ================== ===================================== +version versionsuffix toolchain +=========== ================== ===================================== +``0.5.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``0.6.0`` ``GCCcore/10.3.0``, ``gcccuda/2020b`` +``0.6.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.0.0b1`` ``GCCcore/11.2.0`` +=========== ================== ===================================== .. _list_software_GPy_272: @@ -15897,6 +16028,7 @@ version versionsuffix toolchain ``2.44.1`` ``-Java-11-Python-3.8.2`` ``GCCcore/9.3.0`` ``2.47.0`` ``-Java-11`` ``GCCcore/10.2.0`` ``2.47.2`` ``GCCcore/10.3.0`` +``2.50.0`` ``GCCcore/11.2.0`` ========== ========================= =============================== @@ -16129,6 +16261,8 @@ version versionsuffix toolchain ``2021.3`` ``foss/2021a`` ``2021.3`` ``-CUDA-11.3.1`` ``foss/2021a`` ``2021.3`` ``-CUDA-11.3.1-PLUMED-2.7.2`` ``foss/2021a`` +``2021.5`` ``foss/2021b`` +``2021.5`` ``-CUDA-11.4.1`` ``foss/2021b`` ========== ============================= ============================================================================================================ @@ -16286,6 +16420,7 @@ version toolchain ``1.16.0`` ``GCC/8.2.0-2.31.1`` ``1.16.2`` ``GCC/8.3.0`` ``1.18.4`` ``GCC/10.2.0``, ``GCC/10.3.0`` +``1.18.5`` ``GCC/11.2.0`` =========== ================================================================================================================== @@ -16308,6 +16443,7 @@ version toolchain ``1.16.0`` ``GCC/8.2.0-2.31.1`` ``1.16.2`` ``GCC/8.3.0`` ``1.18.4`` ``GCC/10.2.0``, ``GCC/10.3.0`` +``1.18.5`` ``GCC/11.2.0`` =========== ================================================================================================================== @@ -16489,6 +16625,7 @@ version toolchain ``2.2.2`` ``GCCcore/6.4.0`` ``2.2.4`` ``GCCcore/7.3.0``, ``GCCcore/9.3.0`` ``2.2.7`` ``GCCcore/10.3.0`` +``3.0.7`` ``GCCcore/11.2.0`` ========== ====================================================================================================================================================================================================================== @@ -16563,7 +16700,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_HIP_225` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_hivtrace_854` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_HIP_225` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_histolab_854` - :ref:`list_software_hivtrace_854` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -16935,6 +17072,7 @@ version versionsuffix toolchain ``1.10.5`` ``-serial`` ``GCCcore/8.3.0`` ``1.10.6`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpic/2020a`` ``1.10.7`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpic/2020b`` +``1.10.8`` ``gompi/2021b`` ``1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` ``1.12.1`` ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021b`` ================= ============= ================================================================================================================================================================================================================== @@ -17242,10 +17380,26 @@ version toolchain ``2.0.5`` ``intel/2017a`` ``2.1.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``2.2.0`` ``foss/2018b`` -``2.2.1`` ``foss/2019b``, ``foss/2020a``, ``gompi/2020b`` +``2.2.1`` ``foss/2019b``, ``foss/2020a``, ``gompi/2020b``, ``gompi/2021b`` ============== ================================================================================= +.. _list_software_histolab_854: + +*histolab* +++++++++++ + +Library for Digital Pathology Image Processing + +*homepage*: https://github.com/histolab/histolab + +========= ============================== +version toolchain +========= ============================== +``0.4.1`` ``foss/2021a``, ``foss/2021b`` +========= ============================== + + .. _list_software_hivtrace_854: *hivtrace* @@ -17764,7 +17918,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intervaltree-python_2020` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_IsoNet_594` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intervaltree-python_2020` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_Iris_407` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_IsoNet_594` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -18386,14 +18540,15 @@ Imageio is a Python library that provides an easy interface to read and write a *homepage*: https://imageio.github.io -========= ================= ================================== -version versionsuffix toolchain -========= ================= ================================== -``2.3.0`` ``-Python-3.6.4`` ``intel/2018a`` -``2.5.0`` ``foss/2019a`` -``2.9.0`` ``foss/2020b``, ``fosscuda/2020b`` -``2.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -========= ================= ================================== +========== ================= ================================== +version versionsuffix toolchain +========== ================= ================================== +``2.3.0`` ``-Python-3.6.4`` ``intel/2018a`` +``2.5.0`` ``foss/2019a`` +``2.9.0`` ``foss/2020b``, ``fosscuda/2020b`` +``2.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``2.13.5`` ``foss/2021b`` +========== ================= ================================== .. _list_software_ImageJ_557: @@ -19065,11 +19220,11 @@ An interval tree can be used to efficiently find a set of numeric intervals ove *homepage*: https://github.com/ekg/intervaltree -======= ========================================================= -version toolchain -======= ========================================================= -``0.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -======= ========================================================= +======= ============================================================================= +version toolchain +======= ============================================================================= +``0.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +======= ============================================================================= .. _list_software_intervaltree-python_2020: @@ -19394,6 +19549,22 @@ version versionsuffix toolchain ========== ============= =============================================== +.. _list_software_Iris_407: + +*Iris* +++++++ + +A module for improving the insertion sequences of structural variant calls + +*homepage*: https://github.com/mkirsche/Iris + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``1.0.5`` ``-Java-15`` ``GCC/11.2.0`` +========= ============= ============== + + .. _list_software_IRkernel_796: *IRkernel* @@ -19568,7 +19739,7 @@ version versionsuffix toolchain ``5.0b01`` ``-Python-3.6.6`` ``foss/2018b`` ``5.1.2`` ``foss/2020a``, ``fosscuda/2020a`` ``5.1.2`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` -``5.2.1`` ``foss/2020b`` +``5.2.1`` ``foss/2020b``, ``foss/2021a`` ========== ================== ================================== @@ -19645,7 +19816,7 @@ version toolchain --- -:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_jax_323` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_JSON-GLib_709` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyter-matlab-proxy_2080` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` - :ref:`list_software_jxrlib_651` +:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_Jasmine_711` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_jax_323` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_JSON-GLib_709` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyter-matlab-proxy_2080` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` - :ref:`list_software_jxrlib_651` .. _list_software_JAGS_293: @@ -19682,6 +19853,22 @@ version toolchain ========== ============== +.. _list_software_Jasmine_711: + +*Jasmine* ++++++++++ + +SV Merging Across Samples + +*homepage*: https://github.com/mkirsche/Jasmine + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``1.1.4`` ``-Java-15`` ``GCC/11.2.0`` +========= ============= ============== + + .. _list_software_JasPer_581: *JasPer* @@ -19775,6 +19962,7 @@ version versionsuffix toolchain ``16.0.1`` ``system`` ``17`` ``system`` ``17.0.1`` ``system`` +``17.0.2`` ``system`` ============= ======================== ========== @@ -20154,6 +20342,7 @@ version versionsuffix toolchain ``2.2.8`` ``GCCcore/10.2.0`` ``3.0.16`` ``GCCcore/10.3.0`` ``3.1.6`` ``GCCcore/11.2.0`` +``3.2.8`` ``GCCcore/10.3.0`` ========== ================= ================================== @@ -20665,7 +20854,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LBFGS++_452` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_LERC_294` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaec_608` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libavif_733` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libfabric_926` - :ref:`list_software_libfdf_615` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_LibLZF_515` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libmbd_618` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libnsl_644` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpspio_866` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libSBML_613` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libtree_743` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_longread_umi_1270` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPeg_360` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LBFGS++_452` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_LERC_294` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaec_608` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libavif_733` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libexif_739` - :ref:`list_software_libfabric_926` - :ref:`list_software_libfdf_615` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgdiplus_1071` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_LibLZF_515` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libmbd_618` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libnsl_644` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpspio_866` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libSBML_613` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libtree_743` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_longread_umi_1270` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPeg_360` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -21012,15 +21201,16 @@ version toolchain *lftp* ++++++ -LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind. +LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind. -*homepage*: http://lftp.yar.ru +*homepage*: https://lftp.yar.ru ========= ================== version toolchain ========= ================== ``4.6.4`` ``GNU/4.9.3-2.25`` ``4.8.4`` ``GCCcore/6.4.0`` +``4.9.2`` ``GCCcore/11.2.0`` ========= ================== @@ -21117,11 +21307,12 @@ A C library for handling bigWig files *homepage*: https://github.com/dpryan79/libBigWig -========= ================= -version toolchain -========= ================= -``0.4.4`` ``GCCcore/8.3.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``0.4.4`` ``GCCcore/8.3.0`` +``0.4.6`` ``GCCcore/11.2.0`` +========= ================== .. _list_software_libbitmask_1058: @@ -21329,13 +21520,13 @@ Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. *homepage*: https://github.com/ebiggers/libdeflate -======= ===================================== -version toolchain -======= ===================================== -``1.5`` ``GCCcore/7.3.0`` -``1.7`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``1.8`` ``GCCcore/11.2.0`` -======= ===================================== +======= ========================================================= +version toolchain +======= ========================================================= +``1.5`` ``GCCcore/7.3.0`` +``1.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``1.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +======= ========================================================= .. _list_software_libdivsufsort_1424: @@ -21491,6 +21682,22 @@ version toolchain ========== ====================================================================================== +.. _list_software_libexif_739: + +*libexif* ++++++++++ + +A library for parsing, editing, and saving EXIF data. + +*homepage*: https://libexif.github.io/ + +========== ================== +version toolchain +========== ================== +``0.6.24`` ``GCCcore/11.2.0`` +========== ================== + + .. _list_software_libfabric_926: *libfabric* @@ -21641,6 +21848,22 @@ version toolchain ========= ============================================================================================================ +.. _list_software_libgdiplus_1071: + +*libgdiplus* +++++++++++++ + +Libgdiplus is the Mono library that provides a GDI+-compatible API on non-Windows operating systems. + +*homepage*: https://www.mono-project.com/docs/gui/libgdiplus + +======= ================== +version toolchain +======= ================== +``6.1`` ``GCCcore/11.2.0`` +======= ================== + + .. _list_software_libGDSII_679: *libGDSII* @@ -21798,12 +22021,12 @@ A library to compute the exchange and correlation energy and potential in spher *homepage*: https://gitlab.com/siesta-project/libraries/libgridxc -========= ================================ -version toolchain -========= ================================ -``0.8.5`` ``iimpi/2019b`` -``0.9.6`` ``gompi/2020b``, ``iimpi/2020b`` -========= ================================ +========= ==================================================================================================== +version toolchain +========= ==================================================================================================== +``0.8.5`` ``iimpi/2019b`` +``0.9.6`` ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b`` +========= ==================================================================================================== .. _list_software_libgtextutils_1428: @@ -22322,12 +22545,12 @@ LibPSML provides a Fortran API to parse files in the PSeudopotential Markup Lan *homepage*: https://launchpad.net/libpsml -========== ======================================= -version toolchain -========== ======================================= -``1.1.7`` ``foss/2016b``, ``foss/2017a`` -``1.1.10`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -========== ======================================= +========== =================================================================================================================================== +version toolchain +========== =================================================================================================================================== +``1.1.7`` ``foss/2016b``, ``foss/2017a`` +``1.1.10`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` +========== =================================================================================================================================== .. _list_software_libpsortb_977: @@ -22432,6 +22655,7 @@ version toolchain ``3.6.0`` ``foss/2018b`` ``4.0.0`` ``GCCcore/9.3.0`` ``4.1.0`` ``GCCcore/10.2.0`` +``4.1.2`` ``GCCcore/11.2.0`` ========= ================== @@ -22460,11 +22684,14 @@ A shared memory parallel sparse matrix computations library for the Recursive Sp *homepage*: https://sourceforge.net/projects/librsb/ -=========== ============== -version toolchain -=========== ============== -``1.2.0.9`` ``GCC/10.2.0`` -=========== ============== +============ ============== +version toolchain +============ ============== +``1.2.0.9`` ``GCC/10.2.0`` +``1.2.0.10`` ``GCC/10.2.0`` +``1.2.0.11`` ``GCC/10.2.0`` +``1.3.0.0`` ``GCC/10.2.0`` +============ ============== .. _list_software_librsvg_761: @@ -22747,6 +22974,7 @@ version toolchain ``4.13`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``4.16.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` ``4.17.0`` ``GCCcore/10.3.0`` +``4.18.0`` ``GCCcore/11.2.0`` ========== =================================================== @@ -22847,9 +23075,9 @@ version toolchain *libunistring* ++++++++++++++ -This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. +This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. -*homepage*: http://www.gnu.org/software/libunistring/ +*homepage*: https://www.gnu.org/software/libunistring/ ========== ============================================================================================== version toolchain @@ -22858,6 +23086,7 @@ version toolchain ``0.9.6`` ``GCCcore/5.4.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016b`` ``0.9.7`` ``GCCcore/6.4.0`` ``0.9.10`` ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.0`` ``GCCcore/11.2.0`` ========== ============================================================================================== @@ -23022,22 +23251,22 @@ Libxc is a library of exchange-correlation functionals for density-functional th *homepage*: https://www.tddft.org/programs/libxc -========= ===================================================================================================================================================================================================================================== -version toolchain -========= ===================================================================================================================================================================================================================================== -``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` -``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` -``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``foss/2020b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` -``4.0.1`` ``foss/2017b``, ``intel/2017b`` -``4.0.3`` ``foss/2016b``, ``foss/2017a`` -``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` -``4.3.4`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0`` -``5.1.2`` ``GCC/10.2.0`` -``5.1.3`` ``GCC/10.2.0`` -``5.1.5`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` -``5.1.6`` ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` -========= ===================================================================================================================================================================================================================================== +========= =================================================================================================================================================================================================================================================================================== +version toolchain +========= =================================================================================================================================================================================================================================================================================== +``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` +``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` +``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``foss/2020b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` +``4.0.1`` ``foss/2017b``, ``intel/2017b`` +``4.0.3`` ``foss/2016b``, ``foss/2017a`` +``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` +``4.3.4`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` +``5.1.2`` ``GCC/10.2.0`` +``5.1.3`` ``GCC/10.2.0`` +``5.1.5`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` +``5.1.6`` ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` +========= =================================================================================================================================================================================================================================================================================== .. _list_software_libxcb_628: @@ -23578,6 +23807,7 @@ version toolchain ``5.0.1`` ``GCCcore/8.3.0`` ``5.1.0`` ``GCCcore/9.3.0`` ``5.2.0`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` +``5.2.1`` ``GCCcore/11.2.0`` ========= ===================================================================== @@ -24313,7 +24543,7 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MuJoCo_557` - :ref:`list_software_mujoco-py_931` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: @@ -24660,6 +24890,7 @@ version versionsuffix toolchain ========= ============= ============== ``2.2.1`` ``foss/2021b`` ``2.2.1`` ``-R-4.0.4`` ``foss/2020b`` +``2.2.1`` ``-R-4.1.0`` ``foss/2021a`` ========= ============= ============== @@ -25088,13 +25319,14 @@ version versionsuffix toolchain MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. -*homepage*: https://maxquant.org/maxquant/ +*homepage*: https://maxquant.org/maxquant -============= ============== -version toolchain -============= ============== -``1.6.10.43`` ``foss/2018b`` -============= ============== +============= ================== +version toolchain +============= ================== +``1.6.10.43`` ``foss/2018b`` +``2.0.3.0`` ``GCCcore/11.2.0`` +============= ================== .. _list_software_mayavi_647: @@ -25454,6 +25686,7 @@ version toolchain ============ ========== ``7.0.20-1`` ``system`` ``10.0.5`` ``system`` +``11.0.10`` ``system`` ============ ========== @@ -26003,6 +26236,7 @@ version toolchain ========= ======================================== ``0.4.0`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``0.5.0`` ``iccifort/2019.5.281`` +``0.6.1`` ``GCC/11.2.0`` ========= ======================================== @@ -26019,6 +26253,7 @@ Bisulfite sequencing data processing and differential methylation analysis. version versionsuffix toolchain ========= ================== ============== ``1.1.9`` ``-Python-2.7.13`` ``foss/2017a`` +``1.2.9`` ``foss/2021b`` ========= ================== ============== @@ -26332,6 +26567,7 @@ version toolchain ``2.18`` ``GCCcore/10.2.0`` ``2.20`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``2.22`` ``GCCcore/11.2.0`` +``2.24`` ``GCCcore/11.2.0`` ========== ====================================================== @@ -26382,7 +26618,7 @@ version versionsuffix toolchain ======= ================== =============================== ``1.4`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``1.4`` ``-Python-2.7.16`` ``intel/2019b`` -``1.6`` ``intel/2021b`` +``1.6`` ``GCCcore/11.2.0`` ======= ================== =============================== @@ -26548,13 +26784,13 @@ Python hooks for Intel(R) Math Kernel Library runtime control settings. *homepage*: https://github.com/IntelPython/mkl-service -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``2.0.2`` ``intel/2019a`` -``2.3.0`` ``intel/2020b`` -``2.3.0`` ``-Python-3.7.4`` ``intel/2019b`` -========= ================= =============== +========= ================= ================================ +version versionsuffix toolchain +========= ================= ================================ +``2.0.2`` ``intel/2019a`` +``2.3.0`` ``intel/2020b``, ``intel/2021b`` +``2.3.0`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= ================================ .. _list_software_mkl_fft_739: @@ -26862,6 +27098,7 @@ version toolchain ``5.18.1.0`` ``foss/2018a`` ``6.4.0.198`` ``foss/2018b`` ``6.8.0.105`` ``GCCcore/8.3.0`` +``6.12.0.122`` ``GCCcore/11.2.0`` ============== =============================== @@ -26975,13 +27212,13 @@ Motif refers to both a graphical user interface (GUI) specification and the widg *homepage*: https://motif.ics.com/ -========= =========================================================================================================================================================================== -version toolchain -========= =========================================================================================================================================================================== -``2.3.5`` ``foss/2016a``, ``intel/2016a`` -``2.3.7`` ``intel/2017a`` -``2.3.8`` ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` -========= =========================================================================================================================================================================== +========= =============================================================================================================================================================================================== +version toolchain +========= =============================================================================================================================================================================================== +``2.3.5`` ``foss/2016a``, ``intel/2016a`` +``2.3.7`` ``intel/2017a`` +``2.3.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` +========= =============================================================================================================================================================================================== .. _list_software_MotionCor2_972: @@ -27406,6 +27643,38 @@ version toolchain ============ ========== +.. _list_software_MuJoCo_557: + +*MuJoCo* +++++++++ + +MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose physics engine that aims to facilitate research and development in robotics, biomechanics, graphics and animation, machine learning, and other areas which demand fast and accurate simulation of articulated structures interacting with their environment. + +*homepage*: https://mujoco.org/ + +========= ================== +version toolchain +========= ================== +``2.1.1`` ``GCCcore/11.2.0`` +========= ================== + + +.. _list_software_mujoco-py_931: + +*mujoco-py* ++++++++++++ + +MuJoCo is a physics engine for detailed, efficient rigid body simulations with contacts. mujoco-py allows using MuJoCo from Python 3. + +*homepage*: https://github.com/openai/mujoco-py + +============ ============== +version toolchain +============ ============== +``2.1.2.14`` ``foss/2021b`` +============ ============== + + .. _list_software_multichoose_1196: *multichoose* @@ -27415,11 +27684,11 @@ generate multiset combinations (n multichoose k). *homepage*: https://github.com/ekg/multichoose -========= ========================================================= -version toolchain -========= ========================================================= -``1.0.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -========= ========================================================= +========= ============================================================================= +version toolchain +========= ============================================================================= +``1.0.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========= ============================================================================= .. _list_software_MultiNest_933: @@ -27585,6 +27854,7 @@ version versionsuffix toolchain ``3.8.31`` ``-i86linux64`` ``system`` ``3.8.1551`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` ``5.0.1428`` ``GCCcore/10.3.0`` +``5.1`` ``GCCcore/11.2.0`` ============ =============== ================================================================================================================================================================================================= @@ -27880,7 +28150,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numdiff_745` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_namedlist_961` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numdiff_745` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -27938,6 +28208,22 @@ version versionsuffix toolchain ======== ================ ================================================================ +.. _list_software_namedlist_961: + +*namedlist* ++++++++++++ + +A Python object, similar to namedtuple, but for lists. + +*homepage*: https://gitlab.com/ericvsmith/namedlist + +======= ================== +version toolchain +======= ================== +``1.8`` ``GCCcore/11.2.0`` +======= ================== + + .. _list_software_NanoComp_795: *NanoComp* @@ -28048,11 +28334,12 @@ A set of tools for handling and analysing data at the NanoMAX beamline. *homepage*: https://github.com/maxiv-science/nanomax-analysis-utils -======= ================= ================================== -version versionsuffix toolchain -======= ================= ================================== -``0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -======= ================= ================================== +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``0.4.3`` ``foss/2020b``, ``fosscuda/2020b`` +========= ================= ================================== .. _list_software_nanonet_755: @@ -28217,6 +28504,7 @@ version toolchain ``2.10.4`` ``gompi/2019b`` ``2.10.7`` ``gompi/2020a`` ``2.10.9`` ``gompi/2020b`` +``2.11.2`` ``gompi/2021b`` =========== ================================================ @@ -28319,6 +28607,7 @@ version toolchain ================ ======================= ``4.0-20190718`` ``iccifort/2019.5.281`` ``4.0-20200106`` ``iccifort/2019.5.281`` +``4.0-20200624`` ``GCC/11.2.0`` ================ ======================= @@ -28681,7 +28970,7 @@ version versionsuffix toolchain ``1.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``1.5.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``1.5.5.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``1.5.7`` ``foss/2021a`` +``1.5.7`` ``foss/2021a``, ``intel/2021b`` =========== ============================= =================================================== @@ -28852,7 +29141,7 @@ version versionsuffix toolchain ``2.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``2.5.1`` ``foss/2021a`` ``2.6.2`` ``foss/2020b`` -``2.6.3`` ``foss/2021a``, ``foss/2021b`` +``2.6.3`` ``foss/2021a``, ``foss/2021b``, ``intel/2021b`` ========= ================== ======================================================================== @@ -28925,6 +29214,7 @@ version toolchain ``20.10.0`` ``system`` ``21.03.0`` ``system`` ``21.08.0`` ``system`` +``21.10.6`` ``system`` =========== ========== @@ -29017,6 +29307,7 @@ version versionsuffix toolchain ``2.10.4`` ``-Java-11`` ``GCCcore/8.3.0`` ``2.10.5`` ``GCCcore/9.3.0`` ``2.10.9`` ``GCCcore/10.2.0`` +``2.11.2`` ``GCCcore/11.2.0`` ========== =================== ================================== @@ -29095,22 +29386,22 @@ NiBabel provides read/write access to some common medical and neuroimaging file *homepage*: https://nipy.github.io/nibabel -========= ================================= ================================== -version versionsuffix toolchain -========= ================================= ================================== -``2.0.2`` ``-Python-2.7.11`` ``intel/2016a`` -``2.0.2`` ``-Python-2.7.11-freetype-2.6.3`` ``intel/2016a`` -``2.1.0`` ``-Python-2.7.13`` ``intel/2017a`` -``2.2.1`` ``-Python-3.6.4`` ``intel/2018a`` -``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.3.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.3.0`` ``-Python-3.6.6`` ``foss/2018b`` -``2.4.0`` ``foss/2019a``, ``intel/2019a`` -``2.5.1`` ``-Python-3.6.6`` ``foss/2018b`` -``3.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``3.2.0`` ``-Python-3.8.2`` ``foss/2020a`` -``3.2.1`` ``foss/2020b``, ``fosscuda/2020b`` -========= ================================= ================================== +========= ================================= ================================================== +version versionsuffix toolchain +========= ================================= ================================================== +``2.0.2`` ``-Python-2.7.11`` ``intel/2016a`` +``2.0.2`` ``-Python-2.7.11-freetype-2.6.3`` ``intel/2016a`` +``2.1.0`` ``-Python-2.7.13`` ``intel/2017a`` +``2.2.1`` ``-Python-3.6.4`` ``intel/2018a`` +``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2.3.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.3.0`` ``-Python-3.6.6`` ``foss/2018b`` +``2.4.0`` ``foss/2019a``, ``intel/2019a`` +``2.5.1`` ``-Python-3.6.6`` ``foss/2018b`` +``3.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.2.0`` ``-Python-3.8.2`` ``foss/2020a`` +``3.2.1`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` +========= ================================= ================================================== .. _list_software_NIfTI_410: @@ -29801,6 +30092,7 @@ version toolchain ``1.0.0`` ``fosscuda/2018b`` ``1.1.0`` ``fosscuda/2019b`` ``1.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.2.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ====================================== @@ -29847,7 +30139,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFace_769` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSceneGraph_1394` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCensus-python_1746` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFace_769` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSceneGraph_1394` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -30184,6 +30476,22 @@ version versionsuffix toolchain ======= ================= ============== +.. _list_software_OpenCensus-python_1746: + +*OpenCensus-python* ++++++++++++++++++++ + +OpenCensus for Python. OpenCensus provides a framework to measure a server's resource usage and collect performance stats. This repository contains Python related utilities and supporting software needed by OpenCensus. + +*homepage*: https://opencensus.io/ + +========= ================== +version toolchain +========= ================== +``0.8.0`` ``GCCcore/11.2.0`` +========= ================== + + .. _list_software_OpenCoarrays_1238: *OpenCoarrays* @@ -30251,6 +30559,7 @@ version versionsuffix toolchain ``4.5.1`` ``-contrib`` ``foss/2020b``, ``fosscuda/2020b`` ``4.5.3`` ``-CUDA-11.3.1-contrib`` ``foss/2021a`` ``4.5.3`` ``-contrib`` ``foss/2021a`` +``4.5.5`` ``-contrib`` ``foss/2021b`` ========== ========================= ================================================================ @@ -30718,7 +31027,7 @@ OpenSlide is a C library that provides a simple interface to read whole-slide im ========= =============== ===================================== version versionsuffix toolchain ========= =============== ===================================== -``3.4.1`` ``GCCcore/8.2.0`` +``3.4.1`` ``GCCcore/11.2.0``, ``GCCcore/8.2.0`` ``3.4.1`` ``-largefiles`` ``GCCcore/10.3.0``, ``GCCcore/8.2.0`` ========= =============== ===================================== @@ -30732,11 +31041,12 @@ OpenSlide Python is a Python interface to the OpenSlide library. *homepage*: https://github.com/openslide/openslide-python -========= ================= -version toolchain -========= ================= -``1.1.1`` ``GCCcore/8.2.0`` -========= ================= +========= ====================================== +version toolchain +========= ====================================== +``1.1.1`` ``GCCcore/8.2.0`` +``1.1.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== .. _list_software_OpenSSL_644: @@ -30765,7 +31075,7 @@ version toolchain ``1.1.1d`` ``GCCcore/8.3.0`` ``1.1.1e`` ``GCCcore/9.3.0`` ``1.1.1h`` ``GCCcore/10.2.0`` -``1.1.1k`` ``GCCcore/10.3.0`` +``1.1.1k`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ===================================================================== @@ -31079,7 +31389,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyEVTK_515` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_pyradiomics_1188` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch-Lightning_1690` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -31096,6 +31406,7 @@ version toolchain ========== ====================================================================== ``0.23.2`` ``GCCcore/5.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` ``0.24.0`` ``GCCcore/10.3.0`` +``0.24.1`` ``GCCcore/11.2.0`` ========== ====================================================================== @@ -32081,6 +32392,7 @@ version versionsuffix toolchain ``5.32.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` ``5.32.1`` ``-minimal`` ``GCCcore/10.3.0`` ``5.34.0`` ``GCCcore/11.2.0`` +``5.34.0`` ``-minimal`` ``GCCcore/11.2.0`` ========== ============= ========================================================================================= @@ -32183,13 +32495,14 @@ version versionsuffix toolchain *pftoolsV3* +++++++++++ -The pftools package contains all the software necessary to build protein and DNA generalized profiles and use them to scan and align sequences, and search databases. +A suite of tools to build and search generalized profiles (protein and DNA). -*homepage*: http://web.expasy.org/pftools/ +*homepage*: https://github.com/sib-swiss/pftools3 ============ ============== version toolchain ============ ============== +``3.2.11`` ``foss/2021a`` ``20160324`` ``foss/2016a`` ============ ============== @@ -32604,6 +32917,7 @@ version versionsuffix toolchain ``2.25.0`` ``-Java-11`` ``system`` ``2.25.1`` ``-Java-11`` ``system`` ``2.25.5`` ``-Java-13`` ``system`` +``2.26.10`` ``-Java-15`` ``system`` =========== =================== ========== @@ -32768,12 +33082,12 @@ Pindel can detect breakpoints of large deletions, medium sized insertions, inve *homepage*: http://gmt.genome.wustl.edu/packages/pindel/ -==================== ================== -version toolchain -==================== ================== -``0.2.5b8`` ``foss/2016b`` -``0.2.5b9-20170508`` ``GCC/6.4.0-2.28`` -==================== ================== +==================== ================================== +version toolchain +==================== ================================== +``0.2.5b8`` ``foss/2016b`` +``0.2.5b9-20170508`` ``GCC/11.2.0``, ``GCC/6.4.0-2.28`` +==================== ================================== .. _list_software_Pingouin_841: @@ -33739,11 +34053,11 @@ PRANK is a probabilistic multiple alignment program for DNA, codon and amino-a *homepage*: http://wasabiapp.org/software/prank/ -========== ============================================================== -version toolchain -========== ============================================================== -``170427`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0``, ``intel/2018a`` -========== ============================================================== +========== ============================================================================== +version toolchain +========== ============================================================================== +``170427`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0``, ``intel/2018a`` +========== ============================================================================== .. _list_software_PRC_229: @@ -33809,7 +34123,7 @@ version toolchain ========= =============================== ``2.0.2`` ``foss/2016b`` ``2.0.3`` ``foss/2018b``, ``intel/2018a`` -``3.1.2`` ``GCC/10.3.0`` +``3.1.2`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========= =============================== @@ -34969,6 +35283,7 @@ version versionsuffix toolchain ``1.4.2`` ``GCCcore/8.3.0`` ``2.1.2`` ``GCCcore/10.2.0`` ``2.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``2.2.2`` ``GCCcore/10.3.0`` ========= ================== ================== @@ -35040,6 +35355,23 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_PyEVTK_515: + +*PyEVTK* +++++++++ + +EVTK (Export VTK) package allows exporting data to binary VTK files for visualization and data analysis with any of the visualization packages that support VTK files + +*homepage*: https://github.com/paulo-herrera/PyEVTK + +========= ============== +version toolchain +========= ============== +``1.4.1`` ``foss/2021b`` +``2.0.0`` ``foss/2021b`` +========= ============== + + .. _list_software_pyFAI_441: *pyFAI* @@ -35053,6 +35385,7 @@ Python implementation of fast azimuthal integration. version versionsuffix toolchain ========== ================= ================================== ``0.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``0.20.0`` ``foss/2020b``, ``fosscuda/2020b`` ========== ================= ================================== @@ -35535,12 +35868,12 @@ Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machin *homepage*: https://docs.pymc.io/ -========== ================= =================================== -version versionsuffix toolchain -========== ================= =================================== -``3.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``3.11.1`` ``fosscuda/2020b``, ``intel/2020b`` -========== ================= =================================== +========== ================= ==================================================== +version versionsuffix toolchain +========== ================= ==================================================== +``3.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.11.1`` ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021b`` +========== ================= ==================================================== .. _list_software_pymca_538: @@ -35555,7 +35888,7 @@ The PyMca X-Ray Fluorescence Toolkit, including PyMca5 and fisx. ========= ================= ================================== version versionsuffix toolchain ========= ================= ================================== -``5.6.3`` ``foss/2020b`` +``5.6.3`` ``foss/2020b``, ``fosscuda/2020b`` ``5.6.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========= ================= ================================== @@ -35852,6 +36185,22 @@ version versionsuffix toolchain ========== ================= ================================== +.. _list_software_pyradiomics_1188: + +*pyradiomics* ++++++++++++++ + +Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks. + +*homepage*: https://pyradiomics.readthedocs.io/ + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``3.0.1`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============== + + .. _list_software_PyRe_384: *PyRe* @@ -35998,6 +36347,7 @@ version versionsuffix toolchain ``0.16.0.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` ``0.16.0.1`` ``-Python-2.7.18`` ``GCC/10.2.0`` ``0.17.0`` ``GCC/11.2.0`` +``0.18.0`` ``GCC/11.2.0`` ============ ================== ============================================================================================================== @@ -36322,6 +36672,7 @@ version toolchain ========= ====================================== ``2.1.0`` ``GCCcore/10.2.0`` ``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.5.0`` ``GCCcore/11.2.0`` ========= ====================================== @@ -36452,12 +36803,12 @@ Faster zlib and gzip compatible compression and decompression by providing pyth *homepage*: https://github.com/pycompression/python-isal -========== ================== -version toolchain -========== ================== -``0.11.0`` ``GCCcore/10.3.0`` -``0.11.1`` ``GCCcore/10.2.0`` -========== ================== +========== ====================================== +version toolchain +========== ====================================== +``0.11.0`` ``GCCcore/10.3.0`` +``0.11.1`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` +========== ====================================== .. _list_software_python-Levenshtein_1876: @@ -36588,6 +36939,23 @@ version versionsuffix toolchain ========= =============================== ================================== +.. _list_software_PyTorch-Lightning_1690: + +*PyTorch-Lightning* ++++++++++++++++++++ + +PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers. + +*homepage*: https://pytorchlightning.ai + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``1.5.9`` ``foss/2021a`` +``1.5.9`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== + + .. _list_software_PyTorch3D_832: *PyTorch3D* @@ -37188,6 +37556,7 @@ version versionsuffix toolchain ========= ============= ============== ``2.2.1`` ``-R-3.6.0`` ``foss/2019a`` ``2.2.1`` ``-R-4.0.3`` ``foss/2020b`` +``2.2.1`` ``-R-4.1.2`` ``foss/2021b`` ========= ============= ============== @@ -37385,7 +37754,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_RaGOO_408` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_RAPSearch2_875` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_RaGOO_408` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_RAPSearch2_875` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redis_503` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rising_652` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -37528,9 +37897,9 @@ version versionsuffix toolchain *Racon* +++++++ -Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads +Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. -*homepage*: https://github.com/clara-genomics/racon-gpu +*homepage*: https://github.com/lbcb-sci/racon ========== ====================================== version toolchain @@ -37540,6 +37909,7 @@ version toolchain ``1.4.10`` ``GCC/7.3.0-2.30`` ``1.4.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.4.21`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.5.0`` ``GCCcore/11.2.0`` ========== ====================================== @@ -37796,18 +38166,18 @@ RAxML search algorithm for maximum likelihood based inference of phylogenetic tr *homepage*: https://github.com/stamatak/standard-RAxML -========== ================== ==================================================================================================== -version versionsuffix toolchain -========== ================== ==================================================================================================== -``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` -``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` -``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` -``8.2.12`` ``-hybrid-avx2`` ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2019b``, ``intel/2018b``, ``intel/2019a`` -``8.2.12`` ``-pthreads-avx2`` ``GCC/10.2.0`` -========== ================== ==================================================================================================== +========== ================== ===================================================================================================================== +version versionsuffix toolchain +========== ================== ===================================================================================================================== +``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` +``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` +``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` +``8.2.12`` ``-hybrid-avx2`` ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2019b``, ``intel/2018b``, ``intel/2019a`` +``8.2.12`` ``-pthreads-avx2`` ``GCC/10.2.0`` +========== ================== ===================================================================================================================== .. _list_software_RAxML-NG_614: @@ -38122,6 +38492,22 @@ version toolchain ============== ======================================== +.. _list_software_Redis_503: + +*Redis* ++++++++ + +Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache, and message broker. Redis provides data structures such as strings, hashes, lists, sets, sorted sets with range queries, bitmaps, hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, Lua scripting, LRU eviction, transactions, and different levels of on-disk persistence, and provides high availability via Redis Sentinel and automatic partitioning with Redis Cluster. + +*homepage*: https://redis.io + +========= ============================== +version toolchain +========= ============================== +``6.2.6`` ``GCC/10.3.0``, ``GCC/11.2.0`` +========= ============================== + + .. _list_software_Redundans_932: *Redundans* @@ -38147,27 +38533,28 @@ ReFrame is a framework for writing regression tests for HPC systems. *homepage*: https://github.com/eth-cscs/reframe -========= ========== -version toolchain -========= ========== -``2.18`` ``system`` -``2.19`` ``system`` -``2.20`` ``system`` -``2.21`` ``system`` -``3.0`` ``system`` -``3.2`` ``system`` -``3.3`` ``system`` -``3.4.1`` ``system`` -``3.5.0`` ``system`` -``3.5.1`` ``system`` -``3.5.2`` ``system`` -``3.6.2`` ``system`` -``3.6.3`` ``system`` -``3.7.3`` ``system`` -``3.8.0`` ``system`` -``3.9.0`` ``system`` -``3.9.1`` ``system`` -========= ========== +========== ========== +version toolchain +========== ========== +``2.18`` ``system`` +``2.19`` ``system`` +``2.20`` ``system`` +``2.21`` ``system`` +``3.0`` ``system`` +``3.2`` ``system`` +``3.3`` ``system`` +``3.4.1`` ``system`` +``3.5.0`` ``system`` +``3.5.1`` ``system`` +``3.5.2`` ``system`` +``3.6.2`` ``system`` +``3.6.3`` ``system`` +``3.7.3`` ``system`` +``3.8.0`` ``system`` +``3.9.0`` ``system`` +``3.9.1`` ``system`` +``3.10.1`` ``system`` +========== ========== .. _list_software_RegTools_815: @@ -38551,6 +38938,23 @@ version versionsuffix toolchain ========== ================= =============== +.. _list_software_rising_652: + +*rising* +++++++++ + +Provides everything needed for high performance data loading and augmentation in PyTorch. + +*homepage*: https://rising.rtfd.io/ + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``0.2.2`` ``foss/2021a`` +``0.2.2`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== + + .. _list_software_rjags_535: *rjags* @@ -38956,6 +39360,7 @@ version versionsuffix toolchain ``6.14.06`` ``-Python-2.7.15`` ``foss/2018b`` ``6.14.06`` ``-Python-3.6.6`` ``foss/2018b`` ``6.20.04`` ``-Python-3.7.4`` ``foss/2019b`` +``6.24.06`` ``foss/2021b`` ``v5.34.34`` ``-Python-2.7.11`` ``intel/2016a`` ``v5.34.36`` ``-Python-2.7.11`` ``intel/2016a`` ``v6.06.02`` ``-Python-2.7.12`` ``intel/2016b`` @@ -39268,7 +39673,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_SCopeLoomR_963` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_ShengBTE_720` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_SHTns_464` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_STRUMPACK_698` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_SCopeLoomR_963` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_ShengBTE_720` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_SHTns_464` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SoXt_398` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_STRUMPACK_698` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SURVIVOR_656` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -39605,11 +40010,11 @@ ScaFaCoS is a library of scalable fast coulomb solvers. *homepage*: http://www.scafacos.de/ -========= =============================================================== -version toolchain -========= =============================================================== -``1.0.1`` ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``intel/2020a`` -========= =============================================================== +========= =============================================================================== +version toolchain +========= =============================================================================== +``1.0.1`` ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``intel/2020a`` +========= =============================================================================== .. _list_software_ScaLAPACK_707: @@ -39874,6 +40279,7 @@ version versionsuffix toolchain ``0.17.1`` ``-Python-3.8.2`` ``foss/2020a`` ``0.18.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``0.18.3`` ``foss/2021a`` +``0.19.1`` ``foss/2021b`` ========== ================== =================================================== @@ -40290,6 +40696,7 @@ version toolchain ``2.0.9`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.0.10`` ``GCCcore/8.3.0`` ``2.0.14`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.0.20`` ``GCCcore/11.2.0`` ========== ====================================================================== @@ -40620,6 +41027,7 @@ version toolchain ========== ========== ``0.8.1`` ``system`` ``0.13.2`` ``system`` +``2.1.0`` ``system`` ========== ========== @@ -40681,12 +41089,12 @@ Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FA *homepage*: https://github.com/lh3/seqtk/ -======= ================================================================================================================== -version toolchain -======= ================================================================================================================== -``1.2`` ``foss/2016b``, ``intel/2017a`` -``1.3`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` -======= ================================================================================================================== +======= ================================================================================================================================== +version toolchain +======= ================================================================================================================================== +``1.2`` ``foss/2016b``, ``intel/2017a`` +``1.3`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` +======= ================================================================================================================================== .. _list_software_Serf_400: @@ -41110,6 +41518,7 @@ version versionsuffix toolchain ``4.1-b4`` ``foss/2018b``, ``intel/2018b`` ``4.1-MaX-1.0`` ``intel/2019b`` ``4.1-MaX-1.0`` ``-PEXSI`` ``intel/2019b`` +``4.1.5`` ``foss/2020a`` =============== ============= =============================== @@ -41142,7 +41551,7 @@ The silx project provides a collection of Python packages to support the develo version versionsuffix toolchain ========== ================= ================================== ``0.13.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``0.14.0`` ``foss/2020b`` +``0.14.0`` ``foss/2020b``, ``fosscuda/2020b`` ========== ================= ================================== @@ -41231,6 +41640,7 @@ version versionsuffix toolchain ``1.1.0`` ``-Python-3.6.6`` ``foss/2018b`` ``1.2.4`` ``-Python-3.7.4`` ``foss/2019b`` ``2.1.0`` ``foss/2020b`` +``2.1.1`` ``foss/2021a`` ========= ================== ============== @@ -41588,11 +41998,11 @@ smith-waterman-gotoh alignment algorithm. *homepage*: https://github.com/ekg/smithwaterman -============ ========================================================= -version toolchain -============ ========================================================= -``20160702`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -============ ========================================================= +============ ============================================================================= +version toolchain +============ ============================================================================= +``20160702`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +============ ============================================================================= .. _list_software_Smoldyn_742: @@ -41976,15 +42386,15 @@ version toolchain *SoQt* ++++++ -SoQt is a Qt GUI component toolkit library for Coin. It is also compatible with SGI and TGS Open Inventor, and the API is based on the API of the InventorXt GUI component toolkit. +SoQt is a library which provides the glue between Systems in Motion's Coin high-level 3D visualization library and the Qt 2D user interface library. -*homepage*: https://coin3d.github.io/SoQt/html +*homepage*: https://coin3d.github.io/SoQt/html/ -========= ============== -version toolchain -========= ============== -``1.6.0`` ``GCC/10.3.0`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``1.6.0`` ``GCC/10.3.0``, ``GCC/11.2.0`` +========= ============================== .. _list_software_SortMeRNA_827: @@ -42019,6 +42429,22 @@ version toolchain ========== ============= +.. _list_software_SoXt_398: + +*SoXt* +++++++ + +SoXt is an Xt/Motif glue library for Coin. It can also be used on top of the SGI or TGS implementation of Open Inventor, and is designed to be source code compatible with SGI's InventorXt library. + +*homepage*: https://coin3d.github.io/SoXt/html/ + +========= ============== +version toolchain +========= ============== +``1.4.0`` ``GCC/11.2.0`` +========= ============== + + .. _list_software_SpaceRanger_1099: *SpaceRanger* @@ -42519,6 +42945,7 @@ version versionsuffix toolchain ========= ================== ============== ``0.4.3`` ``-Python-2.7.15`` ``foss/2018b`` ``1.0.0`` ``-Python-2.7.15`` ``foss/2018b`` +``1.5.0`` ``foss/2021b`` ========= ================== ============== @@ -43293,6 +43720,22 @@ version toolchain ========= ========== +.. _list_software_SURVIVOR_656: + +*SURVIVOR* +++++++++++ + +Toolset for SV simulation, comparison and filtering + +*homepage*: https://github.com/fritzsedlazeck/SURVIVOR + +===================== ============== +version toolchain +===================== ============== +``1.0.7-19-ged1ca51`` ``GCC/11.2.0`` +===================== ============== + + .. _list_software_SVDetect_770: *SVDetect* @@ -43570,7 +44013,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TALYS_397` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_termcolor_983` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_ThemisPy_819` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmux_462` - :ref:`list_software_TN93_270` - :ref:`list_software_TOBIAS_450` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` +:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TALYS_397` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboard_1187` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_termcolor_983` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_ThemisPy_819` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmux_462` - :ref:`list_software_TN93_270` - :ref:`list_software_TOBIAS_450` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` .. _list_software_tabix_536: @@ -43582,11 +44025,11 @@ Generic indexer for TAB-delimited genome position files *homepage*: http://samtools.sourceforge.net -========= ================================================================================================================================================ -version toolchain -========= ================================================================================================================================================ -``0.2.6`` ``GCCcore/10.2.0``, ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``intel/2016a``, ``intel/2016b`` -========= ================================================================================================================================================ +========= ==================================================================================================================================================================== +version toolchain +========= ==================================================================================================================================================================== +``0.2.6`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``intel/2016a``, ``intel/2016b`` +========= ==================================================================================================================================================================== .. _list_software_tabixpp_760: @@ -43598,11 +44041,11 @@ C++ wrapper to tabix indexer *homepage*: https://github.com/ekg/tabixpp -========= ============================================= -version toolchain -========= ============================================= -``1.1.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` -========= ============================================= +========= ============================================================= +version toolchain +========= ============================================================= +``1.1.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` +========= ============================================================= .. _list_software_taco_423: @@ -43914,6 +44357,22 @@ version versionsuffix toolchain ========= ================= ============== +.. _list_software_tensorboard_1187: + +*tensorboard* ++++++++++++++ + +TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs. + +*homepage*: https://github.com/tensorflow/tensorboard + +========= ============== +version toolchain +========= ============== +``2.8.0`` ``foss/2021a`` +========= ============== + + .. _list_software_tensorboardX_1275: *tensorboardX* @@ -44227,29 +44686,29 @@ Theano is a Python library that allows you to define, optimize, and evaluate mat *homepage*: https://deeplearning.net/software/theano -========= ================== =================================================== -version versionsuffix toolchain -========= ================== =================================================== -``0.8.2`` ``-Python-2.7.11`` ``foss/2016a`` -``0.8.2`` ``-Python-3.5.1`` ``foss/2016a`` -``0.8.2`` ``-Python-3.5.2`` ``intel/2016b`` -``0.9.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.9.0`` ``-Python-3.6.1`` ``intel/2017a`` -``1.0.0`` ``-Python-2.7.14`` ``intel/2017b`` -``1.0.0`` ``-Python-3.6.3`` ``intel/2017b`` -``1.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.0.2`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` -``1.0.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``1.0.2`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intelcuda/2017b`` -``1.0.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``1.0.4`` ``foss/2019a``, ``fosscuda/2019a`` -``1.0.4`` ``-Python-3.6.4`` ``foss/2018a`` -``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` -``1.0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``1.0.4`` ``-Python-3.8.2`` ``foss/2020a`` -``1.1.2`` ``-PyMC`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -========= ================== =================================================== +========= ================== ==================================================================== +version versionsuffix toolchain +========= ================== ==================================================================== +``0.8.2`` ``-Python-2.7.11`` ``foss/2016a`` +``0.8.2`` ``-Python-3.5.1`` ``foss/2016a`` +``0.8.2`` ``-Python-3.5.2`` ``intel/2016b`` +``0.9.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.9.0`` ``-Python-3.6.1`` ``intel/2017a`` +``1.0.0`` ``-Python-2.7.14`` ``intel/2017b`` +``1.0.0`` ``-Python-3.6.3`` ``intel/2017b`` +``1.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``1.0.2`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``1.0.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``1.0.2`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``1.0.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``1.0.4`` ``foss/2019a``, ``fosscuda/2019a`` +``1.0.4`` ``-Python-3.6.4`` ``foss/2018a`` +``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` +``1.0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``1.0.4`` ``-Python-3.8.2`` ``foss/2020a`` +``1.1.2`` ``-PyMC`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021b`` +========= ================== ==================================================================== .. _list_software_ThemisPy_819: @@ -44520,6 +44979,7 @@ Package containing functions to: perform a negative binomial test on allele version versionsuffix toolchain ========= ============= ============== ``1.0.0`` ``-R-4.0.3`` ``foss/2020b`` +``1.0.1`` ``-R-4.1.2`` ``foss/2021b`` ========= ============= ============== @@ -44743,6 +45203,7 @@ version versionsuffix toolchain ``0.10.0`` ``-PyTorch-1.9.0`` ``fosscuda/2020b`` ``0.11.1`` ``foss/2021a`` ``0.11.1`` ``-CUDA-11.3.1`` ``foss/2021a`` +``0.11.3`` ``foss/2021a`` ========== ==================================== ================================== @@ -45009,7 +45470,7 @@ version versionsuffix toolchain *Trim_Galore* +++++++++++++ -Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. +Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). *homepage*: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ @@ -45030,6 +45491,7 @@ version versionsuffix toolchain ``0.6.5`` ``-Java-11-Python-3.7.4`` ``GCCcore/8.3.0`` ``0.6.6`` ``-Python-2.7.18`` ``GCC/10.2.0`` ``0.6.6`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``0.6.7`` ``GCCcore/10.3.0`` ========= ========================= =============================== @@ -45362,6 +45824,7 @@ version versionsuffix toolchain ``3.7.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``3.7.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``3.10.0.0`` ``GCCcore/10.3.0`` +``3.10.0.2`` ``GCCcore/11.2.0`` ============ ================= ================== @@ -45883,6 +46346,7 @@ version toolchain ``3.14.0`` ``foss/2018b`` ``3.16.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020a`` ``3.17.0`` ``gompi/2021a`` +``3.18.1`` ``gompi/2021b``, ``iimpi/2021b`` ========== ================================================================================= @@ -46095,6 +46559,7 @@ version versionsuffix toolchain ========= ================= ============================== ``1.0.2`` ``GCC/10.2.0``, ``GCC/10.3.0`` ``1.0.2`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``1.0.3`` ``GCC/11.2.0`` ========= ================= ============================== @@ -46592,6 +47057,7 @@ version versionsuffix toolchain ``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` ``8.1.1`` ``-Python-2.7.15`` ``foss/2018b`` ``8.1.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``8.2.0`` ``foss/2021a`` ``8.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ``8.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``8.2.0`` ``-Python-3.7.4`` ``foss/2019b`` @@ -46849,6 +47315,7 @@ version toolchain ``1.20.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ``1.20.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``1.21.1`` ``GCCcore/10.3.0`` +``1.21.2`` ``GCCcore/11.2.0`` ========== ===================================== @@ -47194,15 +47661,15 @@ wxWidgets is a C++ library that lets developers create applications for Windows, *homepage*: https://www.wxwidgets.org -========= ==================== -version toolchain -========= ==================== -``3.0.3`` ``foss/2018a`` -``3.0.4`` ``GCC/8.2.0-2.31.1`` -``3.1.3`` ``GCC/8.3.0`` -``3.1.4`` ``GCC/10.2.0`` -``3.1.5`` ``GCC/10.3.0`` -========= ==================== +========= ============================== +version toolchain +========= ============================== +``3.0.3`` ``foss/2018a`` +``3.0.4`` ``GCC/8.2.0-2.31.1`` +``3.1.3`` ``GCC/8.3.0`` +``3.1.4`` ``GCC/10.2.0`` +``3.1.5`` ``GCC/10.3.0``, ``GCC/11.2.0`` +========= ============================== .. _list_software_letter_x: @@ -47211,7 +47678,7 @@ version toolchain --- -:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_xxHash_628` - :ref:`list_software_XZ_178` +:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtensor_787` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_xxd_340` - :ref:`list_software_xxHash_628` - :ref:`list_software_XZ_178` .. _list_software_X11_186: @@ -47736,12 +48203,12 @@ xmlf90 is a basic XML parsing library written in Fortran. *homepage*: https://launchpad.net/xmlf90 -========= ================================================================ -version toolchain -========= ================================================================ -``1.5.3`` ``foss/2016b``, ``foss/2017a`` -``1.5.4`` ``GCC/10.2.0``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304`` -========= ================================================================ +========= ============================================================================================================================================================ +version toolchain +========= ============================================================================================================================================================ +``1.5.3`` ``foss/2016b``, ``foss/2017a`` +``1.5.4`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` +========= ============================================================================================================================================================ .. _list_software_XMLSec_524: @@ -47899,6 +48366,22 @@ version versionsuffix toolchain ================ ================= =============== +.. _list_software_xtensor_787: + +*xtensor* ++++++++++ + +xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions. + +*homepage*: https://github.com/xtensor-stack/xtensor + +========== ============== +version toolchain +========== ============== +``0.24.0`` ``foss/2021b`` +========== ============== + + .. _list_software_xtrans_672: *xtrans* @@ -47934,6 +48417,22 @@ version toolchain =========== ===================================== +.. _list_software_xxd_340: + +*xxd* ++++++ + +xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files. + +*homepage*: https://www.vim.org + +============ ========================================================== +version toolchain +============ ========================================================== +``8.2.4220`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +============ ========================================================== + + .. _list_software_xxHash_628: *xxHash* @@ -48142,6 +48641,7 @@ version toolchain ``0.6.2`` ``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` ``0.9.0`` ``gompi/2020b`` ``0.9.1`` ``gompi/2021a`` +``0.9.2`` ``iimpi/2021b`` ========= ================================================= diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index f4170b2b..ea13f8d3 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -300,6 +300,7 @@ * EB_Bioconductor * EB_pbdMPI * EB_pbdSLAP + * EB_reticulate * EB_Rmpi * EB_Rserve * EB_XML @@ -441,6 +442,7 @@ * EB_Bioconductor * EB_pbdMPI * EB_pbdSLAP + * EB_reticulate * EB_Rmpi * EB_Rserve * EB_XML From 35a549fcdd5f3e6ee98c58d5730ace162593483b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 11 Feb 2022 17:00:22 +0800 Subject: [PATCH 201/286] update release notes and changelog for EasyBuild v4.5.3 + bump version to 4.5.3 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 105 +++++++++++++++++++++++++++++++++++++++-- docs/conf.py | 4 +- 3 files changed, 105 insertions(+), 5 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index bf546db3..d2f71ebf 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20220211.01** (`Feb 11th 2022`): update release notes for EasyBuild v4.5.3 (see :ref:`release_notes_eb453`) * **release 20220124.01** (`Jan 24th 2022`): update release notes for EasyBuild v4.5.2 (see :ref:`release_notes_eb452`) * **release 20211213.01** (`Dec 13th 2021`): update release notes for EasyBuild v4.5.1 (see :ref:`release_notes_eb451`) * **release 20211029.01** (`Oct 29th 2021`): update release notes for EasyBuild v4.5.0 (see :ref:`release_notes_eb450`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index fbe269d5..3bc5ad01 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,111 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,622** different software packages, -including 36 different (compiler) toolchains. It contains 243 software-specific easyblocks and 37 generic easyblocks, -alongside 14,080 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,647** different software packages, +including 36 different (compiler) toolchains. It contains 244 software-specific easyblocks and 37 generic easyblocks, +alongside 14,282 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb453: + +EasyBuild v4.5.3 (February 11th 2022) +------------------------------------- + +bugfix/update release + +**framework** + +* various enhancements, including: + + * also check for git in ``--check-eb-deps`` (`#3954 `_) + * add end2end test for ``eb --containerize`` (`#3958 `_) + +* various bug fixes, including: + + * take into account that patch files can also be zipped when checking filename extension for patches (`#3936 `_) + * initialize ``BACKUP_PKG_URL`` with empty string in ``install_eb_dep.sh`` script (`#3939 `_) + * fix ``get_os_name`` and ``get_os_version`` to avoid reporting ``UNKNOWN`` in output of ``eb --show-system-info`` (`#3942 `_) + * consistently use ``actions/setup-python@v2`` in CI workflows (`#3944 `_) + * switch to using ``pip3`` for installing EasyBuild in container recipes generated by EasyBuild (`#3945 `_) + * specify ``easybuild.io`` as EasyBuild homepage in ``setup.py`` (`#3947 `_) + * avoid crash in ``get_os_version`` on modern SLES-based OSs (`#3955 `_) + +* other changes: + + * indicate compatibility with Python 3.10 in ``setup.py`` (`#3940 `_) + +**easyblocks** + +* new software-specific easyblock for reticulate R package (`#2668 `_) + +* minor enhancements and updates, including: + + * set CUDA target architecture(s) for GROMACS based on ``cuda_cc_semicolon_sep`` template value (`#2655 `_) + * add support to NAMD easyblock to opt out of building with CUDA support even if CUDA is included as dependency (`#2666 `_) + * update sanity check in CUDA easyblock: CUDA 11.6 no longer includes samples (`#2669 `_) + +* various bug fixes, including: + + * also run easyblocks test suite with Python 3.8-3.10 + consistently use ``actions/setup-python@v2`` in CI workflows (`#2664 `_) + * specify ``easybuild.io`` as EasyBuild homepage in ``setup.py`` (`#2667 `_) + +* other changes: + + * remove vulnerable binaries from sanity check of HDF5, no longer installed by default with HDF5 1.10.8 (`#2670 `_) + +**easyconfigs** + +* added example easyconfig files for 25 new software packages: + + * Arcade-Learning-Environment (`#14753 `_), Bambi (`#14811 `_), CASTEP (`#14420 `_), Crumble (`#14785 `_), deepmedic (`#14953 `_), + FoBiS (`#14771 `_), histolab (`#14945 `_), Iris (`#14788 `_), Jasmine (`#14789 `_), libexif (`#14823 `_), libgdiplus (`#14823 `_), + MuJoCo (`#14965 `_), mujoco-py (`#14776 `_, `#14965 `_), namedlist (`#14814 `_), OpenCensus-python (`#14837 `_), PyEVTK (`#14911 `_), + pyradiomics (`#14851 `_), PyTorch-Lightning (`#14933 `_), Redis (`#14783 `_), rising (`#14952 `_), SoXt (`#14803 `_), + SURVIVOR (`#14786 `_), tensorboard (`#14926 `_), xtensor (`#14944 `_), xxd (`#14846 `_) + +* added additional easyconfigs for various supported software packages, including: + + * aiohttp 3.8.1, AOCC 3.2.0, ArviZ 0.11.4, BeautifulSoup 4.10.0, bokeh 2.4.2, Boost.Python 1.77.0, + Bowtie 1.3.1, CheMPS2 1.8.11, Clang 13.0.1, CLHEP 2.4.5.1, ConnectomeWorkbench 1.5.0, Crumble 0.8.3, + CUDA 11.5.1 + 11.6.0, cutadapt 3.5, dask 2022.1.0, deepdiff 5.7.0, deepTools 3.5.0, dm-tree 0.1.6, + DROP 1.1.1, ecCodes 2.24.2, Emacs 27.2, FDS 6.7.7, file 5.41, Flask 2.0.2, FORD 6.1.6, GATE 9.1, + Geant4 11.0.0, GEMMA 0.98.5, GnuTLS 3.7.3, Go 1.17.6, gpustat 1.0.0b1, Graphviz 2.50.0, GROMACS 2021.5, + Guile 3.0.7, HDF5 1.10.8, imageio 2.13.5, JupyterLab 3.2.8, lftp 4.9.2, libBigWig 0.4.6, libpsml 1.1.10, + libRmath 4.1.2, librsb 1.3.0.0, libtasn1 4.18.0, libunistring 1.0, likwid 5.2.1, MaxQuant 2.0.3.0, + MEGA 11.0.10.eb, MethylDackel 0.6.1, methylpy 1.2.9, minimap2 2.24, Mono 6.12.0.122, MUSCLE 5.1, + nanomax-analysis-utils 0.4.3, ncbi-vdb 2.11.2, NCIPLOT-4.0 20200624, Nextflow 21.10.6, NGS 2.11.2, + nvtop 1.2.2, OpenCV 4.5.5, openslide-python 1.1.2, pftoolsV3 3.2.11, picard 2.26.10, pydicom 2.2.2, + pyFAI 0.20.0, Pysam 0.18.0, pytest-xdist 2.5.0, Racon 1.5.0, RAxML 8.2.12, ReFrame 3.10.1, ROOT 6.24.06, + scikit-image 0.19.1, SDL2 2.0.20, SeqKit 2.1.0, Siesta 4.1.5, SimpleITK 2.1.1, SqueezeMeta 1.5.0, + tMAE 1.0.1, torchvision 0.11.3, Trim_Galore 0.6.7, typing-extensions 3.10.0.2 + +* minor enhancements, including: + + * also install Python bindings for SHTns 3.5.1 (`#14893 `_) + * add catlearn extension to easyconfig for R v4.1.2 (`#14940 `_) + +* various bug fixes, including: + + * update TALYS sources to (hopefully) ensure constant checksums (`#14797 `_) + * add missing graphite2 + HarfBuzz dependencies to Qt5 v5.15.2 (`#14802 `_) + * add missing UCX-CUDA dep to GROMACS for foss-2021a-CUDA-11.3.1 (`#14859 `_) + * specify ``easybuild.io`` as EasyBuild homepage in ``setup.py`` (`#14870 `_) + * add alternative checksum for MASS, class, nnet, spatial extensions in R 4.1.0 (`#14873 `_) and R 4.1.2 (`#14880 `_) easyconfigs + * add patch to fix Kraken2 ncbi ``ftp``/``https`` check in ``rsync_from_ncbi.pl`` for versions 2.0.9-2.1.1 (`#14889 `_) + * disable building of tests/benchmarks for snappy 1.1.8 to avoid failing build (`#14923 `_) + * disable use of ``-Werror`` for recent NSS versions (`#14924 `_) + * fix download URL in UDUNITS v2.2.28 easyconfigs (`#14954 `_) + * remove unnecessary CUDAcore dependency from nvtop v1.2.1 easyconfig (`#14957 `_) + * consistently apply patch for mapDamage 2.2.1 to use external seqtk (`#14961 `_) + * fix typo in templated source URL in RcppGSL 0.3.8 easyconfig: ``$(name)s`` should be ``%(name)s`` (`#14962 `_) + +* other changes: + + * update Java/17 wrapper to Java 17.0.2 (`#14868 `_) + * use ``actions/setup-python@v2`` in CI workflows + trim test configurations for easyconfigs test suite: only test with Python 2.7 + 3.6 and Lmod 7.x + 8.x (`#14857 `_, `#14881 `_) + + .. _release_notes_eb452: EasyBuild v4.5.2 (January 24th 2022) diff --git a/docs/conf.py b/docs/conf.py index a7cbc823..57b39b3b 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.5.2' # this is meant to reference the version of EasyBuild +version = '4.5.3' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20220124.0' # this is meant to reference the version of the documentation itself +release = '20220211.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 9dab837c43ebd1602d57e91312607bd33dee7232 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Feb 2022 10:00:38 +0100 Subject: [PATCH 202/286] indicate compatibility with Python 3.10 in setup.py --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index 19f94dd7..e39e3abf 100644 --- a/setup.py +++ b/setup.py @@ -75,6 +75,7 @@ def read(fname): "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", "Topic :: Scientific/Engineering", "Topic :: Software Development :: Build Tools", ], From 4a061cc8bcb7de4e311357e617f85b794add877a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 11 Feb 2022 18:39:13 +0800 Subject: [PATCH 203/286] bump version to 4.5.3 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index e39e3abf..77d2bc13 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.5.2' +VERSION = '4.5.3' # Utility function to read README file From 969de42bdb54f6acb21a43957b30ff097dadf6f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Mar 2022 20:04:25 +0100 Subject: [PATCH 204/286] document 'clone_into' field in git_config that can be used in 'sources' easyconfig parameter --- docs/Writing_easyconfig_files.rst | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index 1569a350..02ea6c32 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -456,10 +456,13 @@ If a recursive checkout should be made of the repository, the ``recursive`` key To also retain the ``.git`` directory (which holds the Git metadata for the repository), you can set the ``keep_git_dir`` to ``True`` (supported since EasyBuild v4.2.0). +A different name for the top-level directory can be specified via ``clone_into``; +by default the name of the repository is used. + Examples: * creating a source tarball named ``example-main.tar.gz`` of the ``main`` branch of a (fictional) - ``test`` repository from ``https://agitserver.org/example``: + ``test`` repository from ``https://agitserver.org/example``, and use ``example-test`` as top-level directory name: .. code:: @@ -469,6 +472,7 @@ Examples: 'url': 'https://agitserver.org/example', 'repo_name': 'test', 'tag': 'main', + 'clone_into': 'example-test', }, }] From f2b475c5e4544e66583c3d8af1be6f177349a2b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Mar 2022 22:57:51 +0200 Subject: [PATCH 205/286] auto-update docs for EasyBuild v4.5.4 --- docs/version-specific/Supported_software.rst | 1383 ++++++++++++----- docs/version-specific/easyblocks.rst | 39 +- .../easyconfig_parameters.rst | 2 + docs/version-specific/generic_easyblocks.rst | 4 +- docs/version-specific/toolchain_opts.rst | 48 +- docs/version-specific/toolchains.rst | 179 +-- 6 files changed, 1134 insertions(+), 521 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 0f2cf7ab..e21ff695 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2647 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2676 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_alevin-fry_1021` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMD-uProf_779` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_ANGEL_359` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_Arcade-Learning-Environment_2655` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_atropos_776` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Austin_628` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock-GPU_1075` - :ref:`list_software_AutoDock-Vina_1237` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_Abseil_592` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_alevin-fry_1021` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMD-uProf_779` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_AMS_225` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_ANGEL_359` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_Arcade-Learning-Environment_2655` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_ArchR_464` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_atropos_776` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Austin_628` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock-GPU_1075` - :ref:`list_software_AutoDock-Vina_1237` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -86,6 +86,7 @@ version versionsuffix toolchain ``2017`` ``-hotfix-1721`` ``system`` ``2018`` ``-hotfix-1806`` ``system`` ``2020`` ``system`` +``2021`` ``-hotfix-2132`` ``system`` ========== ================= ========== @@ -155,6 +156,22 @@ version versionsuffix toolchain ========= ================ =============== +.. _list_software_Abseil_592: + +*Abseil* +++++++++ + +Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives. + +*homepage*: https://abseil.io/ + +============== ================== +version toolchain +============== ================== +``20210324.2`` ``GCCcore/11.2.0`` +============== ================== + + .. _list_software_abTEM_425: *abTEM* @@ -614,13 +631,16 @@ AlphaFold can predict protein structures with atomic accuracy even where no simi *homepage*: https://deepmind.com/research/case-studies/alphafold -========= ================================== -version toolchain -========= ================================== -``2.0.0`` ``foss/2020b``, ``fosscuda/2020b`` -``2.0.1`` ``foss/2020b``, ``fosscuda/2020b`` -``2.1.1`` ``fosscuda/2020b`` -========= ================================== +========= ===================== ================================== +version versionsuffix toolchain +========= ===================== ================================== +``2.0.0`` ``foss/2020b``, ``fosscuda/2020b`` +``2.0.1`` ``foss/2020b``, ``fosscuda/2020b`` +``2.1.1`` ``fosscuda/2020b`` +``2.1.2`` ``foss/2021a`` +``2.1.2`` ``-CUDA-11.3.1`` ``foss/2021a`` +``2.1.2`` ``-TensorFlow-2.5.0`` ``foss/2020b``, ``fosscuda/2020b`` +========= ===================== ================================== .. _list_software_ALPS_304: @@ -747,6 +767,7 @@ version versionsuffix toolchain ``17`` ``intel/2017b``, ``intel/2018a`` ``17`` ``-Python-2.7.14`` ``foss/2018a`` ``20`` ``-Python-3.8.2`` ``intel/2020a`` +``21`` ``intel/2021b`` ======= ================== ================================ @@ -897,6 +918,22 @@ version toolchain ================ ============= +.. _list_software_AMS_225: + +*AMS* ++++++ + +The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for computational chemistry and materials science, from quantum mechanics to fluid thermodynamics. + +*homepage*: https://www.scm.com/amsterdam-modeling-suite/ + +============ ============= =============== +version versionsuffix toolchain +============ ============= =============== +``2020.102`` ``-intelmpi`` ``iimpi/2020b`` +============ ============= =============== + + .. _list_software_Anaconda2_839: *Anaconda2* @@ -1436,6 +1473,22 @@ version toolchain ======== ========================================================== +.. _list_software_ArchR_464: + +*ArchR* ++++++++ + +ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data. + +*homepage*: https://www.archrproject.com + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``1.0.1`` ``-R-4.1.2`` ``foss/2021b`` +========= ============= ============== + + .. _list_software_archspec_841: *archspec* @@ -1451,6 +1504,7 @@ version versionsuffix toolchain ``0.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``0.1.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``0.1.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``0.1.3`` ``GCCcore/11.2.0`` ========= ================= ====================================== @@ -1719,7 +1773,7 @@ version versionsuffix toolchain ========== ================= =============================== ``0.7.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``0.11.1`` ``intel/2020b`` -``0.11.4`` ``intel/2021b`` +``0.11.4`` ``foss/2021b``, ``intel/2021b`` ========== ================= =============================== @@ -2166,18 +2220,18 @@ AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences *homepage*: https://bioinf.uni-greifswald.de/augustus/ -========= ================== =============================== -version versionsuffix toolchain -========= ================== =============================== -``3.2.3`` ``-Python-2.7.13`` ``intel/2017a`` -``3.3`` ``foss/2018a`` -``3.3.2`` ``intel/2019a`` -``3.3.2`` ``-Python-2.7.13`` ``intel/2017a`` -``3.3.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``3.3.2`` ``-Python-2.7.15`` ``intel/2018b`` -``3.3.3`` ``foss/2019b``, ``intel/2019b`` -``3.4.0`` ``foss/2020a``, ``foss/2020b`` -========= ================== =============================== +========= ================== ============================================== +version versionsuffix toolchain +========= ================== ============================================== +``3.2.3`` ``-Python-2.7.13`` ``intel/2017a`` +``3.3`` ``foss/2018a`` +``3.3.2`` ``intel/2019a`` +``3.3.2`` ``-Python-2.7.13`` ``intel/2017a`` +``3.3.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``3.3.2`` ``-Python-2.7.15`` ``intel/2018b`` +``3.3.3`` ``foss/2019b``, ``intel/2019b`` +``3.4.0`` ``foss/2020a``, ``foss/2020b``, ``foss/2021b`` +========= ================== ============================================== .. _list_software_Austin_628: @@ -2543,11 +2597,11 @@ Bambi is a high-level Bayesian model-building interface written in Python. It wo *homepage*: https://bambinos.github.io/bambi -========= =============== -version toolchain -========= =============== -``0.7.1`` ``intel/2021b`` -========= =============== +========= =============================== +version toolchain +========= =============================== +``0.7.1`` ``foss/2021b``, ``intel/2021b`` +========= =============================== .. _list_software_BAMM_285: @@ -2659,14 +2713,15 @@ version toolchain Bandage is a program for visualising de novo assembly graphs -*homepage*: http://rrwick.github.io/Bandage/ +*homepage*: http://rrwick.github.io/Bandage -========= ============= ========== -version versionsuffix toolchain -========= ============= ========== -``0.8.1`` ``_Centos`` ``system`` -``0.8.1`` ``_Ubuntu`` ``system`` -========= ============= ========== +========= ============= ================== +version versionsuffix toolchain +========= ============= ================== +``0.8.1`` ``_Centos`` ``system`` +``0.8.1`` ``_Ubuntu`` ``system`` +``0.9.0`` ``GCCcore/11.2.0`` +========= ============= ================== .. _list_software_barrnap_742: @@ -3406,7 +3461,7 @@ version versionsuffix toolchain ``2.11`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``2.11`` ``-Perl-5.26.1`` ``intel/2018a`` ``2.11`` ``-Perl-5.28.0`` ``foss/2018b`` -``3.01`` ``GCC/10.2.0`` +``3.01`` ``GCC/10.2.0``, ``GCC/11.2.0`` ``3.01`` ``-Perl-5.28.1`` ``GCC/8.2.0-2.31.1`` ======== ================ =============================== @@ -3549,22 +3604,22 @@ Bioperl is the product of a community effort to produce Perl code which is usefu *homepage*: https://bioperl.org/ -=========== ================ ====================================== -version versionsuffix toolchain -=========== ================ ====================================== -``1.6.924`` ``-Perl-5.20.3`` ``intel/2016a`` -``1.6.924`` ``-Perl-5.22.1`` ``foss/2016a`` -``1.7.0`` ``-Perl-5.24.0`` ``foss/2016b`` -``1.7.1`` ``-Perl-5.24.0`` ``intel/2016b`` -``1.7.1`` ``-Perl-5.24.1`` ``intel/2017a`` -``1.7.2`` ``GCCcore/8.3.0`` -``1.7.2`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``1.7.2`` ``-Perl-5.26.1`` ``intel/2018a`` -``1.7.2`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` -``1.7.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -``1.7.7`` ``GCCcore/9.3.0`` -``1.7.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -=========== ================ ====================================== +=========== ================ ========================================================== +version versionsuffix toolchain +=========== ================ ========================================================== +``1.6.924`` ``-Perl-5.20.3`` ``intel/2016a`` +``1.6.924`` ``-Perl-5.22.1`` ``foss/2016a`` +``1.7.0`` ``-Perl-5.24.0`` ``foss/2016b`` +``1.7.1`` ``-Perl-5.24.0`` ``intel/2016b`` +``1.7.1`` ``-Perl-5.24.1`` ``intel/2017a`` +``1.7.2`` ``GCCcore/8.3.0`` +``1.7.2`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``1.7.2`` ``-Perl-5.26.1`` ``intel/2018a`` +``1.7.2`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` +``1.7.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``1.7.7`` ``GCCcore/9.3.0`` +``1.7.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +=========== ================ ========================================================== .. _list_software_BioPP_442: @@ -3885,6 +3940,7 @@ version versionsuffix toolchain ``2.2`` ``-amd`` ``GCCcore/9.3.0`` ``3.0`` ``-amd`` ``GCCcore/10.3.0`` ``3.0.1`` ``-amd`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``3.1`` ``-amd`` ``GCCcore/11.2.0`` ========= ============= ================================================== @@ -4017,20 +4073,20 @@ Statistical and novel interactive HTML plots for Python *homepage*: https://github.com/bokeh/bokeh -=========== ================== =================================================== -version versionsuffix toolchain -=========== ================== =================================================== -``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` -``0.12.3`` ``-Python-3.5.2`` ``intel/2016b`` -``0.12.15`` ``-Python-3.6.4`` ``intel/2018a`` -``1.0.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.3.4`` ``-Python-3.7.2`` ``foss/2019a`` -``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``2.0.2`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``2.2.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``2.4.1`` ``foss/2021a`` -``2.4.2`` ``foss/2021b`` -=========== ================== =================================================== +=========== ================== ======================================================================== +version versionsuffix toolchain +=========== ================== ======================================================================== +``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` +``0.12.3`` ``-Python-3.5.2`` ``intel/2016b`` +``0.12.15`` ``-Python-3.6.4`` ``intel/2018a`` +``1.0.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.3.4`` ``-Python-3.7.2`` ``foss/2019a`` +``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2.0.2`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``2.2.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +``2.4.1`` ``foss/2021a`` +``2.4.2`` ``foss/2021b`` +=========== ================== ======================================================================== .. _list_software_BoltzTraP_898: @@ -4216,11 +4272,11 @@ Boto3 is the Amazon Web Services (AWS) Software Development Kit (SDK) for Python *homepage*: https://github.com/boto/boto3 -=========== ================== -version toolchain -=========== ================== -``1.20.13`` ``GCCcore/11.2.0`` -=========== ================== +=========== ====================================== +version toolchain +=========== ====================================== +``1.20.13`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +=========== ====================================== .. _list_software_Bottleneck_1035: @@ -4601,6 +4657,7 @@ version versionsuffix toolchain ``2.0.1`` ``-Python-2.7.13`` ``intel/2017a`` ``3.0.2`` ``-Python-2.7.15`` ``intel/2018b`` ``4.0.5`` ``-Python-3.7.4`` ``foss/2019b`` +``4.0.6`` ``foss/2020b`` ``5.0.0`` ``foss/2020b`` ``5.1.2`` ``foss/2020b`` ========= ================== =============== @@ -4803,7 +4860,7 @@ version toolchain --- -:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CASTEP_448` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_Crumble_714` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CASTEP_448` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMAverse_758` - :ref:`list_software_CmdStanR_764` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_CONN_302` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_Crumble_714` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_c-ares_571: @@ -4813,12 +4870,13 @@ version toolchain c-ares is a C library for asynchronous DNS requests (including name resolves) -*homepage*: https://c-ares.haxx.se +*homepage*: https://c-ares.org/ ========== ================== version toolchain ========== ================== ``1.17.2`` ``GCCcore/10.3.0`` +``1.18.1`` ``GCCcore/11.2.0`` ========== ================== @@ -5050,6 +5108,7 @@ version versionsuffix toolchain ``2.1.1`` ``GCCcore/10.2.0`` ``2.1.1`` ``-Java-11`` ``GCCcore/9.3.0`` ``2.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.2`` ``-Java-11`` ``GCCcore/10.3.0`` ========= ================ ====================================== @@ -5096,14 +5155,14 @@ Cap’n Proto is an insanely fast data interchange format and capability-based R *homepage*: https://capnproto.org -========= ====================================== -version toolchain -========= ====================================== -``0.6.1`` ``GCCcore/6.4.0`` -``0.7.0`` ``GCCcore/7.3.0`` -``0.8.0`` ``GCCcore/9.3.0`` -``0.9.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========= ====================================== +========= ========================================================== +version toolchain +========= ========================================================== +``0.6.1`` ``GCCcore/6.4.0`` +``0.7.0`` ``GCCcore/7.3.0`` +``0.8.0`` ``GCCcore/9.3.0`` +``0.9.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ========================================================== .. _list_software_Cargo_492: @@ -5402,12 +5461,13 @@ Clozure CL (often called CCL for short) is a free Common Lisp implementation wi *homepage*: https://ccl.clozure.com/ -========== ================= -version toolchain -========== ================= -``1.11.5`` ``system`` -``1.12`` ``GCCcore/9.3.0`` -========== ================= +========== ================== +version toolchain +========== ================== +``1.11.5`` ``system`` +``1.12`` ``GCCcore/9.3.0`` +``1.12.1`` ``GCCcore/10.3.0`` +========== ================== .. _list_software_cclib_509: @@ -5896,6 +5956,7 @@ version toolchain ``2.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.1.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.2.0`` ``GCCcore/10.2.0`` +``2.3.4`` ``GCCcore/10.3.0`` ========= ==================================== @@ -6356,12 +6417,13 @@ Python bindings for libclang *homepage*: https://clang.llvm.org -========== ================== ================= -version versionsuffix toolchain -========== ================== ================= -``8.0.0`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` -``10.0.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -========== ================== ================= +========== ================== ================== +version versionsuffix toolchain +========== ================== ================== +``8.0.0`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``10.0.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``13.0.1`` ``GCCcore/11.2.0`` +========== ================== ================== .. _list_software_CLAPACK_495: @@ -6604,6 +6666,38 @@ version toolchain ========== ================================================================================================================================================= +.. _list_software_CMAverse_758: + +*CMAverse* +++++++++++ + +The R package CMAverse provides a suite of functions for reproducible causal mediation analysis including cmdag for DAG visualization, cmest for statistical modeling and cmsens for sensitivity analysis. + +*homepage*: https://bs1125.github.io/CMAverse/ + +============ ============== +version toolchain +============ ============== +``20220112`` ``foss/2021b`` +============ ============== + + +.. _list_software_CmdStanR_764: + +*CmdStanR* +++++++++++ + +CmdStanR is a lightweight interface to Stan for R users + +*homepage*: https://mc-stan.org/cmdstanr + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``0.5.0`` ``-R-4.1.2`` ``foss/2021b`` +========= ============= ============== + + .. _list_software_CMSeq_441: *CMSeq* @@ -6908,6 +7002,22 @@ version versionsuffix toolchain ========= ================= ================== +.. _list_software_CONN_302: + +*CONN* +++++++ + +CONN is an open-source Matlab/SPM-based cross-platform software for the computation, display, and analysis of functional connectivity Magnetic Resonance Imaging (fcMRI). CONN is used to analyze resting state data (rsfMRI) as well as task-related designs. + +*homepage*: https://web.conn-toolbox.org/home + +======= ================= ========== +version versionsuffix toolchain +======= ================= ========== +``21a`` ``-MATLAB-2021a`` ``system`` +======= ================= ========== + + .. _list_software_ConnectomeWorkbench_1966: *ConnectomeWorkbench* @@ -8066,7 +8176,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_deepmedic_928` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dlib_411` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dRep_395` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_DualSPHysics_1180` - :ref:`list_software_DUBStepR_713` - :ref:`list_software_dune-core_898` - :ref:`list_software_dune-fem_785` - :ref:`list_software_dxpy_453` - :ref:`list_software_DyMat_479` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_deepmedic_928` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_Devito_619` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dlib_411` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dRep_395` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_DualSPHysics_1180` - :ref:`list_software_DUBStepR_713` - :ref:`list_software_dune-core_898` - :ref:`list_software_dune-fem_785` - :ref:`list_software_dxpy_453` - :ref:`list_software_DyMat_479` .. _list_software_dadi_402: @@ -8192,31 +8302,31 @@ Dask natively scales Python. Dask provides advanced parallelism for analytics, e *homepage*: https://dask.org/ -============ ================== =================================================== -version versionsuffix toolchain -============ ================== =================================================== -``0.8.2`` ``-Python-2.7.11`` ``intel/2016a`` -``0.8.2`` ``-Python-3.5.1`` ``intel/2016a`` -``0.11.0`` ``-Python-2.7.11`` ``foss/2016a`` -``0.11.0`` ``-Python-2.7.12`` ``intel/2016b`` -``0.11.0`` ``-Python-3.5.2`` ``intel/2016b`` -``0.12.0`` ``-Python-2.7.12`` ``intel/2016b`` -``0.12.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``0.16.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``0.16.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``0.17.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` -``0.17.0`` ``-Python-3.6.1`` ``intel/2017a`` -``0.17.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``0.19.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``1.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.1.4`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``2.3.0`` ``-Python-3.7.2`` ``foss/2019a`` -``2.8.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``2.18.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``2021.2.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``2021.9.1`` ``foss/2021a`` -``2022.1.0`` ``foss/2021b`` -============ ================== =================================================== +============ ================== ======================================================================== +version versionsuffix toolchain +============ ================== ======================================================================== +``0.8.2`` ``-Python-2.7.11`` ``intel/2016a`` +``0.8.2`` ``-Python-3.5.1`` ``intel/2016a`` +``0.11.0`` ``-Python-2.7.11`` ``foss/2016a`` +``0.11.0`` ``-Python-2.7.12`` ``intel/2016b`` +``0.11.0`` ``-Python-3.5.2`` ``intel/2016b`` +``0.12.0`` ``-Python-2.7.12`` ``intel/2016b`` +``0.12.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``0.16.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``0.16.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``0.17.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``0.17.0`` ``-Python-3.6.1`` ``intel/2017a`` +``0.17.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.19.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``1.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.1.4`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``2.3.0`` ``-Python-3.7.2`` ``foss/2019a`` +``2.8.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2.18.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``2021.2.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +``2021.9.1`` ``foss/2021a`` +``2022.1.0`` ``foss/2021b`` +============ ================== ======================================================================== .. _list_software_datamash_835: @@ -8291,6 +8401,7 @@ version versionsuffix toolchain ``1.835`` ``-Perl-5.22.1`` ``foss/2016a`` ``1.855`` ``GCCcore/10.2.0`` ``1.856`` ``GCCcore/10.3.0`` +``1.857`` ``GCCcore/11.2.0`` ========= ================ ================== @@ -8381,7 +8492,7 @@ version toolchain *dcm2niix* ++++++++++ -dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format. +dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. *homepage*: https://github.com/rordenlab/dcm2niix @@ -8392,6 +8503,7 @@ version toolchain ``1.0.20190902`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.0.20200331`` ``GCCcore/8.3.0`` ``1.0.20201102`` ``GCCcore/8.3.0`` +``1.0.20211006`` ``GCCcore/10.3.0`` ================ ==================================== @@ -8579,6 +8691,7 @@ version versionsuffix toolchain ``3.3.1`` ``-Python-3.7.4`` ``intel/2019b`` ``3.3.1`` ``-Python-3.8.2`` ``foss/2020a`` ``3.5.0`` ``foss/2021a`` +``3.5.1`` ``foss/2021b`` ========= ================= =============== @@ -8666,6 +8779,22 @@ version toolchain ======== =============== +.. _list_software_Devito_619: + +*Devito* +++++++++ + +Devito is a domain-specific Language (DSL) and code generation framework for performing optimised Finite Difference (FD) computation from high-level symbolic problem definitions. Devito performs automated code generation and Just-In-time (JIT) compilation based on symbolic equations defined in SymPy to create and execute highly optimised Finite Difference stencil kernels on multiple computer platforms. + +*homepage*: https://www.devitoproject.org + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``4.6.1`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_DFA_203: *DFA* @@ -8731,6 +8860,7 @@ version versionsuffix toolchain ``17.1`` ``-Python-2.7.14`` ``intel/2017b`` ``19.1`` ``-Python-2.7.16`` ``foss/2019b`` ``19.1`` ``-Python-2.7.16-mpi`` ``foss/2019b`` +``21.1`` ``intel/2021a`` ========= ====================== =============== @@ -8743,11 +8873,11 @@ This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers *homepage*: https://github.com/dftbplus/dftd3-lib -======= ============= -version toolchain -======= ============= -``0.9`` ``GCC/8.3.0`` -======= ============= +======= =========================================== +version toolchain +======= =========================================== +``0.9`` ``GCC/8.3.0``, ``intel-compilers/2021.2.0`` +======= =========================================== .. _list_software_DGL_215: @@ -8898,12 +9028,13 @@ DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electr *homepage*: http://www.diracprogram.org -======== ============================ =============== -version versionsuffix toolchain -======== ============================ =============== -``19.0`` ``-Python-2.7.18-int64`` ``intel/2020a`` -``19.0`` ``-Python-2.7.18-mpi-int64`` ``intel/2020a`` -======== ============================ =============== +======== ============================ =============================== +version versionsuffix toolchain +======== ============================ =============================== +``19.0`` ``-Python-2.7.18-int64`` ``intel/2020a`` +``19.0`` ``-Python-2.7.18-mpi-int64`` ``intel/2020a`` +``22.0`` ``foss/2021a``, ``intel/2021a`` +======== ============================ =============================== .. _list_software_distributed_1187: @@ -9624,6 +9755,7 @@ version toolchain ``4.5.0`` ``system`` ``4.5.1`` ``system`` ``4.5.2`` ``system`` +``4.5.3`` ``system`` ========== ========== @@ -9665,7 +9797,7 @@ version versionsuffix toolchain ``2.18.0`` ``gompi/2020a`` ``2.20.0`` ``gompi/2020b`` ``2.22.1`` ``gompi/2021a`` -``2.24.2`` ``iimpi/2021b`` +``2.24.2`` ``gompi/2021b``, ``iimpi/2021b`` ========== ================== ================================ @@ -9928,7 +10060,7 @@ version toolchain *ELPA* ++++++ -Eigenvalue SoLvers for Petaflop-Applications . +Eigenvalue SoLvers for Petaflop-Applications. *homepage*: https://elpa.rzg.mpg.de @@ -9945,6 +10077,7 @@ version toolchain ``2020.05.001`` ``intel/2020a`` ``2020.11.001`` ``foss/2020b``, ``intel/2020b`` ``2021.05.001`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` +``2021.11.001`` ``foss/2021b``, ``intel/2021b`` =================== ================================================================================= @@ -10372,14 +10505,14 @@ A Python framework for the analysis and visualization of trees *homepage*: http://etetoolkit.org -============ ================== =============== -version versionsuffix toolchain -============ ================== =============== -``3.0.0b36`` ``-Python-2.7.12`` ``intel/2016b`` -``3.1.1`` ``-Python-3.6.6`` ``foss/2018b`` -``3.1.2`` ``foss/2020b`` -``3.1.2`` ``-Python-3.8.2`` ``foss/2020a`` -============ ================== =============== +============ ================== ============================== +version versionsuffix toolchain +============ ================== ============================== +``3.0.0b36`` ``-Python-2.7.12`` ``intel/2016b`` +``3.1.1`` ``-Python-3.6.6`` ``foss/2018b`` +``3.1.2`` ``foss/2020b``, ``foss/2021b`` +``3.1.2`` ``-Python-3.8.2`` ``foss/2020a`` +============ ================== ============================== .. _list_software_ETSF_IO_553: @@ -11916,7 +12049,7 @@ FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate softwa version toolchain ========== ============================================================= ``1.2.11`` ``GCC/8.3.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b`` -``2.2.00`` ``foss/2018b``, ``foss/2020b`` +``2.2.00`` ``GCC/11.2.0``, ``foss/2018b``, ``foss/2020b`` ========== ============================================================= @@ -12043,6 +12176,7 @@ FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK version toolchain ========= ============================== ``3.0.4`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``3.1.3`` ``GCC/11.2.0`` ========= ============================== @@ -12138,7 +12272,7 @@ version toolchain ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. -*homepage*: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent +*homepage*: https://www.ansys.com/products/fluids/ansys-fluent ========== ========== version toolchain @@ -12151,6 +12285,7 @@ version toolchain ``18.1`` ``system`` ``18.2`` ``system`` ``2021R1`` ``system`` +``2021R2`` ``system`` ========== ========== @@ -13060,7 +13195,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_genozip_764` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPy_272` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_genozip_764` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPy_272` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap_784` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gRPC_332` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -13336,6 +13471,7 @@ version versionsuffix toolchain ``4.2.0.0`` ``-Java-1.8`` ``GCCcore/10.2.0`` ``4.2.0.0`` ``-Java-11`` ``GCCcore/10.2.0`` ``4.2.3.0`` ``-Java-11`` ``GCCcore/11.2.0`` +``4.2.5.0`` ``-Java-11`` ``GCCcore/11.2.0`` ============ =================== ================== @@ -14309,6 +14445,7 @@ version versionsuffix toolchain ``3.6.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.7.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ``3.7.2`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.8.0`` ``GCC/8.3.0`` ``3.8.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ``3.8.1`` ``-Python-3.8.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` ``3.9.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304`` @@ -14361,6 +14498,7 @@ version versionsuffix toolchain ============== ================= ============== ``1.7.2`` ``-Python-3.8.2`` ``foss/2020a`` ``1.7.4-pre2`` ``foss/2020b`` +``1.7.5.3`` ``foss/2021b`` ============== ================= ============== @@ -15247,18 +15385,18 @@ GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x *homepage*: https://github.com/aleaxit/gmpy -============ ================== ====================================================================== -version versionsuffix toolchain -============ ================== ====================================================================== -``2.0.8`` ``-Python-2.7.13`` ``intel/2017a`` -``2.0.8`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.0.8`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b4`` ``GCC/8.3.0`` -``2.1.0b5`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` -``2.1.0rc1`` ``GCC/11.2.0`` -============ ================== ====================================================================== +=========== ================== ====================================================================== +version versionsuffix toolchain +=========== ================== ====================================================================== +``2.0.8`` ``-Python-2.7.13`` ``intel/2017a`` +``2.0.8`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2.0.8`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b4`` ``GCC/8.3.0`` +``2.1.0b5`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` +``2.1.2`` ``GCC/11.2.0`` +=========== ================== ====================================================================== .. _list_software_gmsh_431: @@ -15967,11 +16105,11 @@ Graphite is a "smart font" system developed specifically to handle the complexi *homepage*: https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home -========== ===================================== -version toolchain -========== ===================================== -``1.3.14`` ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` -========== ===================================== +========== ========================================================= +version toolchain +========== ========================================================= +``1.3.14`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` +========== ========================================================= .. _list_software_GraPhlAn_749: @@ -15990,6 +16128,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_GraphMap_784: + +*GraphMap* +++++++++++ + +A highly sensitive and accurate mapper for long, error-prone reads + +*homepage*: https://github.com/isovic/graphmap + +========= ============== +version toolchain +========= ============== +``0.5.2`` ``foss/2019b`` +========= ============== + + .. _list_software_GraphMap2_834: *GraphMap2* @@ -16314,6 +16468,22 @@ version versionsuffix toolchain ========= ============= ========== +.. _list_software_gRPC_332: + +*gRPC* +++++++ + +gRPC is a modern, open source, high-performance remote procedure call (RPC) framework that can run anywhere. gRPC enables client and server applications to communicate transparently, and simplifies the building of connected systems. + +*homepage*: https://grpc.io/ + +========== ================== +version toolchain +========== ================== +``1.44.0`` ``GCCcore/11.2.0`` +========== ================== + + .. _list_software_GSEA_288: *GSEA* @@ -16700,7 +16870,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_HIP_225` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_histolab_854` - :ref:`list_software_hivtrace_854` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_HIP_225` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_histolab_854` - :ref:`list_software_hivtrace_854` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hydra_504` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -17780,6 +17950,22 @@ version toolchain =========== ===================================================================================================================================================================================================================================================== +.. _list_software_Hydra_504: + +*Hydra* ++++++++ + +Hydra is an open-source Python framework that simplifies the development of research and other complex applications. The key feature is the ability to dynamically create a hierarchical configuration by composition and override it through config files and the command line. The name Hydra comes from its ability to run multiple similar jobs - much like a Hydra with multiple heads. + +*homepage*: https://hydra.cc/ + +========= ================== +version toolchain +========= ================== +``1.1.1`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_Hyperopt_859: *Hyperopt* @@ -18266,6 +18452,7 @@ IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable version versionsuffix toolchain ========== ============== ========== ``1.15.0`` ``-x64-linux`` ``system`` +``1.18.0`` ``-x64-linux`` ``system`` ========== ============== ========== @@ -18547,6 +18734,7 @@ version versionsuffix toolchain ``2.5.0`` ``foss/2019a`` ``2.9.0`` ``foss/2020b``, ``fosscuda/2020b`` ``2.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``2.10.5`` ``foss/2021a`` ``2.13.5`` ``foss/2021b`` ========== ================= ================================== @@ -18925,7 +19113,7 @@ Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases version toolchain ========= ================================================================ ``1.1.2`` ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018b`` -``1.1.4`` ``foss/2021b`` +``1.1.4`` ``foss/2020b``, ``foss/2021b`` ========= ================================================================ @@ -19128,14 +19316,15 @@ version toolchain *IntelClusterChecker* +++++++++++++++++++++ -Verifies cluster components work together ― for - better uptime and productivity and lower total - cost of ownership (TCO) +Intel Cluster Checker verifies the configuration and performance of Linux OS-based clusters. Anomalies and performance differences can be identified and practical resolutions provided. -*homepage*: https://software.intel.com/en-us/intel-cluster-checker +*homepage*: https://software.intel.com/en-us/cluster-checker ============== ========== version toolchain ============== ========== ``2017.1.016`` ``system`` +``2021.5.0`` ``system`` ============== ========== @@ -19232,15 +19421,16 @@ version toolchain *intervaltree-python* +++++++++++++++++++++ -A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment +A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment. *homepage*: https://github.com/chaimleib/intervaltree -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` -========= ================= ============== +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` +``3.1.0`` ``GCCcore/10.3.0`` +========= ================= ================== .. _list_software_intltool_885: @@ -19786,11 +19976,12 @@ ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal *homepage*: https://microbiology.se/software/itsx/ -========= ================= -version toolchain -========= ================= -``1.1.2`` ``GCCcore/9.3.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``1.1.2`` ``GCCcore/9.3.0`` +``1.1.3`` ``GCCcore/10.3.0`` +========= ================== .. _list_software_iVar_402: @@ -19816,7 +20007,7 @@ version toolchain --- -:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_Jasmine_711` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_jax_323` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_JSON-GLib_709` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyter-matlab-proxy_2080` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` - :ref:`list_software_jxrlib_651` +:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_Jasmine_711` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_jax_323` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_JSON-GLib_709` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyter-matlab-proxy_2080` - :ref:`list_software_jupyter-server-proxy_2118` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` - :ref:`list_software_jxrlib_651` .. _list_software_JAGS_293: @@ -19828,12 +20019,12 @@ JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian *homepage*: http://mcmc-jags.sourceforge.net/ -========= =================================================================================================================================================== -version toolchain -========= =================================================================================================================================================== -``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` -``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b``, ``intel/2017b`` -========= =================================================================================================================================================== +========= =================================================================================================================================================================== +version toolchain +========= =================================================================================================================================================================== +``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` +``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2020b``, ``intel/2017b`` +========= =================================================================================================================================================================== .. _list_software_Jansson_732: @@ -20255,6 +20446,7 @@ version versionsuffix toolchain ``1.6.5`` ``-linux-x86_64`` ``system`` ``1.7.0`` ``-linux-x86_64`` ``system`` ``1.7.1`` ``-linux-x86_64`` ``system`` +``1.7.2`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -20307,6 +20499,22 @@ version toolchain ========= ================== +.. _list_software_jupyter-server-proxy_2118: + +*jupyter-server-proxy* +++++++++++++++++++++++ + +Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) alongside your notebook server and provide authenticated web access to them using a path like /rstudio next to others like /lab. Alongside the python package that provides the main functionality, the JupyterLab extension (@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window to get to RStudio for example. + +*homepage*: https://github.com/jupyterhub/jupyter-server-proxy + +========= ================== +version toolchain +========= ================== +``3.2.1`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_JupyterHub_1042: *JupyterHub* @@ -20460,6 +20668,7 @@ version toolchain ``0.46.0`` ``intel/2019a`` ``0.46.1`` ``foss/2019b``, ``iimpi/2020a``, ``iimpi/2020b`` ``0.46.2`` ``foss/2020b`` +``0.48.0`` ``gompi/2021b`` ========== ================================================ @@ -20654,6 +20863,7 @@ version versionsuffix toolchain ``3.1.0`` ``foss/2018a``, ``foss/2018b`` ``3.1.1`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` ``3.1.2rc1`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``3.2.1`` ``GCC/11.2.0`` ============ ================= ============================== @@ -21678,7 +21888,7 @@ version toolchain ``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` ``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` ``2.1.11`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.1.12`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.1.12`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``system`` ========== ====================================================================================== @@ -22403,6 +22613,7 @@ ObjCryst++ is Object-Oriented Crystallographic Library for C++ version toolchain ============ =============== ``2017.2.3`` ``intel/2020a`` +``2021.1.2`` ``foss/2021b`` ============ =============== @@ -22578,11 +22789,11 @@ libpspio is a library to read and write pseudopotentials in multiple formats. *homepage*: https://gitlab.e-cam2020.eu/esl/pspio/ -========= ======================================= -version toolchain -========= ======================================= -``0.2.4`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -========= ======================================= +========= ======================================================= +version toolchain +========= ======================================================= +``0.2.4`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` +========= ======================================================= .. _list_software_libpthread-stubs_1661: @@ -23067,6 +23278,7 @@ libtree is a tool that turns ldd into a tree, explains why shared libraries are version toolchain ========= ================== ``2.0.0`` ``GCCcore/10.3.0`` +``3.0.3`` ``system`` ========= ================== @@ -23764,12 +23976,12 @@ Fast and memory-efficient sequencing error corrector *homepage*: https://github.com/mourisl/Lighter -========= ============== -version toolchain -========= ============== -``1.1.1`` ``foss/2018a`` -``1.1.2`` ``foss/2018b`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``1.1.1`` ``foss/2018a`` +``1.1.2`` ``GCC/11.2.0``, ``foss/2018b`` +========= ============================== .. _list_software_liknorm_764: @@ -23797,18 +24009,18 @@ Likwid stands for Like I knew what I am doing. This project contributes easy to *homepage*: https://github.com/RRZE-HPC/likwid -========= ===================================================================== -version toolchain -========= ===================================================================== -``4.0.1`` ``GNU/4.9.3-2.25`` -``4.1.0`` ``GCCcore/4.9.3`` -``4.2.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2017a``, ``intel/2017a`` -``4.3.2`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``5.0.1`` ``GCCcore/8.3.0`` -``5.1.0`` ``GCCcore/9.3.0`` -``5.2.0`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` -``5.2.1`` ``GCCcore/11.2.0`` -========= ===================================================================== +========= ===================================================================================================== +version toolchain +========= ===================================================================================================== +``4.0.1`` ``GNU/4.9.3-2.25`` +``4.1.0`` ``GCCcore/4.9.3`` +``4.2.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2017a``, ``intel/2017a`` +``4.3.2`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``5.0.1`` ``GCCcore/8.3.0`` +``5.1.0`` ``GCCcore/9.3.0`` +``5.2.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0`` +``5.2.1`` ``GCC/11.2.0`` +========= ===================================================================================================== .. _list_software_limix_547: @@ -24191,11 +24403,12 @@ Python implementation of the Loom file format, an efficient file format for larg *homepage*: https://loompy.org/ -========= =============== -version toolchain -========= =============== -``3.0.6`` ``intel/2020b`` -========= =============== +========= =============================== +version toolchain +========= =============================== +``3.0.6`` ``intel/2020b`` +``3.0.7`` ``foss/2021b``, ``intel/2021b`` +========= =============================== .. _list_software_LPeg_360: @@ -24243,7 +24456,7 @@ Mixed Integer Linear Programming (MILP) solver version toolchain ============ ============================================================================================================================================================================================== ``5.5.2.5`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a``, ``intel/2018b`` -``5.5.2.11`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``5.5.2.11`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` ============ ============================================================================================================================================================================================== @@ -24543,7 +24756,23 @@ version toolchain --- -:ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MuJoCo_557` - :ref:`list_software_mujoco-py_931` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M1QN3_336` - :ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_MAGeCK_456` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_matplotlib-inline_1764` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_MEGAN_360` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MNE-Python_911` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MuJoCo_557` - :ref:`list_software_mujoco-py_931` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` + + +.. _list_software_M1QN3_336: + +*M1QN3* ++++++++ + +A solver of large-scale unconstrained minimization problems + +*homepage*: https://who.rocq.inria.fr/Jean-Charles.Gilbert/modulopt/optimization-routines/m1qn3/m1qn3.html + +======= ============== +version toolchain +======= ============== +``3.3`` ``GCC/10.3.0`` +======= ============== .. _list_software_M4_129: @@ -24657,6 +24886,22 @@ version versionsuffix toolchain ========= ==================== ======================================================================================= +.. _list_software_MAGeCK_456: + +*MAGeCK* +++++++++ + +Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute, and is being actively updated by Wei Li lab from Children's National Medical Center. + +*homepage*: https://sourceforge.net/p/mageck/wiki/Home/ + +=========== ============== +version toolchain +=========== ============== +``0.5.9.4`` ``foss/2021a`` +=========== ============== + + .. _list_software_magick_620: *magick* @@ -25017,14 +25262,14 @@ Fast genome and metagenome distance estimation using MinHash *homepage*: http://mash.readthedocs.org -======= ============== -version toolchain -======= ============== -``2.0`` ``foss/2018a`` -``2.1`` ``foss/2018b`` -``2.2`` ``GCC/9.3.0`` -``2.3`` ``GCC/10.3.0`` -======= ============== +======= ============================== +version toolchain +======= ============================== +``2.0`` ``foss/2018a`` +``2.1`` ``foss/2018b`` +``2.2`` ``GCC/9.3.0`` +``2.3`` ``GCC/10.3.0``, ``GCC/11.2.0`` +======= ============================== .. _list_software_MaSuRCA_588: @@ -25204,9 +25449,26 @@ version versionsuffix toolchain ``3.3.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``3.4.2`` ``foss/2021a``, ``intel/2021a`` ``3.4.3`` ``foss/2021b``, ``intel/2021b`` +``3.5.1`` ``foss/2020b``, ``intel/2020b`` ========= ================================= =================================================================================== +.. _list_software_matplotlib-inline_1764: + +*matplotlib-inline* ++++++++++++++++++++ + +Matplotlib Inline Back-end for IPython and Jupyter. + +*homepage*: https://github.com/ipython/matplotlib-inline + +========= ================== +version toolchain +========= ================== +``0.1.3`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_MATSim_523: *MATSim* @@ -25476,6 +25738,8 @@ version versionsuffix toolchain ``R2021a`` ``.0`` ``system`` ``R2021a`` ``.3`` ``system`` ``R2021b`` ``system`` +``R2021b`` ``.2`` ``system`` +``R2022a`` ``system`` ========== ============= ========== @@ -25492,6 +25756,8 @@ MDAnalysis is an object-oriented Python library to analyze trajectories from mol version versionsuffix toolchain ========== ================= =============================== ``0.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.1.1`` ``foss/2020b`` +``2.0.0`` ``foss/2021b``, ``intel/2021b`` ========== ================= =============================== @@ -25595,6 +25861,7 @@ version versionsuffix toolchain ``1.9.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``1.9.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``1.9.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``1.9.7`` ``intel/2021b`` ========= ================= =================================================== @@ -25618,6 +25885,7 @@ version versionsuffix toolchain ``1.2.0`` ``-Python-3.7.4`` ``foss/2019b`` ``1.4.3`` ``foss/2020b`` ``1.4.3`` ``-Python-3.7.4`` ``foss/2019b`` +``1.5.0`` ``foss/2021a`` ========== ================= ============== @@ -25745,6 +26013,22 @@ version toolchain ========= ================================== +.. _list_software_MEGAN_360: + +*MEGAN* ++++++++ + +MEGAN is a comprehensive toolbox for interactively analyzing microbiome data + +*homepage*: http://megan.informatik.uni-tuebingen.de/ + +========== ============= ========== +version versionsuffix toolchain +========== ============= ========== +``6.22.0`` ``-Java-17`` ``system`` +========== ============= ========== + + .. _list_software_Meld_386: *Meld* @@ -25795,6 +26079,7 @@ version versionsuffix toolchain ``5.1.1`` ``-Python-3.6.6`` ``foss/2018b`` ``5.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``5.4.1`` ``GCC/10.3.0`` +``5.4.1`` ``-Python-2.7.18`` ``gompi/2021b`` ========= ============================== =============================== @@ -25932,16 +26217,17 @@ version toolchain *meshalyzer* ++++++++++++ -Graphical program for display time dependent data on 3D finite elment meshes +Graphical program for display time dependent data on 3D finite element meshes *homepage*: https://git.opencarp.org/openCARP/meshalyzer -======= ================= ============== -version versionsuffix toolchain -======= ================= ============== -``2.0`` ``-Python-3.8.2`` ``foss/2020a`` -``2.2`` ``foss/2020b`` -======= ================= ============== +============ ================= ============== +version versionsuffix toolchain +============ ================= ============== +``2.0`` ``-Python-3.8.2`` ``foss/2020a`` +``2.2`` ``foss/2020b`` +``20200308`` ``-Python-3.8.2`` ``foss/2020a`` +============ ================= ============== .. _list_software_meshio_645: @@ -26912,6 +27198,22 @@ version toolchain ========= ================== +.. _list_software_MNE-Python_911: + +*MNE-Python* +++++++++++++ + +MNE-Python software is an open-source Python package for exploring, visualizing, and analyzing human neurophysiological data such as MEG, EEG, sEEG, ECoG, and more. It includes modules for data input/output, preprocessing, visualization, source estimation, time-frequency analysis, connectivity analysis, machine learning, and statistics. + +*homepage*: https://mne.tools/stable/index.html + +========== ============== +version toolchain +========== ============== +``0.24.1`` ``foss/2021a`` +========== ============== + + .. _list_software_MOABS_370: *MOABS* @@ -27557,6 +27859,7 @@ version versionsuffix toolchain ``3.0-rc-20191217`` ``-Python-2.7.16`` ``foss/2019b`` ``3.0-rc-20191217`` ``-Python-3.7.4`` ``foss/2019b`` ``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` +``3.0.3`` ``foss/2021a`` ``3.0_RC2`` ``-Python-2.7.13`` ``foss/2017a`` ``3.0_RC3`` ``-Python-2.7.14`` ``intel/2018a`` =================== ================== =============== @@ -27847,15 +28150,15 @@ MUSCLE is one of the best-performing multiple alignment programs according to p *homepage*: https://drive5.com/muscle/ -============ =============== ================================================================================================================================================================================================= -version versionsuffix toolchain -============ =============== ================================================================================================================================================================================================= -``3.8.31`` ``GCC/7.3.0-2.30``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2017b``, ``foss/2018a``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``3.8.31`` ``-i86linux64`` ``system`` -``3.8.1551`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` -``5.0.1428`` ``GCCcore/10.3.0`` -``5.1`` ``GCCcore/11.2.0`` -============ =============== ================================================================================================================================================================================================= +============ =============== ===================================================================================================================================================================================================================== +version versionsuffix toolchain +============ =============== ===================================================================================================================================================================================================================== +``3.8.31`` ``GCC/7.3.0-2.30``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2017b``, ``foss/2018a``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``3.8.31`` ``-i86linux64`` ``system`` +``3.8.1551`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` +``5.0.1428`` ``GCCcore/10.3.0`` +``5.1`` ``GCCcore/11.2.0`` +============ =============== ===================================================================================================================================================================================================================== .. _list_software_MuSiC_449: @@ -28970,7 +29273,7 @@ version versionsuffix toolchain ``1.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``1.5.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``1.5.5.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``1.5.7`` ``foss/2021a``, ``intel/2021b`` +``1.5.7`` ``foss/2021a``, ``foss/2021b``, ``intel/2021b`` =========== ============================= =================================================== @@ -29138,7 +29441,7 @@ version versionsuffix toolchain ``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``2.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` ``2.4`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` -``2.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``2.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``2.5.1`` ``foss/2021a`` ``2.6.2`` ``foss/2020b`` ``2.6.3`` ``foss/2021a``, ``foss/2021b``, ``intel/2021b`` @@ -29243,13 +29546,13 @@ The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transf *homepage*: https://www-user.tu-chemnitz.de/~potts/nfft/ -========= ================================== -version toolchain -========= ================================== -``3.1.3`` ``foss/2020b``, ``fosscuda/2020b`` -``3.5.1`` ``foss/2018b``, ``foss/2019a`` -``3.5.2`` ``foss/2020a``, ``foss/2021a`` -========= ================================== +========= ============================================== +version toolchain +========= ============================================== +``3.1.3`` ``foss/2020b``, ``fosscuda/2020b`` +``3.5.1`` ``foss/2018b``, ``foss/2019a`` +``3.5.2`` ``foss/2020a``, ``foss/2021a``, ``foss/2021b`` +========= ============================================== .. _list_software_NGLess_556: @@ -29401,6 +29704,7 @@ version versionsuffix toolchain ``3.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.2.0`` ``-Python-3.8.2`` ``foss/2020a`` ``3.2.1`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` +``3.2.2`` ``foss/2021b`` ========= ================================= ================================================== @@ -29598,6 +29902,8 @@ version versionsuffix toolchain ``3.2.4`` ``-Python-2.7.13`` ``intel/2017a`` ``3.5`` ``-Python-3.7.4`` ``foss/2019b`` ``3.5`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``3.6.7`` ``foss/2021a`` +``3.7`` ``foss/2021b`` ========= ================== ================================== @@ -29981,7 +30287,7 @@ version versionsuffix toolchain ``0.52.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``0.52.0`` ``-Python-3.8.2`` ``foss/2020a`` ``0.53.1`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` -``0.54.1`` ``foss/2021b`` +``0.54.1`` ``foss/2021b``, ``intel/2021b`` ========== ================== =================================================== @@ -30028,6 +30334,7 @@ version versionsuffix toolchain ``2.7.1`` ``-Python-2.7.16`` ``intel/2019b`` ``2.7.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.7.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``2.8.1`` ``foss/2021a``, ``intel/2021a`` ========= ================== =================================================== @@ -30139,7 +30446,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCensus-python_1746` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFace_769` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSceneGraph_1394` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ONNX_323` - :ref:`list_software_ONNX-Runtime_1108` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_ont-remora_1028` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCensus-python_1746` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFace_769` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSceneGraph_1394` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_Optuna_631` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -30314,6 +30621,39 @@ version toolchain ========== ================== +.. _list_software_ONNX_323: + +*ONNX* +++++++ + +Open Neural Network Exchange (ONNX) is an open ecosystem that empowers AI developers to choose the right tools as their project evolves. ONNX provides an open source format for AI models, both deep learning and traditional ML. It defines an extensible computation graph model, as well as definitions of built-in operators and standard data types. Currently we focus on the capabilities needed for inferencing (scoring). + +*homepage*: https://onnx.ai/ + +========== ============== +version toolchain +========== ============== +``1.11.0`` ``foss/2021a`` +========== ============== + + +.. _list_software_ONNX-Runtime_1108: + +*ONNX-Runtime* +++++++++++++++ + +ONNX Runtime inference can enable faster customer experiences and lower costs, supporting models from deep learning frameworks such as PyTorch and TensorFlow/Keras as well as classical machine learning libraries such as scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different hardware, drivers, and operating systems, and provides optimal performance by leveraging hardware accelerators where applicable alongside graph optimizations and transforms. + +*homepage*: https://onnxruntime.ai/ + +========== ================ ============== +version versionsuffix toolchain +========== ================ ============== +``1.10.0`` ``foss/2021a`` +``1.10.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +========== ================ ============== + + .. _list_software_ont-fast5-api_1224: *ont-fast5-api* @@ -30328,9 +30668,28 @@ version versionsuffix toolchain ========= ================= ================================== ``3.3.0`` ``foss/2020b``, ``fosscuda/2020b`` ``3.3.0`` ``-Python-3.7.4`` ``foss/2019b`` +``4.0.0`` ``foss/2021a`` +``4.0.2`` ``foss/2021a`` ========= ================= ================================== +.. _list_software_ont-remora_1028: + +*ont-remora* +++++++++++++ + +Methylation/modified base calling separated from basecalling. Remora primarily provides an API to call modified bases for basecaller programs such as Bonito. Remora also provides the tools to prepare datasets, train modified base models and run simple inference. + +*homepage*: https://github.com/nanoporetech/remora + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``0.1.2`` ``foss/2021a`` +``0.1.2`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== + + .. _list_software_OOMPA_380: *OOMPA* @@ -30394,6 +30753,7 @@ A toolkit for developing and comparing reinforcement learning algorithms. version versionsuffix toolchain ========== ================= ============== ``0.17.1`` ``-Python-3.7.4`` ``foss/2019b`` +``0.21.0`` ``foss/2021b`` ========== ================= ============== @@ -30455,6 +30815,7 @@ version versionsuffix toolchain ``0.3.15`` ``GCC/10.3.0`` ``0.3.17`` ``GCC/10.3.0``, ``GCC/11.2.0`` ``0.3.18`` ``GCC/11.2.0`` +``0.3.20`` ``GCC/11.2.0`` ========== ================= ========================================================== @@ -31163,6 +31524,23 @@ version toolchain ========= ================== +.. _list_software_Optuna_631: + +*Optuna* +++++++++ + +Optuna is an automatic hyperparameter optimization software framework, particularly designed for machine learning. It features an imperative, define-by-run style user API. Thanks to our define-by-run API, the code written with Optuna enjoys high modularity, and the user of Optuna can dynamically construct the search spaces for the hyperparameters. + +*homepage*: https://optuna.org/ + +========== ============== +version toolchain +========== ============== +``2.9.1`` ``foss/2021a`` +``2.10.0`` ``foss/2021b`` +========== ============== + + .. _list_software_OR-Tools_735: *OR-Tools* @@ -31203,6 +31581,7 @@ version versionsuffix toolchain ``5.0.1`` ``-static`` ``gompi/2021a`` ``5.0.2`` ``gompi/2021a``, ``gompi/2021b`` ``5.0.2`` ``-static`` ``gompi/2021a``, ``gompi/2021b`` +``5.0.3`` ``gompi/2021b`` ====================== ================== ================================ @@ -31389,7 +31768,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyEVTK_515` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_pyradiomics_1188` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch-Lightning_1690` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patch_528` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_porefoam_857` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_presto_669` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyEVTK_515` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_PyFrag_585` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_pyradiomics_1188` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch-Lightning_1690` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -31773,6 +32152,7 @@ parallel fastq-dump wrapper version versionsuffix toolchain ========= ================= ================= ``0.6.5`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``0.6.6`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ================= ================= @@ -31969,6 +32349,22 @@ version toolchain ========= ============== +.. _list_software_patch_528: + +*patch* ++++++++ + +Patch takes a patch file containing a difference listing produced by the diff program and applies those differences to one or more original files, producing patched versions. + +*homepage*: https://savannah.gnu.org/projects/patch + +========= ========== +version toolchain +========= ========== +``2.7.6`` ``system`` +========= ========== + + .. _list_software_patchelf_839: *patchelf* @@ -33153,6 +33549,7 @@ An automated pipeline for analyses of fungal internal transcribed spacer (ITS) s version versionsuffix toolchain ======= ================= ============== ``2.7`` ``-Python-3.8.2`` ``foss/2020a`` +``2.8`` ``foss/2021a`` ======= ================= ============== @@ -33457,6 +33854,7 @@ version toolchain ``2.00-alpha1-x86_64`` ``system`` ``2.00-alpha2-x86_64`` ``system`` ``2.00-alpha2-x86_64_avx2`` ``system`` +``2.00a2.3`` ``GCC/10.3.0``, ``GCC/11.2.0`` ``2.00a2.3_x86_64`` ``system`` =========================== ============================== @@ -33712,6 +34110,7 @@ version toolchain ``1.4`` ``GCC/8.3.0``, ``gcccuda/2019b`` ``1.5`` ``GCC/9.3.0`` ``1.6`` ``GCC/10.2.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` +``1.8`` ``GCC/11.2.0`` ======= ========================================================== @@ -33853,6 +34252,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_porefoam_857: + +*porefoam* +++++++++++ + +Direct pore-scale simulation of single- and two-phase flow through confined media + +*homepage*: https://github.com/ImperialCollegeLondon/porefoam + +============== ============== +version toolchain +============== ============== +``2021-09-21`` ``foss/2020a`` +============== ============== + + .. _list_software_poretools_999: *poretools* @@ -34127,6 +34542,22 @@ version toolchain ========= =============================== +.. _list_software_presto_669: + +*presto* +++++++++ + +Presto performs a fast Wilcoxon rank sum test and auROC analysis. + +*homepage*: https://github.com/immunogenomics/presto + +================== ============= ============== +version versionsuffix toolchain +================== ============= ============== +``1.0.0-20200718`` ``-R-4.1.2`` ``foss/2021b`` +================== ============= ============== + + .. _list_software_pretty-yaml_1160: *pretty-yaml* @@ -35144,6 +35575,7 @@ version versionsuffix toolchain ``2.0.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.0.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.0.2`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``2.0.4`` ``foss/2021a`` ========= ================= ================================== @@ -35275,16 +35707,16 @@ Pure python package for DICOM medical file reading and writing. *homepage*: https://pydicom.github.io/ -========= ================== ================== -version versionsuffix toolchain -========= ================== ================== -``0.9.9`` ``-Python-2.7.11`` ``intel/2016a`` -``1.2.2`` ``GCCcore/8.2.0`` -``1.4.2`` ``GCCcore/8.3.0`` -``2.1.2`` ``GCCcore/10.2.0`` -``2.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``2.2.2`` ``GCCcore/10.3.0`` -========= ================== ================== +========= ================== ====================================== +version versionsuffix toolchain +========= ================== ====================================== +``0.9.9`` ``-Python-2.7.11`` ``intel/2016a`` +``1.2.2`` ``GCCcore/8.2.0`` +``1.4.2`` ``GCCcore/8.3.0`` +``2.1.2`` ``GCCcore/10.2.0`` +``2.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``2.2.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ================== ====================================== .. _list_software_pydlpoly_893: @@ -35330,13 +35762,14 @@ A basic Python-based EGA download client *homepage*: https://github.com/EGA-archive/ega-download-client -========== ================= ================= -version versionsuffix toolchain -========== ================= ================= -``3.0.33`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``3.4.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``3.4.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -========== ================= ================= +========== ================= ================== +version versionsuffix toolchain +========== ================= ================== +``3.0.33`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``3.4.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``3.4.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``4.0.0`` ``GCCcore/11.2.0`` +========== ================= ================== .. _list_software_pyenchant_970: @@ -35523,6 +35956,22 @@ version versionsuffix toolchain ========= ============================= =================== +.. _list_software_PyFrag_585: + +*PyFrag* +++++++++ + +PyFrag 2019 resolves three main challenges associated with the automatized computational exploration of reaction mechanisms: 1) the management of multiple parallel calculations to automatically find a reaction path; 2) the monitoring of the entire computational process along with the extraction and plotting of relevant information from large amounts of data; and 3) the analysis and presentation of these data in a clear and informative way. This module provides the Activation Strain Analysis (ASA) Module of PyFrag 2019 + +*homepage*: https://pyfragdocument.readthedocs.io/en/latest/includeme.html + +================= ============= =============== +version versionsuffix toolchain +================= ============= =============== +``2019-20220216`` ``-ASA`` ``intel/2020b`` +================= ============= =============== + + .. _list_software_pygccxml_871: *pygccxml* @@ -35868,12 +36317,12 @@ Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machin *homepage*: https://docs.pymc.io/ -========== ================= ==================================================== -version versionsuffix toolchain -========== ================= ==================================================== -``3.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``3.11.1`` ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021b`` -========== ================= ==================================================== +========== ================= ==================================================================== +version versionsuffix toolchain +========== ================= ==================================================================== +``3.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.11.1`` ``foss/2021b``, ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021b`` +========== ================= ==================================================================== .. _list_software_pymca_538: @@ -35939,6 +36388,7 @@ Python bindings to ObjCryst++, the Object-Oriented Crystallographic Library. version versionsuffix toolchain =============== ================= =============== ``2.1.0.post2`` ``-Python-3.8.2`` ``intel/2020a`` +``2.2.1`` ``foss/2021b`` =============== ================= =============== @@ -36146,22 +36596,22 @@ PyQt5 is a set of Python bindings for v5 of the Qt application framework from Th *homepage*: http://www.riverbankcomputing.co.uk/software/pyqt -========== ================== ================================================ -version versionsuffix toolchain -========== ================== ================================================ -``5.7`` ``-Python-2.7.11`` ``foss/2016a`` -``5.7.1`` ``-Python-2.7.12`` ``intel/2016b`` -``5.8.2`` ``-Python-2.7.13`` ``intel/2017a`` -``5.9.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``5.9.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``5.11.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` -``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``5.13.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``5.15.1`` ``GCCcore/10.2.0`` -``5.15.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``5.15.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========== ================== ================================================ +========== ================== ========================================================== +version versionsuffix toolchain +========== ================== ========================================================== +``5.7`` ``-Python-2.7.11`` ``foss/2016a`` +``5.7.1`` ``-Python-2.7.12`` ``intel/2016b`` +``5.8.2`` ``-Python-2.7.13`` ``intel/2017a`` +``5.9.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``5.9.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``5.11.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``5.13.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``5.15.1`` ``GCCcore/10.2.0`` +``5.15.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``5.15.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ================== ========================================================== .. _list_software_PyQtGraph_896: @@ -36197,6 +36647,7 @@ Open-source python package for the extraction of Radiomics features from 2D and ========= ================= ============== version versionsuffix toolchain ========= ================= ============== +``3.0.1`` ``foss/2021a`` ``3.0.1`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -36526,12 +36977,12 @@ Python bindings to spoa. *homepage*: https://github.com/nanoporetech/pyspoa -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``0.0.4`` ``-Python-3.7.4`` ``GCC/8.3.0`` -``0.0.8`` ``GCC/10.2.0`` -========= ================= ============== +========= ================= ============================== +version versionsuffix toolchain +========= ================= ============================== +``0.0.4`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``0.0.8`` ``GCC/10.2.0``, ``GCC/10.3.0`` +========= ================= ============================== .. _list_software_pysqlite_891: @@ -36997,11 +37448,12 @@ PyWavelets is open source wavelet transform software for Python. *homepage*: https://pywavelets.readthedocs.io -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``1.1.1`` ``-Python-3.7.4`` ``intel/2019b`` -========= ================= =============== +========= ================= =================== +version versionsuffix toolchain +========= ================= =================== +``1.1.1`` ``intelcuda/2020b`` +``1.1.1`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= =================== .. _list_software_PyYAML_508: @@ -38404,6 +38856,7 @@ version toolchain ============== ================== ``2020-07-01`` ``GCCcore/8.3.0`` ``2021-06-01`` ``GCCcore/10.2.0`` +``2022-02-01`` ``GCCcore/11.2.0`` ============== ================== @@ -38805,11 +39258,11 @@ RevBayes provides an interactive environment for statistical computation in phy *homepage*: https://revbayes.github.io/ -========= ============== -version toolchain -========= ============== -``1.1.1`` ``GCC/10.2.0`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``1.1.1`` ``GCC/10.2.0``, ``GCC/11.2.0`` +========= ============================== .. _list_software_rgdal_522: @@ -39673,7 +40126,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_SCopeLoomR_963` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_ShengBTE_720` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_SHTns_464` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SoXt_398` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_STRUMPACK_698` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SURVIVOR_656` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_SCopeLoomR_963` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_ShengBTE_720` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_SHTns_464` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_skorch_650` - :ref:`list_software_SlamDunk_799` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SoXt_398` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_SPM_240` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_STRique_685` - :ref:`list_software_Structure_977` - :ref:`list_software_STRUMPACK_698` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SURVIVOR_656` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -39860,12 +40313,12 @@ Filter SAM file for soft and hard clipped alignments. *homepage*: https://github.com/tseemann/samclip -========= ================ ===================================== -version versionsuffix toolchain -========= ================ ===================================== -``0.2`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -``0.4.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========= ================ ===================================== +========= ================ ========================================================= +version versionsuffix toolchain +========= ================ ========================================================= +``0.2`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``0.4.0`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========= ================ ========================================================= .. _list_software_SAMtools_786: @@ -39899,6 +40352,7 @@ version versionsuffix toolchain ``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` ``1.13`` ``GCC/10.3.0`` ``1.14`` ``GCC/11.2.0`` +``1.15`` ``GCC/11.2.0`` ========== ================= ======================================================================================================================================= @@ -39977,11 +40431,12 @@ Steel Bank Common Lisp (SBCL) is a high performance Common Lisp compiler. It is *homepage*: http://sbcl.sourceforge.net/ -========= ================= -version toolchain -========= ================= -``2.0.9`` ``GCCcore/9.3.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``2.0.9`` ``GCCcore/9.3.0`` +``2.2.1`` ``GCCcore/10.3.0`` +========= ================== .. _list_software_sbt_329: @@ -40260,27 +40715,27 @@ scikit-image is a collection of algorithms for image processing. *homepage*: https://scikit-image.org/ -========== ================== =================================================== -version versionsuffix toolchain -========== ================== =================================================== -``0.12.3`` ``-Python-2.7.11`` ``foss/2016a`` -``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` -``0.12.3`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``0.13.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.13.0`` ``-Python-3.6.1`` ``intel/2017a`` -``0.13.0`` ``-Python-3.6.3`` ``foss/2017b`` -``0.13.1`` ``-Python-2.7.14`` ``intel/2017b`` -``0.13.1`` ``-Python-3.6.3`` ``foss/2017b`` -``0.13.1`` ``-Python-3.6.4`` ``foss/2018a`` -``0.14.0`` ``-Python-3.6.4`` ``intel/2018a`` -``0.14.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``0.15.0`` ``-Python-3.7.2`` ``foss/2019a`` -``0.16.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``0.17.1`` ``-Python-3.8.2`` ``foss/2020a`` -``0.18.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``0.18.3`` ``foss/2021a`` -``0.19.1`` ``foss/2021b`` -========== ================== =================================================== +========== ================== ======================================================================== +version versionsuffix toolchain +========== ================== ======================================================================== +``0.12.3`` ``-Python-2.7.11`` ``foss/2016a`` +``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` +``0.12.3`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``0.13.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.13.0`` ``-Python-3.6.1`` ``intel/2017a`` +``0.13.0`` ``-Python-3.6.3`` ``foss/2017b`` +``0.13.1`` ``-Python-2.7.14`` ``intel/2017b`` +``0.13.1`` ``-Python-3.6.3`` ``foss/2017b`` +``0.13.1`` ``-Python-3.6.4`` ``foss/2018a`` +``0.14.0`` ``-Python-3.6.4`` ``intel/2018a`` +``0.14.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``0.15.0`` ``-Python-3.7.2`` ``foss/2019a`` +``0.16.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``0.17.1`` ``-Python-3.8.2`` ``foss/2020a`` +``0.18.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +``0.18.3`` ``foss/2021a`` +``0.19.1`` ``foss/2021b`` +========== ================== ======================================================================== .. _list_software_scikit-learn_1222: @@ -40988,13 +41443,13 @@ SeqAn is an open source C++ library of efficient algorithms and data structures *homepage*: https://www.seqan.de/ -========= ============= =============================================================================================================== -version versionsuffix toolchain -========= ============= =============================================================================================================== -``1.4.2`` ``-library`` ``system`` -``2.3.2`` ``foss/2016b`` -``2.4.0`` ``GCC/8.2.0-2.31.1``, ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2018b`` -========= ============= =============================================================================================================== +========= ============= =================================================================================================================================== +version versionsuffix toolchain +========= ============= =================================================================================================================================== +``1.4.2`` ``-library`` ``system`` +``2.3.2`` ``foss/2016b`` +``2.4.0`` ``GCC/8.2.0-2.31.1``, ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2018b`` +========= ============= =================================================================================================================================== .. _list_software_SeqAn3_523: @@ -41408,12 +41863,13 @@ Faster SPAdes assembly of Illumina reads *homepage*: https://github.com/tseemann/shovill -========= ================== ============== -version versionsuffix toolchain -========= ================== ============== -``0.9.0`` ``-Python-2.7.14`` ``foss/2018a`` -``1.0.4`` ``-Python-2.7.15`` ``foss/2018b`` -========= ================== ============== +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``0.9.0`` ``-Python-2.7.14`` ``foss/2018a`` +``1.0.4`` ``-Python-2.7.15`` ``foss/2018b`` +``1.1.0`` ``gompi/2021b`` +========= ================== =============== .. _list_software_shrinkwrap_1097: @@ -41518,7 +41974,7 @@ version versionsuffix toolchain ``4.1-b4`` ``foss/2018b``, ``intel/2018b`` ``4.1-MaX-1.0`` ``intel/2019b`` ``4.1-MaX-1.0`` ``-PEXSI`` ``intel/2019b`` -``4.1.5`` ``foss/2020a`` +``4.1.5`` ``foss/2020a``, ``intel/2020a`` =============== ============= =============================== @@ -41778,12 +42234,13 @@ SKESA is a de-novo sequence read assembler for cultured single isolate genomes b *homepage*: https://github.com/ncbi/SKESA -========= ============== -version toolchain -========= ============== -``2.2`` ``foss/2018a`` -``2.3.0`` ``foss/2018b`` -========= ============== +========= ================== =============== +version versionsuffix toolchain +========= ================== =============== +``2.2`` ``foss/2018a`` +``2.3.0`` ``foss/2018b`` +``2.4.0`` ``_saute.1.3.0_1`` ``gompi/2021b`` +========= ================== =============== .. _list_software_sketchmap_960: @@ -41834,6 +42291,38 @@ version toolchain ========= ============== +.. _list_software_skorch_650: + +*skorch* +++++++++ + +A scikit-learn compatible neural network library that wraps PyTorch. + +*homepage*: https://skorch.readthedocs.io/ + +========== =================== ============== +version versionsuffix toolchain +========== =================== ============== +``0.11.0`` ``-PyTorch-1.10.0`` ``foss/2021a`` +========== =================== ============== + + +.. _list_software_SlamDunk_799: + +*SlamDunk* +++++++++++ + +SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis. + +*homepage*: https://t-neumann.github.io/slamdunk + +========= ============== +version toolchain +========= ============== +``0.4.3`` ``foss/2021b`` +========= ============== + + .. _list_software_SLATEC_444: *SLATEC* @@ -42346,6 +42835,7 @@ version toolchain ========= ================================= ``4.0.1`` ``GCC/10.2.0``, ``GCCcore/9.3.0`` ``4.0.2`` ``GCC/10.3.0`` +``4.0.3`` ``GCC/11.2.0`` ========= ================================= @@ -42844,6 +43334,22 @@ version toolchain ========= ========== +.. _list_software_SPM_240: + +*SPM* ++++++ + +SPM (Statistical Parametric Mapping) refers to the construction and assessment of spatially extended statistical processes used to test hypo- theses about functional imaging data. These ideas have been instantiated in software that is called SPM. The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG. + +*homepage*: https://www.fil.ion.ucl.ac.uk/spm + +============== ================= ========== +version versionsuffix toolchain +============== ================= ========== +``12.5_r7771`` ``-MATLAB-2021a`` ``system`` +============== ================= ========== + + .. _list_software_spoa_435: *spoa* @@ -42853,14 +43359,14 @@ Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) alg *homepage*: https://github.com/rvaser/spoa -========= ================== -version toolchain -========= ================== -``3.0.1`` ``GCC/7.3.0-2.30`` -``3.4.0`` ``GCC/10.2.0`` -``4.0.0`` ``GCC/8.3.0`` -``4.0.7`` ``GCC/10.2.0`` -========= ================== +========= ============================== +version toolchain +========= ============================== +``3.0.1`` ``GCC/7.3.0-2.30`` +``3.4.0`` ``GCC/10.2.0`` +``4.0.0`` ``GCC/8.3.0`` +``4.0.7`` ``GCC/10.2.0``, ``GCC/10.3.0`` +========= ============================== .. _list_software_SPRNG_394: @@ -43138,7 +43644,7 @@ version toolchain ``2.3e`` ``foss/2018b`` ``2.5`` ``iccifort/2019.5.281`` ``2.41`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2.53`` ``foss/2019b`` +``2.53`` ``foss/2019b``, ``iccifort/2019.5.281`` ``2.54`` ``foss/2020a`` ============== ============================================================================== @@ -43432,6 +43938,22 @@ version toolchain ========== ================================== +.. _list_software_STRique_685: + +*STRique* ++++++++++ + +STRique is a python package to analyze repeat expansion and methylation states of short tandem repeats (STR) in Oxford Nanopore Technology (ONT) long read sequencing data. + +*homepage*: https://github.com/giesselmann/STRique + +========= ============== +version toolchain +========= ============== +``0.4.2`` ``foss/2021b`` +========= ============== + + .. _list_software_Structure_977: *Structure* @@ -43971,6 +44493,7 @@ version versionsuffix toolchain ``1.6.2`` ``-Python-3.8.2`` ``foss/2020a`` ``1.7.1`` ``foss/2020b``, ``intel/2020b`` ``1.8`` ``foss/2021a`` +``1.9`` ``foss/2021b`` ========= ================== =============================== @@ -44450,8 +44973,11 @@ version versionsuffix toolchain ``2.3.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` ``2.4.1`` ``foss/2020b``, ``fosscuda/2020b`` ``2.4.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2.4.4`` ``foss/2021a`` ``2.5.0`` ``foss/2020b``, ``fosscuda/2020b`` ``2.5.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2.5.3`` ``foss/2021a`` +``2.5.3`` ``-CUDA-11.3.1`` ``foss/2021a`` ``2.6.0`` ``foss/2021a`` ``2.6.0`` ``-CUDA-11.3.1`` ``foss/2021a`` ========== ============================= =================================================== @@ -44653,12 +45179,12 @@ TeX is a typesetting language. Instead of visually formatting your text, you ent *homepage*: https://tug.org -============ ================= -version toolchain -============ ================= -``20200406`` ``GCCcore/8.3.0`` -``20210324`` ``GCC/11.2.0`` -============ ================= +============ ============================== +version toolchain +============ ============================== +``20200406`` ``GCCcore/8.3.0`` +``20210324`` ``GCC/10.3.0``, ``GCC/11.2.0`` +============ ============================== .. _list_software_Text-CSV_702: @@ -44686,29 +45212,29 @@ Theano is a Python library that allows you to define, optimize, and evaluate mat *homepage*: https://deeplearning.net/software/theano -========= ================== ==================================================================== -version versionsuffix toolchain -========= ================== ==================================================================== -``0.8.2`` ``-Python-2.7.11`` ``foss/2016a`` -``0.8.2`` ``-Python-3.5.1`` ``foss/2016a`` -``0.8.2`` ``-Python-3.5.2`` ``intel/2016b`` -``0.9.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.9.0`` ``-Python-3.6.1`` ``intel/2017a`` -``1.0.0`` ``-Python-2.7.14`` ``intel/2017b`` -``1.0.0`` ``-Python-3.6.3`` ``intel/2017b`` -``1.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.0.2`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` -``1.0.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``1.0.2`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intelcuda/2017b`` -``1.0.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``1.0.4`` ``foss/2019a``, ``fosscuda/2019a`` -``1.0.4`` ``-Python-3.6.4`` ``foss/2018a`` -``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` -``1.0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``1.0.4`` ``-Python-3.8.2`` ``foss/2020a`` -``1.1.2`` ``-PyMC`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021b`` -========= ================== ==================================================================== +========= ================== ==================================================================================== +version versionsuffix toolchain +========= ================== ==================================================================================== +``0.8.2`` ``-Python-2.7.11`` ``foss/2016a`` +``0.8.2`` ``-Python-3.5.1`` ``foss/2016a`` +``0.8.2`` ``-Python-3.5.2`` ``intel/2016b`` +``0.9.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.9.0`` ``-Python-3.6.1`` ``intel/2017a`` +``1.0.0`` ``-Python-2.7.14`` ``intel/2017b`` +``1.0.0`` ``-Python-3.6.3`` ``intel/2017b`` +``1.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``1.0.2`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``1.0.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``1.0.2`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``1.0.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``1.0.4`` ``foss/2019a``, ``fosscuda/2019a`` +``1.0.4`` ``-Python-3.6.4`` ``foss/2018a`` +``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` +``1.0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``1.0.4`` ``-Python-3.8.2`` ``foss/2020a`` +``1.1.2`` ``-PyMC`` ``foss/2020b``, ``foss/2021b``, ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021b`` +========= ================== ==================================================================================== .. _list_software_ThemisPy_819: @@ -44992,16 +45518,16 @@ tmux is a terminal multiplexer: it enables a number of terminals to be created, *homepage*: https://github.com/tmux/tmux/ -======== ====================================== -version toolchain -======== ====================================== -``1.9a`` ``GCC/4.9.2`` -``2.2`` ``GCCcore/4.9.3`` -``2.3`` ``GCC/5.4.0-2.26``, ``system`` -``3.1c`` ``GCCcore/8.3.0`` -``3.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.2a`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -======== ====================================== +======== ================================================== +version toolchain +======== ================================================== +``1.9a`` ``GCC/4.9.2`` +``2.2`` ``GCCcore/4.9.3`` +``2.3`` ``GCC/5.4.0-2.26``, ``system`` +``3.1c`` ``GCCcore/8.3.0`` +``3.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.2a`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``system`` +======== ================================================== .. _list_software_TN93_270: @@ -46642,12 +47168,12 @@ Sequence assembler for very short reads *homepage*: http://www.ebi.ac.uk/~zerbino/velvet/ -========== ================ ============================================= -version versionsuffix toolchain -========== ================ ============================================= -``1.2.10`` ``-mt-kmer_191`` ``GCC/8.3.0``, ``foss/2018a``, ``foss/2018b`` -``1.2.10`` ``-mt-kmer_37`` ``intel/2017a`` -========== ================ ============================================= +========== ================ ============================================================= +version versionsuffix toolchain +========== ================ ============================================================= +``1.2.10`` ``-mt-kmer_191`` ``GCC/11.2.0``, ``GCC/8.3.0``, ``foss/2018a``, ``foss/2018b`` +``1.2.10`` ``-mt-kmer_37`` ``intel/2017a`` +========== ================ ============================================================= .. _list_software_VEP_235: @@ -46772,6 +47298,7 @@ version toolchain ========= ================= ``2.6.1`` ``foss/2018b`` ``2.6.2`` ``GCCcore/9.3.0`` +``3.0`` ``GCC/11.2.0`` ========= ================= @@ -46963,6 +47490,8 @@ version versionsuffix toolchain ``5.2.5`` ``system`` ``5.2.6`` ``system`` ``5.2.7`` ``system`` +``5.2.9`` ``system`` +``5.2.10`` ``system`` =========== ================================== =============== @@ -47015,6 +47544,7 @@ version toolchain ``2.13.4`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.15.0`` ``GCC/9.3.0`` ``2.18.0`` ``GCC/10.2.0`` +``2.21.1`` ``GCC/10.3.0`` ========== ======================================== @@ -47063,6 +47593,7 @@ version versionsuffix toolchain ``8.2.0`` ``-Python-3.7.4`` ``foss/2019b`` ``8.2.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` ``9.0.1`` ``foss/2020b``, ``foss/2021a`` +``9.1.0`` ``foss/2021b`` ========= ================== =================================================== @@ -47099,6 +47630,7 @@ version toolchain ``2021.6.0`` ``system`` ``2021.9.0`` ``system`` ``2022.0.0`` ``system`` +``2022.2.0`` ``system`` ================= ========== @@ -47363,11 +47895,11 @@ WhatsHap is a software for phasing genomic variants using DNA sequencing reads, *homepage*: https://whatshap.readthedocs.io -======= ============== -version toolchain -======= ============== -``1.1`` ``foss/2020b`` -======= ============== +======= ============================== +version toolchain +======= ============================== +``1.1`` ``foss/2020b``, ``foss/2021a`` +======= ============================== .. _list_software_wheel_533: @@ -47678,7 +48210,7 @@ version toolchain --- -:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtensor_787` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_xxd_340` - :ref:`list_software_xxHash_628` - :ref:`list_software_XZ_178` +:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-Compile_999` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtensor_787` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_xxd_340` - :ref:`list_software_xxHash_628` - :ref:`list_software_XZ_178` .. _list_software_X11_186: @@ -48060,6 +48592,7 @@ version versionsuffix toolchain ``0.72.1`` ``-Python-2.7.14`` ``intel/2017b`` ``0.90`` ``-Python-3.7.4`` ``foss/2019b`` ``1.2.0`` ``-Python-3.8.2`` ``foss/2020a`` +``1.5.0`` ``foss/2021a`` ``20171120`` ``-Java-1.8.0_152`` ``intel/2017b`` ============ =================== =============== @@ -48146,6 +48679,22 @@ version versionsuffix toolchain ================== ================== ================================== +.. _list_software_XML-Compile_999: + +*XML-Compile* ++++++++++++++ + +Perl module for compilation based XML processing + +*homepage*: https://metacpan.org/pod/XML::Compile + +======== ================== +version toolchain +======== ================== +``1.63`` ``GCCcore/11.2.0`` +======== ================== + + .. _list_software_XML-LibXML_806: *XML-LibXML* diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index ea13f8d3..3eaf494b 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -306,6 +306,19 @@ * EB_XML * RubyGem + * Tarball + + * BinariesTarball + * EB_cuDNN + * EB_FoldX + * EB_FreeSurfer + * EB_Gurobi + * EB_Hadoop + * EB_MTL4 + * EB_picard + * EB_RepeatMasker + * EB_RepeatModeler + * GoPackage * IntelBase @@ -375,19 +388,6 @@ * EB_Xmipp - * Tarball - - * BinariesTarball - * EB_cuDNN - * EB_FoldX - * EB_FreeSurfer - * EB_Gurobi - * EB_Hadoop - * EB_MTL4 - * EB_picard - * EB_RepeatMasker - * EB_RepeatModeler - * Waf * **Extension** @@ -448,5 +448,18 @@ * EB_XML * RubyGem + * Tarball + + * BinariesTarball + * EB_cuDNN + * EB_FoldX + * EB_FreeSurfer + * EB_Gurobi + * EB_Hadoop + * EB_MTL4 + * EB_picard + * EB_RepeatMasker + * EB_RepeatModeler + diff --git a/docs/version-specific/easyconfig_parameters.rst b/docs/version-specific/easyconfig_parameters.rst index cf020344..276433e6 100644 --- a/docs/version-specific/easyconfig_parameters.rst +++ b/docs/version-specific/easyconfig_parameters.rst @@ -48,6 +48,7 @@ build parameters ``checksums`` Checksums for sources and patches [] ``configopts`` Extra options passed to configure (default already has --prefix) "" ``cuda_compute_capabilities`` List of CUDA compute capabilities to build with (if supported) [] +``download_instructions`` Specify steps to aquire necessary file, if obtaining it is difficult "" ``easyblock`` EasyBlock to use for building; if set to None, an easyblock is selected based on the software name None ``easybuild_version`` EasyBuild-version this spec-file was written for None ``enhance_sanity_check`` Indicate that additional sanity check commands & paths should enhance the existin sanity check, not replace it False @@ -61,6 +62,7 @@ build parameters ``parallel`` Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit) None ``patches`` List of patches to apply [] ``postinstallcmds`` Commands to run after the install step. [] +``postinstallpatches`` Patch files to apply after running the install step. [] ``prebuildopts`` Extra options pre-passed to build command. "" ``preconfigopts`` Extra options pre-passed to configure. "" ``preinstallopts`` Extra prefix options for installation. "" diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index f4598106..8e1d70b8 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -28,6 +28,7 @@ Extra easyconfig parameters specific to ``BinariesTarball`` easyblock easyconfig parameter description default value ==================== ============================================================================================================================================================= ============= ``install_type`` Defaults to extract tarball into clean directory. Options: 'merge' merges tarball to existing directory, 'subdir' extracts tarball into its own sub-directory ``None`` +``options`` Dictionary with extension options. ``{}`` ``preinstall_cmd`` Command to execute before installation ``None`` ==================== ============================================================================================================================================================= ============= @@ -1247,7 +1248,7 @@ easyconfig parameter description ``Tarball`` =========== -(derives from EasyBlock) +(derives from ExtensionEasyBlock) Precompiled software supplied as a tarball: - will unpack binary and copy it to the install dir @@ -1259,6 +1260,7 @@ Extra easyconfig parameters specific to ``Tarball`` easyblock easyconfig parameter description default value ==================== ============================================================================================================================================================= ============= ``install_type`` Defaults to extract tarball into clean directory. Options: 'merge' merges tarball to existing directory, 'subdir' extracts tarball into its own sub-directory ``None`` +``options`` Dictionary with extension options. ``{}`` ``preinstall_cmd`` Command to execute before installation ``None`` ==================== ============================================================================================================================================================= ============= diff --git a/docs/version-specific/toolchain_opts.rst b/docs/version-specific/toolchain_opts.rst index 865d4d7a..08bad56f 100644 --- a/docs/version-specific/toolchain_opts.rst +++ b/docs/version-specific/toolchain_opts.rst @@ -5,7 +5,7 @@ Available toolchain options (by toolchain) *(see also* ``eb --avail-toolchain-opts `` *)* -ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - nvompic_ - nvpsmpic_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ +ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpit_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - nvompic_ - nvpsmpic_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ .. _ClangGCC: @@ -1443,6 +1443,52 @@ option description ========================= ======================================================================= ========= +.. _gmpit: + +Available options for gmpit toolchain +------------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``f2c`` Generate code compatible with f2c and f77 ``False`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``loop`` Automatic loop parallellisation ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``lto`` Enable Link Time Optimization ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + .. _gmpolf: Available options for gmpolf toolchain diff --git a/docs/version-specific/toolchains.rst b/docs/version-specific/toolchains.rst index eabb54be..f2b67ade 100644 --- a/docs/version-specific/toolchains.rst +++ b/docs/version-specific/toolchains.rst @@ -3,95 +3,96 @@ List of known toolchains ------------------------ -=================== ================ =========== ========================= ======== -Name Compiler(s) MPI Linear algebra FFT -=================== ================ =========== ========================= ======== -**cgmpich** Clang, GCC MPICH *(none)* *(none)* -**cgmpolf** Clang, GCC MPICH OpenBLAS, ScaLAPACK FFTW -**cgmvapich2** Clang, GCC MVAPICH2 *(none)* *(none)* -**cgmvolf** Clang, GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW -**cgompi** Clang, GCC OpenMPI *(none)* *(none)* -**cgoolf** Clang, GCC OpenMPI OpenBLAS, ScaLAPACK FFTW -**ClangGCC** Clang, GCC *(none)* *(none)* *(none)* -**CrayCCE** PrgEnv-cray cray-mpich cray-libsci *(none)* -**CrayGNU** PrgEnv-gnu cray-mpich cray-libsci *(none)* -**CrayIntel** PrgEnv-intel cray-mpich cray-libsci *(none)* -**CrayPGI** PrgEnv-pgi cray-mpich cray-libsci *(none)* -**FCC** lang *(none)* *(none)* *(none)* -**ffmpi** FCC *(none)* *(none)* *(none)* -**foss** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW -**fosscuda** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW -**Fujitsu** FCC *(none)* *(none)* FFTW -**GCC** GCC *(none)* *(none)* *(none)* -**GCCcore** GCCcore *(none)* *(none)* *(none)* -**gcccuda** GCC, CUDA *(none)* *(none)* *(none)* -**gimkl** GCC impi imkl imkl -**gimpi** GCC impi *(none)* *(none)* -**gimpic** GCC, CUDA impi *(none)* *(none)* -**giolf** GCC impi OpenBLAS, ScaLAPACK FFTW -**giolfc** GCC, CUDA impi OpenBLAS, ScaLAPACK FFTW -**gmacml** GCC MVAPICH2 ACML, ScaLAPACK FFTW -**gmkl** GCC *(none)* imkl imkl -**gmklc** GCC, CUDA *(none)* imkl imkl -**gmpich** GCC MPICH *(none)* *(none)* -**gmpich2** GCC MPICH2 *(none)* *(none)* -**gmpolf** GCC MPICH OpenBLAS, ScaLAPACK FFTW -**gmvapich2** GCC MVAPICH2 *(none)* *(none)* -**gmvolf** GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW -**GNU** GCC *(none)* *(none)* *(none)* -**goalf** GCC OpenMPI ATLAS, ScaLAPACK FFTW -**gobff** GCC OpenMPI BLIS, libFLAME, ScaLAPACK FFTW -**goblf** GCC OpenMPI BLIS, LAPACK, ScaLAPACK FFTW -**gofbf** GCC OpenMPI FlexiBLAS, ScaLAPACK FFTW -**golf** GCC *(none)* OpenBLAS FFTW -**golfc** GCC, CUDA *(none)* OpenBLAS FFTW -**gomkl** GCC OpenMPI imkl imkl -**gomklc** GCC, CUDA OpenMPI imkl imkl -**gompi** GCC OpenMPI *(none)* *(none)* -**gompic** GCC, CUDA OpenMPI *(none)* *(none)* -**goolf** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW -**goolfc** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW -**gpsmpi** GCC psmpi *(none)* *(none)* -**gpsolf** GCC psmpi OpenBLAS, ScaLAPACK FFTW -**gqacml** GCC QLogicMPI ACML, ScaLAPACK FFTW -**gsmpi** GCC SpectrumMPI *(none)* *(none)* -**gsolf** GCC SpectrumMPI OpenBLAS, ScaLAPACK FFTW -**iccifort** icc, ifort *(none)* *(none)* *(none)* -**iccifortcuda** icc, ifort, CUDA *(none)* *(none)* *(none)* -**ictce** icc, ifort impi imkl imkl -**iibff** icc, ifort impi BLIS, libFLAME, ScaLAPACK FFTW -**iimkl** icc, ifort *(none)* imkl imkl -**iimklc** icc, ifort, CUDA *(none)* imkl imkl -**iimpi** icc, ifort impi *(none)* *(none)* -**iimpic** icc, ifort, CUDA impi *(none)* *(none)* -**iiqmpi** icc, ifort QLogicMPI *(none)* *(none)* -**impich** icc, ifort MPICH *(none)* *(none)* -**impmkl** icc, ifort MPICH imkl imkl -**intel** icc, ifort impi imkl imkl -**intel-compilers** intel-compilers *(none)* *(none)* *(none)* -**intel-para** icc, ifort psmpi imkl imkl -**intelcuda** icc, ifort, CUDA impi imkl imkl -**iomkl** icc, ifort OpenMPI imkl imkl -**iomklc** icc, ifort, CUDA OpenMPI imkl imkl -**iompi** icc, ifort OpenMPI *(none)* *(none)* -**iompic** icc, ifort, CUDA OpenMPI *(none)* *(none)* -**ipsmpi** icc, ifort psmpi *(none)* *(none)* -**iqacml** icc, ifort QLogicMPI ACML, ScaLAPACK FFTW -**ismkl** icc, ifort MPICH2 imkl imkl -**NVHPC** NVHPC *(none)* *(none)* *(none)* -**nvompic** NVHPC OpenMPI *(none)* *(none)* -**nvpsmpic** NVHPC psmpi *(none)* *(none)* -**PGI** PGI *(none)* *(none)* *(none)* -**pmkl** PGI *(none)* imkl imkl -**pomkl** PGI OpenMPI imkl imkl -**pompi** PGI OpenMPI *(none)* *(none)* -**system** *(none)* *(none)* *(none)* *(none)* -**xlcxlf** xlc, xlf *(none)* *(none)* *(none)* -**xlmpich** xlc, xlf MPICH *(none)* *(none)* -**xlmpich2** xlc, xlf MPICH2 *(none)* *(none)* -**xlmvapich2** xlc, xlf MVAPICH2 *(none)* *(none)* -**xlompi** xlc, xlf OpenMPI *(none)* *(none)* -=================== ================ =========== ========================= ======== +=================== ================ ============= ========================= ======== +Name Compiler(s) MPI Linear algebra FFT +=================== ================ ============= ========================= ======== +**cgmpich** Clang, GCC MPICH *(none)* *(none)* +**cgmpolf** Clang, GCC MPICH OpenBLAS, ScaLAPACK FFTW +**cgmvapich2** Clang, GCC MVAPICH2 *(none)* *(none)* +**cgmvolf** Clang, GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW +**cgompi** Clang, GCC OpenMPI *(none)* *(none)* +**cgoolf** Clang, GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**ClangGCC** Clang, GCC *(none)* *(none)* *(none)* +**CrayCCE** PrgEnv-cray cray-mpich cray-libsci *(none)* +**CrayGNU** PrgEnv-gnu cray-mpich cray-libsci *(none)* +**CrayIntel** PrgEnv-intel cray-mpich cray-libsci *(none)* +**CrayPGI** PrgEnv-pgi cray-mpich cray-libsci *(none)* +**FCC** lang *(none)* *(none)* *(none)* +**ffmpi** FCC *(none)* *(none)* *(none)* +**foss** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**fosscuda** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW +**Fujitsu** FCC *(none)* *(none)* FFTW +**GCC** GCC *(none)* *(none)* *(none)* +**GCCcore** GCCcore *(none)* *(none)* *(none)* +**gcccuda** GCC, CUDA *(none)* *(none)* *(none)* +**gimkl** GCC impi imkl imkl +**gimpi** GCC impi *(none)* *(none)* +**gimpic** GCC, CUDA impi *(none)* *(none)* +**giolf** GCC impi OpenBLAS, ScaLAPACK FFTW +**giolfc** GCC, CUDA impi OpenBLAS, ScaLAPACK FFTW +**gmacml** GCC MVAPICH2 ACML, ScaLAPACK FFTW +**gmkl** GCC *(none)* imkl imkl +**gmklc** GCC, CUDA *(none)* imkl imkl +**gmpich** GCC MPICH *(none)* *(none)* +**gmpich2** GCC MPICH2 *(none)* *(none)* +**gmpit** GCC MPItrampoline *(none)* *(none)* +**gmpolf** GCC MPICH OpenBLAS, ScaLAPACK FFTW +**gmvapich2** GCC MVAPICH2 *(none)* *(none)* +**gmvolf** GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW +**GNU** GCC *(none)* *(none)* *(none)* +**goalf** GCC OpenMPI ATLAS, ScaLAPACK FFTW +**gobff** GCC OpenMPI BLIS, libFLAME, ScaLAPACK FFTW +**goblf** GCC OpenMPI BLIS, LAPACK, ScaLAPACK FFTW +**gofbf** GCC OpenMPI FlexiBLAS, ScaLAPACK FFTW +**golf** GCC *(none)* OpenBLAS FFTW +**golfc** GCC, CUDA *(none)* OpenBLAS FFTW +**gomkl** GCC OpenMPI imkl imkl +**gomklc** GCC, CUDA OpenMPI imkl imkl +**gompi** GCC OpenMPI *(none)* *(none)* +**gompic** GCC, CUDA OpenMPI *(none)* *(none)* +**goolf** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**goolfc** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW +**gpsmpi** GCC psmpi *(none)* *(none)* +**gpsolf** GCC psmpi OpenBLAS, ScaLAPACK FFTW +**gqacml** GCC QLogicMPI ACML, ScaLAPACK FFTW +**gsmpi** GCC SpectrumMPI *(none)* *(none)* +**gsolf** GCC SpectrumMPI OpenBLAS, ScaLAPACK FFTW +**iccifort** icc, ifort *(none)* *(none)* *(none)* +**iccifortcuda** icc, ifort, CUDA *(none)* *(none)* *(none)* +**ictce** icc, ifort impi imkl imkl +**iibff** icc, ifort impi BLIS, libFLAME, ScaLAPACK FFTW +**iimkl** icc, ifort *(none)* imkl imkl +**iimklc** icc, ifort, CUDA *(none)* imkl imkl +**iimpi** icc, ifort impi *(none)* *(none)* +**iimpic** icc, ifort, CUDA impi *(none)* *(none)* +**iiqmpi** icc, ifort QLogicMPI *(none)* *(none)* +**impich** icc, ifort MPICH *(none)* *(none)* +**impmkl** icc, ifort MPICH imkl imkl +**intel** icc, ifort impi imkl imkl +**intel-compilers** intel-compilers *(none)* *(none)* *(none)* +**intel-para** icc, ifort psmpi imkl imkl +**intelcuda** icc, ifort, CUDA impi imkl imkl +**iomkl** icc, ifort OpenMPI imkl imkl +**iomklc** icc, ifort, CUDA OpenMPI imkl imkl +**iompi** icc, ifort OpenMPI *(none)* *(none)* +**iompic** icc, ifort, CUDA OpenMPI *(none)* *(none)* +**ipsmpi** icc, ifort psmpi *(none)* *(none)* +**iqacml** icc, ifort QLogicMPI ACML, ScaLAPACK FFTW +**ismkl** icc, ifort MPICH2 imkl imkl +**NVHPC** NVHPC *(none)* *(none)* *(none)* +**nvompic** NVHPC OpenMPI *(none)* *(none)* +**nvpsmpic** NVHPC psmpi *(none)* *(none)* +**PGI** PGI *(none)* *(none)* *(none)* +**pmkl** PGI *(none)* imkl imkl +**pomkl** PGI OpenMPI imkl imkl +**pompi** PGI OpenMPI *(none)* *(none)* +**system** *(none)* *(none)* *(none)* *(none)* +**xlcxlf** xlc, xlf *(none)* *(none)* *(none)* +**xlmpich** xlc, xlf MPICH *(none)* *(none)* +**xlmpich2** xlc, xlf MPICH2 *(none)* *(none)* +**xlmvapich2** xlc, xlf MVAPICH2 *(none)* *(none)* +**xlompi** xlc, xlf OpenMPI *(none)* *(none)* +=================== ================ ============= ========================= ======== *(see also* ``eb --list-toolchains`` *)* From 5da1959be3ed8eff330ac2a78a2231db01fe0a6a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 30 Mar 2022 22:59:56 +0200 Subject: [PATCH 206/286] update release notes and changelog for EasyBuild v4.5.4 + bump version to 4.5.4 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 133 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 134 insertions(+), 4 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index d2f71ebf..4f007bf2 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20220211.01** (`Mar 31st 2022`): update release notes for EasyBuild v4.5.4 (see :ref:`release_notes_eb454`) * **release 20220211.01** (`Feb 11th 2022`): update release notes for EasyBuild v4.5.3 (see :ref:`release_notes_eb453`) * **release 20220124.01** (`Jan 24th 2022`): update release notes for EasyBuild v4.5.2 (see :ref:`release_notes_eb452`) * **release 20211213.01** (`Dec 13th 2021`): update release notes for EasyBuild v4.5.1 (see :ref:`release_notes_eb451`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 3bc5ad01..6c44142c 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,141 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,647** different software packages, +The latest version of EasyBuild provides support for building and installing **2,667** different software packages, including 36 different (compiler) toolchains. It contains 244 software-specific easyblocks and 37 generic easyblocks, -alongside 14,282 easyconfig files. +alongside 14,449 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb454: + +EasyBuild v4.5.4 (March 31st 2022) +---------------------------------- + +bugfix/update release + +**framework** + +* various enhancements, including: + + * warn about potentially missing patches in --new-pr (#3759, `#3966 `_) + * add support for 'clone_into' field in git_config source spec to specify different name for top-level directory (`#3949 `_) + * add bash completion for easyconfigs from local dir but not robot search path (`#3953 `_) + * add a 'sync pr' message when the PR has a mergeable state but is showing a failed status for the test suite on the last commit (`#3967 `_) + * add gmpit toolchain definition (GCC + MPItrampoline) (`#3971 `_) + * use 'zypper search -i' to check whether specified OS dependency is installed on openSUSE + make sure that rpm is considered for checking OS dependencies on RHEL8 (`#3973 `_) + * add support for post-install patches (`#3974 `_) + * add support for 'download_instructions' easyconfig parameter key to specify some download or installation steps for user in case of complicated way of obtaining needed files (#3976, `#3981 `_) + * also try collecting AMD GPU info (via rocm-smi) for --show-system-info (#3978, `#3982 `_) + +* various bug fixes, including: + + * ensure --review-pr can find dependencies included in PR (`#3979 `_) + * run 'apt-get update' in GitHub Actions workflow for container tests to update container package list before installing anything (`#3985 `_) + +* other changes: + + * enable code linting check for all supported Python versions (`#3725 `_) + * update copyright lines for 2022 (`#3986 `_) + +**easyblocks** + +* minor enhancements and updates, including: + + * update Clang-AOMP easyblock to add support for ROCm v5.0 (`#2681 `_) + * enable system SSL certificates in OpenSSL installations (`#2683 `_) + * enhance MRtrix easyblock: build in parallel + enable OpenMP support for MRtrix >= 3.0 (`#2685 `_) + * avoid dependency on 'which' command in sanity check for Python, use 'command -v' instead (`#2687 `_) + * enhance Tarball easyblock to support using it for installing extensions (`#2688 `_) + * update wxPython easyblock to support wxPython v4.1 (`#2689 `_) + * enhance Gurobi easyblock to also update $MATLABPATH (`#2691 `_) + * build single-file shared libraries for imkl so it can be used as FlexiBLAS backend via $FLEXIBLAS_LIBRARY_PATH (`#2694 `_) + +* various bug fixes, including: + + * added regex to replace /lib/cpp with cpp in OpenFOAM's wmake rules file (`#2331 `_) + * set $NINJAFLAGS to make sure Ninja doesn't use all visible cores when building Qt5 (`#2338 `_) + * update Siesta EasyBlock to use serial FFTW (`#2662 `_) + * fix support for imkl for numexpr 2.8.0+ in numexpr easyblock (`#2678 `_) + * make sure TensorFlow doesn't see the nvptx-none dir when searching for gcc include dir (`#2682 `_) + * force use of bash for Anaconda install script (`#2692 `_) + * add guess for path to add to $MANPATH for intel-compilers (`#2696 `_) + * change permissions of the Java build directory to avoid permission denied error (`#2698 `_) + * also consider $MKLROOT/lib/pkgconfig for $PKG_CONFIG_PATH for imkl (`#2701 `_) + * close log after installing Bundle component (`#2702 `_) + * replace hardcoded /tmp to make sure that Bazel build respects $TMPDIR (`#2703 `_) + +* other changes: + + * minor code cleanup in numexpr easyblock (`#2679 `_) + * update copyright lines for 2022 (`#2705 `_) + +**easyconfigs** + +* added example easyconfig files for 29 new software packages: + + * Abseil (`#15102 `_), AMS (`#1997 `_), ArchR (`#15119 `_), CMAverse (`#14963 `_), CmdStanR (`#15198 `_), CONN (#963), + Devito (#14984, `#15009 `_), GraphMap (`#10299 `_), gRPC (`#14728 `_), Hydra (`#15025 `_), jupyter-server-proxy (`#14844 `_), + M1QN3 (`#15002 `_), MAGeCK (`#15082 `_), matplotlib-inline (`#15084 `_), MEGAN (`#15064 `_), MNE-Python (`#15174 `_), + ONNX (`#15158 `_), ONNX-Runtime (`#15158 `_), ont-remora (`#15162 `_), Optuna (`#15021 `_), patch (`#15035 `_), + porefoam (`#15067 `_), presto (`#15119 `_), PyFrag (`#15184 `_), skorch (`#15175 `_), SlamDunk (`#15197 `_), SPM (`#15050 `_), + STRique (`#14980 `_), XML-Compile (`#15177 `_) + +* added additional easyconfigs for various supported software packages, including: + + * ABAQUS 2021, AlphaFold 2.1.2, AmberTools 21, archspec 0.1.3, Bandage 0.9.0, BLIS 3.1, c-ares 1.18.1, + CCL 1.12.1, CharLS 2.3.4, Clang-Python-bindings 13.0.1, dcm2niix 1.0.20211006, DFTB+ 21.1, DIRAC 22.0, + ELPA 2021.11.001, FlexiBLAS 3.1.3, FLUENT 2021R2, GATK 4.2.5.0, GetOrganelle 1.7.5.3, IgBLAST 1.18.0, + IntelClusterChecker 2021.5.0, intervaltree-python 3.1.0, ITSx 1.1.3, Julia 1.7.2, kallisto 0.48.0, + KMC 3.2.1, libobjcryst 2021.1.2, libtree 3.0.3, loompy 3.0.7, matplotlib 3.5.1, MCR R2022a, + MDAnalysis 1.1.1+ 2.0.0, MDTraj 1.9.7, medaka 1.5.0, meshalyzer 20200308, MRtrix 3.0.3, NiBabel 3.2.2, + NLTK 3.7, numexpr 2.8.1, ont-fast5-api 4.0.2, OpenAI-Gym 0.21.0, OpenBLAS 0.3.20, ORCA 5.0.3, + parallel-fastq-dump 0.6.6, PIPITS 2.8, pocl 1.8, pycocotools 2.0.4, pyEGA3 4.0.0, pyobjcryst 2.2.1, + RE2 2022-02-01, SAMtools 1.15, SBCL 2.2.1, shovill 1.1.0, SKESA 2.4.0, SOCI 4.0.3, sympy 1.9, TensorFlow 2.5.3, + VirtualGL 3.0, vsc-mympirun 5.2.10, VSEARCH 2.21.1, VTK 9.1.0, VTune 2022.2.0, XGBoost 1.5.0 + +* minor enhancements, including: + + * add Flask-Session to Flask v1.1.4 and Flask v2.0.2 (`#15027 `_) + * add check to verify that patch files touched in PRs have a description in place (`#15061 `_) + * add extensions to R v4.1.2 easyconfig: hash (`#15098 `_), nabor + harmony (`#15117 `_), apluster, DataCombine, docstring, gdalUtils, openair, mstate, SNFtool, and deps (`#15141 `_) + * also install rMATS_P commands in rMATS-turbo easyconfig (`#15113 `_) + * add extensions to Bioconductor v3.14 easyconfig: chromVAR (`#15118 `_), EnsDb.Hsapiens.v79 (`#15154 `_), WGCNA (`#15178 `_) + * add extensions to Perl v5.34.0 easyconfigs: Sys::Info, HTML::Template, Log::Report (`#15176 `_), Sys::Info::Driver::Unknown, Sys::Info::Driver::Linux, Unix::Processors (`#15190 `_) + * enable running of tests for MEME with gompi/2021b (#15191, `#15199 `_) + +* various bug fixes, including: + + * add missing xxd build dependency for recent PLUMED versions (2.6.2, 2.7.x) (`#14847 `_) + * downgrade dependency on nodejs + use jupyter-server-proxy in jupyter-matlab-proxy and configurable-http-proxy easyconfigs using GCCcore/10.3.0 toolchain (`#14942 `_) + * add additional valid checksum for extensions in R 4.1.0 and 4.1.2 easyconfigs: norm (`#14987 `_), optmatch (`#14993 `_) + * avoid pollution in the tmp directory when running the AlphaFold tests (`#14989 `_) + * consistently enable usempi toolchain option in OSU-Micro-Benchmarks easyconfigs (`#15039 `_) + * fix GBprocesS easyconfig by switching to source tarball created using git_config (`#15048 `_) + * add patches for mauveAligner to fix build on RHEL8 (`#15049 `_) + * fix installation of RDKit by using -DBoost_NO_BOOST_CMAKE=ON (`#15051 `_) + * add patch to fix linking error for imread extension in scikit-image easyconfigs using intel toolchain (`#15054 `_) + * avoid excessively long shebang in Autoconf/Automake Perl scripts + promote Perl to runtime dependency + fix Perl shebang for intltool (`#15055 `_) + * fix python shebang in cutadapt script for cutadapt 1.18 w/ GCCcore/8.3.0 (`#15059 `_) + * don't use v2.1.0rc1 release candidate of gmpy2, stick to proper release v2.1.2 (`#15060 `_) + * add M4 as build dependency for CCL-1.12 (`#15075 `_) + * configure libffi 3.4.2 with --disable-exec-static-tramp to prevent segfaults (`#15086 `_) + * set XLA_PYTHON_CLIENT_ALLOCATOR=platform for running tests in jax CUDA easyconfigs (`#15097 `_) + * remove disable flag for RTTI in snappy v1.1.9 (`#15099 `_) + * fix grconvert build for Grace/5.1.25 with foss/2021a by adding libtirpc dependency + related patch (`#15121 `_) + * clean up PSolver and futile easyconfigs and add dynamic libs (`#15148 `_) + * enhance vcflib easyconfigs to also install scripts (`#15181 `_) + * add patch to fix shared linking in vcflib (`#15203 `_) + * fix failing sanity check for PRINSEQ (`#15205 `_) + +* other changes: + + * use typing-extensions from Python v3.9.6 easyconfig in ArviZ and PyMC3 (`#15003 `_) + * disable building of documentation for DBus 1.13.18 (`#15010 `_) + * consistently use system toolchain in EasyBuild easyconfigs (`#15126 `_) + * use EasyBuild hwloc in likwid and move to GCC/intel-compiler level due to Fortran modules (`#15149 `_) + + .. _release_notes_eb453: EasyBuild v4.5.3 (February 11th 2022) diff --git a/docs/conf.py b/docs/conf.py index 57b39b3b..24292701 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.5.3' # this is meant to reference the version of EasyBuild +version = '4.5.4' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20220211.0' # this is meant to reference the version of the documentation itself +release = '20220331.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 85048fca4a631eadbb81fd02b8992fb1594c6471 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2022 08:33:44 +0200 Subject: [PATCH 207/286] fix docs release for EasyBuild v4.5.4 --- docs/Changelog.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 4f007bf2..ea95399e 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,7 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) -* **release 20220211.01** (`Mar 31st 2022`): update release notes for EasyBuild v4.5.4 (see :ref:`release_notes_eb454`) +* **release 20220331.01** (`Mar 31st 2022`): update release notes for EasyBuild v4.5.4 (see :ref:`release_notes_eb454`) * **release 20220211.01** (`Feb 11th 2022`): update release notes for EasyBuild v4.5.3 (see :ref:`release_notes_eb453`) * **release 20220124.01** (`Jan 24th 2022`): update release notes for EasyBuild v4.5.2 (see :ref:`release_notes_eb452`) * **release 20211213.01** (`Dec 13th 2021`): update release notes for EasyBuild v4.5.1 (see :ref:`release_notes_eb451`) From 2f1830f9aecacb422a8c96cfc3fb43074641e3e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2022 08:34:03 +0200 Subject: [PATCH 208/286] fixes, tweaks and formatting for EasyBuild v4.5.4 release notes --- docs/Release_notes.rst | 55 ++++++++++++++++++++++-------------------- 1 file changed, 29 insertions(+), 26 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 6c44142c..01f36c83 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -20,20 +20,20 @@ bugfix/update release * various enhancements, including: - * warn about potentially missing patches in --new-pr (#3759, `#3966 `_) - * add support for 'clone_into' field in git_config source spec to specify different name for top-level directory (`#3949 `_) + * warn about potentially missing patches in ``--new-pr`` (`#3759 `_, `#3966 `_) + * add support for '``clone_into``' field in git_config source spec to specify different name for top-level directory (`#3949 `_) * add bash completion for easyconfigs from local dir but not robot search path (`#3953 `_) * add a 'sync pr' message when the PR has a mergeable state but is showing a failed status for the test suite on the last commit (`#3967 `_) - * add gmpit toolchain definition (GCC + MPItrampoline) (`#3971 `_) - * use 'zypper search -i' to check whether specified OS dependency is installed on openSUSE + make sure that rpm is considered for checking OS dependencies on RHEL8 (`#3973 `_) + * add ``gmpit`` toolchain definition (GCC + MPItrampoline) (`#3971 `_) + * use '``zypper search -i``' to check whether specified OS dependency is installed on openSUSE + make sure that rpm is considered for checking OS dependencies on RHEL8 (`#3973 `_) * add support for post-install patches (`#3974 `_) - * add support for 'download_instructions' easyconfig parameter key to specify some download or installation steps for user in case of complicated way of obtaining needed files (#3976, `#3981 `_) - * also try collecting AMD GPU info (via rocm-smi) for --show-system-info (#3978, `#3982 `_) + * add support for '``download_instructions``' easyconfig parameter key to specify some download or installation steps for user in case of complicated way of obtaining needed files (`#3976 `_, `#3981 `_) + * also try collecting AMD GPU info (via ``rocm-smi``) for ``--show-system-info`` (`#3978 `_, `#3982 `_) * various bug fixes, including: - * ensure --review-pr can find dependencies included in PR (`#3979 `_) - * run 'apt-get update' in GitHub Actions workflow for container tests to update container package list before installing anything (`#3985 `_) + * ensure ``--review-pr`` can find dependencies included in PR (`#3979 `_) + * run '``apt-get update``' in GitHub Actions workflow for container tests to update container package list before installing anything (`#3985 `_) * other changes: @@ -47,25 +47,28 @@ bugfix/update release * update Clang-AOMP easyblock to add support for ROCm v5.0 (`#2681 `_) * enable system SSL certificates in OpenSSL installations (`#2683 `_) * enhance MRtrix easyblock: build in parallel + enable OpenMP support for MRtrix >= 3.0 (`#2685 `_) - * avoid dependency on 'which' command in sanity check for Python, use 'command -v' instead (`#2687 `_) + * avoid dependency on '``which``' command in sanity check for Python, use '``command -v``' instead (`#2687 `_) * enhance Tarball easyblock to support using it for installing extensions (`#2688 `_) * update wxPython easyblock to support wxPython v4.1 (`#2689 `_) - * enhance Gurobi easyblock to also update $MATLABPATH (`#2691 `_) - * build single-file shared libraries for imkl so it can be used as FlexiBLAS backend via $FLEXIBLAS_LIBRARY_PATH (`#2694 `_) + * enhance Gurobi easyblock to also update ``$MATLABPATH`` (`#2691 `_) + * build single-file shared libraries for imkl so it can be used as FlexiBLAS backend via ``$FLEXIBLAS_LIBRARY_PATH`` (`#2694 `_) * various bug fixes, including: * added regex to replace /lib/cpp with cpp in OpenFOAM's wmake rules file (`#2331 `_) - * set $NINJAFLAGS to make sure Ninja doesn't use all visible cores when building Qt5 (`#2338 `_) + * set ``$NINJAFLAGS`` to make sure Ninja doesn't use all visible cores when building Qt5 (`#2338 `_) * update Siesta EasyBlock to use serial FFTW (`#2662 `_) * fix support for imkl for numexpr 2.8.0+ in numexpr easyblock (`#2678 `_) - * make sure TensorFlow doesn't see the nvptx-none dir when searching for gcc include dir (`#2682 `_) + * make sure TensorFlow doesn't see the ``nvptx-none`` dir when searching for ``gcc`` include dir (`#2682 `_) * force use of bash for Anaconda install script (`#2692 `_) - * add guess for path to add to $MANPATH for intel-compilers (`#2696 `_) + * add guess for path to add to ``$MANPATH`` for intel-compilers (`#2696 `_) * change permissions of the Java build directory to avoid permission denied error (`#2698 `_) - * also consider $MKLROOT/lib/pkgconfig for $PKG_CONFIG_PATH for imkl (`#2701 `_) + * also consider ``$MKLROOT/lib/pkgconfig`` for ``$PKG_CONFIG_PATH`` for imkl (`#2701 `_) * close log after installing Bundle component (`#2702 `_) - * replace hardcoded /tmp to make sure that Bazel build respects $TMPDIR (`#2703 `_) + + * fixes problem of log leaking across installations (`framework issue #3533 `_) + + * replace hardcoded /tmp to make sure that Bazel build respects ``$TMPDIR`` (`#2703 `_) * other changes: @@ -76,8 +79,8 @@ bugfix/update release * added example easyconfig files for 29 new software packages: - * Abseil (`#15102 `_), AMS (`#1997 `_), ArchR (`#15119 `_), CMAverse (`#14963 `_), CmdStanR (`#15198 `_), CONN (#963), - Devito (#14984, `#15009 `_), GraphMap (`#10299 `_), gRPC (`#14728 `_), Hydra (`#15025 `_), jupyter-server-proxy (`#14844 `_), + * Abseil (`#15102 `_), AMS (`#13155 `_), ArchR (`#15119 `_), CMAverse (`#14963 `_), CmdStanR (`#15198 `_), CONN (`#15052 `_), + Devito (`#14984 `_, `#15009 `_), GraphMap (`#10299 `_), gRPC (`#14728 `_), Hydra (`#15025 `_), jupyter-server-proxy (`#14844 `_), M1QN3 (`#15002 `_), MAGeCK (`#15082 `_), matplotlib-inline (`#15084 `_), MEGAN (`#15064 `_), MNE-Python (`#15174 `_), ONNX (`#15158 `_), ONNX-Runtime (`#15158 `_), ont-remora (`#15162 `_), Optuna (`#15021 `_), patch (`#15035 `_), porefoam (`#15067 `_), presto (`#15119 `_), PyFrag (`#15184 `_), skorch (`#15175 `_), SlamDunk (`#15197 `_), SPM (`#15050 `_), @@ -104,27 +107,27 @@ bugfix/update release * also install rMATS_P commands in rMATS-turbo easyconfig (`#15113 `_) * add extensions to Bioconductor v3.14 easyconfig: chromVAR (`#15118 `_), EnsDb.Hsapiens.v79 (`#15154 `_), WGCNA (`#15178 `_) * add extensions to Perl v5.34.0 easyconfigs: Sys::Info, HTML::Template, Log::Report (`#15176 `_), Sys::Info::Driver::Unknown, Sys::Info::Driver::Linux, Unix::Processors (`#15190 `_) - * enable running of tests for MEME with gompi/2021b (#15191, `#15199 `_) + * enable running of tests for MEME with ``gompi/2021b`` (#15191, `#15199 `_) * various bug fixes, including: * add missing xxd build dependency for recent PLUMED versions (2.6.2, 2.7.x) (`#14847 `_) - * downgrade dependency on nodejs + use jupyter-server-proxy in jupyter-matlab-proxy and configurable-http-proxy easyconfigs using GCCcore/10.3.0 toolchain (`#14942 `_) + * downgrade dependency on nodejs + use jupyter-server-proxy in jupyter-matlab-proxy and configurable-http-proxy easyconfigs using ``GCCcore/10.3.0`` toolchain (`#14942 `_) * add additional valid checksum for extensions in R 4.1.0 and 4.1.2 easyconfigs: norm (`#14987 `_), optmatch (`#14993 `_) * avoid pollution in the tmp directory when running the AlphaFold tests (`#14989 `_) * consistently enable usempi toolchain option in OSU-Micro-Benchmarks easyconfigs (`#15039 `_) - * fix GBprocesS easyconfig by switching to source tarball created using git_config (`#15048 `_) + * fix GBprocesS easyconfig by switching to source tarball created using ``git_config`` (`#15048 `_) * add patches for mauveAligner to fix build on RHEL8 (`#15049 `_) - * fix installation of RDKit by using -DBoost_NO_BOOST_CMAKE=ON (`#15051 `_) + * fix installation of RDKit by using ``-DBoost_NO_BOOST_CMAKE=ON`` (`#15051 `_) * add patch to fix linking error for imread extension in scikit-image easyconfigs using intel toolchain (`#15054 `_) * avoid excessively long shebang in Autoconf/Automake Perl scripts + promote Perl to runtime dependency + fix Perl shebang for intltool (`#15055 `_) - * fix python shebang in cutadapt script for cutadapt 1.18 w/ GCCcore/8.3.0 (`#15059 `_) + * fix ``python`` shebang in cutadapt script for cutadapt 1.18 w/ ``GCCcore/8.3.0`` (`#15059 `_) * don't use v2.1.0rc1 release candidate of gmpy2, stick to proper release v2.1.2 (`#15060 `_) * add M4 as build dependency for CCL-1.12 (`#15075 `_) - * configure libffi 3.4.2 with --disable-exec-static-tramp to prevent segfaults (`#15086 `_) - * set XLA_PYTHON_CLIENT_ALLOCATOR=platform for running tests in jax CUDA easyconfigs (`#15097 `_) + * configure libffi 3.4.2 with ``--disable-exec-static-tramp`` to prevent segfaults (`#15086 `_) + * set ``XLA_PYTHON_CLIENT_ALLOCATOR=platform`` for running tests in jax CUDA easyconfigs (`#15097 `_) * remove disable flag for RTTI in snappy v1.1.9 (`#15099 `_) - * fix grconvert build for Grace/5.1.25 with foss/2021a by adding libtirpc dependency + related patch (`#15121 `_) + * fix grconvert build for Grace 5.1.25 with ``foss/2021a`` by adding libtirpc dependency + related patch (`#15121 `_) * clean up PSolver and futile easyconfigs and add dynamic libs (`#15148 `_) * enhance vcflib easyconfigs to also install scripts (`#15181 `_) * add patch to fix shared linking in vcflib (`#15203 `_) From 7a7e9a7696ce129d350126571bc281ea122273bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2022 12:10:19 +0200 Subject: [PATCH 209/286] bump version to 4.5.4 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 77d2bc13..96c57cd3 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.5.3' +VERSION = '4.5.4' # Utility function to read README file From 3ab16a0651c085dd5a4d530eb37b2b798b9ae70e Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 4 Apr 2022 16:43:38 +0200 Subject: [PATCH 210/286] Added download_instructions documentation --- docs/Writing_easyconfig_files.rst | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index 02ea6c32..e3f35640 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -428,6 +428,25 @@ For example: .. note:: Custom extraction commands can also be specified as a 2-element tuple, but this format has been deprecated in favor of the Python dictionary format described above; see also :ref:`depr_sources_2_element_tuple`. +Using ``download_instructions`` for user-side part of instalation +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +In some cases, getting some files that are needed for the installation are too complicated to provide up-front, +and the process would be much simpler if user provided said files. + +You can use the ``download_instructions`` parameter to specify steps for the user to do. +This parameter takes string value and prints it whenever build fails because any file needed was not found. +If ``download_instructions`` is not specified, Easybuild prints the default message stating the paths that were tested. + +.. code:: python + + download_instructions = """ + Step 1: Go to example.com and download example.jar. + Step 2: Install example.jar (ensure Java is installed). + Step 3: Go to the installation directory and create Tarball of its contents (tar -czvf example.tar.gz *). + Step 4: Move created Tarball into the same directory, where your easyconfig is located and run build again. + """ + .. _common_easyconfig_param_sources_git_config: Downloading from a Git repository From b03d1c38fe5a0a6997f6660c0cc5a3d5b73b7c09 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 8 Apr 2022 12:07:56 +0100 Subject: [PATCH 211/286] fix typo and add extra reason for manual download --- docs/Writing_easyconfig_files.rst | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index e3f35640..ab58d768 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -428,11 +428,13 @@ For example: .. note:: Custom extraction commands can also be specified as a 2-element tuple, but this format has been deprecated in favor of the Python dictionary format described above; see also :ref:`depr_sources_2_element_tuple`. -Using ``download_instructions`` for user-side part of instalation +Using ``download_instructions`` for user-side part of installation ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -In some cases, getting some files that are needed for the installation are too complicated to provide up-front, -and the process would be much simpler if user provided said files. +In some cases, getting some of the files required for an installation cannot be automated. Reasons for this include: + +* there is a manual stage to combine multiple downloaded files into the required installation file +* the file requires a login to download You can use the ``download_instructions`` parameter to specify steps for the user to do. This parameter takes string value and prints it whenever build fails because any file needed was not found. From ee808c940aa1f0544b2dd67f7b89c926fffa3ae4 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 8 Apr 2022 12:08:38 +0100 Subject: [PATCH 212/286] missed extra ^ --- docs/Writing_easyconfig_files.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index ab58d768..f1b4a0dc 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -429,7 +429,7 @@ For example: in favor of the Python dictionary format described above; see also :ref:`depr_sources_2_element_tuple`. Using ``download_instructions`` for user-side part of installation -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ In some cases, getting some of the files required for an installation cannot be automated. Reasons for this include: From 97ca4d4a3a7ffafee1d4293ace833f6281024e91 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 8 Apr 2022 13:06:42 +0100 Subject: [PATCH 213/286] git_config tag option is for getting a tag --- docs/Writing_easyconfig_files.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index f1b4a0dc..571a9897 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -469,7 +469,7 @@ will be created from the cloned repository). In addition, either of the following keys *must* also be defined: -* ``tag``: the specific tag to download (could be a branch name or an actual tag) +* ``tag``: the specific tag to download * ``commit``: the specific commit ID to download If a recursive checkout should be made of the repository, the ``recursive`` key can be set to ``True``. From 511226388aa9c0c1466ac3e63f1214f2c290e502 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 12 Apr 2022 13:35:44 +0200 Subject: [PATCH 214/286] Bad formatting for example --- docs/Writing_easyconfig_files.rst | 27 ++++++++++++++------------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index 02ea6c32..bdbbc995 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -186,21 +186,22 @@ The ``dict`` has a required ``filename`` key, with ``level`` and ``opts`` being Specifying ``filename`` and ``level`` is same as using a ``tuple`` definition. Example: -``` -patches = [ - # a simple patch file - 'name-versions-fix.patch', - # when creating only new files by patch file, you need to specify level: - ('name-versions-fix.patch', 1), - - # copy file to target_path folder - ('Makefile', 'target_path'), +.. code:: python - # specify patch file and optionally level and opts for patch command - {'filename': 'name-versions-fix.patch', 'level': 1, 'opts': '-l'} -] -``` + patches = [ + # a simple patch file + 'name-versions-fix.patch', + + # when creating only new files by patch file, you need to specify level: + ('name-versions-fix.patch', 1), + + # copy file to target_path folder + ('Makefile', 'target_path'), + + # specify patch file and optionally level and opts for patch command + {'filename': 'name-versions-fix.patch', 'level': 1, 'opts': '-l'} + ] .. _common_easyconfig_param_sources_checksums: From c00e43af0918e624a82805859264ba17f6beffab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 29 May 2022 15:37:21 +0200 Subject: [PATCH 215/286] fix formatting issue in patches subsection --- docs/Writing_easyconfig_files.rst | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index 02ea6c32..353e99e9 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -186,21 +186,22 @@ The ``dict`` has a required ``filename`` key, with ``level`` and ``opts`` being Specifying ``filename`` and ``level`` is same as using a ``tuple`` definition. Example: -``` -patches = [ - # a simple patch file - 'name-versions-fix.patch', - # when creating only new files by patch file, you need to specify level: - ('name-versions-fix.patch', 1), +.. code:: python + + patches = [ + # a simple patch file + 'name-versions-fix.patch', - # copy file to target_path folder - ('Makefile', 'target_path'), + # when creating only new files by patch file, you need to specify level: + ('name-versions-fix.patch', 1), - # specify patch file and optionally level and opts for patch command - {'filename': 'name-versions-fix.patch', 'level': 1, 'opts': '-l'} -] -``` + # copy file to target_path folder + ('Makefile', 'target_path'), + + # specify patch file and optionally level and opts for patch command + {'filename': 'name-versions-fix.patch', 'level': 1, 'opts': '-l'} + ] .. _common_easyconfig_param_sources_checksums: From 2bfc2b1003c9a8fc31ecfc1580969a5062ddc113 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 Jun 2022 14:34:39 +0200 Subject: [PATCH 216/286] auto-update docs for EasyBuild v4.5.5 --- docs/scripts/update-all-docs.sh | 4 +- docs/version-specific/Supported_software.rst | 2097 ++++++++++++------ docs/version-specific/easyblocks.rst | 5 +- docs/version-specific/generic_easyblocks.rst | 32 +- docs/version-specific/help.rst | 3 +- docs/version-specific/toolchain_opts.rst | 133 +- docs/version-specific/toolchains.rst | 3 + 7 files changed, 1594 insertions(+), 683 deletions(-) diff --git a/docs/scripts/update-all-docs.sh b/docs/scripts/update-all-docs.sh index 4c0a6f4b..adcf76cb 100755 --- a/docs/scripts/update-all-docs.sh +++ b/docs/scripts/update-all-docs.sh @@ -73,7 +73,7 @@ echo >> $overview ################################################################################################### # api docs -python $generate_api_script +python3 $generate_api_script # inject label to top of API docs sed -i '' -e 's/easybuild package/.. _easybuild_api_top:\ \ @@ -216,7 +216,7 @@ echo "* :ref:\`Overview of configuration options (eb --help) \`" >> $ov # generic easyblocks doc echo ".. _generic_easyblocks:" > $VERSION_SPECIFIC_DIR/generic_easyblocks.rst echo "" >> $VERSION_SPECIFIC_DIR/generic_easyblocks.rst -python $generic_easyblocks_script >> $VERSION_SPECIFIC_DIR/generic_easyblocks.rst +python3 $generic_easyblocks_script >> $VERSION_SPECIFIC_DIR/generic_easyblocks.rst echo "* :ref:\`Overview of generic easyblocks \`" >> $overview diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index e21ff695..d3305ff1 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2676 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2711 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_Abseil_592` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_alevin-fry_1021` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMD-uProf_779` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_AMS_225` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_ANGEL_359` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_Arcade-Learning-Environment_2655` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_ArchR_464` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_atropos_776` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Austin_628` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock-GPU_1075` - :ref:`list_software_AutoDock-Vina_1237` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_Abseil_592` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_Albumentations_1478` - :ref:`list_software_alevin-fry_1021` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMD-uProf_779` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AMPtk_445` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_AMS_225` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_ANGEL_359` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_Arcade-Learning-Environment_2655` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_ArchR_464` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_arosics_756` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_atropos_776` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Austin_628` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock-GPU_1075` - :ref:`list_software_AutoDock-Vina_1237` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -87,6 +87,8 @@ version versionsuffix toolchain ``2018`` ``-hotfix-1806`` ``system`` ``2020`` ``system`` ``2021`` ``-hotfix-2132`` ``system`` +``2022`` ``system`` +``2022`` ``-hotfix-2214`` ``system`` ========== ================= ========== @@ -506,6 +508,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_Albumentations_1478: + +*Albumentations* +++++++++++++++++ + +Albumentations is a Python library for fast and flexible image augmentations + +*homepage*: https://albumentations.ai + +========= ============== +version toolchain +========= ============== +``1.1.0`` ``foss/2021b`` +========= ============== + + .. _list_software_alevin-fry_1021: *alevin-fry* @@ -835,6 +853,7 @@ AMD uProf is a performance analysis tool for applications running on Windows, Li version toolchain =========== ========== ``3.4.502`` ``system`` +``3.5.671`` ``system`` =========== ========== @@ -902,6 +921,22 @@ version versionsuffix toolchain ========== ================= ============== +.. _list_software_AMPtk_445: + +*AMPtk* ++++++++ + +AMPtk is a series of scripts to process NGS amplicon data using USEARCH and VSEARCH, it can also be used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial 16S, and insect COI amplicons. + +*homepage*: https://amptk.readthedocs.io + +========= ============== +version toolchain +========= ============== +``1.5.4`` ``foss/2021b`` +========= ============== + + .. _list_software_AmrPlusPlus_1128: *AmrPlusPlus* @@ -986,6 +1021,7 @@ version toolchain ``2020.11`` ``system`` ``2021.05`` ``system`` ``2021.11`` ``system`` +``2022.05`` ``system`` =========== ========== @@ -1265,12 +1301,12 @@ Convert various sequence formats to FASTA *homepage*: https://github.com/tseemann/any2fasta -========= ================ ============================================================================ -version versionsuffix toolchain -========= ================ ============================================================================ -``0.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.4.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -========= ================ ============================================================================ +========= ================ ================================================================================================ +version versionsuffix toolchain +========= ================ ================================================================================================ +``0.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.4.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +========= ================ ================================================================================================ .. _list_software_AOCC_278: @@ -1406,6 +1442,7 @@ version toolchain ``2.16.0`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` ``2.17.0`` ``GCC/8.3.0`` ``2.19.0`` ``GCC/10.3.0`` +``2.22.1`` ``GCC/11.2.0`` ========== ================================================================================ @@ -1521,6 +1558,7 @@ A parallel, multi-engine simulator for heterogeneous swarm robotics version versionsuffix toolchain ================ ============== ============== ``3.0.0-beta53`` ``-Lua-5.2.4`` ``foss/2018b`` +``3.0.0-beta59`` ``GCC/11.2.0`` ================ ============== ============== @@ -1598,6 +1636,22 @@ version versionsuffix toolchain =========== ================== =============================== +.. _list_software_arosics_756: + +*arosics* ++++++++++ + +AROSICS is a python package to perform automatic subpixel co-registration of two satellite image datasets based on an image matching approach working in the frequency domain, combined with a multistage workflow for effective detection of false-positives. + +*homepage*: https://github.com/GFZ/arosics + +========= ============== +version toolchain +========= ============== +``1.7.6`` ``foss/2021a`` +========= ============== + + .. _list_software_ARPACK++_520: *ARPACK++* @@ -1657,7 +1711,7 @@ version versionsuffix toolchain *Arriba* ++++++++ -Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. +Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. *homepage*: https://github.com/suhrig/arriba @@ -1666,6 +1720,7 @@ version toolchain ========= ============================== ``1.1.0`` ``foss/2018b`` ``2.1.0`` ``GCC/10.2.0``, ``GCC/10.3.0`` +``2.2.1`` ``GCC/11.2.0`` ========= ============================== @@ -1707,6 +1762,7 @@ version versionsuffix toolchain ``0.17.1`` ``-R-4.0.0`` ``foss/2020a`` ``6.0.0.2`` ``-R-4.1.0`` ``foss/2021a`` ``6.0.0.2`` ``-R-4.1.2`` ``foss/2021b`` +``6.0.0.2`` ``-R-4.2.0`` ``foss/2021b`` =========== ============= ============== @@ -1990,6 +2046,7 @@ version versionsuffix toolchain ``4.0.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``4.2.1`` ``intelcuda/2020b`` ``4.3.1`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` +``5.0.4`` ``foss/2021a`` ========== ================== =============================================== @@ -2002,15 +2059,15 @@ AT-SPI 2 toolkit bridge *homepage*: https://wiki.gnome.org/Accessibility -========== ========================================================== -version toolchain -========== ========================================================== -``2.26.3`` ``fosscuda/2018b`` -``2.32.0`` ``GCCcore/8.2.0`` -``2.34.1`` ``GCCcore/8.3.0`` -``2.34.2`` ``GCCcore/9.3.0`` -``2.38.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========== ========================================================== +========== ============================================================================== +version toolchain +========== ============================================================================== +``2.26.3`` ``fosscuda/2018b`` +``2.32.0`` ``GCCcore/8.2.0`` +``2.34.1`` ``GCCcore/8.3.0`` +``2.34.2`` ``GCCcore/9.3.0`` +``2.38.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========== ============================================================================== .. _list_software_at-spi2-core_1110: @@ -2032,6 +2089,7 @@ version toolchain ``2.38.0`` ``GCCcore/10.2.0`` ``2.40.2`` ``GCCcore/10.3.0`` ``2.40.3`` ``GCCcore/11.2.0`` +``2.44.1`` ``GCCcore/11.3.0`` ========== ================== @@ -2057,6 +2115,7 @@ version toolchain ``2.32.0`` ``GCCcore/8.2.0`` ``2.34.1`` ``GCCcore/8.3.0`` ``2.36.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``2.38.0`` ``GCCcore/11.3.0`` ========== ============================================================================= @@ -2280,7 +2339,7 @@ version toolchain ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= ``2.68`` ``foss/2016b`` ``2.69`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.71`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``system`` +``2.71`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= @@ -2404,6 +2463,7 @@ version toolchain ``1.16.2`` ``GCCcore/10.2.0`` ``1.16.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` ``1.16.4`` ``GCCcore/11.2.0`` +``1.16.5`` ``GCCcore/11.3.0`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -2458,6 +2518,7 @@ version toolchain ``20200321`` ``GCCcore/10.2.0`` ``20210128`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` ``20210726`` ``GCCcore/11.2.0`` +``20220317`` ``GCCcore/11.3.0`` ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -2532,12 +2593,13 @@ A fast algorithm for doing Bader's analysis on a charge density grid. *homepage*: http://theory.cm.utexas.edu/henkelman/code/bader/ -======== =============== -version toolchain -======== =============== -``1.02`` ``intel/2018a`` -``1.03`` ``intel/2018b`` -======== =============== +======== ======================= +version toolchain +======== ======================= +``1.02`` ``intel/2018a`` +``1.03`` ``intel/2018b`` +``1.04`` ``iccifort/2020.4.304`` +======== ======================= .. _list_software_BAGEL_347: @@ -2581,11 +2643,11 @@ Count DNA sequence reads in BAM files *homepage*: https://github.com/genome/bam-readcount -========= ============================= -version toolchain -========= ============================= -``0.8.0`` ``GCC/9.3.0``, ``foss/2018b`` -========= ============================= +========= ============================================= +version toolchain +========= ============================================= +``0.8.0`` ``GCC/11.2.0``, ``GCC/9.3.0``, ``foss/2018b`` +========= ============================================= .. _list_software_Bambi_475: @@ -2733,11 +2795,11 @@ Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal *homepage*: https://github.com/tseemann/barrnap -======= ===================================================== -version toolchain -======= ===================================================== -``0.9`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2020b`` -======= ===================================================== +======= ====================================================================== +version toolchain +======= ====================================================================== +``0.9`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2020b``, ``gompi/2021b`` +======= ====================================================================== .. _list_software_basemap_729: @@ -2920,6 +2982,8 @@ version versionsuffix toolchain ``3.6.0`` ``GCCcore/9.3.0`` ``3.7.1`` ``GCCcore/8.3.0`` ``3.7.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` +``4.2.2`` ``GCCcore/11.2.0`` +``5.1.1`` ``GCCcore/11.3.0`` ========== ============= ============================================================================= @@ -3136,6 +3200,7 @@ version versionsuffix toolchain ========= ================== =============== ``1.4.1`` ``-Python-2.7.14`` ``intel/2018a`` ``1.4.1`` ``-Python-3.6.4`` ``intel/2018a`` +``1.6.3`` ``intel/2021b`` ========= ================== =============== @@ -3148,15 +3213,15 @@ beagle-lib is a high-performance library that can perform the core calculations *homepage*: https://github.com/beagle-dev/beagle-lib -========= ================ ====================================================================== -version versionsuffix toolchain -========= ================ ====================================================================== -``2.1.2`` ``foss/2016a``, ``foss/2017a`` -``3.0.1`` ``foss/2018a``, ``intel/2018a`` -``3.0.2`` ``foss/2018b`` -``3.0.2`` ``-CUDA-9.2.88`` ``foss/2018b`` -``3.1.2`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0``, ``gcccuda/2019b`` -========= ================ ====================================================================== +========= ================ ================================================================================================================ +version versionsuffix toolchain +========= ================ ================================================================================================================ +``2.1.2`` ``foss/2016a``, ``foss/2017a`` +``3.0.1`` ``foss/2018a``, ``intel/2018a`` +``3.0.2`` ``foss/2018b`` +``3.0.2`` ``-CUDA-9.2.88`` ``foss/2018b`` +``3.1.2`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0``, ``gcccuda/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +========= ================ ================================================================================================================ .. _list_software_Beast_495: @@ -3443,6 +3508,7 @@ version toolchain ``2.35`` ``GCCcore/10.2.0``, ``system`` ``2.36.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/8.4.0``, ``GCCcore/9.4.0``, ``system`` ``2.37`` ``GCCcore/11.2.0``, ``system`` +``2.38`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.5.0``, ``system`` ========== ======================================================================================================================================================================================== @@ -3523,11 +3589,11 @@ Bioawk is an extension to Brian Kernighan's awk, adding the support of several *homepage*: https://github.com/lh3/bioawk -======= ============================== -version toolchain -======= ============================== -``1.0`` ``GCC/10.3.0``, ``foss/2018b`` -======= ============================== +======= ============================================== +version toolchain +======= ============================================== +``1.0`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``foss/2018b`` +======= ============================================== .. _list_software_biobambam2_972: @@ -3576,6 +3642,7 @@ The BIOM file format (canonically pronounced biome) is designed to be a general version versionsuffix toolchain ========== ================= ============== ``2.1.10`` ``-Python-3.8.2`` ``foss/2020a`` +``2.1.12`` ``foss/2021b`` ========== ================= ============== @@ -3763,7 +3830,7 @@ version toolchain ``3.6.1`` ``GCCcore/10.1.0`` ``3.7.1`` ``GCCcore/10.2.0``, ``system`` ``3.7.6`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0``, ``system`` -``3.8.2`` ``system`` +``3.8.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.5.0``, ``system`` ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -3904,7 +3971,7 @@ version toolchain *Blender* +++++++++ -Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline, modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. +Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline, modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. *homepage*: https://www.blender.org @@ -3917,6 +3984,7 @@ version versionsuffix toolchain ``2.79b`` ``-Python-3.6.6-CUDA-9.2.88`` ``foss/2018b`` ``2.81`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.0.0`` ``-linux-x64`` ``system`` +``3.1.2`` ``-linux-x64`` ``system`` ========= ============================= =============================== @@ -3929,19 +3997,20 @@ AMD's fork of BLIS. BLIS is a portable software framework for instantiating high *homepage*: https://developer.amd.com/amd-cpu-libraries/blas-library/ -========= ============= ================================================== -version versionsuffix toolchain -========= ============= ================================================== -``0.3.2`` ``GCC/7.3.0-2.30`` -``0.6.0`` ``GCC/8.3.0-2.32`` -``0.8.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``0.8.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCCcore/10.3.0`` -``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` -``2.2`` ``-amd`` ``GCCcore/9.3.0`` -``3.0`` ``-amd`` ``GCCcore/10.3.0`` -``3.0.1`` ``-amd`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``3.1`` ``-amd`` ``GCCcore/11.2.0`` -========= ============= ================================================== +========= ============= ====================================================== +version versionsuffix toolchain +========= ============= ====================================================== +``0.3.2`` ``GCC/7.3.0-2.30`` +``0.6.0`` ``GCC/8.3.0-2.32`` +``0.8.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``0.8.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCCcore/10.3.0`` +``0.9.0`` ``GCC/11.3.0`` +``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` +``2.2`` ``-amd`` ``GCCcore/9.3.0`` +``3.0`` ``-amd`` ``GCCcore/10.3.0`` +``3.0.1`` ``-amd`` ``GCC/11.2.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``3.1`` ``-amd`` ``GCCcore/11.2.0`` +========= ============= ====================================================== .. _list_software_Blitz++_603: @@ -4215,8 +4284,10 @@ version versionsuffix toolchain ``1.72.0`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a`` ``1.72.0`` ``-no_mpi`` ``GCCcore/9.3.0`` ``1.74.0`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``1.75.0`` ``GCC/11.2.0`` ``1.76.0`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` ``1.77.0`` ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` +``1.79.0`` ``GCC/11.2.0``, ``GCC/11.3.0`` ========== ================== ==================================================================== @@ -4458,6 +4529,7 @@ version versionsuffix toolchain ========== ============= =============== ``0.35.0`` ``-R-3.6.0`` ``intel/2019a`` ``0.35.4`` ``-R-4.0.0`` ``foss/2020a`` +``0.36.1`` ``foss/2021b`` ========== ============= =============== @@ -4470,11 +4542,11 @@ Brotli is a generic-purpose lossless compression algorithm that compresses data *homepage*: https://github.com/google/brotli -========= ============================================================================= -version toolchain -========= ============================================================================= -``1.0.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` -========= ============================================================================= +========= ================================================================================================= +version toolchain +========= ================================================================================================= +``1.0.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` +========= ================================================================================================= .. _list_software_Brotli-python_1339: @@ -4617,12 +4689,13 @@ This module sets a group of environment variables for compilers, linkers, maths *homepage*: None -=========== ================ ================================================================================================================================================================================================================================================================================================================================================================= -version versionsuffix toolchain -=========== ================ ================================================================================================================================================================================================================================================================================================================================================================= -``default`` ``FCC/4.5.0``, ``Fujitsu/21.05``, ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b`` -``default`` ``-CUDA-11.3.1`` ``foss/2021a`` -=========== ================ ================================================================================================================================================================================================================================================================================================================================================================= +=========== ================ ================================================================================================================================================================================================================================================================================================================================================================================= +version versionsuffix toolchain +=========== ================ ================================================================================================================================================================================================================================================================================================================================================================================= +``default`` ``FCC/4.5.0``, ``Fujitsu/21.05``, ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b`` +``default`` ``-CUDA-11.3.1`` ``foss/2021a`` +``default`` ``-CUDA-11.4.1`` ``foss/2021b`` +=========== ================ ================================================================================================================================================================================================================================================================================================================================================================================= .. _list_software_Bullet_616: @@ -4784,6 +4857,7 @@ version versionsuffix toolchain ``0.8.8`` ``-Python-3.7.4`` ``foss/2019b`` ``0.8.9`` ``-Python-3.8.2`` ``foss/2020a`` ``0.8.11`` ``foss/2021a`` +``0.8.13`` ``foss/2021b`` ========== ================== =============== @@ -4850,7 +4924,7 @@ bzip2 is a freely available, patent free, high-quality data compressor. It typi version toolchain ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.0.6`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -4860,7 +4934,7 @@ version toolchain --- -:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CASTEP_448` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMAverse_758` - :ref:`list_software_CmdStanR_764` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_CONN_302` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_Crumble_714` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CASTEP_448` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_CellTypist_1037` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMAverse_758` - :ref:`list_software_CmdStanR_764` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_CONN_302` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_Crumble_714` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_c-ares_571: @@ -4981,6 +5055,7 @@ version versionsuffix toolchain ``1.14.10`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017b`` ``1.14.12`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.16.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.17.4`` ``GCCcore/11.3.0`` =========== ================ =================================================================================================================== @@ -5700,6 +5775,7 @@ version toolchain ========= ========== ``1.0.1`` ``system`` ``2.0.0`` ``system`` +``2.0.1`` ``system`` ========= ========== @@ -5736,6 +5812,22 @@ version toolchain ========= ============== +.. _list_software_CellTypist_1037: + +*CellTypist* +++++++++++++ + +A tool for semi-automatic cell type annotation + +*homepage*: https://www.celltypist.org/ + +========= ============== +version toolchain +========= ============== +``1.0.0`` ``foss/2021b`` +========= ============== + + .. _list_software_Centrifuge_1036: *Centrifuge* @@ -6017,11 +6109,11 @@ Check is a unit testing framework for C. It features a simple interface for defi *homepage*: https://libcheck.github.io/check/ -========== ========================================================= -version toolchain -========== ========================================================= -``0.15.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -========== ========================================================= +========== ============================================================================= +version toolchain +========== ============================================================================= +``0.15.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========== ============================================================================= .. _list_software_check_510: @@ -6381,14 +6473,16 @@ version versionsuffix toolchain ``8.0.0`` ``-CUDA-10.1.105`` ``GCCcore/8.2.0`` ``8.0.1`` ``-CUDA-10.1.105`` ``GCC/8.2.0-2.31.1`` ``8.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` -``9.0.1`` ``GCCcore/8.3.0`` +``9.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``9.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` ``10.0.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``10.0.1`` ``GCCcore/9.3.0`` ``11.0.0`` ``GCCcore/9.3.0`` ``11.0.1`` ``GCCcore/10.2.0``, ``gcccuda/2020b`` ``12.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``12.0.1`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` ``13.0.1`` ``GCCcore/11.2.0`` +``13.0.1`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` ========== ================== ====================================== @@ -6663,6 +6757,7 @@ version toolchain ``3.20.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.21.1`` ``GCCcore/11.2.0`` ``3.22.1`` ``GCCcore/11.2.0`` +``3.23.1`` ``GCCcore/11.3.0`` ========== ================================================================================================================================================= @@ -7148,12 +7243,12 @@ Coverage.py is a tool for measuring code coverage of Python programs. It monito *homepage*: https://coverage.readthedocs.io -========= ================== ================== -version versionsuffix toolchain -========= ================== ================== -``4.5.1`` ``-Python-2.7.14`` ``intel/2017b`` -``5.5`` ``GCCcore/10.2.0`` -========= ================== ================== +========= ================== ====================================== +version versionsuffix toolchain +========= ================== ====================================== +``4.5.1`` ``-Python-2.7.14`` ``intel/2017b`` +``5.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ================== ====================================== .. _list_software_cowsay_662: @@ -7385,12 +7480,12 @@ Conditional Reciprocal Best BLAST - high confidence ortholog assignment. CRB-BL *homepage*: https://github.com/cboursnell/crb-blast -========= =============== ================================ -version versionsuffix toolchain -========= =============== ================================ -``0.6.9`` ``gompi/2021a``, ``intel/2017a`` -``0.6.9`` ``-Ruby-2.6.1`` ``foss/2018b`` -========= =============== ================================ +========= =============== ================================================= +version versionsuffix toolchain +========= =============== ================================================= +``0.6.9`` ``gompi/2021a``, ``gompi/2021b``, ``intel/2017a`` +``0.6.9`` ``-Ruby-2.6.1`` ``foss/2018b`` +========= =============== ================================================= .. _list_software_CREST_385: @@ -7549,11 +7644,13 @@ cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous rec *homepage*: https://cb.csail.mit.edu/cb/cryodrgn/ -========= ================== -version toolchain -========= ================== -``0.3.2`` ``fosscuda/2020b`` -========= ================== +============== ================ ================== +version versionsuffix toolchain +============== ================ ================== +``0.3.2`` ``fosscuda/2020b`` +``0.3.5`` ``-CUDA-11.3.1`` ``foss/2021a`` +``1.0.0-beta`` ``-CUDA-11.3.1`` ``foss/2021a`` +============== ================ ================== .. _list_software_CryptoMiniSat_1334: @@ -7791,6 +7888,7 @@ version toolchain ``11.5.0`` ``system`` ``11.5.1`` ``system`` ``11.6.0`` ``system`` +``11.7.0`` ``system`` ================= ========================================================================== @@ -7853,7 +7951,10 @@ version versionsuffix toolchain ``8.1.0.77`` ``-CUDA-11.2.1`` ``system`` ``8.1.1.33`` ``-CUDA-11.2.1`` ``system`` ``8.2.1.32`` ``-CUDA-11.3.1`` ``system`` +``8.2.2.26`` ``-CUDA-11.4.0`` ``system`` ``8.2.2.26`` ``-CUDA-11.4.1`` ``system`` +``8.4.0.27`` ``-CUDA-11.6.0`` ``system`` +``8.4.1.50`` ``-CUDA-11.6.0`` ``system`` ============ ================== =========================================================== @@ -7870,7 +7971,7 @@ Transcript assembly, differential expression, and differential regulation for RN version toolchain ============ ================================================================================================= ``2.2.1`` ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``gompi/2019b``, ``intel/2017b``, ``intel/2018a`` -``20190706`` ``GCC/10.2.0``, ``gompi/2019a`` +``20190706`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``gompi/2019a`` ============ ================================================================================================= @@ -7940,6 +8041,7 @@ version toolchain ``7.72.0`` ``GCCcore/10.2.0`` ``7.76.0`` ``GCCcore/10.3.0`` ``7.78.0`` ``GCCcore/11.2.0`` +``7.83.0`` ``GCCcore/11.3.0`` ========== =================================================================================== @@ -8176,7 +8278,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_deepmedic_928` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_Devito_619` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dlib_411` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dRep_395` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_DualSPHysics_1180` - :ref:`list_software_DUBStepR_713` - :ref:`list_software_dune-core_898` - :ref:`list_software_dune-fem_785` - :ref:`list_software_dxpy_453` - :ref:`list_software_DyMat_479` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_deepmedic_928` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detectron2_1018` - :ref:`list_software_detonate_852` - :ref:`list_software_Devito_619` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dlib_411` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dRep_395` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_DualSPHysics_1180` - :ref:`list_software_DUBStepR_713` - :ref:`list_software_dune-core_898` - :ref:`list_software_dune-fem_785` - :ref:`list_software_dxpy_453` - :ref:`list_software_DyMat_479` .. _list_software_dadi_402: @@ -8372,16 +8474,16 @@ Berkeley DB enables the development of custom data management solutions, withou *homepage*: http://www.oracle.com/technetwork/products/berkeleydb -=========== =============================================================================================================== -version toolchain -=========== =============================================================================================================== -``4.8.30`` ``intel/2016a`` -``6.2.23`` ``foss/2016a`` -``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` -``18.1.25`` ``GCCcore/7.3.0`` -``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``18.1.40`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -=========== =============================================================================================================== +=========== =================================================================================================================================== +version toolchain +=========== =================================================================================================================================== +``4.8.30`` ``intel/2016a`` +``6.2.23`` ``foss/2016a`` +``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` +``18.1.25`` ``GCCcore/7.3.0`` +``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``18.1.40`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +=========== =================================================================================================================================== .. _list_software_DB_File_613: @@ -8423,7 +8525,7 @@ version versionsuffix toolchain ``4.046`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``4.046`` ``-Perl-5.26.1`` ``intel/2018a`` ``4.048`` ``-Perl-5.28.0`` ``foss/2018b`` -``4.050`` ``GCC/10.2.0`` +``4.050`` ``GCC/10.2.0``, ``GCC/11.2.0`` ``4.050`` ``-Perl-5.28.1`` ``foss/2019a`` ========= ================ =============================== @@ -8452,7 +8554,7 @@ version toolchain D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed. -*homepage*: http://dbus.freedesktop.org/ +*homepage*: https://dbus.freedesktop.org/ =========== ========================================================== version toolchain @@ -8466,6 +8568,7 @@ version toolchain ``1.13.8`` ``GCCcore/8.2.0`` ``1.13.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.13.18`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.14.0`` ``GCCcore/11.3.0`` =========== ========================================================== @@ -8516,13 +8619,13 @@ DCMTK is a collection of libraries and applications implementing large parts the *homepage*: https://dicom.offis.de/dcmtk -========= ==================================== -version toolchain -========= ==================================== -``3.6.3`` ``GCCcore/7.3.0`` -``3.6.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.6.6`` ``GCCcore/10.3.0`` -========= ==================================== +========= ====================================== +version toolchain +========= ====================================== +``3.6.3`` ``GCCcore/7.3.0`` +``3.6.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.6.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== .. _list_software_dd_200: @@ -8763,6 +8866,22 @@ version versionsuffix toolchain ========= ============= =============== +.. _list_software_detectron2_1018: + +*detectron2* +++++++++++++ + +Detectron2 is a platform for object detection, segmentation and other visual recognition tasks. + +*homepage*: https://github.com/facebookresearch/detectron2 + +======= ================ ============== +version versionsuffix toolchain +======= ================ ============== +``0.6`` ``-CUDA-11.3.1`` ``foss/2021a`` +======= ================ ============== + + .. _list_software_detonate_852: *detonate* @@ -9604,7 +9723,7 @@ version versionsuffix toolchain --- -:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_eht-imaging_1098` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_einops_654` - :ref:`list_software_elastix_762` - :ref:`list_software_elbencho_832` - :ref:`list_software_ELFIO_367` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_elprep_648` - :ref:`list_software_ELSI_301` - :ref:`list_software_ELSI-RCI_568` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_Embree_592` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_epiScanpy_940` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESL-Bundle_875` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExaML_439` - :ref:`list_software_Excel-Writer-XLSX_1559` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_expecttest_1097` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_eht-imaging_1098` - :ref:`list_software_Eigen_488` - :ref:`list_software_EigenExa_774` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_einops_654` - :ref:`list_software_elastix_762` - :ref:`list_software_elbencho_832` - :ref:`list_software_ELFIO_367` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_elprep_648` - :ref:`list_software_ELSI_301` - :ref:`list_software_ELSI-RCI_568` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_Embree_592` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_epiScanpy_940` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESL-Bundle_875` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExaML_439` - :ref:`list_software_Excel-Writer-XLSX_1559` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_expecttest_1097` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_E-ANTIC_481: @@ -9756,6 +9875,7 @@ version toolchain ``4.5.1`` ``system`` ``4.5.2`` ``system`` ``4.5.3`` ``system`` +``4.5.4`` ``system`` ========== ========== @@ -9845,14 +9965,14 @@ Lightweight, super fast library for sequence alignment using edit (Levenshtein) *homepage*: https://martinsos.github.io/edlib -=============== ================= ====================================== -version versionsuffix toolchain -=============== ================= ====================================== -``1.3.8.post1`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``1.3.8.post1`` ``-Python-3.8.2`` ``GCC/9.3.0`` -``1.3.8.post2`` ``-Python-3.8.2`` ``iccifort/2020.1.217`` -``1.3.9`` ``GCC/10.2.0``, ``GCC/10.3.0`` -=============== ================= ====================================== +=============== ================= ============================================== +version versionsuffix toolchain +=============== ================= ============================================== +``1.3.8.post1`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``1.3.8.post1`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``1.3.8.post2`` ``-Python-3.8.2`` ``iccifort/2020.1.217`` +``1.3.9`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0`` +=============== ================= ============================================== .. _list_software_EggLib_554: @@ -9885,6 +10005,7 @@ version versionsuffix toolchain ========= ================== =============== ``1.0.3`` ``-Python-2.7.14`` ``intel/2018a`` ``2.1.4`` ``foss/2020b`` +``2.1.7`` ``foss/2021b`` ========= ================== =============== @@ -9930,10 +10051,26 @@ version toolchain ``3.3.7`` ``GCCcore/9.3.0``, ``system`` ``3.3.8`` ``GCCcore/10.2.0`` ``3.3.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``3.4.0`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` +``3.4.0`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ========================================================== +.. _list_software_EigenExa_774: + +*EigenExa* +++++++++++ + +EigenExa, a part of KMATHLIB, is a high performance eigen-solver. + +*homepage*: https://www.r-ccs.riken.jp/labs/lpnctrt/projects/eigenexa/ + +======== =============== +version toolchain +======== =============== +``2.11`` ``intel/2020b`` +======== =============== + + .. _list_software_EIGENSOFT_676: *EIGENSOFT* @@ -10032,6 +10169,7 @@ version toolchain ``0.182`` ``GCCcore/9.3.0`` ``0.183`` ``GCCcore/10.2.0`` ``0.185`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.187`` ``GCCcore/11.3.0`` ========= ============================================================================ @@ -10077,6 +10215,7 @@ version toolchain ``2020.05.001`` ``intel/2020a`` ``2020.11.001`` ``foss/2020b``, ``intel/2020b`` ``2021.05.001`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` +``2021.05.002`` ``intel/2020b`` ``2021.11.001`` ``foss/2021b``, ``intel/2021b`` =================== ================================================================================= @@ -10199,14 +10338,14 @@ EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a fre *homepage*: http://emboss.sourceforge.net/ -========= ================= ================================================================================================================================================ -version versionsuffix toolchain -========= ================= ================================================================================================================================================ -``6.6.0`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018b``, ``foss/2021a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` -``6.6.0`` ``-Java-11`` ``GCC/8.3.0`` -``6.6.0`` ``-Java-13`` ``GCC/10.2.0`` -``6.6.0`` ``-X11-20170314`` ``intel/2017a`` -========= ================= ================================================================================================================================================ +========= ================= ================================================================================================================================================================ +version versionsuffix toolchain +========= ================= ================================================================================================================================================================ +``6.6.0`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018b``, ``foss/2021a``, ``foss/2021b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` +``6.6.0`` ``-Java-11`` ``GCC/8.3.0`` +``6.6.0`` ``-Java-13`` ``GCC/10.2.0`` +``6.6.0`` ``-X11-20170314`` ``intel/2017a`` +========= ================= ================================================================================================================================================================ .. _list_software_Embree_592: @@ -10445,6 +10584,7 @@ version versionsuffix toolchain ========= ================= =============== ``8.0.0`` ``-Python-3.7.4`` ``intel/2019b`` ``8.0.1`` ``intel/2020b`` +``8.0.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= =============== @@ -10562,6 +10702,7 @@ EvidentialGene is a genome informatics project for "Evidence Directed Gene Cons version versionsuffix toolchain ============== ================ =============== ``2018.01.01`` ``-Perl-5.24.1`` ``intel/2017a`` +``2022.01.14`` ``gompi/2021b`` ============== ================ =============== @@ -10670,11 +10811,11 @@ Exonerate is a generic tool for pairwise sequence comparison. It allows you to *homepage*: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate -========= ============================================================================================================================================================================================================================= -version toolchain -========= ============================================================================================================================================================================================================================= -``2.4.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a`` -========= ============================================================================================================================================================================================================================= +========= ============================================================================================================================================================================================================================================= +version toolchain +========= ============================================================================================================================================================================================================================================= +``2.4.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a`` +========= ============================================================================================================================================================================================================================================= .. _list_software_expat_546: @@ -10698,6 +10839,7 @@ version toolchain ``2.2.7`` ``GCCcore/8.3.0`` ``2.2.9`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``2.4.1`` ``GCCcore/11.2.0`` +``2.4.8`` ``GCCcore/11.3.0`` ========= ========================================================================================================================= @@ -10774,7 +10916,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMPy_348` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoBiS_435` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_Fastaq_608` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_FFTW.MPI_587` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMPy_348` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoBiS_435` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeBarcodes_1189` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -10948,15 +11090,31 @@ FastANI is developed for fast alignment-free computation of whole-genome Averag *homepage*: https://github.com/ParBLiSS/FastANI -======== ============================================================== -version toolchain -======== ============================================================== -``1.1`` ``foss/2018b``, ``intel/2018b`` -``1.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``1.3`` ``iccifort/2019.5.281`` -``1.31`` ``iccifort/2020.1.217`` -``1.33`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` -======== ============================================================== +======== ===================================================================================================== +version toolchain +======== ===================================================================================================== +``1.1`` ``foss/2018b``, ``intel/2018b`` +``1.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``1.3`` ``iccifort/2019.5.281`` +``1.31`` ``iccifort/2020.1.217`` +``1.33`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.4.0`` +======== ===================================================================================================== + + +.. _list_software_Fastaq_608: + +*Fastaq* +++++++++ + +Python3 scripts to manipulate FASTA and FASTQ files. + +*homepage*: https://github.com/sanger-pathogens/Fastaq + +========== ============== +version toolchain +========== ============== +``3.17.0`` ``GCC/10.3.0`` +========== ============== .. _list_software_FastME_544: @@ -10990,7 +11148,7 @@ version toolchain ========== ============================================================ ``0.19.7`` ``foss/2018b`` ``0.20.0`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``0.23.2`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``0.23.2`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` ========== ============================================================ @@ -11039,7 +11197,7 @@ This package provides a number of small and efficient programs to perform commo version toolchain ========= ============================== ``0.8`` ``foss/2016b``, ``foss/2018b`` -``0.8.3`` ``GCC/10.3.0`` +``0.8.3`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========= ============================== @@ -11182,12 +11340,12 @@ FastTree infers approximately-maximum-likelihood phylogenetic trees from alignme *homepage*: http://www.microbesonline.org/fasttree/ -========== =============================================================================================== -version toolchain -========== =============================================================================================== -``2.1.10`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``2.1.11`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== =============================================================================================== +========== =================================================================================================================== +version toolchain +========== =================================================================================================================== +``2.1.10`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``2.1.11`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== =================================================================================================================== .. _list_software_FastViromeExplorer_1873: @@ -11215,11 +11373,11 @@ The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/ *homepage*: http://hannonlab.cshl.edu/fastx_toolkit/ -========== ================================================================================================= -version toolchain -========== ================================================================================================= -``0.0.14`` ``GCC/10.3.0``, ``GCC/9.3.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2018a`` -========== ================================================================================================= +========== ================================================================================================================= +version toolchain +========== ================================================================================================================= +``0.0.14`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2018a`` +========== ================================================================================================================= .. _list_software_fatslim_752: @@ -11418,11 +11576,11 @@ Standalone C library for assembling Illumina short reads in small regions. *homepage*: https://github.com/lh3/fermi-lite -============ ===================================== -version toolchain -============ ===================================== -``20190320`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -============ ===================================== +============ ========================================================= +version toolchain +============ ========================================================= +``20190320`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +============ ========================================================= .. _list_software_Ferret_616: @@ -11613,10 +11771,26 @@ version versionsuffix toolchain ``3.3.8`` ``-amd`` ``gompi/2020a`` ``3.3.8`` ``-serial`` ``GCC/9.3.0`` ``3.3.9`` ``gompi/2021a``, ``intel/2021a`` -``3.3.10`` ``gompi/2021b``, ``iimpi/2021b`` +``3.3.10`` ``GCC/11.3.0``, ``gompi/2021b``, ``iimpi/2021b`` ========== ============= ======================================================================================================================================================================================================================================================================================================================= +.. _list_software_FFTW.MPI_587: + +*FFTW.MPI* +++++++++++ + +FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. + +*homepage*: https://www.fftw.org + +========== ================= +version toolchain +========== ================= +``3.3.10`` ``gompi/2022.05`` +========== ================= + + .. _list_software_fgbio_519: *fgbio* @@ -12134,17 +12308,17 @@ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, some *homepage*: http://flex.sourceforge.net/ -========== =========================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain -========== =========================================================================================================================================================================================================================================================================================================================================================================================================================== -``2.5.35`` ``system`` -``2.5.38`` ``GCC/4.8.2`` -``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` -``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.6.2`` ``intel/2016b`` -``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` -``2.6.4`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``system`` -========== =========================================================================================================================================================================================================================================================================================================================================================================================================================== +========== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +version toolchain +========== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +``2.5.35`` ``system`` +``2.5.38`` ``GCC/4.8.2`` +``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` +``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +``2.6.2`` ``intel/2016b`` +``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` +``2.6.4`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``GCCcore/system``, ``system`` +========== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_Flexbar_708: @@ -12177,6 +12351,7 @@ version toolchain ========= ============================== ``3.0.4`` ``GCC/10.3.0``, ``GCC/11.2.0`` ``3.1.3`` ``GCC/11.2.0`` +``3.2.0`` ``GCC/11.3.0`` ========= ============================== @@ -12226,6 +12401,7 @@ version toolchain ========= =============================================================================================== ``2.5.2`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` ``2.7.1`` ``GCC/10.3.0`` +``2.8.4`` ``GCC/11.2.0`` ========= =============================================================================================== @@ -12454,6 +12630,7 @@ version versionsuffix toolchain ``2.13.92`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``2.13.93`` ``GCCcore/10.3.0`` ``2.13.94`` ``GCCcore/11.2.0`` +``2.14.0`` ``GCCcore/11.3.0`` =========== ================== ====================================================================================== @@ -12519,6 +12696,7 @@ version toolchain ``2020b`` ``system`` ``2021a`` ``system`` ``2021b`` ``system`` +``2022.05`` ``system`` =========== ========== @@ -12553,11 +12731,11 @@ FoX is an XML library written in Fortran 95. It allows software developers to re *homepage*: http://homepages.see.leeds.ac.uk/~earawa/FoX/ -========= =============================================== -version toolchain -========= =============================================== -``4.1.2`` ``GCC/9.3.0``, ``intel/2017b``, ``intel/2018a`` -========= =============================================== +========= =============================================================== +version toolchain +========= =============================================================== +``4.1.2`` ``GCC/11.2.0``, ``GCC/9.3.0``, ``intel/2017b``, ``intel/2018a`` +========= =============================================================== .. _list_software_FPM_227: @@ -12657,20 +12835,37 @@ version toolchain ========= ============== +.. _list_software_FreeBarcodes_1189: + +*FreeBarcodes* +++++++++++++++ + +A package for the generation and decoding of FREE divergence error-correcting DNA barcodes + +*homepage*: https://github.com/hawkjo/freebarcodes + +========== ============== +version toolchain +========== ============== +``3.0.a5`` ``foss/2021b`` +========== ============== + + .. _list_software_freebayes_950: *freebayes* +++++++++++ -FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. +Bayesian haplotype-based genetic polymorphism discovery and genotyping. -*homepage*: https://github.com/ekg/freebayes +*homepage*: https://github.com/freebayes/freebayes ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``1.3.5`` ``GCC/10.2.0`` ``1.3.5`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``1.3.6`` ``-R-4.1.2`` ``foss/2021b`` ========= ================= ============== @@ -12723,6 +12918,7 @@ version versionsuffix toolchain ``3.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` ``3.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``3.2.2`` ``GCCcore/11.3.0`` ========= ================ ====================================================================================================================================================================================== @@ -12735,11 +12931,11 @@ FreeImage is an Open Source library project for developers who would like to sup *homepage*: http://freeimage.sourceforge.net -========== =============================================================================================== -version toolchain -========== =============================================================================================== -``3.18.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== =============================================================================================== +========== =================================================================================================================== +version toolchain +========== =================================================================================================================== +``3.18.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== =================================================================================================================== .. _list_software_FreeSASA_682: @@ -12825,6 +13021,7 @@ version versionsuffix toolchain ``2.10.3`` ``GCCcore/10.2.0`` ``2.10.4`` ``GCCcore/10.3.0`` ``2.11.0`` ``GCCcore/11.2.0`` +``2.12.1`` ``GCCcore/11.3.0`` ========== ================== ====================================================================== @@ -12895,6 +13092,7 @@ version toolchain ``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``1.0.9`` ``GCCcore/9.3.0`` ``1.0.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.0.12`` ``GCCcore/11.3.0`` ========== ========================================================== @@ -13047,12 +13245,12 @@ This tool is intended to deduplicate UMIs from single-end and paired-end sequen *homepage*: https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools -========== ================= ============== -version versionsuffix toolchain -========== ================= ============== -``0.18.2`` ``GCC/10.3.0`` -``0.18.2`` ``-Python-3.6.6`` ``foss/2018b`` -========== ================= ============== +========== ================= ============================== +version versionsuffix toolchain +========== ================= ============================== +``0.18.2`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``0.18.2`` ``-Python-3.6.6`` ``foss/2018b`` +========== ================= ============================== .. _list_software_FUNWAVE-TVD_823: @@ -13195,7 +13393,7 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_genozip_764` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPy_272` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap_784` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gRPC_332` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_gcloud_638` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_genozip_764` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPy_272` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap_784` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gRPC_332` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-bad_1393` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_gsutil_664` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GTK4_282` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: @@ -13661,11 +13859,14 @@ version versionsuffix toolchain ``9.2.0`` ``-2.32`` ``system`` ``9.3.0`` ``system`` ``9.4.0`` ``system`` +``9.5.0`` ``system`` ``10.1.0`` ``system`` ``10.2.0`` ``system`` ``10.3.0`` ``system`` ``11.1.0`` ``system`` ``11.2.0`` ``system`` +``11.3.0`` ``system`` +``12.1.0`` ``system`` ``system`` ``system`` ``system`` ``-2.29`` ``system`` ========== =================== ========== @@ -13706,11 +13907,14 @@ version toolchain ``9.2.0`` ``system`` ``9.3.0`` ``system`` ``9.4.0`` ``system`` +``9.5.0`` ``system`` ``10.1.0`` ``system`` ``10.2.0`` ``system`` ``10.3.0`` ``system`` ``11.1.0`` ``system`` ``11.2.0`` ``system`` +``11.3.0`` ``system`` +``12.1.0`` ``system`` ``system`` ``system`` ========== ========== @@ -13738,6 +13942,22 @@ version toolchain =========== ========== +.. _list_software_gcloud_638: + +*gcloud* +++++++++ + +Libraries and tools for interacting with Google Cloud products and services. + +*homepage*: https://cloud.google.com/sdk + +=========== ========== +version toolchain +=========== ========== +``382.0.0`` ``system`` +=========== ========== + + .. _list_software_GConf_461: *GConf* @@ -13987,7 +14207,7 @@ version versionsuffix toolchain The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. -*homepage*: https://developer.gnome.org/gdk-pixbuf/stable/ +*homepage*: https://docs.gtk.org/gdk-pixbuf/ =========== ==================================================================================== version toolchain @@ -14003,6 +14223,7 @@ version toolchain ``2.38.2`` ``GCCcore/8.3.0`` ``2.40.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``2.42.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.42.8`` ``GCCcore/11.3.0`` =========== ==================================================================================== @@ -14376,14 +14597,15 @@ GeoPandas is a project to add support for geographic data to pandas objects. It *homepage*: https://github.com/geopandas/geopandas -========= ================= ================================== -version versionsuffix toolchain -========= ================= ================================== -``0.7.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``0.8.0`` ``-Python-3.7.2`` ``foss/2019a`` -``0.8.1`` ``-Python-3.7.4`` ``intel/2019b`` -``0.8.1`` ``-Python-3.8.2`` ``foss/2020a`` -========= ================= ================================== +========== ================= ================================== +version versionsuffix toolchain +========== ================= ================================== +``0.7.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``0.8.0`` ``-Python-3.7.2`` ``foss/2019a`` +``0.8.1`` ``-Python-3.7.4`` ``intel/2019b`` +``0.8.1`` ``-Python-3.8.2`` ``foss/2020a`` +``0.10.2`` ``foss/2021a`` +========== ================= ================================== .. _list_software_geopy_548: @@ -14522,7 +14744,7 @@ version versionsuffix toolchain ``0.19.8.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` ``0.19.8.1`` ``-libxml2-2.9.7`` ``GCCcore/6.4.0`` ``0.20.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` -``0.21`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``system`` +``0.21`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` ============ ================== =================================================================================================== @@ -14684,12 +14906,12 @@ giflib is a library for reading and writing gif images. It is API and ABI compat *homepage*: http://giflib.sourceforge.net/ -========= ================================================================================================ -version toolchain -========= ================================================================================================ -``5.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``5.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ================================================================================================ +========= ==================================================================================================================== +version toolchain +========= ==================================================================================================================== +``5.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``5.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ==================================================================================================================== .. _list_software_gifsicle_838: @@ -14873,6 +15095,7 @@ version versionsuffix toolchain ``2.28.0`` ``-nodocs`` ``GCCcore/10.2.0`` ``2.32.0`` ``-nodocs`` ``GCCcore/10.3.0`` ``2.33.1`` ``-nodocs`` ``GCCcore/11.2.0`` +``2.36.0`` ``-nodocs`` ``GCCcore/11.3.0`` =========== ============= ==================================== @@ -15068,6 +15291,7 @@ version toolchain ``2.66.1`` ``GCCcore/10.2.0`` ``2.68.2`` ``GCCcore/10.3.0`` ``2.69.1`` ``GCCcore/11.2.0`` +``2.72.1`` ``GCCcore/11.3.0`` ========== ================================================= @@ -15315,6 +15539,7 @@ version toolchain ``2019-03-15`` ``foss/2018b`` ``2019-09-12`` ``GCC/8.3.0`` ``2020-12-17`` ``GCC/9.3.0`` +``2021-21-17`` ``GCC/11.2.0`` ============== =============== @@ -15338,7 +15563,7 @@ version toolchain ``6.1.1`` ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``6.1.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b`` ``6.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``6.2.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``6.2.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ===================================================================================================================================================== @@ -15565,6 +15790,7 @@ version toolchain ``1.16.6`` ``system`` ``1.17.3`` ``system`` ``1.17.6`` ``system`` +``1.18.1`` ``system`` ========== ================= @@ -15647,6 +15873,7 @@ version versionsuffix toolchain ``1.64.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``1.66.1`` ``GCCcore/10.2.0`` ``1.68.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.72.0`` ``GCCcore/11.3.0`` ========== ================== ====================================== @@ -15749,6 +15976,7 @@ version versionsuffix toolchain ``2020b`` ``system`` ``2021a`` ``system`` ``2021b`` ``system`` +``2022.05`` ``system`` ``system`` ``-2.29`` ``system`` =========== ============= ========== @@ -15894,12 +16122,12 @@ GNU gperf is a perfect hash function generator. For a given list of strings, it *homepage*: https://www.gnu.org/software/gperf/ -========= ========================================================================================================================================================= -version toolchain -========= ========================================================================================================================================================= -``3.0.4`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``3.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ========================================================================================================================================================= +========= ============================================================================================================================================================================= +version toolchain +========= ============================================================================================================================================================================= +``3.0.4`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``3.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ============================================================================================================================================================================= .. _list_software_gperftools_1093: @@ -16001,7 +16229,7 @@ Grace is a WYSIWYG tool to make two-dimensional plots of numerical data. ========== ============= ================================================================================================================= version versionsuffix toolchain ========== ============= ================================================================================================================= -``5.1.25`` ``foss/2016a``, ``foss/2021a``, ``intel/2016a`` +``5.1.25`` ``foss/2016a``, ``foss/2021a``, ``foss/2021b``, ``intel/2016a`` ``5.1.25`` ``-5build1`` ``foss/2017b``, ``foss/2018a``, ``foss/2019a``, ``foss/2019b``, ``intel/2017b``, ``intel/2019a``, ``intel/2019b`` ========== ============= ================================================================================================================= @@ -16068,11 +16296,12 @@ Graphene is a a thin layer of types for graphic libraries *homepage*: https://ebassi.github.io/graphene/ -========= =============== -version toolchain -========= =============== -``1.6.0`` ``intel/2017a`` -========= =============== +========== ================== +version toolchain +========== ================== +``1.6.0`` ``intel/2017a`` +``1.10.8`` ``GCCcore/11.3.0`` +========== ================== .. _list_software_GraphicsMagick_1405: @@ -16347,11 +16576,11 @@ Groff (GNU troff) is a typesetting system that reads plain text mixed with forma *homepage*: https://www.gnu.org/software/groff -========== =============================================================================================================== -version toolchain -========== =============================================================================================================== -``1.22.4`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== =============================================================================================================== +========== =================================================================================================================================== +version toolchain +========== =================================================================================================================================== +``1.22.4`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== =================================================================================================================================== .. _list_software_GroIMP_526: @@ -16535,7 +16764,7 @@ version toolchain ``2.4`` ``GCCcore/6.4.0`` ``2.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.6`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` -``2.7`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` +``2.7`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ========= ============================================================================================================================ @@ -16572,6 +16801,22 @@ version versionsuffix toolchain ========= ================= ================= +.. _list_software_GST-plugins-bad_1393: + +*GST-plugins-bad* ++++++++++++++++++ + +GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. + +*homepage*: https://gstreamer.freedesktop.org/ + +========== ============== +version toolchain +========== ============== +``1.20.2`` ``GCC/11.3.0`` +========== ============== + + .. _list_software_GST-plugins-base_1509: *GST-plugins-base* @@ -16591,6 +16836,7 @@ version toolchain ``1.16.2`` ``GCC/8.3.0`` ``1.18.4`` ``GCC/10.2.0``, ``GCC/10.3.0`` ``1.18.5`` ``GCC/11.2.0`` +``1.20.2`` ``GCC/11.3.0`` =========== ================================================================================================================== @@ -16614,9 +16860,26 @@ version toolchain ``1.16.2`` ``GCC/8.3.0`` ``1.18.4`` ``GCC/10.2.0``, ``GCC/10.3.0`` ``1.18.5`` ``GCC/11.2.0`` +``1.20.2`` ``GCC/11.3.0`` =========== ================================================================================================================== +.. _list_software_gsutil_664: + +*gsutil* +++++++++ + +gsutil is a Python application that lets you access Cloud Storage from the command line. + +*homepage*: https://cloud.google.com/storage/docs/gsutil + +======== ================== +version toolchain +======== ================== +``5.10`` ``GCCcore/11.2.0`` +======== ================== + + .. _list_software_GTDB-Tk_525: *GTDB-Tk* @@ -16635,6 +16898,7 @@ version versionsuffix toolchain ``1.3.0`` ``-Python-3.8.2`` ``intel/2020a`` ``1.5.0`` ``intel/2020b`` ``1.7.0`` ``foss/2020b``, ``foss/2021a``, ``intel/2020b`` +``2.0.0`` ``foss/2021a``, ``intel/2021b`` ========= ================== =============================================== @@ -16693,9 +16957,26 @@ version toolchain =========== ================== ``3.24.29`` ``GCCcore/10.3.0`` ``3.24.31`` ``GCCcore/11.2.0`` +``3.24.33`` ``GCCcore/11.3.0`` =========== ================== +.. _list_software_GTK4_282: + +*GTK4* +++++++ + +GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. + +*homepage*: https://docs.gtk.org/gtk4/ + +========= ============== +version toolchain +========= ============== +``4.7.0`` ``GCC/11.3.0`` +========= ============== + + .. _list_software_GtkSourceView_1330: *GtkSourceView* @@ -16861,6 +17142,7 @@ version toolchain ``1.8`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.9`` ``GCCcore/7.3.0`` ``1.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.12`` ``GCCcore/11.3.0`` ======== =================================================================================================================== @@ -16870,7 +17152,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_HIP_225` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_histolab_854` - :ref:`list_software_hivtrace_854` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hydra_504` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_hector_645` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_HIP_225` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_histolab_854` - :ref:`list_software_hivtrace_854` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hydra_504` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -17071,6 +17353,7 @@ version toolchain ``2.6.7`` ``GCCcore/10.2.0`` ``2.8.1`` ``GCCcore/10.3.0`` ``2.8.2`` ``GCCcore/11.2.0`` +``4.2.1`` ``GCCcore/11.3.0`` ========= ================================================ @@ -17313,6 +17596,22 @@ version toolchain ========= ============== +.. _list_software_hector_645: + +*hector* +++++++++ + +This is the repository for Hector, an open source, object-oriented, simple global climate carbon-cycle model. It runs essentially instantaneously while still representing the most critical global scale earth system processes, and is one of a class of models heavily used for for emulating complex climate models and uncertainty analyses. + +*homepage*: https://github.com/JGCRI/hector + +========= ============== +version toolchain +========= ============== +``2.5.0`` ``GCC/11.2.0`` +========= ============== + + .. _list_software_HeFFTe_498: *HeFFTe* @@ -17367,6 +17666,7 @@ version toolchain ``1.47.15`` ``GCCcore/10.1.0`` ``1.47.16`` ``GCCcore/10.2.0`` ``1.48.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0`` +``1.49.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.5.0`` =========== ================================================================================================================================================================================== @@ -17633,7 +17933,7 @@ version toolchain ``3.1b2`` ``GCC/6.4.0-2.28``, ``foss/2016a``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a``, ``intel/2018a`` ``3.2.1`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iimpi/2019b``, ``intel/2018b`` ``3.3.1`` ``gompi/2020a``, ``iimpi/2020a`` -``3.3.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b``, ``iimpi/2020b`` +``3.3.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021b`` ========= ============================================================================================================================================ @@ -17801,7 +18101,7 @@ version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -17845,7 +18145,7 @@ version versionsuffix toolchain ``0.11.2`` ``-Python-3.6.6`` ``foss/2018b`` ``0.11.2`` ``-Python-3.7.2`` ``foss/2019a`` ``0.11.2`` ``-Python-3.7.4`` ``foss/2019b`` -``0.11.3`` ``foss/2020b`` +``0.11.3`` ``foss/2020b``, ``foss/2021b`` =========== ================== ================================================ @@ -17947,6 +18247,7 @@ version toolchain ``2.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``2.4.1`` ``GCCcore/10.3.0`` ``2.5.0`` ``GCCcore/11.2.0`` +``2.7.1`` ``GCCcore/11.3.0`` =========== ===================================================================================================================================================================================================================================================== @@ -18074,6 +18375,7 @@ version versionsuffix toolchain ``6.7.0`` ``GCCcore/10.2.0`` ``6.13.1`` ``GCCcore/10.3.0`` ``6.14.6`` ``GCCcore/11.2.0`` +``6.46.7`` ``GCCcore/11.3.0`` ========== ================== ================================== @@ -18095,6 +18397,7 @@ version toolchain ``2.18.2`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` ``2.20.0`` ``foss/2020b``, ``intel/2020b`` ``2.21.0`` ``foss/2021a``, ``fosscuda/2020b`` +``2.24.0`` ``intel/2021b`` ========== ================================================================ @@ -18104,7 +18407,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intervaltree-python_2020` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_Iris_407` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_IsoNet_594` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_i7z_282` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intervaltree-python_2020` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_Iris_407` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_IsoNet_594` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -18157,6 +18460,22 @@ version toolchain ======= ========== +.. _list_software_i7z_282: + +*i7z* ++++++ + +A better i7 (and now i3, i5) reporting tool for Linux + +*homepage*: https://github.com/ajaiantilal/i7z + +============ ================== +version toolchain +============ ================== +``20131012`` ``GCCcore/11.2.0`` +============ ================== + + .. _list_software_ICA-AROMA_618: *ICA-AROMA* @@ -18336,7 +18655,7 @@ version versionsuffix toolchain ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. -*homepage*: https://icu-project.org/ +*homepage*: https://icu.unicode.org ======== ====================================== version toolchain @@ -18347,6 +18666,7 @@ version toolchain ``66.1`` ``GCCcore/9.3.0`` ``67.1`` ``GCCcore/10.2.0`` ``69.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``71.1`` ``GCCcore/11.3.0`` ======== ====================================== @@ -18511,6 +18831,7 @@ version versionsuffix toolchain ``2.5.0`` ``-Java-11`` ``system`` ``2.8.0`` ``-Java-11`` ``system`` ``2.9.4`` ``-Java-11`` ``system`` +``2.12.3`` ``-Java-11`` ``system`` ========== ================== ========== @@ -18628,6 +18949,7 @@ version versionsuffix toolchain ``2021a`` ``system`` ``2021b`` ``system`` ``2022.00`` ``system`` +``2022.05`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ===================== ==================== ========== @@ -18826,6 +19148,7 @@ version toolchain ``4.1`` ``foss/2016a``, ``foss/2017a``, ``intel/2017.02``, ``intel/2017a`` ``2018.1`` ``intel/2017a`` ``2019.3`` ``gompi/2019a``, ``iimpi/2019a`` +``2021.3`` ``gompi/2021b`` ========== ================================================================== @@ -18862,6 +19185,7 @@ This python library helps you with augmenting images for your machine learning p version versionsuffix toolchain ========= ================= ============== ``0.2.8`` ``-Python-3.6.6`` ``foss/2018b`` +``0.4.0`` ``foss/2021b`` ``0.4.0`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -18907,6 +19231,7 @@ version versionsuffix toolchain ``2021.3.0`` ``gompi/2021a`` ``2021.4.0`` ``system`` ``2022.0.1`` ``system`` +``2022.1.0`` ``system`` ============== ============= ====================================================================================================================================================================================================================================================================== @@ -18924,6 +19249,7 @@ version toolchain ============ ================================ ``2021.4.0`` ``gompi/2021b``, ``iimpi/2021b`` ``2022.0.1`` ``iimpi/2022.00`` +``2022.1.0`` ``iimpi/2022.05`` ============ ================================ @@ -19026,6 +19352,7 @@ version versionsuffix toolchain ``2021.3.0`` ``intel-compilers/2021.3.0`` ``2021.4.0`` ``intel-compilers/2021.4.0`` ``2021.5.0`` ``intel-compilers/2022.0.1`` +``2021.6.0`` ``intel-compilers/2022.1.0`` ``system`` ``iccifort/system-GCC-system-2.29`` =============== ============= ================================================================================================================================================================================================================================ @@ -19090,14 +19417,15 @@ InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence *homepage*: https://github.com/broadinstitute/inferCNV/wiki -========= ========================= ============================== -version versionsuffix toolchain -========= ========================= ============================== -``1.0.4`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` -``1.2.1`` ``-Python-3.7.4`` ``foss/2019b`` -``1.3.3`` ``foss/2020b``, ``foss/2021a`` -``1.3.3`` ``-Python-3.8.2`` ``foss/2020a`` -========= ========================= ============================== +========== ========================= ============================== +version versionsuffix toolchain +========== ========================= ============================== +``1.0.4`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` +``1.2.1`` ``-Python-3.7.4`` ``foss/2019b`` +``1.3.3`` ``foss/2020b``, ``foss/2021a`` +``1.3.3`` ``-Python-3.8.2`` ``foss/2020a`` +``1.10.1`` ``-R-4.1.2`` ``foss/2021b`` +========== ========================= ============================== .. _list_software_Infernal_815: @@ -19288,6 +19616,7 @@ version versionsuffix toolchain ``2021a`` ``system`` ``2021b`` ``system`` ``2022.00`` ``system`` +``2022.05`` ``system`` ===================== ============= ========== @@ -19308,6 +19637,8 @@ version toolchain ``2021.3.0`` ``system`` ``2021.4.0`` ``system`` ``2022.0.1`` ``system`` +``2022.0.2`` ``system`` +``2022.1.0`` ``system`` ============ ========== @@ -19389,15 +19720,16 @@ version versionsuffix toolchain InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. -*homepage*: http://www.ebi.ac.uk/interpro/ +*homepage*: https://www.ebi.ac.uk/interpro/ -============= =============== -version toolchain -============= =============== -``5.26-65.0`` ``intel/2017b`` -``5.27-66.0`` ``intel/2017b`` -``5.28-67.0`` ``intel/2018a`` -============= =============== +============= ================== +version toolchain +============= ================== +``5.26-65.0`` ``intel/2017b`` +``5.27-66.0`` ``intel/2017b`` +``5.28-67.0`` ``intel/2018a`` +``5.52-86.0`` ``GCCcore/10.3.0`` +============= ================== .. _list_software_intervaltree_1301: @@ -19442,18 +19774,18 @@ intltool is a set of tools to centralize translation of many different file for *homepage*: http://freedesktop.org/wiki/Software/intltool/ -========== ================ =================================================================================================================== -version versionsuffix toolchain -========== ================ =================================================================================================================== -``0.51.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.51.0`` ``-Perl-5.20.3`` ``intel/2016a`` -``0.51.0`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` -``0.51.0`` ``-Perl-5.24.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` -``0.51.0`` ``-Perl-5.24.1`` ``GCCcore/6.3.0``, ``intel/2017a`` -``0.51.0`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` -``0.51.0`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``0.51.0`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -========== ================ =================================================================================================================== +========== ================ ======================================================================================================================================= +version versionsuffix toolchain +========== ================ ======================================================================================================================================= +``0.51.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.51.0`` ``-Perl-5.20.3`` ``intel/2016a`` +``0.51.0`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` +``0.51.0`` ``-Perl-5.24.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` +``0.51.0`` ``-Perl-5.24.1`` ``GCCcore/6.3.0``, ``intel/2017a`` +``0.51.0`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` +``0.51.0`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``0.51.0`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +========== ================ ======================================================================================================================================= .. _list_software_io_lib_622: @@ -19736,6 +20068,7 @@ version versionsuffix toolchain ``1.6.12`` ``foss/2018b``, ``foss/2020a``, ``intel/2019b`` ``2.1.2`` ``foss/2020a``, ``gompi/2020b`` ``2.1.3`` ``gompi/2021a`` +``2.2.1`` ``gompi/2021b`` ========== ============= =============================================== @@ -19800,11 +20133,11 @@ Intelligent Storage Acceleration Library *homepage*: https://github.com/intel/isa-l -========== ========================================================== -version toolchain -========== ========================================================== -``2.30.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========== ========================================================== +========== ============================================================================== +version toolchain +========== ============================================================================== +``2.30.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========== ============================================================================== .. _list_software_ISL_232: @@ -20173,6 +20506,7 @@ version versionsuffix toolchain ``0.2.20`` ``foss/2021a`` ``0.2.24`` ``foss/2021a`` ``0.2.24`` ``-CUDA-11.3.1`` ``foss/2021a`` +``0.3.9`` ``foss/2021a`` ========== ================ ================================== @@ -20201,11 +20535,11 @@ JBIG-KIT is a software implementation of the JBIG1 data compression standard (I *homepage*: https://www.cl.cam.ac.uk/~mgk25/jbigkit/ -======= ====================================================================================================================================== -version toolchain -======= ====================================================================================================================================== -``2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ====================================================================================================================================== +======= ========================================================================================================================================================== +version toolchain +======= ========================================================================================================================================================== +``2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ========================================================================================================================================================== .. _list_software_Jellyfish_938: @@ -20217,15 +20551,15 @@ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. *homepage*: http://www.genome.umd.edu/jellyfish.html -========== =================================================== -version toolchain -========== =================================================== -``1.1.11`` ``foss/2016a``, ``foss/2016b`` -``1.1.12`` ``foss/2018b``, ``intel/2018a`` -``2.2.6`` ``foss/2016b``, ``intel/2017a`` -``2.2.10`` ``foss/2018b``, ``intel/2018a`` -``2.3.0`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` -========== =================================================== +========== =================================================================== +version toolchain +========== =================================================================== +``1.1.11`` ``foss/2016a``, ``foss/2016b`` +``1.1.12`` ``foss/2018b``, ``intel/2018a`` +``2.2.6`` ``foss/2016b``, ``intel/2017a`` +``2.2.10`` ``foss/2018b``, ``intel/2018a`` +``2.3.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` +========== =================================================================== .. _list_software_jemalloc_839: @@ -20346,6 +20680,7 @@ JSON-C implements a reference counting object model that allows you to easily co version toolchain ======== ========================================================== ``0.15`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``0.16`` ``GCCcore/11.3.0`` ======== ========================================================== @@ -20444,6 +20779,7 @@ version versionsuffix toolchain ``1.6.2`` ``-linux-x86_64`` ``system`` ``1.6.4`` ``-linux-x86_64`` ``system`` ``1.6.5`` ``-linux-x86_64`` ``system`` +``1.6.6`` ``-linux-x86_64`` ``system`` ``1.7.0`` ``-linux-x86_64`` ``system`` ``1.7.1`` ``-linux-x86_64`` ``system`` ``1.7.2`` ``-linux-x86_64`` ``system`` @@ -20925,16 +21261,16 @@ Kraken is a system for assigning taxonomic labels to short DNA sequences, usual *homepage*: https://ccb.jhu.edu/software/kraken/ -=============== ================ ===================================== -version versionsuffix toolchain -=============== ================ ===================================== -``0.10.5-beta`` ``-Perl-5.22.1`` ``foss/2016a`` -``0.10.5-beta`` ``-Perl-5.24.0`` ``foss/2016b`` -``1.0`` ``-Perl-5.26.1`` ``intel/2018a`` -``1.1`` ``-Perl-5.28.0`` ``foss/2018b`` -``1.1.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``1.1.1`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -=============== ================ ===================================== +=============== ================ ========================================================= +version versionsuffix toolchain +=============== ================ ========================================================= +``0.10.5-beta`` ``-Perl-5.22.1`` ``foss/2016a`` +``0.10.5-beta`` ``-Perl-5.24.0`` ``foss/2016b`` +``1.0`` ``-Perl-5.26.1`` ``intel/2018a`` +``1.1`` ``-Perl-5.28.0`` ``foss/2018b`` +``1.1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``1.1.1`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +=============== ================ ========================================================= .. _list_software_Kraken2_654: @@ -20946,17 +21282,17 @@ Kraken is a system for assigning taxonomic labels to short DNA sequences, usual *homepage*: https://github.com/DerrickWood/kraken2/wiki -============== ================ =============== -version versionsuffix toolchain -============== ================ =============== -``2.0.6-beta`` ``-Perl-5.26.1`` ``foss/2018a`` -``2.0.7-beta`` ``-Perl-5.28.0`` ``foss/2018b`` -``2.0.8-beta`` ``-Perl-5.30.0`` ``gompi/2019b`` -``2.0.9-beta`` ``-Perl-5.28.0`` ``foss/2018b`` -``2.0.9-beta`` ``-Perl-5.30.2`` ``gompi/2020a`` -``2.1.1`` ``gompi/2020b`` -``2.1.2`` ``gompi/2021a`` -============== ================ =============== +============== ================ ================================ +version versionsuffix toolchain +============== ================ ================================ +``2.0.6-beta`` ``-Perl-5.26.1`` ``foss/2018a`` +``2.0.7-beta`` ``-Perl-5.28.0`` ``foss/2018b`` +``2.0.8-beta`` ``-Perl-5.30.0`` ``gompi/2019b`` +``2.0.9-beta`` ``-Perl-5.28.0`` ``foss/2018b`` +``2.0.9-beta`` ``-Perl-5.30.2`` ``gompi/2020a`` +``2.1.1`` ``gompi/2020b`` +``2.1.2`` ``gompi/2021a``, ``gompi/2021b`` +============== ================ ================================ .. _list_software_Kratos_628: @@ -21064,7 +21400,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LBFGS++_452` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_LERC_294` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaec_608` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libavif_733` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libexif_739` - :ref:`list_software_libfabric_926` - :ref:`list_software_libfdf_615` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgdiplus_1071` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_LibLZF_515` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libmbd_618` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libnsl_644` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpspio_866` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libSBML_613` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libtree_743` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_longread_umi_1270` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPeg_360` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LBFGS++_452` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_LERC_294` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaec_608` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libavif_733` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libde265_669` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libexif_739` - :ref:`list_software_libfabric_926` - :ref:`list_software_libfdf_615` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgdiplus_1071` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libheif_723` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_LibLZF_515` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libmbd_618` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libnsl_644` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpspio_866` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libSBML_613` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libtree_743` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_longread_umi_1270` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPeg_360` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -21160,12 +21496,13 @@ LAPACK is written in Fortran90 and provides routines for solving systems of sim *homepage*: https://www.netlib.org/lapack/ -========= ================== -version toolchain -========= ================== -``3.8.0`` ``GCC/7.3.0-2.30`` -``3.9.1`` ``GCC/10.2.0`` -========= ================== +========== ================== +version toolchain +========== ================== +``3.8.0`` ``GCC/7.3.0-2.30`` +``3.9.1`` ``GCC/10.2.0`` +``3.10.1`` ``GCC/11.2.0`` +========== ================== .. _list_software_LAST_308: @@ -21473,6 +21810,7 @@ version toolchain ``3.4.2`` ``GCCcore/9.3.0`` ``3.4.3`` ``GCCcore/10.2.0`` ``3.5.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` +``3.6.1`` ``GCCcore/11.3.0`` ========= ========================================================= @@ -21721,6 +22059,22 @@ version versionsuffix toolchain ========== ================== ========================================================= +.. _list_software_libde265_669: + +*libde265* +++++++++++ + +libde265 is an open source implementation of the h.265 video codec + +*homepage*: https://github.com/strukturag/libde265 + +========= ============== +version toolchain +========= ============== +``1.0.8`` ``GCC/11.2.0`` +========= ============== + + .. _list_software_libdeflate_1036: *libdeflate* @@ -21730,13 +22084,14 @@ Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. *homepage*: https://github.com/ebiggers/libdeflate -======= ========================================================= -version toolchain -======= ========================================================= -``1.5`` ``GCCcore/7.3.0`` -``1.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``1.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -======= ========================================================= +======== ========================================================= +version toolchain +======== ========================================================= +``1.5`` ``GCCcore/7.3.0`` +``1.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``1.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.10`` ``GCCcore/11.3.0`` +======== ========================================================= .. _list_software_libdivsufsort_1424: @@ -21780,6 +22135,7 @@ version toolchain ``2.4.102`` ``GCCcore/10.2.0`` ``2.4.106`` ``GCCcore/10.3.0`` ``2.4.107`` ``GCCcore/11.2.0`` +``2.4.110`` ``GCCcore/11.3.0`` =========== ================================================== @@ -21835,6 +22191,7 @@ version toolchain ``20150325`` ``GNU/4.9.3-2.25`` ``20180525`` ``GCCcore/6.4.0`` ``20191231`` ``GCCcore/9.3.0`` +``20210910`` ``GCCcore/11.2.0`` ============ ================== @@ -21863,14 +22220,15 @@ Epoxy is a library for handling OpenGL function pointer management for you *homepage*: https://github.com/anholt/libepoxy -========= ======================================================== -version toolchain -========= ======================================================== -``1.5.2`` ``foss/2018a`` -``1.5.3`` ``GCCcore/8.2.0``, ``fosscuda/2018b`` -``1.5.4`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.5.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========= ======================================================== +========== ======================================================== +version toolchain +========== ======================================================== +``1.5.2`` ``foss/2018a`` +``1.5.3`` ``GCCcore/8.2.0``, ``fosscuda/2018b`` +``1.5.4`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.5.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.5.10`` ``GCCcore/11.3.0`` +========== ======================================================== .. _list_software_libevent_857: @@ -21882,14 +22240,14 @@ The libevent API provides a mechanism to execute a callback function when a spec *homepage*: http://libevent.org/ -========== ====================================================================================== -version toolchain -========== ====================================================================================== -``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` -``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` -``2.1.11`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.1.12`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``system`` -========== ====================================================================================== +========== ========================================================================================== +version toolchain +========== ========================================================================================== +``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` +``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` +``2.1.11`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.1.12`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` +========== ========================================================================================== .. _list_software_libexif_739: @@ -21927,6 +22285,7 @@ version toolchain ``1.13.0`` ``GCCcore/11.2.0`` ``1.13.1`` ``GCCcore/11.2.0`` ``1.13.2`` ``GCCcore/11.2.0`` +``1.15.1`` ``GCCcore/11.3.0`` ========== ===================================== @@ -21978,7 +22337,7 @@ version toolchain ========= ============================================================================================================================================================================================================================================================================================================= ``3.2.1`` ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``system`` ``3.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``3.4.2`` ``GCCcore/11.2.0`` +``3.4.2`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ============================================================================================================================================================================================================================================================================================================= @@ -22158,7 +22517,7 @@ version versionsuffix toolchain ``9.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b``, ``iomkl/2018a`` ``9.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` ``9.0.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``9.0.2`` ``GCCcore/11.2.0`` +``9.0.2`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ================ =========================================================================================================================================================================================================================================================================================================================================== @@ -22177,6 +22536,7 @@ version toolchain ``1.2.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.3.2`` ``GCCcore/10.2.0`` ``1.3.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.4.0`` ``GCCcore/11.3.0`` ========= ======================================================= @@ -22264,11 +22624,27 @@ libHaru is a free, cross platform, open source library for generating PDF files. *homepage*: http://libharu.org/ -========= ============================================================================================================================================================= -version toolchain -========= ============================================================================================================================================================= -``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2021a``, ``intel/2017a``, ``intel/2018b`` -========= ============================================================================================================================================================= +========= ================================================================================================================================================================================================= +version toolchain +========= ================================================================================================================================================================================================= +``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2021a``, ``foss/2021b``, ``intel/2017a``, ``intel/2018b`` +========= ================================================================================================================================================================================================= + + +.. _list_software_libheif_723: + +*libheif* ++++++++++ + +libheif is an HEIF and AVIF file format decoder and encoder + +*homepage*: https://github.com/strukturag/libheif + +========== ============== +version toolchain +========== ============== +``1.12.0`` ``GCC/11.2.0`` +========== ============== .. _list_software_libibmad_820: @@ -22435,6 +22811,7 @@ version versionsuffix toolchain ``2.0.4`` ``GCCcore/9.3.0`` ``2.0.5`` ``GCCcore/10.2.0`` ``2.0.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.1.3`` ``GCCcore/11.3.0`` ========= ================= ================================================================== @@ -22676,13 +23053,13 @@ Generic PCI access library. *homepage*: https://cgit.freedesktop.org/xorg/lib/libpciaccess/ -========== ================================================================================================ -version toolchain -========== ================================================================================================ -``0.13.4`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` -``0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.16`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -========== ================================================================================================ +========== ==================================================================================================================== +version toolchain +========== ==================================================================================================================== +``0.13.4`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` +``0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.16`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +========== ==================================================================================================================== .. _list_software_libpng_636: @@ -22694,23 +23071,23 @@ libpng is the official PNG reference library *homepage*: http://www.libpng.org/pub/png/libpng.html -========== ================================================================================================ -version toolchain -========== ================================================================================================ -``1.2.58`` ``system`` -``1.2.59`` ``system`` -``1.6.21`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``1.6.23`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``1.6.24`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` -``1.6.26`` ``foss/2016b``, ``intel/2016b`` -``1.6.27`` ``intel/2016b`` -``1.6.28`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``gimkl/2017a`` -``1.6.29`` ``GCCcore/6.3.0`` -``1.6.32`` ``GCCcore/6.4.0`` -``1.6.34`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.6.36`` ``GCCcore/8.2.0`` -``1.6.37`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ================================================================================================ +========== ==================================================================================================================== +version toolchain +========== ==================================================================================================================== +``1.2.58`` ``system`` +``1.2.59`` ``system`` +``1.6.21`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``1.6.23`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` +``1.6.24`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` +``1.6.26`` ``foss/2016b``, ``intel/2016b`` +``1.6.27`` ``intel/2016b`` +``1.6.28`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``gimkl/2017a`` +``1.6.29`` ``GCCcore/6.3.0`` +``1.6.32`` ``GCCcore/6.4.0`` +``1.6.34`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.6.36`` ``GCCcore/8.2.0`` +``1.6.37`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ==================================================================================================================== .. _list_software_libpsl_646: @@ -22841,14 +23218,15 @@ The GNU Readline library provides a set of functions for use by applications th *homepage*: https://tiswww.case.edu/php/chet/readline/rltop.html -======= =================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain -======= =================================================================================================================================================================================================================================================================================================================================================================================== -``6.3`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``7.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``8.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` -``8.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -======= =================================================================================================================================================================================================================================================================================================================================================================================== +========= =================================================================================================================================================================================================================================================================================================================================================================================== +version toolchain +========= =================================================================================================================================================================================================================================================================================================================================================================================== +``6.3`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +``7.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``8.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +``8.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``8.1.2`` ``GCCcore/11.3.0`` +========= =================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_libRmath_819: @@ -22902,6 +23280,7 @@ version toolchain ``1.2.0.10`` ``GCC/10.2.0`` ``1.2.0.11`` ``GCC/10.2.0`` ``1.3.0.0`` ``GCC/10.2.0`` +``1.3.0.1`` ``GCC/10.2.0`` ============ ============== @@ -22920,6 +23299,7 @@ version toolchain ``2.40.15`` ``intel/2016a`` ``2.48.4`` ``foss/2019a`` ``2.51.2`` ``GCCcore/10.3.0`` +``2.52.8`` ``GCCcore/11.2.0`` =========== ================== @@ -23142,14 +23522,14 @@ LIBSVM is an integrated software for support vector classification, (C-SVC, nu-S *homepage*: https://www.csie.ntu.edu.tw/~cjlin/libsvm/ -======== ================================ -version toolchain -======== ================================ -``3.22`` ``intel/2016b``, ``intel/2017b`` -``3.23`` ``foss/2018b``, ``intel/2018b`` -``3.24`` ``GCCcore/9.3.0`` -``3.25`` ``GCCcore/10.2.0`` -======== ================================ +======== ====================================== +version toolchain +======== ====================================== +``3.22`` ``intel/2016b``, ``intel/2017b`` +``3.23`` ``foss/2018b``, ``intel/2018b`` +``3.24`` ``GCCcore/9.3.0`` +``3.25`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` +======== ====================================== .. _list_software_libtar_638: @@ -23224,7 +23604,7 @@ version toolchain ``4.0.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``4.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.2.0`` ``GCCcore/10.3.0`` -``4.3.0`` ``GCCcore/11.2.0`` +``4.3.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ========================================================================================================= @@ -23252,9 +23632,9 @@ version toolchain *libtool* +++++++++ -GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. +GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. -*homepage*: http://www.gnu.org/software/libtool +*homepage*: https://www.gnu.org/software/libtool ========= ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain @@ -23262,6 +23642,7 @@ version toolchain ``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` ``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` ``2.4.6`` ``FCC/4.5.0``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +``2.4.7`` ``GCCcore/11.3.0`` ========= ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -23319,6 +23700,7 @@ version toolchain ``1.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.4.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.5.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.6.2`` ``GCCcore/11.3.0`` ========= ======================================================================= @@ -23379,12 +23761,12 @@ libvdwxc is a general library for evaluating energy and potential for exchange-c *homepage*: https://libvdwxc.org -========= ================================================================================================================ -version toolchain -========= ================================================================================================================ -``0.3.2`` ``foss/2018b`` -``0.4.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``intel/2020b``, ``intel/2021a`` -========= ================================================================================================================ +========= ================================================================================================================================================= +version toolchain +========= ================================================================================================================================================= +``0.3.2`` ``foss/2018b`` +``0.4.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` +========= ================================================================================================================================================= .. _list_software_libvorbis_972: @@ -23702,6 +24084,7 @@ version versionsuffix toolchain ``2.9.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.9.9`` ``GCCcore/8.3.0`` ``2.9.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``2.9.13`` ``GCCcore/11.3.0`` ========== ================== ================================================================================================================================================================================== @@ -24155,6 +24538,7 @@ version toolchain ``11.0.0`` ``GCCcore/10.2.0`` ``11.1.0`` ``GCCcore/10.3.0`` ``12.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``14.0.3`` ``GCCcore/11.3.0`` ========== ======================================================================== @@ -24260,6 +24644,7 @@ version versionsuffix toolchain =========== ================= ============== ``1.9.2`` ``foss/2016b`` ``1.9.2.2`` ``-Python-3.6.6`` ``foss/2018b`` +``1.9.2.3`` ``foss/2021b`` =========== ================= ============== @@ -24506,13 +24891,13 @@ Least-squares methods to estimate rates and dates from phylogenies *homepage*: https://github.com/tothuhien/lsd2 -========= ================== -version toolchain -========= ================== -``1.9.7`` ``GCCcore/9.3.0`` -``2.2`` ``GCCcore/10.2.0`` -``2.3`` ``GCCcore/10.3.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.9.7`` ``GCCcore/9.3.0`` +``2.2`` ``GCCcore/10.2.0`` +``2.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== .. _list_software_LSMS_319: @@ -24718,19 +25103,19 @@ version versionsuffix toolchain *lz4* +++++ -LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core. +LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core. *homepage*: https://lz4.github.io/lz4/ -========= ======================================================== -version toolchain -========= ======================================================== -``1.8.2`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0`` -``1.9.0`` ``GCCcore/7.3.0`` -``1.9.1`` ``GCCcore/8.2.0`` -``1.9.2`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.9.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========= ======================================================== +========= ========================================================== +version toolchain +========= ========================================================== +``1.8.2`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0`` +``1.9.0`` ``GCCcore/7.3.0`` +``1.9.1`` ``GCCcore/8.2.0`` +``1.9.2`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.9.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ========================================================== .. _list_software_LZO_245: @@ -24756,7 +25141,7 @@ version toolchain --- -:ref:`list_software_M1QN3_336` - :ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_MAGeCK_456` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_matplotlib-inline_1764` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_MEGAN_360` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MNE-Python_911` - :ref:`list_software_MOABS_370` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MuJoCo_557` - :ref:`list_software_mujoco-py_931` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M1QN3_336` - :ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_MAGeCK_456` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_matplotlib-inline_1764` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_MEGAN_360` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MNE-Python_911` - :ref:`list_software_MOABS_370` - :ref:`list_software_ModelTest-NG_1107` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MuJoCo_557` - :ref:`list_software_mujoco-py_931` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M1QN3_336: @@ -24790,7 +25175,7 @@ version toolchain ``1.4.16`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.4.18`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` -``1.4.19`` ``GCCcore/11.2.0``, ``GCCcore/9.4.0``, ``system`` +``1.4.19`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``system`` ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -24817,7 +25202,7 @@ version toolchain Model Based Analysis for ChIP-Seq data -*homepage*: https://github.com/taoliu/MACS/ +*homepage*: https://github.com/taoliu/MACS ================== ================== =============================== version versionsuffix toolchain @@ -24826,6 +25211,7 @@ version versionsuffix toolchain ``2.1.2.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2.1.2.1`` ``-Python-2.7.15`` ``intel/2019a`` ``2.2.5`` ``-Python-3.6.6`` ``foss/2018b`` +``2.2.7.1`` ``foss/2021b`` ================== ================== =============================== @@ -24955,6 +25341,7 @@ version versionsuffix toolchain ``2.5.1`` ``fosscuda/2019a``, ``fosscuda/2019b`` ``2.5.4`` ``fosscuda/2019a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intelcuda/2019b``, ``intelcuda/2020b`` ``2.6.1`` ``-CUDA-11.3.1`` ``foss/2021a`` +``2.6.2`` ``-CUDA-11.4.1`` ``foss/2021b`` ========= ================ ======================================================================================================================== @@ -25071,7 +25458,7 @@ makeinfo is part of the Texinfo project, the official documentation format of th version versionsuffix toolchain ======= ============= =========================================================================================== ``6.7`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``6.7`` ``-minimal`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``6.7`` ``-minimal`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``6.8`` ``GCCcore/11.2.0`` ======= ============= =========================================================================================== @@ -25099,6 +25486,7 @@ version versionsuffix toolchain ``1.1.2`` ``GCCcore/9.3.0`` ``1.1.3`` ``GCCcore/10.2.0`` ``1.1.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.2.0`` ``GCCcore/11.3.0`` ========= ================== ================================================================================================================================================================= @@ -25262,14 +25650,14 @@ Fast genome and metagenome distance estimation using MinHash *homepage*: http://mash.readthedocs.org -======= ============================== -version toolchain -======= ============================== -``2.0`` ``foss/2018a`` -``2.1`` ``foss/2018b`` -``2.2`` ``GCC/9.3.0`` -``2.3`` ``GCC/10.3.0``, ``GCC/11.2.0`` -======= ============================== +======= ============================================================ +version toolchain +======= ============================================================ +``2.0`` ``foss/2018a`` +``2.1`` ``foss/2018b`` +``2.2`` ``GCC/9.3.0`` +``2.3`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` +======= ============================================================ .. _list_software_MaSuRCA_588: @@ -25314,6 +25702,7 @@ version toolchain ``11.3.0`` ``system`` ``12.0.0`` ``system`` ``12.1.1`` ``system`` +``13.0.0`` ``system`` ========== ========== @@ -25699,14 +26088,14 @@ The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable *homepage*: http://micans.org/mcl/ -========== ================ ========================================================================================= -version versionsuffix toolchain -========== ================ ========================================================================================= -``02.063`` ``intel/2016b`` -``14.137`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``intel/2016b`` -``14.137`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``14.137`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -========== ================ ========================================================================================= +========== ================ ============================================================================================================= +version versionsuffix toolchain +========== ================ ============================================================================================================= +``02.063`` ``intel/2016b`` +``14.137`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``intel/2016b`` +``14.137`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``14.137`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +========== ================ ============================================================================================================= .. _list_software_MCR_226: @@ -25738,8 +26127,10 @@ version versionsuffix toolchain ``R2021a`` ``.0`` ``system`` ``R2021a`` ``.3`` ``system`` ``R2021b`` ``system`` +``R2021b`` ``.1`` ``system`` ``R2021b`` ``.2`` ``system`` ``R2022a`` ``system`` +``R2022a`` ``.1`` ``system`` ========== ============= ========== @@ -26078,7 +26469,7 @@ version versionsuffix toolchain ``5.0.4`` ``-Perl-5.26.0-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``5.1.1`` ``-Python-3.6.6`` ``foss/2018b`` ``5.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``5.4.1`` ``GCC/10.3.0`` +``5.4.1`` ``GCC/10.3.0``, ``gompi/2021b`` ``5.4.1`` ``-Python-2.7.18`` ``gompi/2021b`` ========= ============================== =============================== @@ -26193,6 +26584,7 @@ version toolchain ``20.2.1`` ``GCCcore/10.2.0`` ``21.1.1`` ``GCCcore/10.3.0`` ``21.1.7`` ``GCCcore/11.2.0`` +``22.0.3`` ``GCCcore/11.3.0`` ========== ==================================================================== @@ -26289,6 +26681,7 @@ version versionsuffix toolchain ``0.58.0`` ``GCCcore/10.3.0`` ``0.58.2`` ``GCCcore/11.2.0`` ``0.59.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.62.1`` ``GCCcore/11.3.0`` ========== ================= ================================== @@ -26915,15 +27308,16 @@ version versionsuffix toolchain MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the latter at the moment only CCS and error-corrected CLR reads). -*homepage*: https://sourceforge.net/projects/mira-assembler/ +*homepage*: https://sourceforge.net/p/mira-assembler/wiki/Home/ -========= ================== ================================================ -version versionsuffix toolchain -========= ================== ================================================ -``4.0.2`` ``foss/2018b``, ``gompi/2019b``, ``intel/2017b`` -``4.0.2`` ``-Python-2.7.11`` ``foss/2016a`` -``4.9.6`` ``intel/2017b`` -========= ================== ================================================ +========== ================== ================================================ +version versionsuffix toolchain +========== ================== ================================================ +``4.0.2`` ``foss/2018b``, ``gompi/2019b``, ``intel/2017b`` +``4.0.2`` ``-Python-2.7.11`` ``foss/2016a`` +``4.9.6`` ``intel/2017b`` +``5.0rc2`` ``foss/2020b`` +========== ================== ================================================ .. _list_software_miRDeep2_728: @@ -27132,15 +27526,16 @@ version versionsuffix toolchain *Mmg* +++++ -Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries +Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries *homepage*: https://www.mmgtools.org/ -========= ============== -version toolchain -========= ============== -``5.3.9`` ``foss/2017b`` -========= ============== +========= =============== +version toolchain +========= =============== +``5.3.9`` ``foss/2017b`` +``5.6.0`` ``gompi/2021b`` +========= =============== .. _list_software_MMSEQ_387: @@ -27230,6 +27625,22 @@ version toolchain =========== =============== +.. _list_software_ModelTest-NG_1107: + +*ModelTest-NG* +++++++++++++++ + +ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces. + +*homepage*: https://github.com/ddarriba/modeltest + +========= =============== +version toolchain +========= =============== +``0.1.7`` ``gompi/2021b`` +========= =============== + + .. _list_software_modred_635: *modred* @@ -27278,6 +27689,7 @@ version toolchain ========= ================== ``0.9.6`` ``GCCcore/11.2.0`` ``1.0.0`` ``GCCcore/11.2.0`` +``1.2.1`` ``GCCcore/11.3.0`` ========= ================== @@ -27484,6 +27896,7 @@ version toolchain ``0.2.2`` ``intel/2018a`` ``0.2.3`` ``intel/2018a`` ``0.2.4`` ``foss/2018b`` +``0.3.3`` ``GCC/11.2.0`` ========= =============== @@ -27769,12 +28182,13 @@ MrBayes is a program for Bayesian inference and model choice across a wide rang *homepage*: https://nbisweden.github.io/MrBayes/ -========= ================================= -version toolchain -========= ================================= -``3.2.6`` ``foss/2016a``, ``foss/2017a`` -``3.2.7`` ``gompi/2020b``, ``gompic/2019b`` -========= ================================= +========== =============================================== +version toolchain +========== =============================================== +``3.2.6`` ``foss/2016a``, ``foss/2017a``, ``gompi/2020b`` +``3.2.7`` ``gompi/2020b``, ``gompic/2019b`` +``3.2.7a`` ``foss/2020a``, ``iimpi/2019a`` +========== =============================================== .. _list_software_mrcfile_738: @@ -28035,6 +28449,7 @@ version versionsuffix toolchain ``1.9`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``1.10.1`` ``foss/2020b`` ``1.11`` ``foss/2021a`` +``1.12`` ``foss/2021b`` ========== ================== =============================== @@ -28089,6 +28504,8 @@ version versionsuffix toolchain ``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` ``5.3.5`` ``-metis`` ``foss/2020b``, ``intel/2020b`` ``5.4.0`` ``-metis`` ``foss/2021a`` +``5.4.1`` ``-metis`` ``intel/2021b`` +``5.5.0`` ``-metis`` ``foss/2021a`` ========= ============== ================================================================================================================= @@ -28106,6 +28523,7 @@ version toolchain ========= ===================================== ``2.2.5`` ``GCCcore/6.4.0`` ``2.3.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.3.3`` ``GCCcore/10.3.0`` ========= ===================================== @@ -28155,7 +28573,7 @@ version versionsuffix toolchain ============ =============== ===================================================================================================================================================================================================================== ``3.8.31`` ``GCC/7.3.0-2.30``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2017b``, ``foss/2018a``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ``3.8.31`` ``-i86linux64`` ``system`` -``3.8.1551`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` +``3.8.1551`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` ``5.0.1428`` ``GCCcore/10.3.0`` ``5.1`` ``GCCcore/11.2.0`` ============ =============== ===================================================================================================================================================================================================================== @@ -28453,7 +28871,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_namedlist_961` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numdiff_745` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_namedlist_961` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_num2words_945` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numdiff_745` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -28732,7 +29150,7 @@ version toolchain ``2.13.01`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``2.13.03`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.14.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.15.05`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.15.05`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` =========== ==================================================================================== @@ -28886,14 +29304,14 @@ Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find *homepage*: https://dev.yorhel.nl/ncdu -========== ================= -version toolchain -========== ================= -``1.13`` ``GCCcore/7.3.0`` -``1.14`` ``GCCcore/7.3.0`` -``1.15.1`` ``GCCcore/9.3.0`` -``1.16`` ``GCC/10.3.0`` -========== ================= +========== ============================== +version toolchain +========== ============================== +``1.13`` ``GCCcore/7.3.0`` +``1.14`` ``GCCcore/7.3.0`` +``1.15.1`` ``GCCcore/9.3.0`` +``1.16`` ``GCC/10.3.0``, ``GCC/11.2.0`` +========== ============================== .. _list_software_NCIPLOT_537: @@ -28996,7 +29414,7 @@ version toolchain *ncurses* +++++++++ -The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. +The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. *homepage*: https://www.gnu.org/software/ncurses/ @@ -29007,6 +29425,7 @@ version toolchain ``6.0`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``6.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` ``6.2`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``system`` +``6.3`` ``GCCcore/11.3.0`` ======= ============================================================================================================================================================================================================================================================================================================================================================================= @@ -29137,6 +29556,7 @@ version versionsuffix toolchain =========== ================= ============== ``0.4.129`` ``-Python-3.8.2`` ``foss/2020a`` ``0.10.5`` ``foss/2020b`` +``0.16.2`` ``foss/2021a`` =========== ================= ============== @@ -29518,6 +29938,7 @@ version toolchain ``21.03.0`` ``system`` ``21.08.0`` ``system`` ``21.10.6`` ``system`` +``22.04.0`` ``system`` =========== ========== @@ -29530,11 +29951,11 @@ NextGenMap is a flexible highly sensitive short read mapping tool that handles *homepage*: http://cibiv.github.io/NextGenMap/ -========= ============== -version toolchain -========= ============== -``0.5.5`` ``foss/2016b`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``0.5.5`` ``GCC/11.2.0``, ``foss/2016b`` +========= ============================== .. _list_software_NFFT_302: @@ -29777,6 +30198,7 @@ version toolchain ``1.0.0`` ``GCCcore/8.3.0`` ``1.4.6`` ``GCCcore/10.2.0`` ``1.4.8`` ``GCCcore/10.3.0`` +``1.6.6`` ``GCCcore/11.2.0`` ========== ================== @@ -29812,7 +30234,7 @@ version toolchain ``1.9.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` ``1.10.0`` ``GCCcore/9.3.0`` ``1.10.1`` ``GCCcore/10.2.0`` -``1.10.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.10.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ==================================================================================== @@ -30167,11 +30589,11 @@ ntCard is a streaming algorithm for estimating the frequencies of k-mers in geno *homepage*: https://www.bcgsc.ca/resources/software/ntcard -========= ============= -version toolchain -========= ============= -``1.2.1`` ``GCC/8.3.0`` -========= ============= +========= ============================= +version toolchain +========= ============================= +``1.2.1`` ``GCC/11.2.0``, ``GCC/8.3.0`` +========= ============================= .. _list_software_ntEdit_616: @@ -30236,9 +30658,26 @@ version toolchain ========= =============================== ``2.5.1`` ``foss/2020b``, ``intel/2020b`` ``2.7.0`` ``foss/2021a``, ``intel/2021a`` +``2.7.1`` ``intel/2020b`` ========= =============================== +.. _list_software_num2words_945: + +*num2words* ++++++++++++ + +Modules to convert numbers to words. 42 --> forty-two + +*homepage*: https://github.com/savoirfairelinux/num2words + +========== ================== +version toolchain +========== ================== +``0.5.10`` ``GCCcore/10.3.0`` +========== ================== + + .. _list_software_numactl_756: *numactl* @@ -30256,7 +30695,7 @@ version toolchain ``2.0.11`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.3.0-2.26``, ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``GCC/6.2.0-2.27``, ``GCC/6.3.0-2.27``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` ``2.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.0.13`` ``GCCcore/10.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -``2.0.14`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.0.14`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ============================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -30288,6 +30727,7 @@ version versionsuffix toolchain ``0.52.0`` ``-Python-3.8.2`` ``foss/2020a`` ``0.53.1`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` ``0.54.1`` ``foss/2021b``, ``intel/2021b`` +``0.54.1`` ``-CUDA-11.4.1`` ``foss/2021b`` ========== ================== =================================================== @@ -30446,7 +30886,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ONNX_323` - :ref:`list_software_ONNX-Runtime_1108` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_ont-remora_1028` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCensus-python_1746` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFace_769` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSceneGraph_1394` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_Optuna_631` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OGDF_288` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ONNX_323` - :ref:`list_software_ONNX-Runtime_1108` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_ont-remora_1028` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCensus-python_1746` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFace_769` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSceneGraph_1394` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_Optuna_631` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -30589,6 +31029,22 @@ version toolchain ========= ============== +.. _list_software_OGDF_288: + +*OGDF* +++++++ + +OGDF is a self-contained C++ library for graph algorithms, in particular for (but not restricted to) automatic graph drawing. It offers sophisticated algorithms and data structures to use within your own applications or scientific projects. + +*homepage*: https://ogdf.uos.de/ + +================== ============== +version toolchain +================== ============== +``dogwood-202202`` ``GCC/11.2.0`` +================== ============== + + .. _list_software_OMA_221: *OMA* @@ -30815,7 +31271,7 @@ version versionsuffix toolchain ``0.3.15`` ``GCC/10.3.0`` ``0.3.17`` ``GCC/10.3.0``, ``GCC/11.2.0`` ``0.3.18`` ``GCC/11.2.0`` -``0.3.20`` ``GCC/11.2.0`` +``0.3.20`` ``GCC/11.2.0``, ``GCC/11.3.0`` ========== ================= ========================================================== @@ -31239,6 +31695,7 @@ version versionsuffix toolchain ``4.1.0`` ``GCC/10.2.0`` ``4.1.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0`` ``4.1.2`` ``GCC/11.2.0`` +``4.1.4`` ``GCC/11.3.0`` ``system`` ``GCC/system-2.29`` ========== ================ ==================================================================================================================== @@ -31323,6 +31780,7 @@ version versionsuffix toolchain ``2.6.4`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` ``3.0.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``3.0.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``3.0.9`` ``GCCcore/11.2.0`` ========= ================== ====================================== @@ -31352,11 +31810,11 @@ The OpenSceneGraph is an open source high performance 3D graphics toolkit, used *homepage*: http://www.openscenegraph.org/ -========= ============== -version toolchain -========= ============== -``3.6.5`` ``foss/2021a`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``3.6.5`` ``foss/2021a``, ``foss/2021b`` +========= ============================== .. _list_software_OpenSees_802: @@ -31437,6 +31895,7 @@ version toolchain ``1.1.1e`` ``GCCcore/9.3.0`` ``1.1.1h`` ``GCCcore/10.2.0`` ``1.1.1k`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.1.1n`` ``GCCcore/11.3.0`` ========== ===================================================================== @@ -31453,6 +31912,7 @@ OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the version toolchain ========= ================== ``5.5.0`` ``GCCcore/10.2.0`` +``5.8.0`` ``GCCcore/11.2.0`` ========= ================== @@ -31708,6 +32168,8 @@ version versionsuffix toolchain ``5.7.1`` ``ffmpi/4.5.0``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021a``, ``iompi/2021a`` ``5.7.1`` ``-CUDA-11.3.1`` ``gompi/2021a`` ``5.8`` ``iimpi/2021b`` +``5.9`` ``gompi/2022.05`` +``5.9`` ``-CUDA-11.3.1`` ``gompi/2021a`` ========= ================ ============================================================================================================================================================================================= @@ -31768,7 +32230,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patch_528` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_porefoam_857` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_presto_669` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyEVTK_515` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_PyFrag_585` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_pyradiomics_1188` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch-Lightning_1690` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_panito_651` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parameterized_1389` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patch_528` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_porefoam_857` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_presto_669` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_purge_dups_1086` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyEVTK_515` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_PyFrag_585` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_pyradiomics_1188` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch-Lightning_1690` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -31890,6 +32352,7 @@ pagmo is a C++ scientific library for massively parallel optimization. version toolchain ========== ============== ``2.17.0`` ``foss/2020b`` +``2.18.0`` ``foss/2021a`` ========== ============== @@ -32064,6 +32527,7 @@ version toolchain ``1.47.0`` ``GCCcore/10.2.0`` ``1.48.5`` ``GCCcore/10.3.0`` ``1.48.8`` ``GCCcore/11.2.0`` +``1.50.7`` ``GCCcore/11.3.0`` =========== ==================================== @@ -32085,6 +32549,22 @@ version versionsuffix toolchain ========== ========================== ============== +.. _list_software_panito_651: + +*panito* +++++++++ + +Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment. + +*homepage*: https://github.com/sanger-pathogens/panito + +========= ============== +version toolchain +========= ============== +``0.0.1`` ``GCC/10.3.0`` +========= ============== + + .. _list_software_PAPI_298: *PAPI* @@ -32153,6 +32633,7 @@ version versionsuffix toolchain ========= ================= ================= ``0.6.5`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``0.6.6`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``0.6.7`` ``gompi/2020b`` ========= ================= ================= @@ -32172,6 +32653,22 @@ version toolchain ========== =============== +.. _list_software_parameterized_1389: + +*parameterized* ++++++++++++++++ + +Parameterized testing with any Python test framework + +*homepage*: https://github.com/wolever/parameterized + +========= ================== +version toolchain +========= ================== +``0.8.1`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_parasail_845: *parasail* @@ -32643,7 +33140,7 @@ version toolchain ``8.42`` ``GCCcore/6.4.0`` ``8.43`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``8.44`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``8.45`` ``GCCcore/11.2.0`` +``8.45`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ======== ================================================================================== @@ -32666,6 +33163,7 @@ version toolchain ``10.35`` ``GCCcore/10.2.0`` ``10.36`` ``GCCcore/10.3.0`` ``10.37`` ``GCCcore/11.2.0`` +``10.40`` ``GCCcore/11.3.0`` ========= ==================================== @@ -32781,6 +33279,7 @@ version versionsuffix toolchain ``5.28.0`` ``GCCcore/7.3.0`` ``5.28.1`` ``GCCcore/8.2.0`` ``5.30.0`` ``GCCcore/8.3.0`` +``5.30.0`` ``-minimal`` ``GCCcore/8.3.0`` ``5.30.2`` ``GCCcore/9.3.0`` ``5.30.2`` ``-minimal`` ``GCCcore/9.3.0`` ``5.32.0`` ``GCCcore/10.2.0`` @@ -32789,6 +33288,7 @@ version versionsuffix toolchain ``5.32.1`` ``-minimal`` ``GCCcore/10.3.0`` ``5.34.0`` ``GCCcore/11.2.0`` ``5.34.0`` ``-minimal`` ``GCCcore/11.2.0`` +``5.34.1`` ``GCCcore/11.3.0`` ========== ============= ========================================================================================= @@ -32895,12 +33395,12 @@ A suite of tools to build and search generalized profiles (protein and DNA). *homepage*: https://github.com/sib-swiss/pftools3 -============ ============== -version toolchain -============ ============== -``3.2.11`` ``foss/2021a`` -``20160324`` ``foss/2016a`` -============ ============== +============ ================================== +version toolchain +============ ================================== +``3.2.11`` ``GCCcore/10.3.0``, ``foss/2021a`` +``20160324`` ``foss/2016a`` +============ ================================== .. _list_software_pFUnit_598: @@ -33408,6 +33908,7 @@ version versionsuffix toolchain ``8.2.0`` ``GCCcore/10.3.0`` ``8.3.1`` ``GCCcore/11.2.0`` ``8.3.2`` ``GCCcore/11.2.0`` +``9.1.0`` ``GCCcore/10.3.0`` ========= ================================= =================================================== @@ -33632,7 +34133,7 @@ version toolchain ``0.34.0`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``0.38.0`` ``GCCcore/8.2.0`` ``0.38.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.40.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``0.40.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ============================================================================================================================================ @@ -33680,11 +34181,11 @@ pkgconf is a program which helps to configure compiler and linker flags for deve *homepage*: https://github.com/pkgconf/pkgconf -========= ================== -version toolchain -========= ================== -``1.8.0`` ``GCCcore/11.2.0`` -========= ================== +========= ================================================== +version toolchain +========= ================================================== +``1.8.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` +========= ================================================== .. _list_software_pkgconfig_952: @@ -33856,6 +34357,7 @@ version toolchain ``2.00-alpha2-x86_64_avx2`` ``system`` ``2.00a2.3`` ``GCC/10.3.0``, ``GCC/11.2.0`` ``2.00a2.3_x86_64`` ``system`` +``2.00a3.1`` ``GCC/11.2.0`` =========================== ============================== @@ -34054,6 +34556,7 @@ version toolchain ``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``3.2.3`` ``GCCcore/10.3.0`` ``4.1.0`` ``GCCcore/11.2.0`` +``4.1.2`` ``GCCcore/11.3.0`` ========= ======================================================= @@ -35260,6 +35763,22 @@ version toolchain ========= ============== +.. _list_software_purge_dups_1086: + +*purge_dups* +++++++++++++ + +purge haplotigs and overlaps in an assembly based on read depth + +*homepage*: https://github.com/dfguan/purge_dups + +========= ============== +version toolchain +========= ============== +``1.2.5`` ``foss/2021b`` +========= ============== + + .. _list_software_py_233: *py* @@ -35356,6 +35875,7 @@ version versionsuffix toolchain ========= ================== =============================== ``3.0.1`` ``-Python-2.7.11`` ``intel/2016a`` ``4.0.0`` ``foss/2020b``, ``intel/2020b`` +``4.2.3`` ``foss/2021a`` ========= ================== =============================== @@ -35450,6 +35970,7 @@ version versionsuffix toolchain ``2.6.2`` ``GCCcore/10.3.0`` ``2.7.1`` ``GCCcore/11.2.0`` ``2.7.1`` ``-Python-2.7.18`` ``GCCcore/11.2.0`` +``2.9.2`` ``GCCcore/11.3.0`` ========= ================== ================== @@ -35475,6 +35996,7 @@ version versionsuffix toolchain ``1.18.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.20.0`` ``GCCcore/10.2.0`` ``1.20.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.21.0`` ``GCCcore/11.3.0`` ========== ================== ====================================== @@ -35745,12 +36267,12 @@ Python interface to Graphviz's Dot language. *homepage*: https://github.com/pydot/pydot -========= ================================= -version toolchain -========= ================================= -``1.4.1`` ``GCCcore/9.3.0``, ``foss/2019b`` -``1.4.2`` ``GCCcore/10.2.0`` -========= ================================= +========= ====================================== +version toolchain +========= ====================================== +``1.4.1`` ``GCCcore/9.3.0``, ``foss/2019b`` +``1.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_pyEGA3_489: @@ -36054,6 +36576,7 @@ pygmo is a scientific Python library for massively parallel optimization. version toolchain ========== ============== ``2.16.1`` ``foss/2020b`` +``2.18.0`` ``foss/2021a`` ========== ============== @@ -36066,17 +36589,18 @@ PyGObject is a Python package which provides bindings for GObject based librarie *homepage*: https://pygobject.readthedocs.io/ -========== ================== ================= -version versionsuffix toolchain -========== ================== ================= -``2.28.6`` ``-Python-2.7.11`` ``intel/2016a`` -``2.28.6`` ``-Python-2.7.14`` ``intel/2017b`` -``2.28.7`` ``-Python-2.7.14`` ``intel/2018a`` -``2.28.7`` ``-Python-2.7.15`` ``foss/2018b`` -``3.34.0`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` -``3.34.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``3.34.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -========== ================== ================= +========== ================== ================== +version versionsuffix toolchain +========== ================== ================== +``2.28.6`` ``-Python-2.7.11`` ``intel/2016a`` +``2.28.6`` ``-Python-2.7.14`` ``intel/2017b`` +``2.28.7`` ``-Python-2.7.14`` ``intel/2018a`` +``2.28.7`` ``-Python-2.7.15`` ``foss/2018b`` +``3.34.0`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +``3.34.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``3.34.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``3.42.1`` ``GCCcore/11.3.0`` +========== ================== ================== .. _list_software_pygraphviz_1108: @@ -37168,10 +37692,11 @@ version versionsuffix toolchain ``2.7.14`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2018a`` ``2.7.14`` ``-bare`` ``GCCcore/6.4.0`` ``2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``2.7.15`` ``-bare`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``2.7.15`` ``-bare`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.7.16`` ``GCCcore/8.3.0`` +``2.7.16`` ``-bare`` ``GCCcore/8.3.0`` ``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``2.7.18`` ``-bare`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.7.18`` ``-bare`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ``3.5.1`` ``foss/2016a``, ``intel/2016a`` ``3.5.2`` ``foss/2016.04``, ``foss/2016b``, ``intel/2016b`` ``3.5.2`` ``-bare`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` @@ -37189,6 +37714,8 @@ version versionsuffix toolchain ``3.9.5`` ``-bare`` ``GCCcore/10.3.0`` ``3.9.6`` ``GCCcore/11.2.0`` ``3.9.6`` ``-bare`` ``GCCcore/11.2.0`` +``3.10.4`` ``GCCcore/11.3.0`` +``3.10.4`` ``-bare`` ``GCCcore/11.3.0`` ========== ================= ================================================================================================================================================================= @@ -38067,17 +38594,17 @@ QUAST evaluates genome assemblies by computing various metrics. It works both wi *homepage*: https://github.com/ablab/quast -========= ================== ============================== -version versionsuffix toolchain -========= ================== ============================== -``4.6.0`` ``-Python-3.5.2`` ``foss/2016b`` -``4.6.3`` ``-Python-3.6.4`` ``foss/2018a`` -``5.0.2`` ``foss/2020b``, ``foss/2021a`` -``5.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` -``5.0.2`` ``-Python-2.7.18`` ``foss/2020b`` -``5.0.2`` ``-Python-3.7.2`` ``foss/2019a`` -``5.0.2`` ``-Python-3.8.2`` ``foss/2020a`` -========= ================== ============================== +========= ================== ============================================== +version versionsuffix toolchain +========= ================== ============================================== +``4.6.0`` ``-Python-3.5.2`` ``foss/2016b`` +``4.6.3`` ``-Python-3.6.4`` ``foss/2018a`` +``5.0.2`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` +``5.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` +``5.0.2`` ``-Python-2.7.18`` ``foss/2020b`` +``5.0.2`` ``-Python-3.7.2`` ``foss/2019a`` +``5.0.2`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================== ============================================== .. _list_software_QuaZIP_538: @@ -38206,7 +38733,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_RaGOO_408` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_RAPSearch2_875` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redis_503` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rising_652` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_RaGOO_408` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_RAPSearch2_875` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redis_503` - :ref:`list_software_redis-py_813` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rising_652` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_ruamel.yaml_1127` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -38245,6 +38772,7 @@ version versionsuffix toolchain ``4.0.5`` ``foss/2020b``, ``fosscuda/2020b`` ``4.1.0`` ``foss/2021a`` ``4.1.2`` ``foss/2021b`` +``4.2.0`` ``foss/2021b`` ========= ============================= =================================================== @@ -38274,6 +38802,7 @@ version versionsuffix toolchain ``3.12`` ``-R-4.0.3`` ``foss/2020b`` ``3.13`` ``-R-4.1.0`` ``foss/2021a`` ``3.14`` ``-R-4.1.2`` ``foss/2021b`` +``3.15`` ``-R-4.2.0`` ``foss/2021b`` ======== ============= =============================== @@ -38488,11 +39017,11 @@ A fast JSON parser/generator for C++ with both SAX/DOM style API *homepage*: https://rapidjson.org -========= =========================================================================== -version toolchain -========= =========================================================================== -``1.1.0`` ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= =========================================================================== +========= =============================================================================================== +version toolchain +========= =============================================================================================== +``1.1.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= =============================================================================================== .. _list_software_rapidtide_950: @@ -38648,6 +39177,7 @@ version toolchain ``1.0.1`` ``gompi/2019b`` ``1.0.2`` ``gompi/2020b`` ``1.0.3`` ``GCC/10.2.0`` +``1.1.0`` ``GCC/11.2.0`` ========= ============================== @@ -38851,13 +39381,13 @@ RE2 is a fast, safe, thread-friendly alternative to backtracking regular express *homepage*: https://github.com/google/re2 -============== ================== -version toolchain -============== ================== -``2020-07-01`` ``GCCcore/8.3.0`` -``2021-06-01`` ``GCCcore/10.2.0`` -``2022-02-01`` ``GCCcore/11.2.0`` -============== ================== +============== ====================================== +version toolchain +============== ====================================== +``2020-07-01`` ``GCCcore/8.3.0`` +``2021-06-01`` ``GCCcore/10.2.0`` +``2022-02-01`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +============== ====================================== .. _list_software_re2c_364: @@ -38961,6 +39491,22 @@ version toolchain ========= ============================== +.. _list_software_redis-py_813: + +*redis-py* +++++++++++ + +The Python interface to the Redis key-value store. + +*homepage*: https://github.com/redis/redis-py + +========= ============== +version toolchain +========= ============== +``4.3.1`` ``foss/2021a`` +========= ============== + + .. _list_software_Redundans_932: *Redundans* @@ -39007,6 +39553,7 @@ version toolchain ``3.9.0`` ``system`` ``3.9.1`` ``system`` ``3.10.1`` ``system`` +``3.11.0`` ``system`` ========== ========== @@ -39430,6 +39977,7 @@ version versionsuffix toolchain ``4-10`` ``-R-4.0.4`` ``foss/2020b``, ``fosscuda/2020b`` ``4-10`` ``-R-4.0.5`` ``foss/2020b``, ``fosscuda/2020b`` ``4-10`` ``-R-4.1.0`` ``foss/2021a`` +``4-12`` ``-R-4.1.2`` ``foss/2021b`` ======== ============= ================================== @@ -39494,11 +40042,12 @@ RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. *homepage*: https://github.com/bcgsc/RNA-Bloom -========= ============= -version toolchain -========= ============= -``1.2.3`` ``GCC/8.3.0`` -========= ============= +========= ============== +version toolchain +========= ============== +``1.2.3`` ``GCC/8.3.0`` +``1.4.3`` ``GCC/11.2.0`` +========= ============== .. _list_software_RNA-SeQC_602: @@ -39598,6 +40147,7 @@ version versionsuffix toolchain ========= ================== ============== ``1.5.2`` ``-Python-2.7.15`` ``foss/2018b`` ``2.2.0`` ``-Python-3.8.2`` ``foss/2020a`` +``2.2.2`` ``foss/2021b`` ========= ================== ============== @@ -39642,13 +40192,13 @@ Rapid large-scale prokaryote pan genome analysis *homepage*: https://github.com/sanger-pathogens/Roary -========== ================ =============== -version versionsuffix toolchain -========== ================ =============== -``3.12.0`` ``system`` -``3.12.0`` ``-Perl-5.26.1`` ``intel/2018a`` -``3.13.0`` ``foss/2020a`` -========== ================ =============== +========== ================ ============================== +version versionsuffix toolchain +========== ================ ============================== +``3.12.0`` ``system`` +``3.12.0`` ``-Perl-5.26.1`` ``intel/2018a`` +``3.13.0`` ``foss/2020a``, ``foss/2021a`` +========== ================ ============================== .. _list_software_ROCm_337: @@ -39953,15 +40503,15 @@ RSeQC provides a number of useful modules that can comprehensively evaluate hig *homepage*: http://rseqc.sourceforge.net/ -========= ========================== =============== -version versionsuffix toolchain -========= ========================== =============== -``2.6.4`` ``-Python-2.7.12-R-3.3.1`` ``foss/2016b`` -``2.6.4`` ``-Python-2.7.14`` ``intel/2018a`` -``3.0.0`` ``-Python-3.6.6`` ``foss/2018b`` -``4.0.0`` ``foss/2021a`` -``4.0.0`` ``-Python-3.8.2`` ``foss/2020a`` -========= ========================== =============== +========= ========================== ============================== +version versionsuffix toolchain +========= ========================== ============================== +``2.6.4`` ``-Python-2.7.12-R-3.3.1`` ``foss/2016b`` +``2.6.4`` ``-Python-2.7.14`` ``intel/2018a`` +``3.0.0`` ``-Python-3.6.6`` ``foss/2018b`` +``4.0.0`` ``foss/2021a``, ``foss/2021b`` +``4.0.0`` ``-Python-3.8.2`` ``foss/2020a`` +========= ========================== ============================== .. _list_software_RStan_488: @@ -40049,6 +40599,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_ruamel.yaml_1127: + +*ruamel.yaml* ++++++++++++++ + +ruamel.yaml is a YAML 1.2 loader/dumper package for Python. + +*homepage*: https://sourceforge.net/projects/ruamel-yaml + +=========== ================== +version toolchain +=========== ================== +``0.17.21`` ``GCCcore/11.2.0`` +=========== ================== + + .. _list_software_Ruby_418: *Ruby* @@ -40117,6 +40683,8 @@ version toolchain ``1.42.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.52.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.54.0`` ``GCCcore/11.2.0`` +``1.56.0`` ``GCCcore/11.2.0`` +``1.60.0`` ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` ========== ========================================================================== @@ -40126,7 +40694,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_SCopeLoomR_963` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_ShengBTE_720` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_SHTns_464` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_skorch_650` - :ref:`list_software_SlamDunk_799` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SoXt_398` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_SPM_240` - :ref:`list_software_spoa_435` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_STRique_685` - :ref:`list_software_Structure_977` - :ref:`list_software_STRUMPACK_698` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SURVIVOR_656` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_SCGid_426` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_SCopeLoomR_963` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_scPred_609` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_ShengBTE_720` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_SHTns_464` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_skorch_650` - :ref:`list_software_SlamDunk_799` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_slow5tools_1067` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_smooth-topk_1157` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SoXt_398` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_SPM_240` - :ref:`list_software_spoa_435` - :ref:`list_software_SPOTPY_495` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_STRique_685` - :ref:`list_software_Structure_977` - :ref:`list_software_STRUMPACK_698` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SURVIVOR_656` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -40233,7 +40801,7 @@ version versionsuffix toolchain ``1.1.0`` ``gompi/2019b`` ``1.2.0`` ``gompi/2019b`` ``1.3.0`` ``gompi/2020a`` -``1.4.0`` ``gompi/2020b`` +``1.4.0`` ``GCC/11.2.0``, ``gompi/2020b`` ========== ================== ================================ @@ -40268,6 +40836,7 @@ version toolchain ``0.6.6`` ``system`` ``0.7.1`` ``system`` ``0.8.0`` ``GCC/10.2.0`` +``0.8.2`` ``GCC/10.3.0`` ========= ============== @@ -40280,12 +40849,12 @@ samblaster is a fast and flexible program for marking duplicates in read-id gro *homepage*: https://github.com/GregoryFaust/samblaster -========== ============== -version toolchain -========== ============== -``0.1.24`` ``foss/2018b`` -``0.1.26`` ``GCC/10.2.0`` -========== ============== +========== ============================== +version toolchain +========== ============================== +``0.1.24`` ``foss/2018b`` +``0.1.26`` ``GCC/10.2.0``, ``GCC/10.3.0`` +========== ============================== .. _list_software_Samcef_591: @@ -40334,7 +40903,7 @@ SAM Tools provide various utilities for manipulating alignments in the SAM forma version versionsuffix toolchain ========== ================= ======================================================================================================================================= ``0.1.17`` ``intel/2017a`` -``0.1.19`` ``foss/2016a``, ``foss/2016b`` +``0.1.19`` ``GCC/10.3.0``, ``foss/2016a``, ``foss/2016b`` ``0.1.20`` ``GCC/8.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b`` ``1.2`` ``foss/2016b`` ``1.3`` ``foss/2016a``, ``intel/2016a`` @@ -40353,6 +40922,7 @@ version versionsuffix toolchain ``1.13`` ``GCC/10.3.0`` ``1.14`` ``GCC/11.2.0`` ``1.15`` ``GCC/11.2.0`` +``1.15.1`` ``GCC/11.2.0`` ========== ================= ======================================================================================================================================= @@ -40477,7 +41047,7 @@ version toolchain *ScaLAPACK* +++++++++++ -The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. +The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. *homepage*: https://www.netlib.org/scalapack/ @@ -40501,6 +41071,7 @@ version versionsuffix toolchain ``2.1.0`` ``-bl`` ``gompi/2020b`` ``2.1.0`` ``-fb`` ``gompi/2021a``, ``gompi/2021b`` ``2.2`` ``-amd`` ``gompi/2020a`` +``2.2.0`` ``-fb`` ``gompi/2022.05`` ========= ================================= ============================================================================================================================================ @@ -40588,6 +41159,22 @@ version toolchain ========= ============== +.. _list_software_SCGid_426: + +*SCGid* ++++++++ + +A consensus approach to contig filtering and genome prediction from single-cell sequencing libraries + +*homepage*: https://github.com/amsesk/SCGid + +========= ============== +version toolchain +========= ============== +``0.9b0`` ``foss/2021b`` +========= ============== + + .. _list_software_Schrodinger_1144: *Schrodinger* @@ -40890,6 +41477,7 @@ version versionsuffix toolchain ``2021.05`` ``foss/2021a``, ``intel/2021a`` ``2021.10`` ``foss/2021b``, ``intel/2021b`` ``2021.10`` ``-Python-2.7.18`` ``foss/2021b`` +``2022.05`` ``foss/2022.05``, ``intel/2022.05`` =========== ================== ======================================================================== @@ -41031,7 +41619,7 @@ version versionsuffix toolchain ``6.0.6`` ``foss/2018a``, ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2018a`` ``6.0.9`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` ``6.1.0`` ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2020b`` -``6.1.2`` ``gompi/2021b`` +``6.1.2`` ``gompi/2021b``, ``iimpi/2021b`` =================== ============= ===================================================================================================================================================== @@ -41053,6 +41641,22 @@ version versionsuffix toolchain ========== ================== =============== +.. _list_software_scPred_609: + +*scPred* +++++++++ + +scPred package for cell type prediction from scRNA-seq data + +*homepage*: https://github.com/powellgenomicslab/scPred + +========= ============= ============== +version versionsuffix toolchain +========= ============= ============== +``1.9.2`` ``-R-4.1.2`` ``foss/2021b`` +========= ============= ============== + + .. _list_software_Scrappie_823: *Scrappie* @@ -41291,12 +41895,12 @@ segemehl is a software to map short sequencer reads to reference genomes. Unli *homepage*: http://www.bioinf.uni-leipzig.de/Software/segemehl/ -========= ============================================================= -version toolchain -========= ============================================================= -``0.2.0`` ``foss/2016b``, ``intel/2017b``, ``intel/2018a`` -``0.3.4`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``foss/2018b`` -========= ============================================================= +========= ============================================================================= +version toolchain +========= ============================================================================= +``0.2.0`` ``foss/2016b``, ``intel/2017b``, ``intel/2018a`` +``0.3.4`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``foss/2018b`` +========= ============================================================================= .. _list_software_segmentation-models_1983: @@ -41483,6 +42087,7 @@ version toolchain ``0.8.1`` ``system`` ``0.13.2`` ``system`` ``2.1.0`` ``system`` +``2.2.0`` ``system`` ========== ========== @@ -41495,11 +42100,11 @@ C++ interface to HTSlib, BWA-MEM and Fermi. *homepage*: https://github.com/walaj/SeqLib -========= ============================= -version toolchain -========= ============================= -``1.2.0`` ``GCC/10.2.0``, ``GCC/9.3.0`` -========= ============================= +========= ============================================= +version toolchain +========= ============================================= +``1.2.0`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` +========= ============================================= .. _list_software_Seqmagick_917: @@ -41747,14 +42352,15 @@ Shapely is a BSD-licensed Python package for manipulation and analysis of planar *homepage*: https://github.com/Toblerity/Shapely -========= ================= ======================================================= -version versionsuffix toolchain -========= ================= ======================================================= -``1.7.0`` ``-Python-3.7.2`` ``foss/2019a`` -``1.7.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``1.7.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` -``1.8a1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` -========= ================= ======================================================= +=============== ================= ======================================================= +version versionsuffix toolchain +=============== ================= ======================================================= +``1.7.0`` ``-Python-3.7.2`` ``foss/2019a`` +``1.7.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``1.7.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``1.8.1.post1`` ``GCC/11.2.0`` +``1.8a1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` +=============== ================= ======================================================= .. _list_software_sharutils_991: @@ -42430,6 +43036,22 @@ version toolchain ======= ============= +.. _list_software_slow5tools_1067: + +*slow5tools* +++++++++++++ + +slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. + +*homepage*: https://hasindu2008.github.io/slow5tools + +========= =============== +version toolchain +========= =============== +``0.4.0`` ``gompi/2021b`` +========= =============== + + .. _list_software_smafa_520: *smafa* @@ -42510,6 +43132,23 @@ version toolchain ======== ============== +.. _list_software_smooth-topk_1157: + +*smooth-topk* ++++++++++++++ + +Smooth Loss Functions for Deep Top-k Classification + +*homepage*: https://github.com/oval-group/smooth-topk + +================ ================ ============== +version versionsuffix toolchain +================ ================ ============== +``1.0-20210817`` ``foss/2021a`` +``1.0-20210817`` ``-CUDA-11.3.1`` ``foss/2021a`` +================ ================ ============== + + .. _list_software_SMRT-Link_769: *SMRT-Link* @@ -42656,7 +43295,7 @@ version toolchain *snippy* ++++++++ -Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). Rapid haploid variant calling and core genome alignment. +Rapid haploid variant calling and core genome alignment *homepage*: https://github.com/tseemann/snippy @@ -42666,6 +43305,7 @@ version versionsuffix toolchain ``4.4.1`` ``-Perl-5.28.0`` ``foss/2018b`` ``4.6.0`` ``GCC/10.2.0`` ``4.6.0`` ``-Java-13-Python-3.8.2`` ``GCC/9.3.0`` +``4.6.0`` ``-R-4.1.2`` ``foss/2021b`` ========= ========================= ============== @@ -42678,11 +43318,11 @@ Finds SNP sites from a multi-FASTA alignment file. *homepage*: https://sanger-pathogens.github.io/snp-sites/ -========= ========================================================= -version toolchain -========= ========================================================= -``2.5.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -========= ========================================================= +========= ============================================================================= +version toolchain +========= ============================================================================= +``2.5.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========= ============================================================================= .. _list_software_snpEff_610: @@ -42702,6 +43342,7 @@ version versionsuffix toolchain ``4.3t`` ``-Java-1.8`` ``system`` ``5.0`` ``-Java-13`` ``system`` ``5.0`` ``-Java-13-Python-3.8.2`` ``GCCcore/9.3.0`` +``5.0e`` ``-Java-11`` ``GCCcore/11.2.0`` ``5.0e`` ``-Java-13`` ``GCCcore/10.2.0`` ======== ========================= ================== @@ -42950,6 +43591,7 @@ version toolchain ``1.1.0`` ``GCC/9.3.0`` ``1.2.2`` ``GCC/9.3.0`` ``1.3.0`` ``GCC/10.3.0`` +``1.3.1`` ``GCC/11.2.0`` ========= ============== @@ -42970,6 +43612,7 @@ version toolchain ``0.12.1`` ``system`` ``0.16.2`` ``system`` ``0.17.0`` ``system`` +``0.17.2`` ``system`` ========== ========== @@ -43048,6 +43691,7 @@ version versionsuffix toolchain ``3.0.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``3.1.1`` ``foss/2020b``, ``fosscuda/2020b`` ``3.1.1`` ``-Python-3.8.2`` ``foss/2020a`` +``3.2.1`` ``foss/2021b`` ========= =========================================== ================================== @@ -43369,6 +44013,22 @@ version toolchain ========= ============================== +.. _list_software_SPOTPY_495: + +*SPOTPY* +++++++++ + +SPOTPY is a Python framework that enables the use of Computational optimization techniques for calibration, uncertainty and sensitivity analysis techniques of almost every (environmental-) model. + +*homepage*: https://spotpy.readthedocs.io + +========== =============== +version toolchain +========== =============== +``1.5.14`` ``intel/2021b`` +========== =============== + + .. _list_software_SPRNG_394: *SPRNG* @@ -43434,6 +44094,7 @@ version toolchain ``3.33.0`` ``GCCcore/10.2.0`` ``3.35.4`` ``GCCcore/10.3.0`` ``3.36`` ``GCCcore/11.2.0`` +``3.38.3`` ``GCCcore/11.3.0`` ============ ==================================================================================================================================================================== @@ -43576,11 +44237,11 @@ SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Si *homepage*: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library -======= ===================================== -version toolchain -======= ===================================== -``1.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -======= ===================================== +======= ========================================================= +version toolchain +======= ========================================================= +``1.1`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +======= ========================================================= .. _list_software_STACEY_457: @@ -43935,6 +44596,7 @@ version toolchain ``2.1.3`` ``GCC/8.3.0``, ``GCC/9.3.0`` ``2.1.4`` ``GCC/8.3.0``, ``GCC/9.3.0`` ``2.1.7`` ``GCC/10.3.0`` +``2.2.1`` ``GCC/11.2.0`` ========== ================================== @@ -44131,12 +44793,13 @@ version toolchain *homepage*: https://sumo.dlr.de/ -========= ================= ================= -version versionsuffix toolchain -========= ================= ================= -``1.3.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``1.7.0`` ``-Python-3.8.2`` ``foss/2020a`` -========= ================= ================= +========== ================= ================= +version versionsuffix toolchain +========== ================= ================= +``1.3.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``1.7.0`` ``-Python-3.8.2`` ``foss/2020a`` +``1.12.0`` ``foss/2021b`` +========== ================= ================= .. _list_software_SUNDIALS_611: @@ -44179,7 +44842,7 @@ version versionsuffix toolchain *SuperLU* +++++++++ -SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. +SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. *homepage*: https://crd-legacy.lbl.gov/~xiaoye/SuperLU/ @@ -44189,6 +44852,7 @@ version toolchain ``5.1.1`` ``foss/2016a``, ``intel/2016a`` ``5.2.1`` ``foss/2017b``, ``intel/2017b`` ``5.2.2`` ``foss/2020a``, ``intel/2020a`` +``5.3.0`` ``foss/2021a`` ========= =============================== @@ -44536,7 +45200,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TALYS_397` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboard_1187` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_termcolor_983` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_ThemisPy_819` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmux_462` - :ref:`list_software_TN93_270` - :ref:`list_software_TOBIAS_450` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` +:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TALYS_397` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboard_1187` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_termcolor_983` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_ThemisPy_819` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmap_434` - :ref:`list_software_tmux_462` - :ref:`list_software_TN93_270` - :ref:`list_software_TOBIAS_450` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` .. _list_software_tabix_536: @@ -44751,6 +45415,7 @@ version versionsuffix toolchain ``25.8`` ``-linux64`` ``system`` ``20180227`` ``-linux64`` ``system`` ``20200302`` ``-linux64`` ``system`` +``20220427`` ``-linux64`` ``system`` ============ ============= ========== @@ -44792,6 +45457,7 @@ version toolchain ``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``8.6.10`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``8.6.11`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``8.6.12`` ``GCCcore/11.3.0`` ========== ========================================================================================================================================================================= @@ -44809,6 +45475,7 @@ version toolchain ========= ===================================== ``1.2.2`` ``GCCcore/8.3.0`` ``1.2.4`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.2.5`` ``GCCcore/11.2.0`` ========= ===================================== @@ -44829,6 +45496,7 @@ version toolchain ``6.22.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``6.22.03`` ``GCCcore/10.2.0`` ``6.22.04`` ``GCCcore/10.3.0`` +``6.24.01`` ``GCCcore/11.2.0`` =========== ======================================================= @@ -45184,6 +45852,7 @@ version toolchain ============ ============================== ``20200406`` ``GCCcore/8.3.0`` ``20210324`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``20220321`` ``GCC/11.2.0`` ============ ============================== @@ -45509,6 +46178,22 @@ version versionsuffix toolchain ========= ============= ============== +.. _list_software_tmap_434: + +*tmap* +++++++ + +tmap is a very fast visualization library for large, high-dimensional data sets. Currently, tmap is available for Python. tmap's graph layouts are based on the OGDF library. + +*homepage*: https://tmap.gdb.tools + +============ ============== +version toolchain +============ ============== +``20220502`` ``GCC/11.2.0`` +============ ============== + + .. _list_software_tmux_462: *tmux* @@ -45579,6 +46264,7 @@ version versionsuffix toolchain ``1.4.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``1.4.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.4.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.5.0`` ``foss/2020b``, ``intel/2020b`` ========== ================== =============================== @@ -45917,11 +46603,11 @@ TreeMix is a method for inferring the patterns of population splits and mixtures *homepage*: http://bitbucket.org/nygcresearch/treemix -======== =============================== -version toolchain -======== =============================== -``1.13`` ``GCC/10.3.0``, ``intel/2018a`` -======== =============================== +======== =============================================== +version toolchain +======== =============================================== +``1.13`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel/2018a`` +======== =============================================== .. _list_software_TreeShrink_1023: @@ -45949,12 +46635,12 @@ Tandem Repeats Finder: a program to analyze DNA sequences. *homepage*: https://tandem.bu.edu/trf/trf.html -========== ============= ===================================== -version versionsuffix toolchain -========== ============= ===================================== -``4.09`` ``-linux64`` ``system`` -``4.09.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========== ============= ===================================== +========== ============= ========================================================= +version versionsuffix toolchain +========== ============= ========================================================= +``4.09`` ``-linux64`` ``system`` +``4.09.1`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========== ============= ========================================================= .. _list_software_Triangle_822: @@ -46360,7 +47046,23 @@ version versionsuffix toolchain --- -:ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_UCX-CUDA_570` - :ref:`list_software_ucx-py_614` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_unimap_650` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_UShER_423` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` +:ref:`list_software_UCC_219` - :ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_UCX-CUDA_570` - :ref:`list_software_ucx-py_614` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_unimap_650` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_UShER_423` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` + + +.. _list_software_UCC_219: + +*UCC* ++++++ + +UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. + +*homepage*: https://www.openucx.org/ + +========= ================== +version toolchain +========= ================== +``1.0.0`` ``GCCcore/11.3.0`` +========= ================== .. _list_software_UCLUST_480: @@ -46404,6 +47106,7 @@ version versionsuffix toolchain ``1.10.0`` ``GCCcore/10.3.0`` ``1.11.0`` ``GCCcore/11.2.0`` ``1.11.2`` ``GCCcore/11.2.0`` +``1.12.1`` ``GCCcore/11.3.0`` ============ ================ ======================================================= @@ -46686,11 +47389,11 @@ UnZip is an extraction utility for archives compressed in .zip format (also call *homepage*: http://www.info-zip.org/UnZip.html -======= ===================================================================================================================================================================== -version toolchain -======= ===================================================================================================================================================================== -``6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` -======= ===================================================================================================================================================================== +======= ========================================================================================================================================================================================= +version toolchain +======= ========================================================================================================================================================================================= +``6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +======= ========================================================================================================================================================================================= .. _list_software_UQTk_357: @@ -46808,6 +47511,7 @@ version toolchain ``2.35`` ``GCCcore/9.3.0`` ``2.36`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``2.37`` ``GCCcore/11.2.0`` +``2.38`` ``GCCcore/11.3.0`` ========== ====================================== @@ -46972,6 +47676,7 @@ version versionsuffix toolchain ``2.3.6`` ``-Java-1.7.0_80`` ``system`` ``2.4.1`` ``-Java-1.7.0_80`` ``system`` ``2.4.4`` ``-Java-1.8`` ``system`` +``2.4.4`` ``-Java-11`` ``system`` ========= ================== ========== @@ -47085,7 +47790,7 @@ version versionsuffix toolchain ========= ================= ============================== ``1.0.2`` ``GCC/10.2.0``, ``GCC/10.3.0`` ``1.0.2`` ``-Python-3.8.2`` ``GCC/9.3.0`` -``1.0.3`` ``GCC/11.2.0`` +``1.0.3`` ``-R-4.1.2`` ``foss/2021b`` ========= ================= ============================== @@ -47194,6 +47899,7 @@ version versionsuffix toolchain ``95.0`` ``-Perl-5.28.0`` ``foss/2018b`` ``96.0`` ``-Perl-5.28.1`` ``foss/2019a`` ``103.1`` ``GCC/10.2.0`` +``105`` ``GCC/11.2.0`` ========= ================ =============================== @@ -47247,6 +47953,7 @@ version versionsuffix toolchain ``2.4.10`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.4.11`` ``-Python-3.6.6`` ``foss/2018b`` ``2.4.14`` ``-Python-3.6.6`` ``foss/2018b`` +``2.5.0`` ``foss/2021b`` ========== ================== =============================== @@ -47492,6 +48199,7 @@ version versionsuffix toolchain ``5.2.7`` ``system`` ``5.2.9`` ``system`` ``5.2.10`` ``system`` +``5.2.11`` ``system`` =========== ================================== =============== @@ -47557,11 +48265,11 @@ A tool set for short variant discovery in genetic sequence data. *homepage*: http://genome.sph.umich.edu/wiki/Vt -=========== ============================================= -version toolchain -=========== ============================================= -``0.57721`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``foss/2018b`` -=========== ============================================= +=========== ============================================================= +version toolchain +=========== ============================================================= +``0.57721`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/9.3.0``, ``foss/2018b`` +=========== ============================================================= .. _list_software_VTK_245: @@ -47672,7 +48380,7 @@ version toolchain --- -:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_WCT_238` - :ref:`list_software_wcwidth_762` - :ref:`list_software_webin-cli_890` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wgsim_551` - :ref:`list_software_WHAM_301` - :ref:`list_software_WhatsHap_800` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` +:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_Wayland_720` - :ref:`list_software_WCT_238` - :ref:`list_software_wcwidth_762` - :ref:`list_software_webin-cli_890` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wgsim_551` - :ref:`list_software_WHAM_301` - :ref:`list_software_WhatsHap_800` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` .. _list_software_wandb_524: @@ -47729,6 +48437,22 @@ version toolchain ========= =============== +.. _list_software_Wayland_720: + +*Wayland* ++++++++++ + +Wayland is a project to define a protocol for a compositor to talk to its clients as well as a library implementation of the protocol. The compositor can be a standalone display server running on Linux kernel modesetting and evdev input devices, an X application, or a wayland client itself. The clients can be traditional applications, X servers (rootless or fullscreen) or other display servers. + +*homepage*: https://wayland.freedesktop.org/ + +========== ================== +version toolchain +========== ================== +``1.20.0`` ``GCCcore/11.3.0`` +========== ================== + + .. _list_software_WCT_238: *WCT* @@ -47860,11 +48584,11 @@ Wgsim is a small tool for simulating sequence reads from a reference genome. *homepage*: https://github.com/lh3/wgsim/ -============ ============== -version toolchain -============ ============== -``20111017`` ``GCC/10.2.0`` -============ ============== +============ ============================== +version toolchain +============ ============================== +``20111017`` ``GCC/10.2.0``, ``GCC/11.2.0`` +============ ============================== .. _list_software_WHAM_301: @@ -48048,6 +48772,7 @@ version versionsuffix toolchain ``1.6.8`` ``-intel-2018b`` ``system`` ``1.6.11`` ``intel/2019b`` ``1.6.12`` ``foss/2019a``, ``foss/2021b`` +``1.6.13`` ``iimpi/2021b`` ========== ================ ============================== @@ -48210,7 +48935,7 @@ version toolchain --- -:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-Compile_999` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtensor_787` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_xxd_340` - :ref:`list_software_xxHash_628` - :ref:`list_software_XZ_178` +:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_XGrafix_697` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-Compile_999` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_XPLOR-NIH_673` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtensor_787` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_xxd_340` - :ref:`list_software_xxHash_628` - :ref:`list_software_XZ_178` .. _list_software_X11_186: @@ -48237,6 +48962,7 @@ version toolchain ``20201008`` ``GCCcore/10.2.0`` ``20210518`` ``GCCcore/10.3.0`` ``20210802`` ``GCCcore/11.2.0`` +``20220504`` ``GCCcore/11.3.0`` ============ ================================================== @@ -48535,11 +49261,12 @@ xESMF: Universal Regridder for Geospatial Data *homepage*: https://xesmf.readthedocs.io -========= =============== -version toolchain -========= =============== -``0.3.0`` ``intel/2020b`` -========= =============== +========= ================= =============== +version versionsuffix toolchain +========= ================= =============== +``0.3.0`` ``intel/2020b`` +``0.3.0`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= =============== .. _list_software_xextproto_1021: @@ -48597,6 +49324,22 @@ version versionsuffix toolchain ============ =================== =============== +.. _list_software_XGrafix_697: + +*XGrafix* ++++++++++ + +A graphics library and controller for physics simulation programs. 3-d surface plots, scatter plots, 2-d line plots. + +*homepage*: https://ptsg.egr.msu.edu/ + +======== ================= +version toolchain +======== ================= +``2.41`` ``GCCcore/9.3.0`` +======== ================= + + .. _list_software_xineramaproto_1417: *xineramaproto* @@ -48823,10 +49566,26 @@ version toolchain ``1.19.0`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``1.19.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.19.2`` ``GCCcore/10.2.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -``1.19.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.19.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ==================================================================================================================================== +.. _list_software_XPLOR-NIH_673: + +*XPLOR-NIH* ++++++++++++ + +A System for X-ray Crystallography and NMR + +*homepage*: https://nmr.cit.nih.gov/xplor-nih/ + +======= ================= ========== +version versionsuffix toolchain +======= ================= ========== +``3.4`` ``-Linux_x86_64`` ``system`` +======= ================= ========== + + .. _list_software_xprop_569: *xprop* @@ -49016,7 +49775,7 @@ version versionsuffix toolchain ``5.2.2`` ``-gettext-0.19.7`` ``foss/2016a``, ``intel/2016a`` ``5.2.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``gimkl/2017a`` ``5.2.4`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` -``5.2.5`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``5.2.5`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ========= =================== =========================================================================================================================================================== @@ -49182,16 +49941,17 @@ Yet Another eXchange Tool *homepage*: https://www.dkrz.de/redmine/projects/yaxt -========= ================================================= -version toolchain -========= ================================================= -``0.5.1`` ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``0.6.0`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``0.6.2`` ``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` -``0.9.0`` ``gompi/2020b`` -``0.9.1`` ``gompi/2021a`` -``0.9.2`` ``iimpi/2021b`` -========= ================================================= +=========== ================================================= +version toolchain +=========== ================================================= +``0.5.1`` ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +``0.6.0`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +``0.6.2`` ``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` +``0.9.0`` ``gompi/2020b`` +``0.9.1`` ``gompi/2021a`` +``0.9.2`` ``iimpi/2021b`` +``0.9.2.1`` ``gompi/2021b`` +=========== ================================================= .. _list_software_Yices_509: @@ -49235,6 +49995,7 @@ version toolchain ``4.8.10`` ``GCCcore/10.2.0`` ``4.8.11`` ``GCCcore/10.3.0`` ``4.8.12`` ``GCCcore/11.2.0`` +``4.8.16`` ``GCCcore/11.3.0`` ========== ==================================== @@ -49337,11 +50098,11 @@ Zip is a compression and file packaging/archive utility. Although highly compati *homepage*: http://www.info-zip.org/Zip.html -======= ====================================================================================================================================== -version toolchain -======= ====================================================================================================================================== -``3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ====================================================================================================================================== +======= ========================================================================================================================================================== +version toolchain +======= ========================================================================================================================================================== +``3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ========================================================================================================================================================== .. _list_software_zlib_433: @@ -49360,6 +50121,7 @@ version toolchain ``1.2.8`` ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.2.10`` ``system`` ``1.2.11`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` +``1.2.12`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.5.0``, ``system`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -49451,7 +50213,7 @@ version toolchain *zstd* ++++++ -Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set. +Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set. *homepage*: https://facebook.github.io/zstd @@ -49464,5 +50226,6 @@ version toolchain ``1.4.5`` ``GCCcore/10.2.0`` ``1.4.9`` ``GCCcore/10.3.0`` ``1.5.0`` ``GCCcore/11.2.0`` +``1.5.2`` ``GCCcore/11.3.0`` ========= ==================================================== diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index 3eaf494b..99c9de7d 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -88,6 +88,7 @@ * EB_Libint * EB_LLVM * EB_netCDF + * EB_NEURON * EB_OpenBabel * EB_OpenCV * EB_PSI @@ -120,6 +121,9 @@ * EB_Extrae * EB_Ferret * EB_FFTW + + * EB_FFTW_period_MPI + * EB_flex * EB_FreeFEM * EB_freetype @@ -158,7 +162,6 @@ * EB_NCCL * EB_ncurses * EB_netCDF_minus_Fortran - * EB_NEURON * EB_NWChem * EB_OCaml * EB_Octave diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index 8e1d70b8..1335df5f 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -195,12 +195,13 @@ easyconfig parameter description ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``generator`` Build file generator to use. None to use CMakes default ``None`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` +``install_cmd`` Install command to use ``"make install"`` ``install_target_subdir`` Subdirectory to use as installation target ``None`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` ``separate_build_dir`` Perform build in a separate directory ``True`` ``srcdir`` Source directory location to provide to cmake command ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` ========================= ================================================================================================================================================================================================== ================== Customised steps in ``CMakeMake`` easyblock @@ -273,12 +274,13 @@ easyconfig parameter description ``files_to_copy`` List of files or dirs to copy ``None`` ``generator`` Build file generator to use. None to use CMakes default ``None`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` +``install_cmd`` Install command to use ``"make install"`` ``install_target_subdir`` Subdirectory to use as installation target ``None`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` ``separate_build_dir`` Perform build in a separate directory ``True`` ``srcdir`` Source directory location to provide to cmake command ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` ``with_configure`` Run configure script before building ``False`` ========================= ================================================================================================================================================================================================== ================== @@ -312,12 +314,13 @@ easyconfig parameter description ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``generator`` Build file generator to use. None to use CMakes default ``"Ninja"`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` +``install_cmd`` Install command to use ``"make install"`` ``install_target_subdir`` Subdirectory to use as installation target ``None`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` ``separate_build_dir`` Perform build in a separate directory ``True`` ``srcdir`` Source directory location to provide to cmake command ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` ========================= ================================================================================================================================================================================================== ================== Customised steps in ``CMakeNinja`` easyblock @@ -360,7 +363,7 @@ easyconfig parameter description ``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` ``generator`` Build file generator to use. None to use CMakes default ``None`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` +``install_cmd`` Install command to use ``"make install"`` ``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` ``install_target`` Option to pass to setup.py ``"install"`` ``install_target_subdir`` Subdirectory to use as installation target ``None`` @@ -376,6 +379,7 @@ easyconfig parameter description ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` ``srcdir`` Source directory location to provide to cmake command ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` ``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` ``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` @@ -415,9 +419,10 @@ easyconfig parameter description ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``files_to_copy`` List of files or dirs to copy ``None`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` +``install_cmd`` Install command to use ``"make install"`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` ``with_configure`` Run configure script before building ``False`` ======================== =================================================================================================================================================================================================== ==================================================== @@ -477,9 +482,10 @@ easyconfig parameter description ``configure_cmd`` Configure command to use ``"./configure"`` ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` +``install_cmd`` Install command to use ``"make install"`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` ======================== =================================================================================================================================================================================================== ================== Commonly used easyconfig parameters with ``ConfigureMake`` easyblock @@ -558,7 +564,7 @@ easyconfig parameter description ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` +``install_cmd`` Install command to use ``"make install"`` ``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` ``install_target`` Option to pass to setup.py ``"install"`` ``options`` Dictionary with extension options. ``{}`` @@ -571,6 +577,7 @@ easyconfig parameter description ``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` ``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` ``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` ``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` @@ -790,9 +797,10 @@ easyconfig parameter description ``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` ``files_to_copy`` List of files or dirs to copy ``None`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` +``install_cmd`` Install command to use ``"make install"`` ``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` ``with_configure`` Run configure script before building ``False`` ======================== =================================================================================================================================================================================================== ================== @@ -1167,7 +1175,7 @@ easyconfig parameter description ``generate_standalone_module`` Add known path/library extensions and environment variables for the compiler to the final module ``False`` ``generic`` Build GCC and support libraries such that it runs on all processors of the target architecture (use False to enforce non-generic regardless of configuration) ``None`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` +``install_cmd`` Install command to use ``"make install"`` ``languages`` List of languages to build GCC for (--enable-languages) ``[]`` ``license_activation`` License activation type ``"license_server"`` ``m32`` Enable 32-bit toolchain ``False`` @@ -1181,7 +1189,8 @@ easyconfig parameter description ``sanity_check_components`` List of components for which to run sanity checks ``[]`` ``serial_number`` Serial number for the product ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``use_gold_linker`` Configure GCC to use GOLD as default linker ``True`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` +``use_gold_linker`` Configure GCC to use GOLD as default linker (default: True for GCC < 11.3.0) ``None`` ``usetmppath`` Use temporary path for installation ``False`` ``withamdgcn`` Build GCC with AMD GCN offload support ``False`` ``withcloog`` Build GCC with CLooG support ``False`` @@ -1224,7 +1233,7 @@ easyconfig parameter description ``default_easyblock`` Default easyblock to use for components ``None`` ``generate_standalone_module`` Add known path extensions and environment variables for the MPI installation to the final module ``False`` ``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Build command to use ``"make install"`` +``install_cmd`` Install command to use ``"make install"`` ``libfabric_configopts`` Configure options for the provided libfabric ``""`` ``libfabric_rebuild`` Try to rebuild internal libfabric instead of using provided binary ``True`` ``license_activation`` License activation type ``"license_server"`` @@ -1240,6 +1249,7 @@ easyconfig parameter description ``set_mpi_wrappers_all`` Set (default) compiler for all MPI wrapper commands ``False`` ``set_mpi_wrappers_compiler`` Override default compiler used by MPI wrapper commands ``False`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` ``usetmppath`` Use temporary path for installation ``False`` ================================= =================================================================================================================================================================================================== ==================== diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index 5234ae99..e8a6675a 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -108,7 +108,7 @@ Option flag Option desc ``--packagepath=PACKAGEPATH`` The destination path for the packages built by package-tool (default: /home/example/.local/easybuild/packages) ``--prefix=PREFIX`` Change prefix for buildpath, installpath, sourcepath and repositorypath (used prefix for defaults /home/example/.local/easybuild) ``--recursive-module-unload`` Enable generating of modules that unload recursively. (default: False) -``--repository=REPOSITORY`` Repository type, using repositorypath (type choice; default: FileRepository) (choices: FileRepository, GitRepository, HgRepository) +``--repository=REPOSITORY`` Repository type, using repositorypath (type choice; default: FileRepository) (choices: FileRepository, GitRepository, HgRepository) ``--repositorypath=REPOSITORYPATH`` Repository path, used by repository (is passed as list of arguments to create the repository instance). For more info, use --avail-repositories. (type comma-separated list; default: /home/example/.local/easybuild/ebfiles_repo) ``--sourcepath=SOURCEPATH`` Path(s) to where sources should be downloaded (string, colon-separated) (default: /home/example/.local/easybuild/sources) ``--subdir-modules=SUBDIR-MODULES`` Installpath subdir for modules (default: modules) @@ -238,6 +238,7 @@ Option flag Option description ``--job-backend-config=BACKEND-CONFIG`` Configuration file for job backend ``--job-cores=CORES`` Number of cores to request per job (type int) ``--job-deps-type=DEPS-TYPE`` Type of dependency to set between jobs (default depends on job backend) (type choice) (choices: abort_on_error, always_run) +``--job-eb-cmd=EB-CMD`` EasyBuild command to use in jobs (type str; default: eb) ``--job-max-jobs=MAX-JOBS`` Maximum number of concurrent jobs (queued and running, 0 = unlimited) (type int; default: 0) ``--job-max-walltime=MAX-WALLTIME`` Maximum walltime for jobs (in hours) (type int; default: 24) ``--job-output-dir=OUTPUT-DIR`` Output directory for jobs (default: current directory) (default: /Volumes/work/easybuild/docs) diff --git a/docs/version-specific/toolchain_opts.rst b/docs/version-specific/toolchain_opts.rst index 08bad56f..3cc874f1 100644 --- a/docs/version-specific/toolchain_opts.rst +++ b/docs/version-specific/toolchain_opts.rst @@ -5,7 +5,7 @@ Available toolchain options (by toolchain) *(see also* ``eb --avail-toolchain-opts `` *)* -ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpit_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - nvompic_ - nvpsmpic_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ +ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gfbf_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpit_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - nvompi_ - nvompic_ - nvpsmpi_ - nvpsmpic_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ .. _ClangGCC: @@ -985,6 +985,51 @@ option description ========================= ======================================================================= ========= +.. _gfbf: + +Available options for gfbf toolchain +------------------------------------ + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``f2c`` Generate code compatible with f2c and f77 ``False`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``loop`` Automatic loop parallellisation ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``lto`` Enable Link Time Optimization ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + .. _gimkl: Available options for gimkl toolchain @@ -3414,6 +3459,49 @@ option description ========================= ======================================================================= ========= +.. _nvompi: + +Available options for nvompi toolchain +-------------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + .. _nvompic: Available options for nvompic toolchain @@ -3457,6 +3545,49 @@ option description ========================= ======================================================================= ========= +.. _nvpsmpi: + +Available options for nvpsmpi toolchain +--------------------------------------- + +========================= ======================================================================= ========= +option description default +========================= ======================================================================= ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``noopt`` Disable compiler optimizations ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ======================================================================= ========= + + .. _nvpsmpic: Available options for nvpsmpic toolchain diff --git a/docs/version-specific/toolchains.rst b/docs/version-specific/toolchains.rst index f2b67ade..b42d7525 100644 --- a/docs/version-specific/toolchains.rst +++ b/docs/version-specific/toolchains.rst @@ -25,6 +25,7 @@ Name Compiler(s) MPI Linear algebra **GCC** GCC *(none)* *(none)* *(none)* **GCCcore** GCCcore *(none)* *(none)* *(none)* **gcccuda** GCC, CUDA *(none)* *(none)* *(none)* +**gfbf** GCC *(none)* FlexiBLAS FFTW **gimkl** GCC impi imkl imkl **gimpi** GCC impi *(none)* *(none)* **gimpic** GCC, CUDA impi *(none)* *(none)* @@ -80,7 +81,9 @@ Name Compiler(s) MPI Linear algebra **iqacml** icc, ifort QLogicMPI ACML, ScaLAPACK FFTW **ismkl** icc, ifort MPICH2 imkl imkl **NVHPC** NVHPC *(none)* *(none)* *(none)* +**nvompi** NVHPC OpenMPI *(none)* *(none)* **nvompic** NVHPC OpenMPI *(none)* *(none)* +**nvpsmpi** NVHPC psmpi *(none)* *(none)* **nvpsmpic** NVHPC psmpi *(none)* *(none)* **PGI** PGI *(none)* *(none)* *(none)* **pmkl** PGI *(none)* imkl imkl From 3c97574ff927a3ea4da8753ac0295135cd5f7bf6 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 7 Jun 2022 20:43:16 +0200 Subject: [PATCH 217/286] update release notes and changelog for EasyBuild v4.5.5 + bump version to 4.5.5 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 147 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 148 insertions(+), 4 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index ea95399e..a8b6842e 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20220608.01** (`Jun 8th 2022`): update release notes for EasyBuild v4.5.5 (see :ref:`release_notes_eb455`) * **release 20220331.01** (`Mar 31st 2022`): update release notes for EasyBuild v4.5.4 (see :ref:`release_notes_eb454`) * **release 20220211.01** (`Feb 11th 2022`): update release notes for EasyBuild v4.5.3 (see :ref:`release_notes_eb453`) * **release 20220124.01** (`Jan 24th 2022`): update release notes for EasyBuild v4.5.2 (see :ref:`release_notes_eb452`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 01f36c83..15092b83 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,155 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,667** different software packages, +The latest version of EasyBuild provides support for building and installing **2,711** different software packages, including 36 different (compiler) toolchains. It contains 244 software-specific easyblocks and 37 generic easyblocks, -alongside 14,449 easyconfig files. +alongside 14,816 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb455: + +EasyBuild v4.5.5 (June 8th 2022) +-------------------------------- + +bugfix/update release + +**framework** + +* various enhancements, including: + + * add toolchain definitions for ``nvompi`` (NVHPC + OpenMPI) (`#3969 `_), ``nvpsmpi`` (NVHPC + ParaStationMPI) (`#3970 `_), gfbf (GCC, FlexiBLAS, FFTW) (`#4006 `_) + * add support for ``FFTW.MPI`` toolchain component (``$FFT*DIR`` variables) (`#4012 `_) + * add support for customizing EasyBuild command used in jobs via ``--job-eb-cmd`` (`#4016 `_) + +* various bug fixes, including: + + * fix copying of easyconfig file with ``--copy-ec`` without ``--rebuild`` if module is already installed (`#3993 `_) + * ignore deprecation warnings regarding cryptography in Python 3.6 + Blowfish with Python 3.10 in test suite output (`#3999 `_) + * fix typo in debug log message in ``easyblock.py`` (`#4000 `_) + * fix printing of list of attempted download URLs when url-encoded characters are used in URL (`#4005 `_) + * set ``$FFT(W)_LIB_DIR`` to imkl-FFTW's lib path in build environment if usempi toolchain option is enabled (`#4011 `_) + * correctly identify Apple Silicon M1 as Arm 64-bit by also considering arm64 next to aarch64 (`#4014 `_) + * fix '``eb --show-system-info``' on Apple M1 system (`#4015 `_) + +* other changes: + + * change '``eb``' command to ``import easybuild.framework`` to check if EasyBuild framework is available (#3995, `#3998 `_) + +**easyblocks** + +* new software-specific easyblock for FFTW.MPI (`#2724 `_) + +* minor enhancements and updates, including: + + * update NEURON easyblock to use CMakeMake for recent versions (`#2304 `_) + * enhance Clang easyblock to add support for building with AMDGPU offload (#2684, `#2729 `_) + * update sanity check in OpenMPI easyblock to support OpenMPI v5.0.0 (`#2709 `_) + * don't use ``gold`` linker by default for GCC >= 11.3 (`#2711 `_) + * update sanity check in R easyblock for versions >= 4.2.0, since S.h is not included anymore (`#2713 `_) + * update ABAQUS easyblock for ABAQUS 2022 (`#2716 `_) + * update LLVM easyblock for LLVM v14.0.x (`#2718 `_) + * update Mesa easyblock to remove swr driver configopts for versions 22+ (`#2719 `_) + * enhance Clang easyblock to support also installing Python bindings (#2721, `#2725 `_) + * enhance SuperLU easyblock to support building on top of FlexiBLAS and be compatible with SuperLU v5.3 (`#2722 `_) + * update TensorFlow easyblock for version 2.8.0 (`#2723 `_) + * modify FFTW's sanity check step to allow checking only for MPI parts of FFTW installation (`#2724 `_) + * add support to ConfigureMake for tweaking (first part of) test command via '``test_cmd``' (#2726, `#2737 `_) + * enhance MrBayes easyblock with custom sanity check command (`#2727 `_) + * update cudnnarch string templates used to compose source tarball names from cuDNN 8.3.3 onwards (`#2728 `_) + * add sanity check command to OpenSSL wrapper easyblock to verify that system certificates are available to OpenSSL (`#2735 `_) + * ignore exit code of ``pkg-config`` command in OpenSSL wrapper easyblock, since with ``pkgconf`` they exit with a non-zero exit code if the OS package is not installed (`#2736 `_) + +* various bug fixes, including: + + * remove system-compiled binutils dirs from ``$LDFLAGS`` in binutils easyblock (`#2712 `_) + * fix for FreeSurfer easyblock: define ``$FREESURFER`` needed by recon_all (`#2717 `_) + * also symlink ``cert.pem`` in from-source OpenSSL installation (if it exists) (`#2735 `_) + +**easyconfigs** + +* add candidates for 2022a common toolchains: ``foss/2022.05`` (`#15561 `_), intel/2022.05 (`#15485 `_) + +* added example easyconfig files for 35 new software packages: + * Albumentations (`#15302 `_), AMPtk (`#15435 `_), arosics (`#15249 `_), CellTypist (`#15530 `_), detectron2 (`#15442 `_), + EigenExa (`#15234 `_), Fastaq (`#15332 `_), FFTW.MPI (`#15561 `_), FreeBarcodes (`#15350 `_), gcloud (`#15443 `_), + GST-plugins-bad (`#15446 `_), gsutil (`#15507 `_), GTK4 (`#15447 `_), hector (`#15397 `_), i7z (`#15236 `_), libde265 (`#15395 `_), + libheif (`#15395 `_), ModelTest-NG (`#15448 `_), num2words (`#15473 `_), OGDF (`#15407 `_), panito (`#15314 `_), + parameterized (`#15481 `_), purge_dups (`#15385 `_), redis-py (`#15475 `_), ruamel.yaml (`#15531 `_), SCGid (`#15065 `_), + scPred (`#15575 `_), slow5tools (`#15457 `_), smooth-topk (`#15506 `_), SPOTPY (`#15326 `_), tmap (`#4601 `_), UCC (`#4291 `_), + Wayland (`#11107 `_), XGrafix (`#15268 `_), XPLOR-NIH (`#15479 `_) + +* added additional easyconfigs for various supported software packages, including: + * ABAQUS 2022, Arb 2.22.1, ARGoS 3.0.0, Arriba 2.2.1, astropy 5.0.4, ATK 2.38.0, Autotools 20220317, + Bader 1.04, Bazel 4.2.2 + 5.1.1, BDBag 1.6.3, binutils 2.38, biom-format 2.1.12, BLIS 0.9.0, Boost 1.79.0, + breseq 0.36.1, bx-python 0.8.13, cairo 1.17.4, CellRanger-ARC 2.0.1, CMake 3.23.1, cryoDRGN 1.0.0, + CUDA 11.7.0, cuDNN 8.4.1.50, cURL 7.83.0, DBus 1.14.0, eggnog-mapper 2.1.7, elfutils 0.187, + EvidentialGene 2022.01.14, expat 2.4.8, FlexiBLAS 3.2.0, FLINT 2.8.4, fontconfig 2.14.0, freebayes 1.3.6, + freeglut 3.2.2, freetype 2.12.1, FriBidi 1.0.12, GCC 9.5.0 + 11.3.0 + GCC 12.1.0, Gdk-Pixbuf 2.42.8, + geopandas 0.10.2, git 2.36.0, GLib 2.72.1, GMAP-GSNAP 2021-21-17, Go 1.18.1, GObject-Introspection 1.72.0, + Graphene 1.10.8, GST-plugins-base 1.20.2, GStreamer 1.20.2, GTDB-Tk 2.0.0, GTK3 3.24.33, gzip 1.12, + HarfBuzz 4.2.1, help2man 1.49.2, hwloc 2.7.1, hypothesis 6.46.7, Hypre 2.24.0, ICU 71.1, IGV 2.12.3, + IMB 2021.3, inferCNV 1.10.1, InterProScan 5.52, IQ-TREE 2.2.1, jax 0.3.9, json-c 0.16, LAPACK 3.10.1, + libarchive 3.6.1, libdeflate 1.10, libdrm 2.4.110, libedit 20210910, libepoxy 1.5.10, libfabric 1.15.1, + libglvnd 1.4.0, libjpeg-turbo 2.1.3, libreadline 8.1.2, librsb 1.3.0.1, librsvg 2.52.8, libtool 2.4.7, + libunwind 1.6.2, libxml2 2.9.13, LLVM 14.0.3, LocARNA 1.9.2.3, MACS2 2.2.7.1, magma 2.6.2, Mako 1.2.0, + Mathematica 13.0.0, MCL 14.137, MCR R2022a.1, Mesa 22.0.3, Meson 0.62.1, MIRA 5.0rc2, Mmg 5.6.0, mold 1.2.1, + mosdepth 0.3.3, MrBayes 3.2.7a, MultiQC 1.12, MUMPS 5.5.0, muParser 2.3.3, ncurses 6.3, neptune-client 0.16.2, + Nextflow 22.04.0, Nim 1.6.6, NTPoly 2.7.1, OpenMPI 4.1.4, openpyxl 3.0.9, OpenSSL 1.1.1n, OpenStackClient 5.8.0, + OSU-Micro-Benchmarks 5.9, pagmo 2.18.0, Pango 1.50.7, parallel-fastq-dump 0.6.7, PCRE2 10.40, Perl 5.34.1, + Pillow 9.1.0, PLINK 2.00a3.1, PMIx 4.1.2, PyAMG 4.2.3, pybind11 2.9.2, PyCairo 1.21.0, pygmo 2.18.0, + PyGObject 3.42.1, Python 3.10.4, R 4.2.0, RAxML-NG 1.1.0, R-bundle-Bioconductor 3.15, ReFrame 3.11.0, + RNA-Bloom 1.4.3, rnaQUAST 2.2.2, Rust 1.60.0, Sambamba 0.8.2, SAMtools 1.15.1, ScaLAPACK 2.2.0, + SciPy-bundle 2022.05, SeqKit 2.2.0, Shapely 1.8.1.post1, SpaceRanger 1.3.1, Spack 0.17.2, Spark 3.2.1, + SQLite 3.38.3, StringTie 2.2.1, SUMO 1.12.0, SuperLU 5.3.0, tbl2asn 20220427, Tcl 8.6.12, TCLAP 1.2.5, + tcsh 6.24.01, texlive 20220321, ToFu 1.5.0, UCX 1.12.1, util-linux 2.38, VEP 105, ViennaRNA 2.5.0, + vsc-mympirun 5.2.11, worker 1.6.13, X11 2022050, YAXT 0.9.2.1, Z3 4.8.16, Zip 3.0, zlib 1.2.12, zstd 1.5.2 + +* minor enhancements, including: + + * use OpenSSL wrapper dependency for CMake 3.18.4 with system toolchain (`#15227 `_) + * also build BLIS backend for FlexiBLAS v3.0.4 with GCC/10.3.0 (`#15347 `_) + * add extensions to R v4.1.2 + v4.2.0 easyconfigs: + * Hmsc (`#15393 `_), MonteCarlo + RhpcBLASctl (`#15438 `_), chkptstanr (`#15540 `_), chkptstanr + MLmetrics + renv (`#15573 `_) + * add extensions to R-bundle-Bioconductor 3.14 easyconfig: DNABarcodes (`#15405 `_) + * use redist source_urls for cuDNN > 7.5 (`#15411 `_) + * add download_instructions to Java 1.8 > 200 (`#15412 `_) + * update Arrow to use EB versions of some dependencies and enable all compression codecs (`#15512 `_) + * add csh -> tcsh symlink in recent tcsh easyconfigs (`#15571 `_) + * allow external tools to be located elsewhere for ETE (`#15578 `_) + * add additional sanity check commands for IQ-TREE v2.2.1 (`#15596 `_) +* various bug fixes, including: + * fix source URL for freetype 2.6.5 with ``foss/2016b`` (`#14204 `_) + * fix installation of easybuild-easyconfigs with setuptools>=61 by explicitly declaring there are no Python packages (`#15206 `_) + * use x.py to bootstrap Rust so that build options are properly passed through (`#15211 `_) + * fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15615, `#15615 `_) + * add hwloc dependency to tbb v2021.4.0 (`#15294 `_) + * tweak find command used in preconfigopts in easyconfig for pkg-config v0.29.2 with system toolchain to avoid descending into other filesystems (`#15313 `_) + * remove pkg-config use from SeqLib configure patch (avoids problem due to faulty autoconf macro) (`#15316 `_) + * update source URL for isl in GCCcore easyconfigs (`#15320 `_) + * update source URLs for YAXT 0.9.x to fix download (`#15323 `_) + * define ``$HHLIB`` as path to HH-suite installation directory, required by Perl scripts (`#15324 `_) + * add missing parallel and tbl2asn dependencies for prokka 1.14.5 (#15360, `#15381 `_) + * add missing dependencies for libheif (libpng, libjpeg-turbo) (`#15408 `_) + * switch to configuring build of libheif with CMake so libde265 dependency is picked up (`#15408 `_) + * disable use of ``-ftree-vectorize`` for OpenFOAM v2112 with ``foss/2021b`` (`#15495 `_) + * add patch for OpenMPI 4.1.1 to support building using ``--with-cuda=internal`` (#15528, `#15589 `_) + * add patch to fix support for external PMIx v3.1 in OpenMPI v3.1.3 (`#15566 `_) + * also build shared library + fix ``$PYTHONPATH`` for gmsh 4.9.0 (`#15579 `_) + * add patch for GLib 2.68.2 to fix use of close_range (`#15594 `_) + * fix download of thrift 0.12.0 for Arrow 0.16.0 (`#15597 `_) + * add Bison and flex build dependencies to SCOTCH 6.1.x (`#15618 `_) + * add alternative checksums for class, nnet, spatial extensions in R v4.2.0 easyconfig (`#15619 `_) + * add missing dependencies + switch to non-static build for Arriba v2.1.0 (`#15623 `_) + +* other changes: + + * add R dependency to vcflib 1.0.3, and move from GCC/11.2.0 to ``foss/2021b`` toochain (`#15216 `_) + * update fallback version for OpenSSL 1.1 wrapper to v1.1.1o (`#15592 `_) + * install sklearn meta-package with scikit-learn v1.0.1 (`#15613 `_) + * switch from ``pkg-config`` to ``pkgconf`` as build dependency for OpenSSL wrapper easyconfigs (#15616, `#15617 `_) + + .. _release_notes_eb454: EasyBuild v4.5.4 (March 31st 2022) diff --git a/docs/conf.py b/docs/conf.py index 24292701..ef73c784 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.5.4' # this is meant to reference the version of EasyBuild +version = '4.5.5' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20220331.0' # this is meant to reference the version of the documentation itself +release = '20220608.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 563bf6feb401028e7060f660c2239a82b719e2d2 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 7 Jun 2022 21:43:05 +0200 Subject: [PATCH 218/286] fixes, tweaks and formatting for EasyBuild v4.5.5 and older release notes --- docs/Release_notes.rst | 47 ++++++++++++++++++++++-------------------- 1 file changed, 25 insertions(+), 22 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 15092b83..65bcd01d 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -20,7 +20,7 @@ bugfix/update release * various enhancements, including: - * add toolchain definitions for ``nvompi`` (NVHPC + OpenMPI) (`#3969 `_), ``nvpsmpi`` (NVHPC + ParaStationMPI) (`#3970 `_), gfbf (GCC, FlexiBLAS, FFTW) (`#4006 `_) + * add toolchain definitions for ``nvompi`` (NVHPC + OpenMPI) (`#3969 `_), ``nvpsmpi`` (NVHPC + ParaStationMPI) (`#3970 `_), ```gfbf`` (GCC, FlexiBLAS, FFTW) (`#4006 `_) * add support for ``FFTW.MPI`` toolchain component (``$FFT*DIR`` variables) (`#4012 `_) * add support for customizing EasyBuild command used in jobs via ``--job-eb-cmd`` (`#4016 `_) @@ -36,7 +36,7 @@ bugfix/update release * other changes: - * change '``eb``' command to ``import easybuild.framework`` to check if EasyBuild framework is available (#3995, `#3998 `_) + * change '``eb``' command to ``import easybuild.framework`` to check if EasyBuild framework is available (`#3995 `_, `#3998 `_) **easyblocks** @@ -45,18 +45,18 @@ bugfix/update release * minor enhancements and updates, including: * update NEURON easyblock to use CMakeMake for recent versions (`#2304 `_) - * enhance Clang easyblock to add support for building with AMDGPU offload (#2684, `#2729 `_) + * enhance Clang easyblock to add support for building with AMDGPU offload (`#2684 `_, `#2729 `_) * update sanity check in OpenMPI easyblock to support OpenMPI v5.0.0 (`#2709 `_) * don't use ``gold`` linker by default for GCC >= 11.3 (`#2711 `_) * update sanity check in R easyblock for versions >= 4.2.0, since S.h is not included anymore (`#2713 `_) * update ABAQUS easyblock for ABAQUS 2022 (`#2716 `_) * update LLVM easyblock for LLVM v14.0.x (`#2718 `_) * update Mesa easyblock to remove swr driver configopts for versions 22+ (`#2719 `_) - * enhance Clang easyblock to support also installing Python bindings (#2721, `#2725 `_) + * enhance Clang easyblock to support also installing Python bindings (`#2721 `_, `#2725 `_) * enhance SuperLU easyblock to support building on top of FlexiBLAS and be compatible with SuperLU v5.3 (`#2722 `_) * update TensorFlow easyblock for version 2.8.0 (`#2723 `_) * modify FFTW's sanity check step to allow checking only for MPI parts of FFTW installation (`#2724 `_) - * add support to ConfigureMake for tweaking (first part of) test command via '``test_cmd``' (#2726, `#2737 `_) + * add support to ConfigureMake for tweaking (first part of) test command via '``test_cmd``' (`#2726 `_, `#2737 `_) * enhance MrBayes easyblock with custom sanity check command (`#2727 `_) * update cudnnarch string templates used to compose source tarball names from cuDNN 8.3.3 onwards (`#2728 `_) * add sanity check command to OpenSSL wrapper easyblock to verify that system certificates are available to OpenSSL (`#2735 `_) @@ -73,12 +73,13 @@ bugfix/update release * add candidates for 2022a common toolchains: ``foss/2022.05`` (`#15561 `_), intel/2022.05 (`#15485 `_) * added example easyconfig files for 35 new software packages: + * Albumentations (`#15302 `_), AMPtk (`#15435 `_), arosics (`#15249 `_), CellTypist (`#15530 `_), detectron2 (`#15442 `_), EigenExa (`#15234 `_), Fastaq (`#15332 `_), FFTW.MPI (`#15561 `_), FreeBarcodes (`#15350 `_), gcloud (`#15443 `_), GST-plugins-bad (`#15446 `_), gsutil (`#15507 `_), GTK4 (`#15447 `_), hector (`#15397 `_), i7z (`#15236 `_), libde265 (`#15395 `_), libheif (`#15395 `_), ModelTest-NG (`#15448 `_), num2words (`#15473 `_), OGDF (`#15407 `_), panito (`#15314 `_), parameterized (`#15481 `_), purge_dups (`#15385 `_), redis-py (`#15475 `_), ruamel.yaml (`#15531 `_), SCGid (`#15065 `_), - scPred (`#15575 `_), slow5tools (`#15457 `_), smooth-topk (`#15506 `_), SPOTPY (`#15326 `_), tmap (`#4601 `_), UCC (`#4291 `_), + scPred (`#15575 `_), slow5tools (`#15457 `_), smooth-topk (`#15506 `_), SPOTPY (`#15326 `_), tmap (`#14601 `_), UCC (`#14291 `_), Wayland (`#11107 `_), XGrafix (`#15268 `_), XPLOR-NIH (`#15479 `_) * added additional easyconfigs for various supported software packages, including: @@ -120,22 +121,24 @@ bugfix/update release * add csh -> tcsh symlink in recent tcsh easyconfigs (`#15571 `_) * allow external tools to be located elsewhere for ETE (`#15578 `_) * add additional sanity check commands for IQ-TREE v2.2.1 (`#15596 `_) + * various bug fixes, including: + * fix source URL for freetype 2.6.5 with ``foss/2016b`` (`#14204 `_) * fix installation of easybuild-easyconfigs with setuptools>=61 by explicitly declaring there are no Python packages (`#15206 `_) * use x.py to bootstrap Rust so that build options are properly passed through (`#15211 `_) - * fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15615, `#15615 `_) + * fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (`#15280 `_, `#15615 `_) * add hwloc dependency to tbb v2021.4.0 (`#15294 `_) * tweak find command used in preconfigopts in easyconfig for pkg-config v0.29.2 with system toolchain to avoid descending into other filesystems (`#15313 `_) * remove pkg-config use from SeqLib configure patch (avoids problem due to faulty autoconf macro) (`#15316 `_) * update source URL for isl in GCCcore easyconfigs (`#15320 `_) * update source URLs for YAXT 0.9.x to fix download (`#15323 `_) * define ``$HHLIB`` as path to HH-suite installation directory, required by Perl scripts (`#15324 `_) - * add missing parallel and tbl2asn dependencies for prokka 1.14.5 (#15360, `#15381 `_) + * add missing parallel and tbl2asn dependencies for prokka 1.14.5 (`#15360 `_, `#15381 `_) * add missing dependencies for libheif (libpng, libjpeg-turbo) (`#15408 `_) * switch to configuring build of libheif with CMake so libde265 dependency is picked up (`#15408 `_) * disable use of ``-ftree-vectorize`` for OpenFOAM v2112 with ``foss/2021b`` (`#15495 `_) - * add patch for OpenMPI 4.1.1 to support building using ``--with-cuda=internal`` (#15528, `#15589 `_) + * add patch for OpenMPI 4.1.1 to support building using ``--with-cuda=internal`` (`#15528 `_, `#15589 `_) * add patch to fix support for external PMIx v3.1 in OpenMPI v3.1.3 (`#15566 `_) * also build shared library + fix ``$PYTHONPATH`` for gmsh 4.9.0 (`#15579 `_) * add patch for GLib 2.68.2 to fix use of close_range (`#15594 `_) @@ -149,7 +152,7 @@ bugfix/update release * add R dependency to vcflib 1.0.3, and move from GCC/11.2.0 to ``foss/2021b`` toochain (`#15216 `_) * update fallback version for OpenSSL 1.1 wrapper to v1.1.1o (`#15592 `_) * install sklearn meta-package with scikit-learn v1.0.1 (`#15613 `_) - * switch from ``pkg-config`` to ``pkgconf`` as build dependency for OpenSSL wrapper easyconfigs (#15616, `#15617 `_) + * switch from ``pkg-config`` to ``pkgconf`` as build dependency for OpenSSL wrapper easyconfigs (`#15616 `_, `#15617 `_) .. _release_notes_eb454: @@ -250,7 +253,7 @@ bugfix/update release * also install rMATS_P commands in rMATS-turbo easyconfig (`#15113 `_) * add extensions to Bioconductor v3.14 easyconfig: chromVAR (`#15118 `_), EnsDb.Hsapiens.v79 (`#15154 `_), WGCNA (`#15178 `_) * add extensions to Perl v5.34.0 easyconfigs: Sys::Info, HTML::Template, Log::Report (`#15176 `_), Sys::Info::Driver::Unknown, Sys::Info::Driver::Linux, Unix::Processors (`#15190 `_) - * enable running of tests for MEME with ``gompi/2021b`` (#15191, `#15199 `_) + * enable running of tests for MEME with ``gompi/2021b`` (`#15191 `_, `#15199 `_) * various bug fixes, including: @@ -933,7 +936,7 @@ bugfix/update release biogeme (`#13735 `_), Bio-SearchIO-hmmer (`#13419 `_), BuDDy (`#13907 `_), c-ares (`#13709 `_), CellRank (`#13408 `_), Coin (`#13818 `_), Co-phylog (`#13769 `_), cppy (`#13823 `_), CREST (`#13648 `_), CRISPR-DAV (`#13139 `_), CSBLAST (`#13794 `_), DGL (`#13793 `_), DistributedStream (`#13659 `_), Excel-Writer-XLSX (`#13139 `_), FBPIC (`#13500 `_), freebayes (`#12859 `_), freud-analysis (`#13354 `_), - fumi_tools (`#13517 `_), GEGL (`#13216 `_), GIMP (`#13216 `_), glib-networking (`#13216 `_), GOATOOLS (#13364, `#13629 `_), + fumi_tools (`#13517 `_), GEGL (`#13216 `_), GIMP (`#13216 `_), glib-networking (`#13216 `_), GOATOOLS (`#13364 `_, `#13629 `_), gofasta (`#13651 `_), GTK2 (`#13900 `_), GTK3 (`#13900 `_), Highway (`#13453 `_), hipSYCL (`#13837 `_), ISA-L (`#13663 `_), jax (`#13760 `_), JSON-GLib (`#13216 `_), Kalign (`#13463 `_), LADR (`#13351 `_), lDDT (`#13794 `_), libdivsufsort (`#13768 `_), libjxl (`#13453 `_, `#13829 `_), libmypaint (`#13216 `_), libtecla (`#13908 `_), lie_learn (`#13793 `_), longestrunsubsequence (`#13800 `_), Maude (`#13909 `_), @@ -1730,7 +1733,7 @@ bugfix/update release cuTENSOR (`#11914 `_), dd (`#11978 `_), decona (`#11891 `_), dicom2nifti (`#11955 `_), eccodes-python (`#12083 `_), fftlib (`#11944 `_), flatbuffers-python (`#12148 `_), fpocket (`#11980 `_), gh (`#11851 `_), intel-compilers (oneAPI) (`#11982 `_), libGDSII (`#7026 `_), libpci (`#11871 `_), liknorm (`#7456 `_, `#11867 `_), limix (`#7456 `_, `#11867 `_), logaddexp (`#11867 `_), neptune-client (`#11985 `_), - plinkQC (`#12068 `_), preCICE (`#11886 `_), py-aiger (`#11999 `_), py-aiger-bdd (`#11999 `_), pytest-xdist (#11883, `#11893 `_), + plinkQC (`#12068 `_), preCICE (`#11886 `_), py-aiger (`#11999 `_), py-aiger-bdd (`#11999 `_), pytest-xdist (`#11883 `_, `#11893 `_), samblaster (`#7378 `_), terastructure (`#12197 `_), typing-extensions (`#11636 `_), webin-cli (`#8674 `_) * added additional easyconfigs for various supported software packages, including: @@ -1770,7 +1773,7 @@ bugfix/update release * add EnsDb.Hsapiens.v86 to Bioconductor 3.11 (`#12078 `_) * add sanity check command for bam-readcount v0.8.0 to check ``--version`` output (`#12092 `_) * add EnsDb.Hsapiens.v75 + Signac extensions to R-bundle-Bioconductor 3.12 (`#12174 `_) - * add tensorboard profile plugin to recent TensorFlow 2.x easyconfigs (#12136, `#12137 `_) + * add tensorboard profile plugin to recent TensorFlow 2.x easyconfigs (`#12136 `_, `#12137 `_) * various bug fixes, including: @@ -2220,7 +2223,7 @@ feature release * make ``RPATH`` wrapper script more robust by using ``python -E -s -S`` to run ``rpath_args.py`` (`#3422 `_) * don't inject ``-Wl,-rpath`` options when ``-x c++-header`` compiler option is used (`#3424 `_) * fix lack of ``-mno-recip`` on aarch64 by tweaking GCC options used when ``precise`` toolchain option is enabled (`#3425 `_) - * make sure ``self.start_dir`` is set in ``ExtensionEasyBlock`` (#3426, `#3435 `_) + * make sure ``self.start_dir`` is set in ``ExtensionEasyBlock`` (`#3426 `_, `#3435 `_) * exclude local variables from typo check in easyconfig files (`#3427 `_) * other changes: @@ -2500,7 +2503,7 @@ bugfix/update release * add patch for h5py 2.10.0 to avoid triggering ``MPI_Init`` at import (`#10687 `_) * add alternative checksum for pkgmaker, doRNG, cobs extension in R 3.6.0 easyconfigs (`#10692 `_) * update UDUNITS ``source_urls`` to https sources (`#10693 `_) - * add missing M4 to netCDF-Fortran easyconfigs using 2020a toolchain (#10695, `#10697 `_) + * add missing M4 to netCDF-Fortran easyconfigs using 2020a toolchain (`#10695 `_, `#10697 `_) * add Rgraphviz patch to R-bundle-Bioconductor easyconfigs (`#10710 `_) * add M4 builddependency to SuiteSparse 2019b easyconfigs (`#10720 `_) * make sure WHAM is built with correct compiler (`#10736 `_) @@ -2880,7 +2883,7 @@ feature release * add additional extensions for R: ``HiddenMarkov`` (`#9685 `_), ``lmerTest`` (`#9853 `_), ``VSURF`` + ``Rborist`` (`#10355 `_) * change Mesa 19.1.7 + 19.2.1 easyconfigs to use custom easyblock for Mesa (`#9764 `_) * build shared libs and install header files for Ghostscript (`#9785 `_) - * add MUMPS as dependency in PETSc 3.12.4 easyconfigs (#9880, `#9891 `_) + * add MUMPS as dependency in PETSc 3.12.4 easyconfigs (`#9880 `_, `#9891 `_) * add Perl extensions: ``Term::ReadLine::Gnu`` (`#9901 `_), ``URI::Escape`` and ``Set::IntervalTree`` (`#10049 `_) * add dat directory to aNCI (`#9929 `_) * add patch to create a symlink from ``libsvm.so.$(SHVER)`` to ``libsvm.so`` in LIBSVM easyconfigs (`#10045 `_) @@ -2905,7 +2908,7 @@ feature release * fix inline asm in dscal: mark x, x1 as clobbered, in OpenBLAS 0.3.8 (`#9867 `_) * add missing ``sanity_check_commands`` to cutadapt v1.18 and v2.7 easyconfigs (`#9869 `_) * don't overwrite ``configopts`` in BLAST+ easyconfigs, append to it (`#9875 `_) - * add alternate checksum for ``LaplacesDemon`` in R 3.6.x easyconfigs (#9879, `#10382 `_) + * add alternate checksum for ``LaplacesDemon`` in R 3.6.x easyconfigs (`#9879 `_, `#10382 `_) * fix redefining of preconfigopts in OpenCV easyconfigs (`#9895 `_) * use symlinks for terminfo files instead of hard links in ncurses 6.1 easyconfigs (`#9912 `_) * fix NCIPLOT build flags (`#9915 `_) @@ -2930,7 +2933,7 @@ feature release * other changes: - * use new custom easyblock in recent CMake easyconfigs (#9871, `#9923 `_) + * use new custom easyblock in recent CMake easyconfigs (`#9871 `_, `#9923 `_) * add check for redefined easyconfig parameters in easyconfig tests (`#9876 `_) * use M4-1.4.18.eb for test installation in easyconfigs test suite (`#9926 `_) * use ``https://`` in ``homepage``/``source_urls`` of ``zlib-1.2.11.eb`` (`#10018 `_) @@ -3605,7 +3608,7 @@ bugfix/update release * other changes: - * deprecate toolchains older than ``gompi/2016a`` and ``foss/2016a`` (#2951) + * deprecate toolchains older than ``gompi/2016a`` and ``foss/2016a`` (`#2951 `_) **easyblocks** @@ -7582,7 +7585,7 @@ feature + bugfix release * various other enhancements, including: * enhance BWA easyblock to also install man pages (`#650 `_) - * enhance tbb easyblock to consider lib dirs in order and also define ``$CPATH``, ``$LIBRARY_PATH``, ``$TBBROOT`` (#653, #654) + * enhance tbb easyblock to consider lib dirs in order and also define ``$CPATH``, ``$LIBRARY_PATH``, ``$TBBROOT`` (`#653 `_, `#654 `_) * call ``PythonPackage.configure_step`` in ``ConfigureMakePythonPackage.configure_step`` (`#668 `_) * add '``foldx3b6``' as possible binary name in FoldX easyblock (`#671 `_) * enhance/cleanup MATLAB easyblock (`#672 `_) @@ -9632,7 +9635,7 @@ feature + bugfix release * various 'bug' fixes, including: - * add ``--enable-mpirun-prefix-by-default`` configure option for all OpenMPI easyconfigs (#205) + * add ``--enable-mpirun-prefix-by-default`` configure option for all OpenMPI easyconfigs (`#205 `_) EasyBuild v1.3.0 (April 1st 2013) --------------------------------- From 2a565f74ae5e032dbad63e4df29fd806234e3cca Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 7 Jun 2022 21:52:40 +0200 Subject: [PATCH 219/286] fixes, tweaks and formatting for EasyBuild v4.5.5 and older release notes --- docs/Release_notes.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 65bcd01d..77ddba5b 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -20,7 +20,7 @@ bugfix/update release * various enhancements, including: - * add toolchain definitions for ``nvompi`` (NVHPC + OpenMPI) (`#3969 `_), ``nvpsmpi`` (NVHPC + ParaStationMPI) (`#3970 `_), ```gfbf`` (GCC, FlexiBLAS, FFTW) (`#4006 `_) + * add toolchain definitions for ``nvompi`` (NVHPC + OpenMPI) (`#3969 `_), ``nvpsmpi`` (NVHPC + ParaStationMPI) (`#3970 `_), ``gfbf`` (GCC, FlexiBLAS, FFTW) (`#4006 `_) * add support for ``FFTW.MPI`` toolchain component (``$FFT*DIR`` variables) (`#4012 `_) * add support for customizing EasyBuild command used in jobs via ``--job-eb-cmd`` (`#4016 `_) From d4b83c93c5b7a2a67782bc38b784a83d2e3b788e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 7 Jun 2022 22:12:30 +0200 Subject: [PATCH 220/286] fixes, tweaks and formatting for EasyBuild v4.5.5 and older release notes --- docs/Release_notes.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 77ddba5b..8d0a1f40 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -83,6 +83,7 @@ bugfix/update release Wayland (`#11107 `_), XGrafix (`#15268 `_), XPLOR-NIH (`#15479 `_) * added additional easyconfigs for various supported software packages, including: + * ABAQUS 2022, Arb 2.22.1, ARGoS 3.0.0, Arriba 2.2.1, astropy 5.0.4, ATK 2.38.0, Autotools 20220317, Bader 1.04, Bazel 4.2.2 + 5.1.1, BDBag 1.6.3, binutils 2.38, biom-format 2.1.12, BLIS 0.9.0, Boost 1.79.0, breseq 0.36.1, bx-python 0.8.13, cairo 1.17.4, CellRanger-ARC 2.0.1, CMake 3.23.1, cryoDRGN 1.0.0, From 99b2a6af70328e422df0a6e094c5b874d41fed07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jun 2022 08:44:08 +0200 Subject: [PATCH 221/286] use python3 command in script to create EasyBuild release source tarballs --- scripts/create_source_tarball.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/create_source_tarball.sh b/scripts/create_source_tarball.sh index 0c9cbcbe..9105d24d 100755 --- a/scripts/create_source_tarball.sh +++ b/scripts/create_source_tarball.sh @@ -132,7 +132,7 @@ if [[ "$repo" == "easybuild" ]]; then # - easybuild-4.1.2 which requires easybuild-easyblocks and easybuild-easyconfigs v4.1.1 # - easybuild-4.2.0.post0 which requires easybuild-{framework,easyblocks,easyconfigs} v4.2.0 echo ">> checking whether required packages for 'easybuild' are what's expected ... " - python setup.py --requires 2> /dev/null | grep '^easybuild' | tee $tmpdir/easybuild_requires.txt + python3 setup.py --requires 2> /dev/null | grep '^easybuild' | tee $tmpdir/easybuild_requires.txt for dep in framework easyblocks easyconfigs; do echo -n ">>>> $dep ... " pattern="^easybuild_${dep}(==${curr_version})" @@ -178,7 +178,7 @@ if [[ "$repo" == "easybuild-easyconfigs" ]]; then fi # create source tarball -sdist_cmd="python setup.py sdist" +sdist_cmd="python3 setup.py sdist" out=$tmpdir/sdist.out echo -n ">> running '$sdist_cmd'... " eval $sdist_cmd &> $out From b4e4f826d3cf9fb77f47470ce29bdc954886ec7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jun 2022 08:44:21 +0200 Subject: [PATCH 222/286] bump version to 4.5.5 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 96c57cd3..1e1f973c 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.5.4' +VERSION = '4.5.5' # Utility function to read README file From 33118c5f2122b06bbc7882dd5cab4b146180a18a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jun 2022 09:20:46 +0200 Subject: [PATCH 223/286] update test workflow for create_source_tarball.sh script to inject fake 'python3' command --- .github/workflows/scripts.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/scripts.yml b/.github/workflows/scripts.yml index 909c1380..affae66a 100644 --- a/.github/workflows/scripts.yml +++ b/.github/workflows/scripts.yml @@ -103,15 +103,15 @@ jobs: echo "================================================================================================" - # create fake 'python' command: + # create fake 'python3' command: # just exits when 1st argument is setup.py, but calls out to origin Python command otherwise; # this is important w.r.t. the Python version checks run by the 'eb' script mkdir -p /tmp/$USER/bin export PATH=/tmp/$USER/bin:$PATH - echo '#!/bin/bash' > /tmp/$USER/bin/python - chmod u+x /tmp/$USER/bin/python - echo 'orig_python=$(which -a python | head -2 | tail -1)' >> /tmp/$USER/bin/python - echo 'if [[ "$1" == "setup.py" ]]; then exit 0; else $orig_python "$@"; fi' >> /tmp/$USER/bin/python + echo '#!/bin/bash' > /tmp/$USER/bin/python3 + chmod u+x /tmp/$USER/bin/python3 + echo 'orig_python3=$(which -a python3 | head -2 | tail -1)' >> /tmp/$USER/bin/python3 + echo 'if [[ "$1" == "setup.py" ]]; then exit 0; else $orig_python3 "$@"; fi' >> /tmp/$USER/bin/python3 # script should fail if expected source tarball did not get created in dist/ ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true @@ -124,15 +124,15 @@ jobs: echo "================================================================================================" # make fake python command fail if 1st argument is setup.py - sed -i 's/exit 0/exit 1/g' /tmp/$USER/bin/python + sed -i 's/exit 0/exit 1/g' /tmp/$USER/bin/python3 - # script should deal well with failing 'python setup.py sdist' + # script should deal well with failing 'python3 setup.py sdist' ($GITHUB_WORKSPACE/scripts/create_source_tarball.sh ${{matrix.repo}} $version 2>&1 | tee $out) || true grep "ERROR: Creating source tarball failed" $out echo "Expected error found in output: OK!" # cleanup - rm -f /tmp/$USER/bin/python easybuild/easyconfigs/.eb-path-index + rm -f /tmp/$USER/bin/python3 easybuild/easyconfigs/.eb-path-index echo "================================================================================================" From f149e1bf6e2c1a6ff96ad76e4be47a3ea7a11c4e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Jul 2022 16:30:04 +0200 Subject: [PATCH 224/286] update overview of common toolchains: include 2022a versions, list deprecated versions in separate section --- docs/Common-toolchains.rst | 95 +++++++++++++++++++++++--------------- 1 file changed, 59 insertions(+), 36 deletions(-) diff --git a/docs/Common-toolchains.rst b/docs/Common-toolchains.rst index 2d1c80e3..d42441f4 100644 --- a/docs/Common-toolchains.rst +++ b/docs/Common-toolchains.rst @@ -154,24 +154,6 @@ Component versions in ``foss`` toolchain +----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ | ``foss`` | *date* |*binutils* | *GCC* | *Open MPI* | *FlexiBLAS* | *OpenBLAS* | *LAPACK* | *ScaLAPACK* | *FFTW* | +================+=============+============+===========+============+=============+============+=======================+==============+=============+ -| ``2014b`` | Jul '14 | '*(none)* | 4.8.3 | 1.8.1 | *(none)* | 0.2.9 | 3.5.0 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2015a`` | Jan '15 | '*(none)* | 4.9.2 | 1.8.4 | *(none)* | 0.2.13 | 3.5.0 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2015b`` | Jul '15 | 2.25 | 4.9.3 | 1.8.8 | *(none)* | 0.2.14 | 3.5.0 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2016a`` | Jan '16 | 2.25 | 4.9.3 | 1.10.2 | *(none)* | 0.2.15 | 3.6.0 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2016b`` | Jul '16 | 2.26 | 5.4.0 | 1.10.3 | *(none)* | 0.2.18 | 3.6.1 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2017a`` | Jan '17 | 2.27 | 6.3.0 | 2.0.2 | *(none)* | 0.2.19 | 3.7.0 | 2.0.2 | 3.3.6(-pl2) | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2017b`` | Jul '17 | 2.28 | 6.4.0 | 2.1.1 | *(none)* | 0.2.20* | (incl. with OpenBLAS) | 2.0.2 | 3.3.6(-pl2) | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2018a`` | Jan '18 | 2.28 | 6.4.0 | 2.1.2 | *(none)* | 0.2.20* | (incl. with OpenBLAS) | 2.0.2 | 3.3.7 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2018b`` | Jul '18 | 2.30 | 7.3.0 | 3.1.1 | *(none)* | 0.3.1 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ | ``2019a`` | Jan '19 | 2.31.1 | 8.2.0 | 3.1.3 | *(none)* | 0.3.5 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | +----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ | ``2019b`` | Sept '19 | 2.32 | 8.3.0 | 3.1.4 | *(none)* | 0.3.7 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | @@ -184,6 +166,8 @@ Component versions in ``foss`` toolchain +----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ | ``2021b`` | Oct '21 | 2.37 | 11.2.0 | 4.1.1 | 3.0.4 | 0.3.18 | (incl. with OpenBLAS) | 2.1.0 | 3.3.10 | +----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2022a`` | Jun '21 | 2.38 | 11.3.0 | 4.1.4 | 3.2.0 | 0.3.20 | (incl. with OpenBLAS) | 2.2.0 | 3.3.10 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ *(components marked with* * *were patched)* @@ -192,15 +176,69 @@ Component versions in ``foss`` toolchain Component versions in ``intel`` toolchain ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ++----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ +| ``intel`` | *date* | *binutils* | *GCC* | *Intel compilers* | *Intel MPI* | *Intel MKL* | ++================+=============+=============+===========+====================+=============+==============+ +| ``2019a`` | Jan '19 | 2.31.1 | 8.2.0 | 2019.1.144 | 2018.4.274 | 2019.1.144 | ++----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ +| ``2019b`` | Sept '19 | 2.32 | 8.3.0 | 2019.5.281 | 2018.5.288 | 2019.5.281 | ++----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ +| ``2020a`` | May'20 | 2.34 | 9.3.0 | 2020.1.217 | 2019.7.217 | 2020.1.217 | ++----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ +| ``2020b`` | Nov'20 | 2.35 | 10.2.0 | 2020.4.304 | 2019.9.304 | 2020.4.304 | ++----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ +| ``2021a`` | May'21 | 2.36.1 | 10.3.0 | 2021.2.0 | 2021.2.0 | 2021.2.0 | ++----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ +| ``2021b`` | Oct'21 | 2.37 | 11.2.0 | 2021.4.0 | 2021.4.0 | 2021.4.0 | ++----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ +| ``2022a`` | Jun'21 | 2.38 | 11.3.0 | 2022.1.0 | 2021.6.0 | 2022.1.0 | ++----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ + +.. _common_toolchains_overview_deprecated: + +Overview of common toolchains (deprecated versions) +--------------------------------------------------- + +.. _common_toolchains_overview_foss_deprecated: + +Component versions in ``foss`` toolchain (deprecated versions) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``foss`` | *date* |*binutils* | *GCC* | *Open MPI* | *FlexiBLAS* | *OpenBLAS* | *LAPACK* | *ScaLAPACK* | *FFTW* | ++================+=============+============+===========+============+=============+============+=======================+==============+=============+ +| ``2014b`` | Jul '14 | '*(none)* | 4.8.3 | 1.8.1 | *(none)* | 0.2.9 | 3.5.0 | 2.0.2 | 3.3.4 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2015a`` | Jan '15 | '*(none)* | 4.9.2 | 1.8.4 | *(none)* | 0.2.13 | 3.5.0 | 2.0.2 | 3.3.4 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2015b`` | Jul '15 | 2.25 | 4.9.3 | 1.8.8 | *(none)* | 0.2.14 | 3.5.0 | 2.0.2 | 3.3.4 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2016a`` | Jan '16 | 2.25 | 4.9.3 | 1.10.2 | *(none)* | 0.2.15 | 3.6.0 | 2.0.2 | 3.3.4 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2016b`` | Jul '16 | 2.26 | 5.4.0 | 1.10.3 | *(none)* | 0.2.18 | 3.6.1 | 2.0.2 | 3.3.4 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2017a`` | Jan '17 | 2.27 | 6.3.0 | 2.0.2 | *(none)* | 0.2.19 | 3.7.0 | 2.0.2 | 3.3.6(-pl2) | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2017b`` | Jul '17 | 2.28 | 6.4.0 | 2.1.1 | *(none)* | 0.2.20* | (incl. with OpenBLAS) | 2.0.2 | 3.3.6(-pl2) | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2018a`` | Jan '18 | 2.28 | 6.4.0 | 2.1.2 | *(none)* | 0.2.20* | (incl. with OpenBLAS) | 2.0.2 | 3.3.7 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2018b`` | Jul '18 | 2.30 | 7.3.0 | 3.1.1 | *(none)* | 0.3.1 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ + +.. _common_toolchains_overview_intel_deprecated: + +Component versions in ``intel`` toolchain (deprecated versions) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ | ``intel`` | *date* | *binutils* | *GCC* | *Intel compilers* | *Intel MPI* | *Intel MKL* | +================+=============+=============+===========+====================+=============+==============+ -| ``2014b (*)`` | Jul '14 | '*(none)* | 4.8.3 | 2013.5.192 | 4.1.3.049 | 11.1.2.144 | +| ``2014b`` | Jul '14 | '*(none)* | 4.8.3 | 2013.5.192 | 4.1.3.049 | 11.1.2.144 | +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2015a (*)`` | Jan '15 | '*(none)* | 4.9.2 | 2015.1.133 | 5.0.2.044 | 11.2.1.133 | +| ``2015a`` | Jan '15 | '*(none)* | 4.9.2 | 2015.1.133 | 5.0.2.044 | 11.2.1.133 | +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2015b (*)`` | Jul '15 | 2.25 | 4.9.3 | 2015.3.187 | 5.0.3.048 | 11.2.3.187 | +| ``2015b`` | Jul '15 | 2.25 | 4.9.3 | 2015.3.187 | 5.0.3.048 | 11.2.3.187 | +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ | ``2016a`` | Jan '16 | 2.26 | 4.9.3 | 2016.1.150 | 5.1.2.150 | 11.3.1.150 | +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ @@ -214,20 +252,6 @@ Component versions in ``intel`` toolchain +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ | ``2018b`` | Jul '18 | 2.30 | 7.3.0 | 2018.3.222 | 2018.3.222 | 2018.3.222 | +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2019a`` | Jan '19 | 2.31.1 | 8.2.0 | 2019.1.144 | 2018.4.274 | 2019.1.144 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2019b`` | Sept '19 | 2.32 | 8.3.0 | 2019.5.281 | 2018.5.288 | 2019.5.281 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2020a`` | May'20 | 2.34 | 9.3.0 | 2020.1.217 | 2019.7.217 | 2020.1.217 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2020b`` | Nov'20 | 2.35 | 10.2.0 | 2020.4.304 | 2019.9.304 | 2020.4.304 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2021a`` | May'21 | 2.36.1 | 10.3.0 | 2021.2.0 | 2021.2.0 | 2021.2.0 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2021b`` | Oct'21 | 2.37 | 11.2.0 | 2021.4.0 | 2021.4.0 | 2021.4.0 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ - -``(*)``: This toolchain is deprecated, see :ref:`deprecated_easyconfigs_toolchains` for more information. .. _common_toolchains_customizing: @@ -249,4 +273,3 @@ More information about toolchains Please see the :ref:`toolchains_table` for how to obtain a listing of the currently known toolchains. For a detailed listing of the compiler options available with each toolchain, please see :ref:`avail_toolchain_opts`. - From 4d149f08c8188e57943644686c04e6c0f670902b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Jul 2022 21:09:42 +0200 Subject: [PATCH 225/286] auto-update docs for EasyBuild v4.6.0 --- docs/version-specific/Supported_software.rst | 1307 ++++++++++++------ docs/version-specific/easyblocks.rst | 1 + docs/version-specific/help.rst | 1 + docs/version-specific/toolchain_opts.rst | 7 + 4 files changed, 919 insertions(+), 397 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index d3305ff1..37fb551b 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2711 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2736 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -517,11 +517,12 @@ Albumentations is a Python library for fast and flexible image augmentations *homepage*: https://albumentations.ai -========= ============== -version toolchain -========= ============== -``1.1.0`` ``foss/2021b`` -========= ============== +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``1.1.0`` ``foss/2021b`` +``1.1.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== .. _list_software_alevin-fry_1021: @@ -658,6 +659,8 @@ version versionsuffix toolchain ``2.1.2`` ``foss/2021a`` ``2.1.2`` ``-CUDA-11.3.1`` ``foss/2021a`` ``2.1.2`` ``-TensorFlow-2.5.0`` ``foss/2020b``, ``fosscuda/2020b`` +``2.2.2`` ``foss/2021a`` +``2.2.2`` ``-CUDA-11.3.1`` ``foss/2021a`` ========= ===================== ================================== @@ -1711,7 +1714,7 @@ version versionsuffix toolchain *Arriba* ++++++++ -Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. +Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. *homepage*: https://github.com/suhrig/arriba @@ -1721,6 +1724,7 @@ version toolchain ``1.1.0`` ``foss/2018b`` ``2.1.0`` ``GCC/10.2.0``, ``GCC/10.3.0`` ``2.2.1`` ``GCC/11.2.0`` +``2.3.0`` ``GCC/11.2.0`` ========= ============================== @@ -1744,6 +1748,7 @@ version versionsuffix toolchain ``0.17.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``6.0.0`` ``foss/2021a``, ``foss/2021b`` ``6.0.1`` ``foss/2021a`` +``8.0.0`` ``foss/2022.05`` ========== ================== =================================================== @@ -2549,7 +2554,7 @@ version versionsuffix toolchain --- -:ref:`list_software_BabelStream_1090` - :ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_Bambi_475` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_bamtofastq_1074` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_bcbio-gff_863` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biom-format_1117` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_Blosc2_549` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_boost_histogram_1620` - :ref:`list_software_boto3_487` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_Brotli-python_1339` - :ref:`list_software_Brunsli_735` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` +:ref:`list_software_BabelStream_1090` - :ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_Bambi_475` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_bamtofastq_1074` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_bcbio-gff_863` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biom-format_1117` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_Blosc2_549` - :ref:`list_software_BLT_226` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_boost_histogram_1620` - :ref:`list_software_boto3_487` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_Brotli-python_1339` - :ref:`list_software_Brunsli_735` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` .. _list_software_BabelStream_1090: @@ -4004,7 +4009,7 @@ version versionsuffix toolchain ``0.6.0`` ``GCC/8.3.0-2.32`` ``0.8.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``0.8.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCCcore/10.3.0`` -``0.9.0`` ``GCC/11.3.0`` +``0.9.0`` ``GCC/11.3.0``, ``intel-compilers/2022.1.0`` ``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` ``2.2`` ``-amd`` ``GCCcore/9.3.0`` ``3.0`` ``-amd`` ``GCCcore/10.3.0`` @@ -4085,6 +4090,22 @@ version toolchain ========= ================== +.. _list_software_BLT_226: + +*BLT* ++++++ + +BLT is an extension to the Tk toolkit, adding new widgets, geometry managers, and miscellaneous commands. + +*homepage*: http://blt.sourceforge.net/ + +============ ================== +version toolchain +============ ================== +``20181223`` ``GCCcore/11.2.0`` +============ ================== + + .. _list_software_bmtagger_841: *bmtagger* @@ -4479,6 +4500,7 @@ version toolchain ========= ================== ``2.6.0`` ``GCCcore/9.3.0`` ``2.6.2`` ``GCCcore/11.2.0`` +``2.7`` ``GCCcore/11.2.0`` ========= ================== @@ -4934,7 +4956,7 @@ version toolchain --- -:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CASTEP_448` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_CellTypist_1037` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMAverse_758` - :ref:`list_software_CmdStanR_764` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_CONN_302` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_Crumble_714` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CASTEP_448` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_category_encoders_1808` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_CellTypist_1037` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMAverse_758` - :ref:`list_software_CmdStanR_764` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_CONN_302` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_Crumble_714` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_c-ares_571: @@ -5376,6 +5398,22 @@ version toolchain ========== ========== +.. _list_software_category_encoders_1808: + +*category_encoders* ++++++++++++++++++++ + +A set of scikit-learn-style transformers for encoding categorical variables into numeric by means of different techniques. + +*homepage*: https://github.com/scikit-learn-contrib/category_encoders + +========= ============== +version toolchain +========= ============== +``2.4.1`` ``foss/2021b`` +========= ============== + + .. _list_software_CatMAP_502: *CatMAP* @@ -5758,6 +5796,7 @@ version toolchain ``6.0.1`` ``system`` ``6.0.2`` ``system`` ``6.1.2`` ``system`` +``7.0.0`` ``system`` ========= ========== @@ -6639,6 +6678,7 @@ version toolchain ========== ============================== ``1.17.3`` ``foss/2018b`` ``1.17.6`` ``foss/2020b``, ``foss/2021a`` +``1.17.7`` ``foss/2021b`` ========== ============================== @@ -6971,6 +7011,7 @@ version toolchain ========== ================================== ``2.11.3`` ``GCCcore/7.3.0``, ``foss/2018b`` ``2.11.4`` ``GCC/10.3.0``, ``GCCcore/10.2.0`` +``2.11.6`` ``GCC/11.2.0`` ========== ================================== @@ -7355,6 +7396,7 @@ A small C++ header library which makes it easier to write Python extension modul version toolchain ========= ====================================== ``1.1.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.2.1`` ``GCCcore/11.3.0`` ========= ====================================== @@ -7955,6 +7997,7 @@ version versionsuffix toolchain ``8.2.2.26`` ``-CUDA-11.4.1`` ``system`` ``8.4.0.27`` ``-CUDA-11.6.0`` ``system`` ``8.4.1.50`` ``-CUDA-11.6.0`` ``system`` +``8.4.1.50`` ``-CUDA-11.7.0`` ``system`` ============ ================== =========================================================== @@ -8657,6 +8700,7 @@ deal.II is a C++ program library targeted at the computational solution of part version toolchain ========= =============== ``9.1.1`` ``intel/2019a`` +``9.3.3`` ``foss/2021a`` ========= =============== @@ -9411,6 +9455,7 @@ version toolchain ``3.0.3`` ``foss/2018a`` ``3.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``3.2.0`` ``GCCcore/11.3.0`` ========= ============================================================================= @@ -9452,6 +9497,7 @@ version toolchain ``1.8.17`` ``GCCcore/9.3.0`` ``1.8.20`` ``GCCcore/10.2.0`` ``1.9.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.9.4`` ``GCCcore/11.3.0`` =========== ======================================================================================================================================================= @@ -9876,6 +9922,7 @@ version toolchain ``4.5.2`` ``system`` ``4.5.3`` ``system`` ``4.5.4`` ``system`` +``4.5.5`` ``system`` ========== ========== @@ -10216,7 +10263,7 @@ version toolchain ``2020.11.001`` ``foss/2020b``, ``intel/2020b`` ``2021.05.001`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` ``2021.05.002`` ``intel/2020b`` -``2021.11.001`` ``foss/2021b``, ``intel/2021b`` +``2021.11.001`` ``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` =================== ================================================================================= @@ -10916,7 +10963,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_Fastaq_608` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_FFTW.MPI_587` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMPy_348` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoBiS_435` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeBarcodes_1189` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_Fastaq_608` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_FFTW.MPI_587` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_fio_318` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMPy_348` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoBiS_435` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeBarcodes_1189` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FSON_310` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -11784,11 +11831,11 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: https://www.fftw.org -========== ================= -version toolchain -========== ================= -``3.3.10`` ``gompi/2022.05`` -========== ================= +========== ================================== +version toolchain +========== ================================== +``3.3.10`` ``gompi/2022.05``, ``gompi/2022a`` +========== ================================== .. _list_software_fgbio_519: @@ -12045,6 +12092,22 @@ version toolchain ========= =============== +.. _list_software_fio_318: + +*fio* ++++++ + +Flexible I/O tester + +*homepage*: https://github.com/axboe/fio + +======== ================== +version toolchain +======== ================== +``3.30`` ``GCCcore/10.3.0`` +======== ================== + + .. _list_software_Fiona_493: *Fiona* @@ -12061,6 +12124,7 @@ version versionsuffix toolchain ``1.8.13.post1`` ``-Python-3.7.2`` ``foss/2019a`` ``1.8.16`` ``-Python-3.8.2`` ``foss/2020a`` ``1.8.20`` ``foss/2020b``, ``foss/2021a``, ``intel/2020b`` +``1.8.21`` ``foss/2021b`` ================ ================= =================================================== @@ -12173,6 +12237,7 @@ FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but l version toolchain ========= ========================================================== ``1.3.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.3.4`` ``GCCcore/11.3.0`` ========= ========================================================== @@ -12257,12 +12322,12 @@ FlatBuffers: Memory Efficient Serialization Library *homepage*: https://github.com/google/flatbuffers/ -========== ======================================================== -version toolchain -========== ======================================================== -``1.12.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.0.0`` ``GCCcore/10.3.0`` -========== ======================================================== +========== ========================================================== +version toolchain +========== ========================================================== +``1.12.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.0.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========== ========================================================== .. _list_software_flatbuffers-python_1891: @@ -12274,13 +12339,13 @@ Python Flatbuffers runtime library. *homepage*: https://github.com/google/flatbuffers/ -======== ================= ================== -version versionsuffix toolchain -======== ================= ================== -``1.12`` ``GCCcore/10.2.0`` -``1.12`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``2.0`` ``GCCcore/10.3.0`` -======== ================= ================== +======== ================= ========================================================== +version versionsuffix toolchain +======== ================= ========================================================== +``1.12`` ``GCCcore/10.2.0`` +``1.12`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +======== ================= ========================================================== .. _list_software_FLEUR_382: @@ -12569,6 +12634,7 @@ version toolchain ``5.3.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``6.2.1`` ``GCCcore/9.3.0`` ``7.0.3`` ``GCCcore/9.3.0`` +``7.1.1`` ``GCCcore/11.2.0`` ========= ==================================== @@ -12697,6 +12763,7 @@ version toolchain ``2021a`` ``system`` ``2021b`` ``system`` ``2022.05`` ``system`` +``2022a`` ``system`` =========== ========== @@ -13137,23 +13204,24 @@ FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain ima *homepage*: https://www.fmrib.ox.ac.uk/fsl/ -========== ============================== ================================================ -version versionsuffix toolchain -========== ============================== ================================================ -``5.0.9`` ``intel/2016a`` -``5.0.9`` ``-Mesa-11.2.1`` ``intel/2016a`` -``5.0.9`` ``-centos6_64`` ``system`` -``5.0.10`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``5.0.11`` ``foss/2018b`` -``5.0.11`` ``-Python-3.6.6`` ``foss/2018b`` -``6.0.1`` ``-Python-2.7.15`` ``foss/2019a`` -``6.0.1`` ``-Python-3.7.2`` ``foss/2019a`` -``6.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` -``6.0.2`` ``-Python-2.7.15-CUDA-9.2.88`` ``foss/2018b`` -``6.0.2`` ``-Python-3.7.2`` ``foss/2019a`` -``6.0.3`` ``-Python-3.7.4`` ``foss/2019b`` -``6.0.4`` ``-Python-3.7.4`` ``foss/2019b`` -========== ============================== ================================================ +=========== ============================== ================================================ +version versionsuffix toolchain +=========== ============================== ================================================ +``5.0.9`` ``intel/2016a`` +``5.0.9`` ``-Mesa-11.2.1`` ``intel/2016a`` +``5.0.9`` ``-centos6_64`` ``system`` +``5.0.10`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``5.0.11`` ``foss/2018b`` +``5.0.11`` ``-Python-3.6.6`` ``foss/2018b`` +``6.0.1`` ``-Python-2.7.15`` ``foss/2019a`` +``6.0.1`` ``-Python-3.7.2`` ``foss/2019a`` +``6.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` +``6.0.2`` ``-Python-2.7.15-CUDA-9.2.88`` ``foss/2018b`` +``6.0.2`` ``-Python-3.7.2`` ``foss/2019a`` +``6.0.3`` ``-Python-3.7.4`` ``foss/2019b`` +``6.0.4`` ``-Python-3.7.4`` ``foss/2019b`` +``6.0.5.1`` ``foss/2021a`` +=========== ============================== ================================================ .. _list_software_FSLeyes_667: @@ -13188,6 +13256,22 @@ version toolchain ============ ============================================================================= +.. _list_software_FSON_310: + +*FSON* +++++++ + +Fortran 95 JSON Parser + +*homepage*: https://github.com/josephalevin/fson + +========= ============== +version toolchain +========= ============== +``1.0.5`` ``GCC/10.2.0`` +========= ============== + + .. _list_software_FTGL_301: *FTGL* @@ -13393,7 +13477,23 @@ version toolchain --- -:ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_gcloud_638` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_genozip_764` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPy_272` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap_784` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gRPC_332` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-bad_1393` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_gsutil_664` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GTK4_282` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_G-PhoCS_561` - :ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_gcloud_638` - :ref:`list_software_GConf_461` - :ref:`list_software_GCTA_287` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_genozip_764` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_gfbf_405` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_Gibbs2_537` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPy_272` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap_784` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gRPC_332` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-bad_1393` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_gsutil_664` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GTK4_282` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` + + +.. _list_software_G-PhoCS_561: + +*G-PhoCS* ++++++++++ + +G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences. G-PhoCS accepts as input a set of multiple sequence alignments from separate neutrally evolving loci along the genome. Parameter inference is done in a Bayesian manner, using a Markov Chain Monte Carlo (MCMC) to jointly sample model parameters and genealogies at the input loci. + +*homepage*: http://compgen.cshl.edu/GPhoCS/ + +========= ======================================== +version toolchain +========= ======================================== +``1.2.3`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +========= ======================================== .. _list_software_g2clib_563: @@ -13409,7 +13509,7 @@ Library contains GRIB2 encoder/decoder ('C' version). version toolchain ========= ======================================================================================================================== ``1.6.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``1.6.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.6.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ======================================================================================================================== @@ -13427,7 +13527,7 @@ version toolchain ========= ===================================================================== ``1.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.1.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2018b`` -``3.2.0`` ``GCCcore/10.3.0`` +``3.2.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ===================================================================== @@ -13974,6 +14074,22 @@ version toolchain ========= ======================================================================================================================================== +.. _list_software_GCTA_287: + +*GCTA* +++++++ + +GCTA (Genome-wide Complex Trait Analysis) is a software package, which was initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been extensively extended for many other analyses of data from genome-wide association studies (GWASs). + +*homepage*: https://yanglab.westlake.edu.cn/software/gcta/ + +============== ============================== +version toolchain +============== ============================== +``1.94.0beta`` ``foss/2021b``, ``gfbf/2022a`` +============== ============================== + + .. _list_software_Gctf_388: *Gctf* @@ -14047,6 +14163,7 @@ version versionsuffix toolchain ``3.2.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``3.3.0`` ``foss/2021a`` ``3.3.2`` ``foss/2021b`` +``3.5.0`` ``foss/2022a`` ========= ============================== ================================================================ @@ -14101,15 +14218,16 @@ version versionsuffix toolchain *gdbm* ++++++ -GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database. +GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing and work similar to the standard UNIX dbm. These routines are provided to a programmer needing to create and manipulate a hashed database. -*homepage*: https://www.gnu.org.ua/software/gdbm/ +*homepage*: https://www.gnu.org.ua/software/gdbm/gdbm.html -========== ============== -version toolchain -========== ============== -``1.18.1`` ``foss/2020a`` -========== ============== +========== ================== +version toolchain +========== ================== +``1.18.1`` ``foss/2020a`` +``1.21`` ``GCCcore/10.2.0`` +========== ================== .. _list_software_gdc-client_986: @@ -14243,7 +14361,7 @@ version versionsuffix toolchain ``2.1`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` ``2.1`` ``-CUDA-11.2.1`` ``GCCcore/10.2.0`` ``2.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.3`` ``GCCcore/11.2.0`` +``2.3`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ======= ================ ====================================== @@ -14605,6 +14723,7 @@ version versionsuffix toolchain ``0.8.1`` ``-Python-3.7.4`` ``intel/2019b`` ``0.8.1`` ``-Python-3.8.2`` ``foss/2020a`` ``0.10.2`` ``foss/2021a`` +``0.11.0`` ``foss/2021b`` ========== ================= ================================== @@ -14651,27 +14770,28 @@ GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (J *homepage*: https://trac.osgeo.org/geos -========= ================== ======================================================================= -version versionsuffix toolchain -========= ================== ======================================================================= -``3.5.0`` ``-Python-2.7.11`` ``intel/2016a`` -``3.5.0`` ``-Python-2.7.12`` ``intel/2016b`` -``3.6.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.6.1`` ``-Python-2.7.13`` ``intel/2017a`` -``3.6.1`` ``-Python-3.6.1`` ``intel/2017a`` -``3.6.2`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``3.6.2`` ``-Python-2.7.15`` ``foss/2018b`` -``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` -``3.6.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.01`` -``3.6.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` -``3.6.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.7.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` -``3.7.2`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.8.0`` ``GCC/8.3.0`` -``3.8.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``3.8.1`` ``-Python-3.8.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` -``3.9.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304`` -========= ================== ======================================================================= +========== ================== ======================================================================= +version versionsuffix toolchain +========== ================== ======================================================================= +``3.5.0`` ``-Python-2.7.11`` ``intel/2016a`` +``3.5.0`` ``-Python-2.7.12`` ``intel/2016b`` +``3.6.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.6.1`` ``-Python-2.7.13`` ``intel/2017a`` +``3.6.1`` ``-Python-3.6.1`` ``intel/2017a`` +``3.6.2`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``3.6.2`` ``-Python-2.7.15`` ``foss/2018b`` +``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` +``3.6.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.01`` +``3.6.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` +``3.6.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.7.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` +``3.7.2`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.8.0`` ``GCC/8.3.0`` +``3.8.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``3.8.1`` ``-Python-3.8.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` +``3.9.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304`` +``3.10.3`` ``GCC/11.3.0`` +========== ================== ======================================================================= .. _list_software_Gerris_620: @@ -14764,6 +14884,22 @@ version toolchain ========== ================== +.. _list_software_gfbf_405: + +*gfbf* +++++++ + +GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW. + +*homepage*: (none) + +========= ========== +version toolchain +========= ========== +``2022a`` ``system`` +========= ========== + + .. _list_software_GffCompare_986: *GffCompare* @@ -14894,9 +15030,26 @@ version versionsuffix toolchain ``9.52`` ``GCCcore/9.3.0`` ``9.53.3`` ``GCCcore/10.2.0`` ``9.54.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``9.56.1`` ``GCCcore/11.3.0`` ========== ================== ================================================== +.. _list_software_Gibbs2_537: + +*Gibbs2* +++++++++ + +Gibbs2 is a program for the calculation of thermodynamic properties in periodic solids under arbitrary conditions of temperature and pressure. Gibbs2 uses the results of periodic solid-state quantum-mechanical calculations, specifically the energy-volume curve and possibly the harmonic phonon frequencies, to compute the thermodynamic properties of the solid within the framework of the quasiharmonic approximation. + +*homepage*: https://aoterodelaroza.github.io/gibbs2/ + +======= ============== +version toolchain +======= ============== +``1.0`` ``GCC/10.3.0`` +======= ============== + + .. _list_software_giflib_621: *giflib* @@ -15342,6 +15495,7 @@ C++ bindings for Glib version toolchain ========== ======================================================= ``2.49.7`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.66.4`` ``GCCcore/10.3.0`` ========== ======================================================= @@ -15484,7 +15638,7 @@ version toolchain ``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` ``4.61`` ``intel/2017a`` ``4.65`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``5.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``5.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ======== ================================================================================================================= @@ -15977,6 +16131,7 @@ version versionsuffix toolchain ``2021a`` ``system`` ``2021b`` ``system`` ``2022.05`` ``system`` +``2022a`` ``system`` ``system`` ``-2.29`` ``system`` =========== ============= ========== @@ -16034,7 +16189,7 @@ version toolchain ``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b`` ``1.8.1`` ``GCCcore/8.2.0`` ``1.10.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.11.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.11.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ===================================================================== @@ -16334,11 +16489,11 @@ Graphite is a "smart font" system developed specifically to handle the complexi *homepage*: https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home -========== ========================================================= -version toolchain -========== ========================================================= -``1.3.14`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` -========== ========================================================= +========== ============================================================================= +version toolchain +========== ============================================================================= +``1.3.14`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` +========== ============================================================================= .. _list_software_GraPhlAn_749: @@ -16694,6 +16849,7 @@ Groovy is a powerful, optionally typed and dynamic language, with static-typing version versionsuffix toolchain ========= ============= ========== ``2.5.9`` ``-Java-11`` ``system`` +``4.0.3`` ``-Java-11`` ``system`` ========= ============= ========== @@ -17093,6 +17249,7 @@ GULP is a program for performing a variety of types of simulation on materials version toolchain ======= =============== ``5.1`` ``intel/2019a`` +``6.1`` ``foss/2021b`` ======= =============== @@ -17235,6 +17392,7 @@ version versionsuffix toolchain ``3.1.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``3.2.1`` ``foss/2021a`` ``3.6.0`` ``foss/2021b``, ``intel/2021b`` +``3.7.0`` ``foss/2022a`` ========== ===================================== ==================================================================================== @@ -17450,16 +17608,16 @@ HDF (also known as HDF4) is a library and multi-object file format for storing *homepage*: https://www.hdfgroup.org/products/hdf4/ -========== ============== ============================================================================= -version versionsuffix toolchain -========== ============== ============================================================================= -``4.2.11`` ``intel/2016a`` -``4.2.12`` ``intel/2017a`` -``4.2.13`` ``GCCcore/6.4.0`` -``4.2.13`` ``-no-netcdf`` ``intel/2017a`` -``4.2.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``4.2.15`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -========== ============== ============================================================================= +========== ============== ================================================================================================= +version versionsuffix toolchain +========== ============== ================================================================================================= +``4.2.11`` ``intel/2016a`` +``4.2.12`` ``intel/2017a`` +``4.2.13`` ``GCCcore/6.4.0`` +``4.2.13`` ``-no-netcdf`` ``intel/2017a`` +``4.2.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``4.2.15`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +========== ============== ================================================================================================= .. _list_software_HDF-EOS_486: @@ -17528,6 +17686,7 @@ version versionsuffix toolchain ``1.10.8`` ``gompi/2021b`` ``1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` ``1.12.1`` ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021b`` +``1.13.1`` ``gompi/2022a``, ``iimpi/2022a`` ================= ============= ================================================================================================================================================================================================================== @@ -17746,11 +17905,12 @@ Hifiasm: a haplotype-resolved assembler for accurate Hifi reads. *homepage*: https://github.com/chhylp123/hifiasm -========== ================= -version toolchain -========== ================= -``0.15.2`` ``GCCcore/9.3.0`` -========== ================= +========== ===================================== +version toolchain +========== ===================================== +``0.15.2`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``0.16.1`` ``GCCcore/10.3.0`` +========== ===================================== .. _list_software_Highway_721: @@ -18101,7 +18261,7 @@ version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -18407,7 +18567,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_i7z_282` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intervaltree-python_2020` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_Iris_407` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_IsoNet_594` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_i7z_282` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_InterProScan_data_1713` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intervaltree-python_2020` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_Iris_407` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_IsoNet_594` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -18785,11 +18945,12 @@ IGMPlot is a free open-source program developed to identify molecular interactio *homepage*: http://igmplot.univ-reims.fr -========= ====================================== -version toolchain -========= ====================================== -``2.4.2`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -========= ====================================== +========== ====================================== +version toolchain +========== ====================================== +``2.4.2`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``2.6.9b`` ``GCC/11.2.0`` +========== ====================================== .. _list_software_igraph_635: @@ -18950,6 +19111,7 @@ version versionsuffix toolchain ``2021b`` ``system`` ``2022.00`` ``system`` ``2022.05`` ``system`` +``2022a`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ===================== ==================== ========== @@ -19113,6 +19275,7 @@ version versionsuffix toolchain ``7.0.10-35`` ``GCCcore/10.2.0`` ``7.0.11-14`` ``GCCcore/10.3.0`` ``7.1.0-4`` ``GCCcore/11.2.0`` +``7.1.0-37`` ``GCCcore/11.3.0`` ============= =================================== =============================== @@ -19186,6 +19349,7 @@ version versionsuffix toolchain ========= ================= ============== ``0.2.8`` ``-Python-3.6.6`` ``foss/2018b`` ``0.4.0`` ``foss/2021b`` +``0.4.0`` ``-CUDA-11.3.1`` ``foss/2021a`` ``0.4.0`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -19244,13 +19408,13 @@ FFTW interfaces using Intel oneAPI Math Kernel Library *homepage*: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html -============ ================================ -version toolchain -============ ================================ -``2021.4.0`` ``gompi/2021b``, ``iimpi/2021b`` -``2022.0.1`` ``iimpi/2022.00`` -``2022.1.0`` ``iimpi/2022.05`` -============ ================================ +============ ================================== +version toolchain +============ ================================== +``2021.4.0`` ``gompi/2021b``, ``iimpi/2021b`` +``2022.0.1`` ``iimpi/2022.00`` +``2022.1.0`` ``iimpi/2022.05``, ``iimpi/2022a`` +============ ================================== .. _list_software_Imlib2_543: @@ -19617,6 +19781,7 @@ version versionsuffix toolchain ``2021b`` ``system`` ``2022.00`` ``system`` ``2022.05`` ``system`` +``2022a`` ``system`` ===================== ============= ========== @@ -19718,7 +19883,7 @@ version versionsuffix toolchain *InterProScan* ++++++++++++++ -InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. +InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource [code only: libraries and external binaries but no data]. *homepage*: https://www.ebi.ac.uk/interpro/ @@ -19729,9 +19894,26 @@ version toolchain ``5.27-66.0`` ``intel/2017b`` ``5.28-67.0`` ``intel/2018a`` ``5.52-86.0`` ``GCCcore/10.3.0`` +``5.55-88.0`` ``foss/2021a`` ============= ================== +.. _list_software_InterProScan_data_1713: + +*InterProScan_data* ++++++++++++++++++++ + +InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource [data only]. + +*homepage*: https://www.ebi.ac.uk/interpro/ + +============= ============== +version toolchain +============= ============== +``5.55-88.0`` ``foss/2021a`` +============= ============== + + .. _list_software_intervaltree_1301: *intervaltree* @@ -20105,6 +20287,7 @@ version versionsuffix toolchain ``1.1`` ``-R-3.6.3-Python-3.8.2`` ``foss/2020a`` ``1.2`` ``-R-4.0.0-Python-3.8.2`` ``foss/2020a`` ``1.2`` ``-R-4.1.0`` ``foss/2021a`` +``1.3`` ``-R-4.2.0`` ``foss/2021b`` ========== ========================== ================================== @@ -20246,24 +20429,24 @@ Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite *homepage*: https://itk.org -========== ================== ================================== -version versionsuffix toolchain -========== ================== ================================== -``4.12.2`` ``-Python-2.7.12`` ``foss/2016b`` -``4.13.0`` ``-Python-2.7.14`` ``foss/2018a`` -``4.13.0`` ``-Python-3.6.4`` ``foss/2018a`` -``4.13.1`` ``-Python-2.7.14`` ``foss/2018a`` -``4.13.1`` ``-Python-2.7.15`` ``foss/2018b`` -``4.13.1`` ``-Python-3.6.4`` ``foss/2018a`` -``4.13.1`` ``-Python-3.6.6`` ``foss/2018b`` -``4.13.1`` ``-Python-3.7.4`` ``foss/2019b`` -``5.0.1`` ``-Python-3.7.2`` ``foss/2019a`` -``5.0.1`` ``-Python-3.7.4`` ``foss/2019b`` -``5.0b01`` ``-Python-3.6.6`` ``foss/2018b`` -``5.1.2`` ``foss/2020a``, ``fosscuda/2020a`` -``5.1.2`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` -``5.2.1`` ``foss/2020b``, ``foss/2021a`` -========== ================== ================================== +========== ================== ============================================== +version versionsuffix toolchain +========== ================== ============================================== +``4.12.2`` ``-Python-2.7.12`` ``foss/2016b`` +``4.13.0`` ``-Python-2.7.14`` ``foss/2018a`` +``4.13.0`` ``-Python-3.6.4`` ``foss/2018a`` +``4.13.1`` ``-Python-2.7.14`` ``foss/2018a`` +``4.13.1`` ``-Python-2.7.15`` ``foss/2018b`` +``4.13.1`` ``-Python-3.6.4`` ``foss/2018a`` +``4.13.1`` ``-Python-3.6.6`` ``foss/2018b`` +``4.13.1`` ``-Python-3.7.4`` ``foss/2019b`` +``5.0.1`` ``-Python-3.7.2`` ``foss/2019a`` +``5.0.1`` ``-Python-3.7.4`` ``foss/2019b`` +``5.0b01`` ``-Python-3.6.6`` ``foss/2018b`` +``5.1.2`` ``foss/2020a``, ``fosscuda/2020a`` +``5.1.2`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``5.2.1`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` +========== ================== ============================================== .. _list_software_itpp_445: @@ -20340,7 +20523,7 @@ version toolchain --- -:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_Jasmine_711` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_jax_323` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_JSON-GLib_709` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyter-matlab-proxy_2080` - :ref:`list_software_jupyter-server-proxy_2118` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` - :ref:`list_software_jxrlib_651` +:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_Jasmine_711` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_jax_323` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_Jorg_402` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_JSON-GLib_709` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyter-matlab-proxy_2080` - :ref:`list_software_jupyter-server-proxy_2118` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` - :ref:`list_software_jxrlib_651` .. _list_software_JAGS_293: @@ -20412,7 +20595,7 @@ version toolchain ``2.0.16`` ``GCCcore/9.3.0`` ``2.0.24`` ``GCCcore/10.2.0`` ``2.0.28`` ``GCCcore/10.3.0`` -``2.0.33`` ``GCCcore/11.2.0`` +``2.0.33`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` =========== ========================================================================================================================================================== @@ -20507,6 +20690,7 @@ version versionsuffix toolchain ``0.2.24`` ``foss/2021a`` ``0.2.24`` ``-CUDA-11.3.1`` ``foss/2021a`` ``0.3.9`` ``foss/2021a`` +``0.3.9`` ``-CUDA-11.3.1`` ``foss/2021a`` ========== ================ ================================== @@ -20582,6 +20766,7 @@ version toolchain ``5.1.0`` ``GCCcore/7.3.0`` ``5.2.0`` ``GCCcore/8.2.0`` ``5.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``5.3.0`` ``GCCcore/11.3.0`` ========= ================================================================================================ @@ -20634,6 +20819,22 @@ version versionsuffix toolchain =================== ================== ========== +.. _list_software_Jorg_402: + +*Jorg* +++++++ + +A MAG Circularization Method By Lauren Lui, Torben Nielsen, and Adam Arkin + +*homepage*: https://github.com/lmlui/Jorg + +========= ============== +version toolchain +========= ============== +``1.0.1`` ``foss/2020b`` +========= ============== + + .. _list_software_joypy_571: *joypy* @@ -20715,6 +20916,7 @@ version toolchain ``0.10.7`` ``GCCcore/8.2.0`` ``1.9.3`` ``GCCcore/8.3.0`` ``1.9.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``1.9.5`` ``GCCcore/11.3.0`` ========== ============================================================================= @@ -20783,6 +20985,7 @@ version versionsuffix toolchain ``1.7.0`` ``-linux-x86_64`` ``system`` ``1.7.1`` ``-linux-x86_64`` ``system`` ``1.7.2`` ``-linux-x86_64`` ``system`` +``1.7.3`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -21400,7 +21603,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LBFGS++_452` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_LERC_294` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaec_608` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libavif_733` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libde265_669` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libexif_739` - :ref:`list_software_libfabric_926` - :ref:`list_software_libfdf_615` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgdiplus_1071` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libheif_723` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_LibLZF_515` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libmbd_618` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libnsl_644` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpspio_866` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libSBML_613` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libtree_743` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_longread_umi_1270` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPeg_360` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LBFGS++_452` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_LERC_294` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaec_608` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libavif_733` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libde265_669` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libexif_739` - :ref:`list_software_libfabric_926` - :ref:`list_software_libfdf_615` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgdiplus_1071` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libheif_723` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_LibLZF_515` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libmbd_618` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libnsl_644` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libopus_766` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpspio_866` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libSBML_613` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libtree_743` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_longread_umi_1270` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPeg_360` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -21444,12 +21647,12 @@ LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGP *homepage*: http://lame.sourceforge.net/ -========== ========================================================================================================================================================================== -version toolchain -========== ========================================================================================================================================================================== -``3.99.5`` ``foss/2016b``, ``intel/2017a`` -``3.100`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` -========== ========================================================================================================================================================================== +========== ============================================================================================================================================================================================== +version toolchain +========== ============================================================================================================================================================================================== +``3.99.5`` ``foss/2016b``, ``intel/2017a`` +``3.100`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` +========== ============================================================================================================================================================================================== .. _list_software_LAMMPS_458: @@ -21685,12 +21888,13 @@ Leptonica is a collection of pedagogically-oriented open source software that i *homepage*: http://www.leptonica.org -========== ================= -version toolchain -========== ================= -``1.77.0`` ``GCCcore/7.3.0`` -``1.78.0`` ``GCCcore/8.2.0`` -========== ================= +========== ================== +version toolchain +========== ================== +``1.77.0`` ``GCCcore/7.3.0`` +``1.78.0`` ``GCCcore/8.2.0`` +``1.82.0`` ``GCCcore/10.3.0`` +========== ================== .. _list_software_LERC_294: @@ -22465,6 +22669,7 @@ version toolchain ``1.5.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.7.0`` ``GCCcore/11.2.0`` +``1.7.1`` ``GCCcore/11.3.0`` ========= ======================================================= @@ -22483,6 +22688,7 @@ version toolchain ``1.0.0`` ``GCCcore/8.3.0`` ``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``1.1.1`` ``GCCcore/11.2.0`` +``1.4.3`` ``GCCcore/11.3.0`` ========= ========================================================= @@ -22709,6 +22915,7 @@ version toolchain ======== =================================================================================================================== ``1.15`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``1.16`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.17`` ``GCCcore/11.3.0`` ======== =================================================================================================================== @@ -23007,10 +23214,26 @@ Ogg is a multimedia container format, and the native file and stream format for version toolchain ========= ====================================== ``1.3.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``1.3.5`` ``GCCcore/11.2.0`` +``1.3.5`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ====================================== +.. _list_software_libopus_766: + +*libopus* ++++++++++ + +Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s SILK codec and Xiph.Org’s CELT codec. + +*homepage*: https://www.opus-codec.org/ + +========= ================== +version toolchain +========= ================== +``1.3.1`` ``GCCcore/11.3.0`` +========= ================== + + .. _list_software_libosmium_977: *libosmium* @@ -23224,7 +23447,7 @@ version toolchain ``6.3`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``7.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``8.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` -``8.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``8.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``8.1.2`` ``GCCcore/11.3.0`` ========= =================================================================================================================================================================================================================================================================================================================================================================================== @@ -23245,6 +23468,7 @@ version toolchain ``4.0.0`` ``GCCcore/9.3.0`` ``4.1.0`` ``GCCcore/10.2.0`` ``4.1.2`` ``GCCcore/11.2.0`` +``4.2.0`` ``GCCcore/10.3.0`` ========= ================== @@ -23350,6 +23574,7 @@ version toolchain ``2.10.0`` ``GCCcore/6.4.0`` ``2.10.1`` ``GCCcore/7.3.0`` ``2.10.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.10.8`` ``GCCcore/10.3.0`` ========== ==================================== @@ -23401,6 +23626,7 @@ version toolchain ========== ================================================================================================================================== ``1.0.28`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a`` ``1.0.31`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.1.0`` ``GCCcore/11.3.0`` ========== ================================================================================================================================== @@ -23522,14 +23748,14 @@ LIBSVM is an integrated software for support vector classification, (C-SVC, nu-S *homepage*: https://www.csie.ntu.edu.tw/~cjlin/libsvm/ -======== ====================================== -version toolchain -======== ====================================== -``3.22`` ``intel/2016b``, ``intel/2017b`` -``3.23`` ``foss/2018b``, ``intel/2018b`` -``3.24`` ``GCCcore/9.3.0`` -``3.25`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` -======== ====================================== +======== ========================================================== +version toolchain +======== ========================================================== +``3.22`` ``intel/2016b``, ``intel/2017b`` +``3.23`` ``foss/2018b``, ``intel/2018b`` +``3.24`` ``GCCcore/9.3.0`` +``3.25`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +======== ========================================================== .. _list_software_libtar_638: @@ -23617,14 +23843,14 @@ Libtirpc is a port of Suns Transport-Independent RPC library to Linux. *homepage*: https://sourceforge.net/projects/libtirpc/ -========= ====================================== -version toolchain -========= ====================================== -``1.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.2.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.3.1`` ``GCCcore/10.2.0`` -``1.3.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========= ====================================== +========= ========================================================== +version toolchain +========= ========================================================== +``1.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.2.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.3.1`` ``GCCcore/10.2.0`` +``1.3.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ========================================================== .. _list_software_libtool_757: @@ -23778,11 +24004,11 @@ Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-pu *homepage*: https://xiph.org/vorbis/ -========= ========================================================== -version toolchain -========= ========================================================== -``1.3.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========= ========================================================== +========= ============================================================================== +version toolchain +========= ============================================================================== +``1.3.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ============================================================================== .. _list_software_libwebp_741: @@ -23860,6 +24086,7 @@ version toolchain ``5.1.3`` ``GCC/10.2.0`` ``5.1.5`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` ``5.1.6`` ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` +``5.2.3`` ``GCC/11.3.0``, ``intel-compilers/2022.1.0`` ========= =================================================================================================================================================================================================================================================================================== @@ -24057,6 +24284,7 @@ libxml++ is a C++ wrapper for the libxml XML parser library. version toolchain ========== ======================================================= ``2.40.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.42.1`` ``GCC/10.3.0`` ========== ======================================================= @@ -24195,17 +24423,17 @@ Libxslt is the XSLT C library developed for the GNOME project (but usable outsi *homepage*: http://xmlsoft.org/ -========== ================== ================================================================================================ -version versionsuffix toolchain -========== ================== ================================================================================================ -``1.1.28`` ``foss/2016a``, ``intel/2016a`` -``1.1.28`` ``-Python-2.7.11`` ``intel/2016a`` -``1.1.29`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``1.1.30`` ``GCCcore/6.3.0`` -``1.1.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.1.33`` ``GCCcore/8.2.0`` -``1.1.34`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ================== ================================================================================================ +========== ================== ==================================================================================================================== +version versionsuffix toolchain +========== ================== ==================================================================================================================== +``1.1.28`` ``foss/2016a``, ``intel/2016a`` +``1.1.28`` ``-Python-2.7.11`` ``intel/2016a`` +``1.1.29`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``1.1.30`` ``GCCcore/6.3.0`` +``1.1.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.1.33`` ``GCCcore/8.2.0`` +``1.1.34`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ================== ==================================================================================================================== .. _list_software_libxsmm_764: @@ -24451,6 +24679,7 @@ line_profiler is a module for doing line-by-line profiling of functions. kernpro version versionsuffix toolchain ========= ================= ============== ``3.1.0`` ``-Python-3.8.2`` ``foss/2020a`` +``3.5.1`` ``foss/2021b`` ========= ================= ============== @@ -24479,15 +24708,16 @@ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, *homepage*: http://www.littlecms.com/ -======== ============================================================================================================================================== -version toolchain -======== ============================================================================================================================================== -``2.7`` ``intel/2016a`` -``2.8`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``2.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` -``2.11`` ``GCCcore/10.2.0`` -``2.12`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -======== ============================================================================================================================================== +========== ============================================================================================================================================== +version toolchain +========== ============================================================================================================================================== +``2.7`` ``intel/2016a`` +``2.8`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``2.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` +``2.11`` ``GCCcore/10.2.0`` +``2.12`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.13.1`` ``GCCcore/11.3.0`` +========== ============================================================================================================================================== .. _list_software_LLDB_286: @@ -24560,7 +24790,7 @@ version toolchain ``0.9.23`` ``GCCcore/8.2.0`` ``0.9.24`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.9.28`` ``GCCcore/10.3.0`` -``0.9.29`` ``GCCcore/11.2.0`` +``0.9.29`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ======================================================== @@ -24841,7 +25071,7 @@ Mixed Integer Linear Programming (MILP) solver version toolchain ============ ============================================================================================================================================================================================== ``5.5.2.5`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a``, ``intel/2018b`` -``5.5.2.11`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` +``5.5.2.11`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` ============ ============================================================================================================================================================================================== @@ -25141,7 +25371,7 @@ version toolchain --- -:ref:`list_software_M1QN3_336` - :ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_MAGeCK_456` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_matplotlib-inline_1764` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_MEGAN_360` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MNE-Python_911` - :ref:`list_software_MOABS_370` - :ref:`list_software_ModelTest-NG_1107` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MuJoCo_557` - :ref:`list_software_mujoco-py_931` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M1QN3_336` - :ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_MAGeCK_456` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_matplotlib-inline_1764` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_MEGAN_360` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_Minipolish_1052` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_mm-common_912` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MNE-Python_911` - :ref:`list_software_MOABS_370` - :ref:`list_software_ModelTest-NG_1107` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_MONA_299` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MuJoCo_557` - :ref:`list_software_mujoco-py_931` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M1QN3_336: @@ -25421,12 +25651,12 @@ The makedepend package contains a C-preprocessor like utility to determine build *homepage*: https://linux.die.net/man/1/makedepend -========= ======================================================================================= -version toolchain -========= ======================================================================================= -``1.0.5`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``1.0.6`` ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ======================================================================================= +========= =============================================================================================== +version toolchain +========= =============================================================================================== +``1.0.5`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``1.0.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= =============================================================================================== .. _list_software_makedepf90_934: @@ -25667,7 +25897,7 @@ version toolchain MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). -*homepage*: http://www.genome.umd.edu/masurca.html +*homepage*: https://www.genome.umd.edu/masurca.html ========= ================ ============== version versionsuffix toolchain @@ -25678,6 +25908,7 @@ version versionsuffix toolchain ``3.2.5`` ``-Perl-5.26.0`` ``foss/2017b`` ``3.3.1`` ``-Perl-5.28.0`` ``foss/2018b`` ``4.0.1`` ``-Perl-5.30.2`` ``foss/2020a`` +``4.0.9`` ``-Perl-5.32.1`` ``foss/2021a`` ========= ================ ============== @@ -25996,6 +26227,7 @@ version versionsuffix toolchain ``4.6.2`` ``-Python-3.6.6`` ``foss/2018b`` ``4.7.1`` ``-Python-2.7.15`` ``foss/2019a`` ``4.7.1`` ``-Python-3.7.2`` ``foss/2019a`` +``4.7.4`` ``foss/2021b`` ========= ================== =============== @@ -26781,6 +27013,7 @@ MetaEuk is a modular toolkit designed for large-scale gene discovery and annotat version toolchain ======= ============== ``4`` ``GCC/10.2.0`` +``5`` ``GCC/10.3.0`` ======= ============== @@ -27250,6 +27483,22 @@ version toolchain ========== ====================================================== +.. _list_software_Minipolish_1052: + +*Minipolish* +++++++++++++ + +A tool for Racon polishing of miniasm assemblies + +*homepage*: https://github.com/rrwick/Minipolish + +========= ============== +version toolchain +========= ============== +``0.1.3`` ``GCC/11.2.0`` +========= ============== + + .. _list_software_MiniSat_693: *MiniSat* @@ -27521,6 +27770,22 @@ version versionsuffix toolchain ========== ================= ============== +.. _list_software_mm-common_912: + +*mm-common* ++++++++++++ + +The mm-common module provides the build infrastructure and utilities shared among the GNOME C++ binding libraries. + +*homepage*: https://gitlab.gnome.org/GNOME/mm-common + +========= ================== +version toolchain +========= ================== +``1.0.4`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_Mmg_289: *Mmg* @@ -27690,6 +27955,7 @@ version toolchain ``0.9.6`` ``GCCcore/11.2.0`` ``1.0.0`` ``GCCcore/11.2.0`` ``1.2.1`` ``GCCcore/11.3.0`` +``1.3.0`` ``GCCcore/11.3.0`` ========= ================== @@ -27774,6 +28040,22 @@ version versionsuffix toolchain ============= ======================== ========== +.. _list_software_MONA_299: + +*MONA* +++++++ + +MONA is a tool that translates formulas to finite-state automata. The formulas may express search patterns, temporal properties of reactive systems, parse tree constraints, etc. MONA analyses the automaton resulting from the compilation and prints out "valid" or a counter-example. + +*homepage*: https://www.brics.dk/mona/index.html + +========== ============== +version toolchain +========== ============== +``1.4-18`` ``GCC/11.2.0`` +========== ============== + + .. _list_software_mongolite_974: *mongolite* @@ -27945,15 +28227,15 @@ MotionCor2 correct anisotropic image motion at the single pixel level across the *homepage*: https://msg.ucsf.edu/ -========= ================== -version toolchain -========= ================== -``1.2.6`` ``GCCcore/8.2.0`` -``1.3.1`` ``GCCcore/8.3.0`` -``1.3.2`` ``GCCcore/8.3.0`` -``1.4.2`` ``GCCcore/10.2.0`` -``1.4.4`` ``GCCcore/10.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.2.6`` ``GCCcore/8.2.0`` +``1.3.1`` ``GCCcore/8.3.0`` +``1.3.2`` ``GCCcore/8.3.0`` +``1.4.2`` ``GCCcore/10.2.0`` +``1.4.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_motionSegmentation_1924: @@ -28032,17 +28314,17 @@ The MPFR library is a C library for multiple-precision floating-point computati *homepage*: https://www.mpfr.org -========= ================================================================ -version toolchain -========= ================================================================ -``2.4.2`` ``system`` -``3.1.4`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``3.1.5`` ``GCCcore/6.4.0``, ``intel/2017a`` -``3.1.6`` ``GCCcore/6.4.0`` -``4.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``4.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========= ================================================================ +========= ============================================================================== +version toolchain +========= ============================================================================== +``2.4.2`` ``system`` +``3.1.4`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``3.1.5`` ``GCCcore/6.4.0``, ``intel/2017a`` +``3.1.6`` ``GCCcore/6.4.0`` +``4.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``4.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ============================================================================== .. _list_software_mpi4py_611: @@ -28504,7 +28786,7 @@ version versionsuffix toolchain ``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` ``5.3.5`` ``-metis`` ``foss/2020b``, ``intel/2020b`` ``5.4.0`` ``-metis`` ``foss/2021a`` -``5.4.1`` ``-metis`` ``intel/2021b`` +``5.4.1`` ``-metis`` ``foss/2021b``, ``intel/2021b`` ``5.5.0`` ``-metis`` ``foss/2021a`` ========= ============== ================================================================================================================= @@ -28871,7 +29153,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_namedlist_961` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_num2words_945` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numdiff_745` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_namedlist_961` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_NetPyNE_643` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_num2words_945` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numdiff_745` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -29238,21 +29520,22 @@ The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and mul *homepage*: https://developer.nvidia.com/nccl -========== =================== ============================== -version versionsuffix toolchain -========== =================== ============================== -``2.1.4`` ``-CUDA-9.0.176`` ``system`` -``2.2.13`` ``-CUDA-9.2.148.1`` ``system`` -``2.3.7`` ``fosscuda/2018b`` -``2.4.2`` ``gcccuda/2019a`` -``2.4.8`` ``gcccuda/2019b`` -``2.8.3`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0``, ``system`` -``2.8.3`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0``, ``system`` -``2.9.9`` ``-CUDA-11.3.1`` ``system`` -``2.10.3`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` -``2.10.3`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` -``2.11.4`` ``gcccuda/2019b`` -========== =================== ============================== +=========== =================== ============================== +version versionsuffix toolchain +=========== =================== ============================== +``2.1.4`` ``-CUDA-9.0.176`` ``system`` +``2.2.13`` ``-CUDA-9.2.148.1`` ``system`` +``2.3.7`` ``fosscuda/2018b`` +``2.4.2`` ``gcccuda/2019a`` +``2.4.8`` ``gcccuda/2019b`` +``2.8.3`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0``, ``system`` +``2.8.3`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0``, ``system`` +``2.9.9`` ``-CUDA-11.3.1`` ``system`` +``2.10.3`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` +``2.10.3`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` +``2.11.4`` ``gcccuda/2019b`` +``2.12.12`` ``-CUDA-11.7.0`` ``GCCcore/11.3.0`` +=========== =================== ============================== .. _list_software_NCCL-tests_896: @@ -29341,13 +29624,13 @@ NCL is an interpreted language designed specifically for scientific data analysi *homepage*: https://www.ncl.ucar.edu -========= ================================================================================================= -version toolchain -========= ================================================================================================= -``6.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``6.5.0`` ``intel/2018a`` -``6.6.2`` ``foss/2018b``, ``foss/2020a``, ``foss/2021a``, ``intel/2018b``, ``intel/2019b``, ``intel/2020a`` -========= ================================================================================================= +========= ================================================================================================================= +version toolchain +========= ================================================================================================================= +``6.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +``6.5.0`` ``intel/2018a`` +``6.6.2`` ``foss/2018b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``intel/2018b``, ``intel/2019b``, ``intel/2020a`` +========= ================================================================================================================= .. _list_software_ncl_317: @@ -29442,7 +29725,7 @@ Ncview is a visual browser for netCDF format files. Typically you would use ncv version toolchain ========= ====================================================================================================================================================================================== ``2.1.7`` ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``gompi/2019a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b``, ``iomkl/2018b`` -``2.1.8`` ``gompi/2020a``, ``gompi/2021a`` +``2.1.8`` ``gompi/2020a``, ``gompi/2021a``, ``gompi/2021b`` ========= ====================================================================================================================================================================================== @@ -29605,6 +29888,7 @@ version versionsuffix toolchain ``4.7.4`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2020b`` ``4.8.0`` ``gompi/2021a``, ``iimpi/2021a`` ``4.8.1`` ``gompi/2021b``, ``iimpi/2021b`` +``4.9.0`` ``gompi/2022a`` =========== ================ ========================================================================================================================== @@ -29796,6 +30080,22 @@ version toolchain ========= ================================ +.. _list_software_NetPyNE_643: + +*NetPyNE* ++++++++++ + +NetPyNE is an open-source Python package to facilitate the development, parallel simulation, analysis, and optimization of biological neuronal networks using the NEURON simulator. + +*homepage*: http://www.netpyne.org + +=========== ============== +version toolchain +=========== ============== +``1.0.2.1`` ``foss/2021b`` +=========== ============== + + .. _list_software_nettle_652: *nettle* @@ -29817,6 +30117,7 @@ version toolchain ``3.6`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``3.7.2`` ``GCCcore/10.3.0`` ``3.7.3`` ``GCCcore/11.2.0`` +``3.8`` ``GCCcore/11.3.0`` ========= =========================================================================================================================================== @@ -29865,6 +30166,7 @@ version versionsuffix toolchain ``2.5.1`` ``foss/2021a`` ``2.6.2`` ``foss/2020b`` ``2.6.3`` ``foss/2021a``, ``foss/2021b``, ``intel/2021b`` +``2.8.4`` ``foss/2022a`` ========= ================== ======================================================================== @@ -29891,13 +30193,14 @@ version versionsuffix toolchain Empirically-based simulations of neurons and networks of neurons. -*homepage*: http://www.neuron.yale.edu/neuron +*homepage*: https://www.neuron.yale.edu/neuron ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``7.4`` ``intel/2016b`` ``7.6.5`` ``-Python-2.7.15`` ``intel/2018b`` +``7.8.2`` ``foss/2021b`` ========= ================== =============== @@ -30018,21 +30321,21 @@ NGS is a new, domain-specific API for accessing reads, alignments and pileups pr *homepage*: https://github.com/ncbi/ngs -========== =================== ================================== -version versionsuffix toolchain -========== =================== ================================== -``1.2.3`` ``foss/2016b``, ``intel/2016a`` -``1.2.5`` ``foss/2016b`` -``1.3.0`` ``GCCcore/6.4.0``, ``intel/2017a`` -``2.9.1`` ``-Java-1.8.0_162`` ``foss/2018a``, ``intel/2018a`` -``2.9.3`` ``-Java-1.8`` ``foss/2018b`` -``2.10.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` -``2.10.0`` ``-Java-11`` ``GCCcore/8.2.0`` -``2.10.4`` ``-Java-11`` ``GCCcore/8.3.0`` -``2.10.5`` ``GCCcore/9.3.0`` -``2.10.9`` ``GCCcore/10.2.0`` -``2.11.2`` ``GCCcore/11.2.0`` -========== =================== ================================== +========== =================== ====================================== +version versionsuffix toolchain +========== =================== ====================================== +``1.2.3`` ``foss/2016b``, ``intel/2016a`` +``1.2.5`` ``foss/2016b`` +``1.3.0`` ``GCCcore/6.4.0``, ``intel/2017a`` +``2.9.1`` ``-Java-1.8.0_162`` ``foss/2018a``, ``intel/2018a`` +``2.9.3`` ``-Java-1.8`` ``foss/2018b`` +``2.10.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` +``2.10.0`` ``-Java-11`` ``GCCcore/8.2.0`` +``2.10.4`` ``-Java-11`` ``GCCcore/8.3.0`` +``2.10.5`` ``GCCcore/9.3.0`` +``2.10.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.11.2`` ``GCCcore/11.2.0`` +========== =================== ====================================== .. _list_software_NGS-Python_919: @@ -30286,6 +30589,7 @@ version toolchain ========== ================== ``3.10.0`` ``GCCcore/10.3.0`` ``3.10.4`` ``GCCcore/11.2.0`` +``3.10.5`` ``GCCcore/11.3.0`` ========== ================== @@ -30305,6 +30609,7 @@ version toolchain ``2.6.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.6.2`` ``GCCcore/10.2.0`` ``2.7.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.7.1`` ``GCCcore/11.3.0`` ========= =================================================================================================================================================================================================================================================== @@ -30383,6 +30688,7 @@ version toolchain ``14.17.0`` ``GCCcore/10.3.0`` ``14.17.2`` ``GCCcore/10.3.0`` ``14.17.6`` ``GCCcore/11.2.0`` +``16.15.1`` ``GCCcore/11.3.0`` =========== ======================================================= @@ -30539,6 +30845,7 @@ version toolchain ``4.29`` ``GCCcore/10.2.0`` ``4.30`` ``GCCcore/10.3.0`` ``4.32`` ``GCCcore/11.2.0`` +``4.34`` ``GCCcore/11.3.0`` ======== ==================================== @@ -30561,6 +30868,7 @@ version toolchain ``3.57`` ``GCCcore/10.2.0`` ``3.65`` ``GCCcore/10.3.0`` ``3.69`` ``GCCcore/11.2.0`` +``3.79`` ``GCCcore/11.3.0`` ========== ==================================== @@ -30577,6 +30885,7 @@ nsync is a C library that exports various synchronization primitives, such as mu version toolchain ========== ================================================================================================ ``1.24.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.25.0`` ``GCCcore/11.3.0`` ========== ================================================================================================ @@ -30840,6 +31149,7 @@ version toolchain ``1.1.0`` ``fosscuda/2019b`` ``1.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.2.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.0.2`` ``GCCcore/11.3.0`` ========= ====================================== @@ -31125,7 +31435,7 @@ version versionsuffix toolchain ``3.3.0`` ``foss/2020b``, ``fosscuda/2020b`` ``3.3.0`` ``-Python-3.7.4`` ``foss/2019b`` ``4.0.0`` ``foss/2021a`` -``4.0.2`` ``foss/2021a`` +``4.0.2`` ``foss/2021a``, ``foss/2021b`` ========= ================= ================================== @@ -32130,6 +32440,7 @@ version toolchain =========== ================================== ``0.108.5`` ``GCCcore/7.3.0``, ``foss/2018b`` ``0.108.6`` ``GCC/10.3.0``, ``GCCcore/10.2.0`` +``0.108.7`` ``GCC/11.2.0`` =========== ================================== @@ -32168,7 +32479,7 @@ version versionsuffix toolchain ``5.7.1`` ``ffmpi/4.5.0``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021a``, ``iompi/2021a`` ``5.7.1`` ``-CUDA-11.3.1`` ``gompi/2021a`` ``5.8`` ``iimpi/2021b`` -``5.9`` ``gompi/2022.05`` +``5.9`` ``gompi/2022.05``, ``gompi/2022a`` ``5.9`` ``-CUDA-11.3.1`` ``gompi/2021a`` ========= ================ ============================================================================================================================================================================================= @@ -32230,7 +32541,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_panito_651` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parameterized_1389` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patch_528` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_porefoam_857` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_presto_669` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_purge_dups_1086` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyEVTK_515` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_PyFrag_585` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_pyradiomics_1188` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch-Lightning_1690` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_panito_651` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parameterized_1389` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patch_528` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pfind_529` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_porefoam_857` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_presto_669` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_purge_dups_1086` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyEVTK_515` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_PyFrag_585` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_pyradiomics_1188` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch-Lightning_1690` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -32280,6 +32591,7 @@ p4est is a C library to manage a collection (a forest) of multiple connected ada version toolchain ======= =============== ``2.2`` ``intel/2019a`` +``2.8`` ``foss/2021a`` ======= =============== @@ -32686,6 +32998,7 @@ version toolchain ``2.4.1`` ``GCC/8.3.0``, ``intel/2019b`` ``2.4.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` ``2.4.3`` ``GCC/10.2.0``, ``GCC/10.3.0`` +``2.5`` ``GCC/11.2.0`` ========= ====================================== @@ -33289,6 +33602,7 @@ version versionsuffix toolchain ``5.34.0`` ``GCCcore/11.2.0`` ``5.34.0`` ``-minimal`` ``GCCcore/11.2.0`` ``5.34.1`` ``GCCcore/11.3.0`` +``5.34.1`` ``-minimal`` ``GCCcore/11.3.0`` ========== ============= ========================================================================================= @@ -33386,6 +33700,22 @@ version versionsuffix toolchain ========== ================= ============== +.. _list_software_pfind_529: + +*pfind* ++++++++ + +Drop-in replacement for find, implemented for using parallel access and MPI. + +*homepage*: https://github.com/VI4IO/pfind + +============ =============== +version toolchain +============ =============== +``20220613`` ``gompi/2021b`` +============ =============== + + .. _list_software_pftoolsV3_912: *pftoolsV3* @@ -33909,6 +34239,7 @@ version versionsuffix toolchain ``8.3.1`` ``GCCcore/11.2.0`` ``8.3.2`` ``GCCcore/11.2.0`` ``9.1.0`` ``GCCcore/10.3.0`` +``9.1.1`` ``GCCcore/11.3.0`` ========= ================================= =================================================== @@ -34216,7 +34547,7 @@ version versionsuffix toolchain ``1.5.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``1.5.1`` ``-python`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0`` ``1.5.4`` ``-python`` ``GCCcore/10.3.0`` -``1.5.5`` ``-python`` ``GCCcore/11.2.0`` +``1.5.5`` ``-python`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ================== =================================================== @@ -34513,6 +34844,7 @@ version versionsuffix toolchain ``2.7.0`` ``foss/2020b`` ``2.7.2`` ``foss/2021a``, ``intel/2021a`` ``2.7.3`` ``foss/2021b`` +``2.8.0`` ``foss/2021b`` ========= ================== ================================================ @@ -34593,6 +34925,7 @@ version toolchain ``1.10.0`` ``foss/2018b``, ``intel/2018b`` ``1.12.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2020a`` ``1.12.2`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2021a`` +``1.12.3`` ``gompi/2021b`` ========== ===================================================================================== @@ -34694,14 +35027,14 @@ Poppler is a PDF rendering library *homepage*: https://poppler.freedesktop.org -=========== ================= -version toolchain -=========== ================= -``0.70.1`` ``foss/2018b`` -``0.90.1`` ``GCCcore/8.3.0`` -``21.06.1`` ``GCC/10.3.0`` -``22.01.0`` ``GCC/11.2.0`` -=========== ================= +=========== ============================== +version toolchain +=========== ============================== +``0.70.1`` ``foss/2018b`` +``0.90.1`` ``GCCcore/8.3.0`` +``21.06.1`` ``GCC/10.2.0``, ``GCC/10.3.0`` +``22.01.0`` ``GCC/11.2.0`` +=========== ============================== .. _list_software_popscle_758: @@ -35143,6 +35476,7 @@ PRISMS-PF is a powerful, massively parallel finite element code for conducting p version toolchain ========= =============== ``2.1.1`` ``intel/2019a`` +``2.2`` ``foss/2021a`` ========= =============== @@ -35216,6 +35550,7 @@ version toolchain ``7.2.1`` ``GCCcore/10.2.0`` ``8.0.1`` ``GCCcore/10.3.0`` ``8.1.0`` ``GCCcore/11.2.0`` +``9.0.0`` ``GCCcore/11.3.0`` ========= ================================================================================= @@ -35367,6 +35702,7 @@ version toolchain ``3.13.0`` ``GCCcore/9.3.0`` ``3.14.0`` ``GCCcore/10.2.0`` ``3.17.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``3.19.4`` ``GCCcore/11.3.0`` =========== ==================================================================== @@ -35399,6 +35735,7 @@ version versionsuffix toolchain ``3.13.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` ``3.14.0`` ``GCCcore/10.2.0`` ``3.17.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``3.19.4`` ``GCCcore/11.3.0`` ========== ================== ====================================== @@ -36359,6 +36696,7 @@ version versionsuffix toolchain ``0.5.9.5`` ``GCCcore/10.2.0`` ``0.5.9.5`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``0.6.3.1`` ``GCCcore/10.3.0`` +``0.7.0`` ``GCCcore/11.2.0`` =========== ================= ================== @@ -36986,6 +37324,7 @@ version versionsuffix toolchain ``3.1.3b2`` ``-Python-2.7.14`` ``intel/2018a`` ``3.1.3b2`` ``-Python-2.7.15`` ``foss/2018b`` ``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0`` +``3.1.6`` ``GCCcore/11.2.0`` =========== ================== ========================================================= @@ -37055,6 +37394,7 @@ version versionsuffix toolchain ``2.6.1.post1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``3.0.1`` ``GCCcore/10.2.0`` ``3.1.0`` ``GCCcore/10.3.0`` +``3.3.1`` ``GCCcore/11.2.0`` =============== ================= ================== @@ -37501,12 +37841,12 @@ Python bindings to spoa. *homepage*: https://github.com/nanoporetech/pyspoa -========= ================= ============================== -version versionsuffix toolchain -========= ================= ============================== -``0.0.4`` ``-Python-3.7.4`` ``GCC/8.3.0`` -``0.0.8`` ``GCC/10.2.0``, ``GCC/10.3.0`` -========= ================= ============================== +========= ================= ============================================== +version versionsuffix toolchain +========= ================= ============================================== +``0.0.4`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``0.0.8`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0`` +========= ================= ============================================== .. _list_software_pysqlite_891: @@ -37696,7 +38036,7 @@ version versionsuffix toolchain ``2.7.16`` ``GCCcore/8.3.0`` ``2.7.16`` ``-bare`` ``GCCcore/8.3.0`` ``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``2.7.18`` ``-bare`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``2.7.18`` ``-bare`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ``3.5.1`` ``foss/2016a``, ``intel/2016a`` ``3.5.2`` ``foss/2016.04``, ``foss/2016b``, ``intel/2016b`` ``3.5.2`` ``-bare`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` @@ -37816,16 +38156,16 @@ Python Bindings for the Parasail C Library *homepage*: https://github.com/jeffdaily/parasail-python -========== ================== =================================================== -version versionsuffix toolchain -========== ================== =================================================== -``1.1.12`` ``-Python-2.7.14`` ``intel/2018a`` -``1.1.16`` ``-Python-3.6.6`` ``foss/2018b`` -``1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``1.2.2`` ``-Python-3.8.2`` ``intel/2020a`` -``1.2.3`` ``-Python-3.8.2`` ``foss/2020a`` -``1.2.4`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` -========== ================== =================================================== +========== ================== ================================================================== +version versionsuffix toolchain +========== ================== ================================================================== +``1.1.12`` ``-Python-2.7.14`` ``intel/2018a`` +``1.1.16`` ``-Python-3.6.6`` ``foss/2018b`` +``1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``1.2.2`` ``-Python-3.8.2`` ``intel/2020a`` +``1.2.3`` ``-Python-3.8.2`` ``foss/2020a`` +``1.2.4`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2020b`` +========== ================== ================================================================== .. _list_software_python-weka-wrapper3_2008: @@ -37894,6 +38234,7 @@ version versionsuffix toolchain ``1.9.0`` ``-imkl`` ``fosscuda/2020b`` ``1.10.0`` ``foss/2021a``, ``fosscuda/2020b`` ``1.10.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``1.11.0`` ``-CUDA-11.3.1`` ``foss/2021a`` ========== ============================= ================================== @@ -38232,7 +38573,7 @@ version toolchain ========== ============================================================================================================================================================================= ``2015.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``2019.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2020.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2020.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ============================================================================================================================================================================= @@ -38418,6 +38759,7 @@ version toolchain ``5.14.1`` ``GCCcore/9.3.0`` ``5.14.2`` ``GCCcore/10.2.0`` ``5.15.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``5.15.5`` ``GCCcore/11.3.0`` ========== ==================================================================================== @@ -38582,6 +38924,7 @@ version versionsuffix toolchain ``6.6`` ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2019b`` ``6.7`` ``foss/2019b``, ``foss/2020b``, ``foss/2021a``, ``intel/2019b``, ``intel/2021a``, ``iomkl/2019b`` ``6.8`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` +``7.1`` ``foss/2022a``, ``intel/2022a`` ========= ============= ================================================================================================= @@ -38708,6 +39051,7 @@ version toolchain ``6.1.3`` ``foss/2016b``, ``intel/2016b`` ``6.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` ``6.1.5`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``6.2.0`` ``GCCcore/10.3.0`` ========= ==================================================== @@ -38733,7 +39077,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_RaGOO_408` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_RAPSearch2_875` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redis_503` - :ref:`list_software_redis-py_813` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rising_652` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_ruamel.yaml_1127` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_RaGOO_408` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_RAPSearch2_875` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redis_503` - :ref:`list_software_redis-py_813` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_regionmask_1072` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rising_652` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_ruamel.yaml_1127` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -38773,6 +39117,7 @@ version versionsuffix toolchain ``4.1.0`` ``foss/2021a`` ``4.1.2`` ``foss/2021b`` ``4.2.0`` ``foss/2021b`` +``4.2.1`` ``foss/2022a`` ========= ============================= =================================================== @@ -39017,11 +39362,11 @@ A fast JSON parser/generator for C++ with both SAX/DOM style API *homepage*: https://rapidjson.org -========= =============================================================================================== -version toolchain -========= =============================================================================================== -``1.1.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= =============================================================================================== +========= ======================================================================================================================================= +version toolchain +========= ======================================================================================================================================= +``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ======================================================================================================================================= .. _list_software_rapidtide_950: @@ -39098,12 +39443,13 @@ Rasterio reads and writes geospatial raster data. *homepage*: https://github.com/mapbox/rasterio -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``1.1.7`` ``-Python-3.8.2`` ``foss/2020a`` -``1.2.3`` ``foss/2020b`` -========= ================= ============== +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``1.1.7`` ``-Python-3.8.2`` ``foss/2020a`` +``1.2.3`` ``foss/2020b`` +``1.2.10`` ``foss/2021b`` +========== ================= ============== .. _list_software_rasterstats_1216: @@ -39206,12 +39552,13 @@ Ray is a fast and simple framework for building and running distributed applicat *homepage*: https://docs.ray.io/en/latest/ -========= ================= ================== -version versionsuffix toolchain -========= ================= ================== -``0.8.4`` ``-Python-3.7.4`` ``foss/2019b`` -``1.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` -========= ================= ================== +========== ================= ================== +version versionsuffix toolchain +========== ================= ================== +``0.8.4`` ``-Python-3.7.4`` ``foss/2019b`` +``1.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.13.0`` ``foss/2021b`` +========== ================= ================== .. _list_software_Raysect_731: @@ -39387,6 +39734,7 @@ version toolchain ``2020-07-01`` ``GCCcore/8.3.0`` ``2021-06-01`` ``GCCcore/10.2.0`` ``2022-02-01`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2022-06-01`` ``GCCcore/11.3.0`` ============== ====================================== @@ -39399,16 +39747,16 @@ re2c is a free and open-source lexer generator for C and C++. Its main goal is g *homepage*: https://re2c.org/ -========= ================== -version toolchain -========= ================== -``1.1.1`` ``GCCcore/8.2.0`` -``1.2.1`` ``GCCcore/8.3.0`` -``1.3`` ``GCCcore/9.3.0`` -``2.0.3`` ``GCCcore/10.2.0`` -``2.1.1`` ``GCCcore/10.3.0`` -``2.2`` ``GCCcore/11.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.1.1`` ``GCCcore/8.2.0`` +``1.2.1`` ``GCCcore/8.3.0`` +``1.3`` ``GCCcore/9.3.0`` +``2.0.3`` ``GCCcore/10.2.0`` +``2.1.1`` ``GCCcore/10.3.0`` +``2.2`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ====================================== .. _list_software_Reads2snp_882: @@ -39504,6 +39852,7 @@ The Python interface to the Redis key-value store. version toolchain ========= ============== ``4.3.1`` ``foss/2021a`` +``4.3.3`` ``foss/2021b`` ========= ============== @@ -39554,9 +39903,28 @@ version toolchain ``3.9.1`` ``system`` ``3.10.1`` ``system`` ``3.11.0`` ``system`` +``3.11.1`` ``system`` +``3.11.2`` ``system`` ========== ========== +.. _list_software_regionmask_1072: + +*regionmask* +++++++++++++ + +regionmask creates masks of geographical regions. It determines to which geographic region each grid point belongs. + +*homepage*: https://regionmask.readthedocs.io + +========= ================= ============== +version versionsuffix toolchain +========= ================= ============== +``0.9.0`` ``foss/2021b`` +``0.9.0`` ``-Python-3.8.2`` ``foss/2020a`` +========= ================= ============== + + .. _list_software_RegTools_815: *RegTools* @@ -39935,6 +40303,7 @@ version versionsuffix toolchain ``0.0.12`` ``-Python-3.7.2`` ``intel/2019a`` ``0.0.24`` ``-Python-3.7.4`` ``foss/2019b`` ``0.1.1`` ``-Python-3.8.2`` ``foss/2020a`` +``0.11.1`` ``foss/2021b`` ========== ================= =============== @@ -40055,15 +40424,16 @@ version toolchain *RNA-SeQC* ++++++++++ -RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis. +Fast, efficient RNA-Seq metrics for quality control and process optimization -*homepage*: https://software.broadinstitute.org/cancer/cga/rna-seqc +*homepage*: https://github.com/getzlab/rnaseqc ========= =================== ============== version versionsuffix toolchain ========= =================== ============== ``1.1.8`` ``-Java-1.8`` ``foss/2018b`` ``1.1.8`` ``-Java-1.8.0_121`` ``foss/2016b`` +``2.4.2`` ``foss/2021a`` ========= =================== ============== @@ -40694,7 +41064,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_SCGid_426` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_SCopeLoomR_963` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_scPred_609` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_ShengBTE_720` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_SHTns_464` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_skorch_650` - :ref:`list_software_SlamDunk_799` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_slow5tools_1067` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_smooth-topk_1157` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SoXt_398` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_SPM_240` - :ref:`list_software_spoa_435` - :ref:`list_software_SPOTPY_495` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_STRique_685` - :ref:`list_software_Structure_977` - :ref:`list_software_STRUMPACK_698` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SURVIVOR_656` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_samplot_768` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_SCGid_426` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_SCopeLoomR_963` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_scPred_609` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_ShengBTE_720` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_SHTns_464` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SISSO_401` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-pandas_1428` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_skorch_650` - :ref:`list_software_SlamDunk_799` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_slow5tools_1067` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_smooth-topk_1157` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SoXt_398` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_SPM_240` - :ref:`list_software_spoa_435` - :ref:`list_software_SPOTPY_495` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-CCM+_613` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_STRique_685` - :ref:`list_software_Structure_977` - :ref:`list_software_STRUMPACK_698` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SURVIVOR_656` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_SWIPE_392` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -40890,6 +41260,22 @@ version versionsuffix toolchain ========= ================ ========================================================= +.. _list_software_samplot_768: + +*samplot* ++++++++++ + +Plot structural variant signals from many BAMs and CRAMs. + +*homepage*: https://github.com/ryanlayer/samplot + +========= ============== +version toolchain +========= ============== +``1.3.0`` ``foss/2021b`` +========= ============== + + .. _list_software_SAMtools_786: *SAMtools* @@ -41071,7 +41457,7 @@ version versionsuffix toolchain ``2.1.0`` ``-bl`` ``gompi/2020b`` ``2.1.0`` ``-fb`` ``gompi/2021a``, ``gompi/2021b`` ``2.2`` ``-amd`` ``gompi/2020a`` -``2.2.0`` ``-fb`` ``gompi/2022.05`` +``2.2.0`` ``-fb`` ``gompi/2022.05``, ``gompi/2022a`` ========= ================================= ============================================================================================================================================ @@ -41189,6 +41575,7 @@ version toolchain ========== ========== ``2020-4`` ``system`` ``2021-4`` ``system`` +``2022-2`` ``system`` ========== ========== @@ -41365,7 +41752,7 @@ version versionsuffix toolchain ``0.23.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``0.23.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``0.24.2`` ``foss/2021a``, ``intel/2021a`` -``1.0.1`` ``foss/2021b`` +``1.0.1`` ``foss/2021b``, ``intel/2021b`` ========== ================================= ======================================================================== @@ -41477,7 +41864,7 @@ version versionsuffix toolchain ``2021.05`` ``foss/2021a``, ``intel/2021a`` ``2021.10`` ``foss/2021b``, ``intel/2021b`` ``2021.10`` ``-Python-2.7.18`` ``foss/2021b`` -``2022.05`` ``foss/2022.05``, ``intel/2022.05`` +``2022.05`` ``foss/2022.05``, ``foss/2022a``, ``intel/2022.05``, ``intel/2022a`` =========== ================== ======================================================================== @@ -42359,6 +42746,7 @@ version versionsuffix toolchain ``1.7.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ``1.7.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` ``1.8.1.post1`` ``GCC/11.2.0`` +``1.8.2`` ``foss/2021b`` ``1.8a1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` =============== ================= ======================================================= @@ -42570,18 +42958,18 @@ SIESTA is both a method and its computer program implementation, to perform effi *homepage*: http://departments.icmab.es/leem/siesta -=============== ============= =============================== -version versionsuffix toolchain -=============== ============= =============================== -``4.0`` ``foss/2017b``, ``intel/2017a`` -``4.0.1`` ``intel/2017a`` -``4.1-b2`` ``intel/2017a`` -``4.1-b3`` ``intel/2017a`` -``4.1-b4`` ``foss/2018b``, ``intel/2018b`` -``4.1-MaX-1.0`` ``intel/2019b`` -``4.1-MaX-1.0`` ``-PEXSI`` ``intel/2019b`` -``4.1.5`` ``foss/2020a``, ``intel/2020a`` -=============== ============= =============================== +=============== ============= =============================================================== +version versionsuffix toolchain +=============== ============= =============================================================== +``4.0`` ``foss/2017b``, ``intel/2017a`` +``4.0.1`` ``intel/2017a`` +``4.1-b2`` ``intel/2017a`` +``4.1-b3`` ``intel/2017a`` +``4.1-b4`` ``foss/2018b``, ``intel/2018b`` +``4.1-MaX-1.0`` ``intel/2019b`` +``4.1-MaX-1.0`` ``-PEXSI`` ``intel/2019b`` +``4.1.5`` ``foss/2020a``, ``foss/2021a``, ``foss/2021b``, ``intel/2020a`` +=============== ============= =============================================================== .. _list_software_SignalP_686: @@ -42692,18 +43080,19 @@ version versionsuffix toolchain SimpleITK is a simplified programming interface to the algorithms and data structures of the Insight Toolkit (ITK). -*homepage*: http://www.simpleitk.org +*homepage*: https://www.simpleitk.org -========= ================== ============== -version versionsuffix toolchain -========= ================== ============== -``1.1.0`` ``-Python-2.7.15`` ``foss/2018b`` -``1.1.0`` ``-Python-3.6.4`` ``foss/2018a`` -``1.1.0`` ``-Python-3.6.6`` ``foss/2018b`` -``1.2.4`` ``-Python-3.7.4`` ``foss/2019b`` -``2.1.0`` ``foss/2020b`` -``2.1.1`` ``foss/2021a`` -========= ================== ============== +=========== ================== ============== +version versionsuffix toolchain +=========== ================== ============== +``1.1.0`` ``-Python-2.7.15`` ``foss/2018b`` +``1.1.0`` ``-Python-3.6.4`` ``foss/2018a`` +``1.1.0`` ``-Python-3.6.6`` ``foss/2018b`` +``1.2.4`` ``-Python-3.7.4`` ``foss/2019b`` +``2.1.0`` ``foss/2020b`` +``2.1.1`` ``foss/2021a`` +``2.1.1.2`` ``foss/2021b`` +=========== ================== ============== .. _list_software_simpy_562: @@ -42831,6 +43220,22 @@ version versionsuffix toolchain =========== ================== ================================================================ +.. _list_software_SISSO_401: + +*SISSO* ++++++++ + +A data-driven method combining symbolic regression and compressed sensing toward accurate & interpretable models. + +*homepage*: https://github.com/rouyang2017/SISSO + +========= =============== +version toolchain +========= =============== +``3.0.2`` ``iimpi/2021b`` +========= =============== + + .. _list_software_SKESA_375: *SKESA* @@ -42881,6 +43286,22 @@ version toolchain ========= =============== +.. _list_software_sklearn-pandas_1428: + +*sklearn-pandas* +++++++++++++++++ + +This module provides a bridge between Scikit-Learn's machine learning methods and pandas-style Data Frames. In particular, it provides a way to map DataFrame columns to transformations, which are later recombined into features. + +*homepage*: https://github.com/scikit-learn-contrib/sklearn-pandas + +========= ============== +version toolchain +========= ============== +``2.2.0`` ``foss/2021b`` +========= ============== + + .. _list_software_sklearn-som_1132: *sklearn-som* @@ -43286,7 +43707,7 @@ version toolchain ``1.1.6`` ``system`` ``1.1.7`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``intel/2017b`` ``1.1.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``1.1.9`` ``GCCcore/11.2.0`` +``1.1.9`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ============================================================================================================ @@ -43755,11 +44176,12 @@ Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. *homepage*: https://spectralib.org/ -========= ============== -version toolchain -========= ============== -``1.0.0`` ``GCC/10.2.0`` -========= ============== +========= ====================================== +version toolchain +========= ====================================== +``1.0.0`` ``GCC/10.2.0`` +``1.0.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ====================================== .. _list_software_spectral.methods_1664: @@ -44003,14 +44425,14 @@ Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) alg *homepage*: https://github.com/rvaser/spoa -========= ============================== -version toolchain -========= ============================== -``3.0.1`` ``GCC/7.3.0-2.30`` -``3.4.0`` ``GCC/10.2.0`` -``4.0.0`` ``GCC/8.3.0`` -``4.0.7`` ``GCC/10.2.0``, ``GCC/10.3.0`` -========= ============================== +========= ============================================== +version toolchain +========= ============================================== +``3.0.1`` ``GCC/7.3.0-2.30`` +``3.4.0`` ``GCC/10.2.0`` +``4.0.0`` ``GCC/8.3.0`` +``4.0.7`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0`` +========= ============================================== .. _list_software_SPOTPY_495: @@ -44394,6 +44816,22 @@ version toolchain ========== ============================================================== +.. _list_software_STAR-CCM+_613: + +*STAR-CCM+* ++++++++++++ + +STAR-CCM+ is a complete multidisciplinary platform for the simulation of products and designs operating under real-world conditions. + +*homepage*: https://mdx.plm.automation.siemens.com/star-ccm-plus + +============= ========== +version toolchain +============= ========== +``13.04.011`` ``system`` +============= ========== + + .. _list_software_STAR-Fusion_987: *STAR-Fusion* @@ -45069,6 +45507,22 @@ version versionsuffix toolchain ========== ============================ ================================================================ +.. _list_software_SWIPE_392: + +*SWIPE* ++++++++ + +Smith-Waterman database searches with inter-sequence SIMD parallelisation + +*homepage*: https://github.com/torognes/swipe + +========= ============== +version toolchain +========= ============== +``2.1.1`` ``GCC/10.3.0`` +========= ============== + + .. _list_software_swissknife_1094: *swissknife* @@ -45190,7 +45644,7 @@ Szip compression software, providing lossless compression of scientific data version toolchain ========= ============================================================================================================================================================================================================================================================================================= ``2.1`` ``GCC/4.8.1``, ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``gmpolf/2017.10``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================================================================================================================================================================================================= @@ -45200,7 +45654,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TALYS_397` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboard_1187` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_termcolor_983` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_ThemisPy_819` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmap_434` - :ref:`list_software_tmux_462` - :ref:`list_software_TN93_270` - :ref:`list_software_TOBIAS_450` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` +:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TALYS_397` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboard_1187` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_termcolor_983` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_ThemisPy_819` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmap_434` - :ref:`list_software_tmux_462` - :ref:`list_software_TN93_270` - :ref:`list_software_TOBIAS_450` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_topaz_558` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` .. _list_software_tabix_536: @@ -45470,13 +45924,13 @@ TCLAP is a small, flexible library that provides a simple interface for defining *homepage*: http://tclap.sourceforge.net/ -========= ===================================== -version toolchain -========= ===================================== -``1.2.2`` ``GCCcore/8.3.0`` -``1.2.4`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``1.2.5`` ``GCCcore/11.2.0`` -========= ===================================== +========= ====================================== +version toolchain +========= ====================================== +``1.2.2`` ``GCCcore/8.3.0`` +``1.2.4`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.2.5`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== .. _list_software_tcsh_434: @@ -45648,6 +46102,8 @@ version versionsuffix toolchain ``2.5.3`` ``-CUDA-11.3.1`` ``foss/2021a`` ``2.6.0`` ``foss/2021a`` ``2.6.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``2.7.1`` ``foss/2021b`` +``2.7.1`` ``-CUDA-11.4.1`` ``foss/2021b`` ========== ============================= =================================================== @@ -45741,12 +46197,12 @@ Tesseract is an optical character recognition engine *homepage*: https://github.com/tesseract-ocr/tesseract -========= ================= -version toolchain -========= ================= -``4.0.0`` ``GCCcore/7.3.0`` -``4.1.0`` ``GCCcore/8.2.0`` -========= ================= +========= ===================================== +version toolchain +========= ===================================== +``4.0.0`` ``GCCcore/7.3.0`` +``4.1.0`` ``GCCcore/10.3.0``, ``GCCcore/8.2.0`` +========= ===================================== .. _list_software_testpath_877: @@ -46110,6 +46566,7 @@ version versionsuffix toolchain ``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``8.6.10`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``8.6.11`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``8.6.12`` ``GCCcore/11.3.0`` ========== ================= ================================================================================================================================================ @@ -46142,6 +46599,7 @@ version versionsuffix toolchain ``3.8.6`` ``GCCcore/10.2.0`` ``3.9.5`` ``GCCcore/10.3.0`` ``3.9.6`` ``GCCcore/11.2.0`` +``3.10.4`` ``GCCcore/11.3.0`` ========== ================== ========================================================================================================= @@ -46316,6 +46774,23 @@ version toolchain ========= ======================================= +.. _list_software_topaz_558: + +*topaz* ++++++++ + +A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph denoising using deep de- noising models. + +*homepage*: https://github.com/tbepler/topaz + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``0.2.5`` ``foss/2021a`` +``0.2.5`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== + + .. _list_software_TopHat_592: *TopHat* @@ -46522,11 +46997,12 @@ State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0 *homepage*: https://github.com/huggingface/transformers -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``4.2.1`` ``-Python-3.8.2`` ``foss/2020a`` -========= ================= ============== +========== ================= ============== +version versionsuffix toolchain +========== ================= ============== +``4.2.1`` ``-Python-3.8.2`` ``foss/2020a`` +``4.20.1`` ``foss/2021a`` +========== ================= ============== .. _list_software_Transrate_948: @@ -47046,7 +47522,7 @@ version versionsuffix toolchain --- -:ref:`list_software_UCC_219` - :ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_UCX-CUDA_570` - :ref:`list_software_ucx-py_614` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_unimap_650` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_UShER_423` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` +:ref:`list_software_UCC_219` - :ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_UCX-CUDA_570` - :ref:`list_software_ucx-py_614` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_uncertainty-calibration_2411` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_unimap_650` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_UShER_423` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` .. _list_software_UCC_219: @@ -47125,6 +47601,7 @@ version versionsuffix toolchain ``1.10.0`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` ``1.11.0`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` ``1.11.2`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` +``1.12.1`` ``-CUDA-11.7.0`` ``GCCcore/11.3.0`` ========== ================ ================== @@ -47177,7 +47654,7 @@ version toolchain ``2.2.24`` ``intel/2017a`` ``2.2.25`` ``foss/2017b``, ``intel/2017b`` ``2.2.26`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``2.2.28`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.2.28`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== =============================================================================================================================================================================================== @@ -47280,6 +47757,22 @@ version versionsuffix toolchain ======= ================ =============== +.. _list_software_uncertainty-calibration_2411: + +*uncertainty-calibration* ++++++++++++++++++++++++++ + +Python library to measure the calibration error of models, including confidence intervals computed by Bootstrap resampling, and code to recalibrate models. + +*homepage*: https://github.com/p-lambda/verified_calibration + +========= ============== +version toolchain +========= ============== +``0.0.9`` ``foss/2021b`` +========= ============== + + .. _list_software_Unicycler_942: *Unicycler* @@ -47480,6 +47973,7 @@ version toolchain ``2.3.0`` ``GCCcore/8.2.0`` ``2.5.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.6.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.7.0`` ``GCCcore/11.3.0`` ========= ======================================================== @@ -47521,7 +48015,7 @@ version toolchain --- -:ref:`list_software_V8_142` - :ref:`list_software_Vala_388` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_Vampire_724` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_vawk_441` - :ref:`list_software_VBZ-Compression_1457` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcflib_630` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VisPy_507` - :ref:`list_software_VMD_231` - :ref:`list_software_VMTK_322` - :ref:`list_software_voltools_898` - :ref:`list_software_vorbis-tools_1267` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` +:ref:`list_software_V8_142` - :ref:`list_software_Vala_388` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_Vampire_724` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_vawk_441` - :ref:`list_software_VBZ-Compression_1457` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcflib_630` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_Virtuoso-opensource_2011` - :ref:`list_software_VisPy_507` - :ref:`list_software_VMD_231` - :ref:`list_software_VMTK_322` - :ref:`list_software_voltools_898` - :ref:`list_software_vorbis-tools_1267` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` .. _list_software_V8_142: @@ -48009,6 +48503,22 @@ version toolchain ========= ================= +.. _list_software_Virtuoso-opensource_2011: + +*Virtuoso-opensource* ++++++++++++++++++++++ + +Virtuoso is a high-performance and scalable Multi-Model RDBMS, Data Integration Middleware, Linked Data Deployment, and HTTP Application Server Platform. + +*homepage*: https://github.com/openlink/virtuoso-opensource + +=========== ============== +version toolchain +=========== ============== +``7.2.6.1`` ``GCC/10.3.0`` +=========== ============== + + .. _list_software_VisPy_507: *VisPy* @@ -48265,11 +48775,11 @@ A tool set for short variant discovery in genetic sequence data. *homepage*: http://genome.sph.umich.edu/wiki/Vt -=========== ============================================================= -version toolchain -=========== ============================================================= -``0.57721`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/9.3.0``, ``foss/2018b`` -=========== ============================================================= +=========== ============================================================================= +version toolchain +=========== ============================================================================= +``0.57721`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0``, ``foss/2018b`` +=========== ============================================================================= .. _list_software_VTK_245: @@ -48623,6 +49133,7 @@ WhatsHap is a software for phasing genomic variants using DNA sequencing reads, version toolchain ======= ============================== ``1.1`` ``foss/2020b``, ``foss/2021a`` +``1.4`` ``foss/2021b`` ======= ============================== @@ -48679,11 +49190,11 @@ Wild Magic 5.17 *homepage*: https://www.geometrictools.com/index.html -======== ============== -version toolchain -======== ============== -``5.17`` ``foss/2018b`` -======== ============== +======== ================================== +version toolchain +======== ================================== +``5.17`` ``GCCcore/10.3.0``, ``foss/2018b`` +======== ================================== .. _list_software_Winnowmap_960: @@ -48789,6 +49300,7 @@ WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WR version versionsuffix toolchain ========= ============= =============== ``3.8.0`` ``-dmpar`` ``intel/2016a`` +``3.9.1`` ``-dmpar`` ``foss/2020b`` ``4.0.1`` ``-dmpar`` ``intel/2018b`` ``4.0.2`` ``-dmpar`` ``foss/2018b`` ``4.1`` ``-dmpar`` ``intel/2019b`` @@ -49722,6 +50234,7 @@ version toolchain ``1.20.9`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``1.20.11`` ``GCCcore/10.3.0`` ``1.20.13`` ``GCCcore/11.2.0`` +``21.1.3`` ``GCCcore/11.3.0`` =========== ===================================== diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index 99c9de7d..f535af5b 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -246,6 +246,7 @@ * EB_SAS * EB_SCOTCH * EB_SNPhylo + * EB_STAR_minus_CCM_plus_ * EB_TINKER * EB_Trinity * EB_VEP diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index e8a6675a..7ac56ffa 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -260,6 +260,7 @@ Option flag Opt ``--allow-modules-tool-mismatch`` Allow mismatch of modules tool and definition of 'module' function (default: False) ``--allow-use-as-root-and-accept-consequences`` Allow using of EasyBuild as root (NOT RECOMMENDED!) (default: False) ``--backup-modules`` Back up an existing module file, if any. Only works when using --module-only +``--backup-patched-files`` Create a backup (*.orig) file when applying a patch (default: False) ``--banned-linked-shared-libs=BANNED-LINKED-SHARED-LIBS`` Comma-separated list of shared libraries (names, file names, or paths) which are not allowed to be linked in any installed binary/library (type comma-separated list) ``--check-ebroot-env-vars=CHECK-EBROOT-ENV-VARS`` Action to take when defined $EBROOT* environment variables are found for which there is no matching loaded module; supported values: error, ignore, unset, warn (default: warn) ``--cleanup-builddir`` Cleanup build dir after successful installation. (default: True; disable with --disable-cleanup-builddir) diff --git a/docs/version-specific/toolchain_opts.rst b/docs/version-specific/toolchain_opts.rst index 3cc874f1..b0534e95 100644 --- a/docs/version-specific/toolchain_opts.rst +++ b/docs/version-specific/toolchain_opts.rst @@ -2569,6 +2569,7 @@ option description ``lowopt`` Low compiler optimizations ``False`` ``no-icc`` Don't set Intel specific macros ``False`` ``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` ``optarch`` Enable architecture optimizations ``True`` @@ -2615,6 +2616,7 @@ option description ``lowopt`` Low compiler optimizations ``False`` ``no-icc`` Don't set Intel specific macros ``False`` ``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` ``optarch`` Enable architecture optimizations ``True`` @@ -2751,6 +2753,7 @@ option description ``lowopt`` Low compiler optimizations ``False`` ``no-icc`` Don't set Intel specific macros ``False`` ``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` ``optarch`` Enable architecture optimizations ``True`` @@ -2981,6 +2984,7 @@ option description ``lowopt`` Low compiler optimizations ``False`` ``no-icc`` Don't set Intel specific macros ``False`` ``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` ``optarch`` Enable architecture optimizations ``True`` @@ -3072,6 +3076,7 @@ option description ``lowopt`` Low compiler optimizations ``False`` ``no-icc`` Don't set Intel specific macros ``False`` ``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` ``optarch`` Enable architecture optimizations ``True`` @@ -3164,6 +3169,7 @@ option description ``lowopt`` Low compiler optimizations ``False`` ``no-icc`` Don't set Intel specific macros ``False`` ``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` ``optarch`` Enable architecture optimizations ``True`` @@ -3256,6 +3262,7 @@ option description ``lowopt`` Low compiler optimizations ``False`` ``no-icc`` Don't set Intel specific macros ``False`` ``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` ``optarch`` Enable architecture optimizations ``True`` From 891e7ef146e441b8135c8d9c49d62d0a133beb2d Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 7 Jul 2022 22:05:58 +0200 Subject: [PATCH 226/286] update release notes and changelog for EasyBuild v4.6.0 + bump version to 4.6.0 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 108 +++++++++++++++++++++++++++++++++++++++-- docs/conf.py | 4 +- 3 files changed, 108 insertions(+), 5 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index a8b6842e..b3c53c4f 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20220708.01** (`Jul 8th 2022`): update release notes for EasyBuild v4.6.0 (see :ref:`release_notes_eb460`) * **release 20220608.01** (`Jun 8th 2022`): update release notes for EasyBuild v4.5.5 (see :ref:`release_notes_eb455`) * **release 20220331.01** (`Mar 31st 2022`): update release notes for EasyBuild v4.5.4 (see :ref:`release_notes_eb454`) * **release 20220211.01** (`Feb 11th 2022`): update release notes for EasyBuild v4.5.3 (see :ref:`release_notes_eb453`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 8d0a1f40..b8348d01 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,114 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,711** different software packages, -including 36 different (compiler) toolchains. It contains 244 software-specific easyblocks and 37 generic easyblocks, -alongside 14,816 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,736** different software packages, +including 37 different (compiler) toolchains. It contains 246 software-specific easyblocks and 37 generic easyblocks, +alongside 15,020 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb460: + +EasyBuild v4.6.0 (July 8th 2022) +-------------------------------- + +feature release + +**framework** + +* various enhancements, including: + + * allow searching for sources/patches in alternative location by specifying 'alt_location' in source/patch spec (`#3994 `_) + * show URLs used for download attempts in trace output (`#4026 `_) + * add support for setting environment variables via 'pushenv' with modextravars (`#4030 `_) + * add support for OneAPI compilers using toolchain option 'oneapi' (`#4031 `_, `#4032 `_, `#4039 `_) + * make check_linked_shared_libs more robust by taking into account that 'ldd' may fail (`#4033 `_) + * fall back to sequential extension install if parallel install is not implemented (`#4034 `_) + * add support for using template values in name/version of extensions (`#4036 `_) + +* various bug fixes, including: + + * make sure that ARCH constant has 'aarch64' (rather than 'arm64') as value on macOS ARM (`#4018 `_) + * tweak 'eb' wrapper script to correctly handle errors when python command being considered fails to run (`#4019 `_) + * tweak is_patch_for function to make it more robust (`#4028 `_) + +* other changes: + + * update Lmod used to run tests to version 8.7.6 (`#4027 `_, `#4030 `_) + * tweak apply_patch to not create .orig files (by default) when applying patch files (`#4038 `_) + +**easyblocks** + +* new software-specific easyblock for STAR-CCM+ (`#1613 `_) + +* minor enhancements and updates, including: + + * update Siesta EasyBlock to support GCC 10+ by adding -fallow-argument-mismatch Fortran compiler option (`#2690 `_) + * enable building of shared library for Libint 2.7+ (`#2738 `_) + * allow some PyTorch tests to fail + print warning if one or more tests fail (`#2742 `_) + * also support OpenSSL 3.0 in OpenSSL wrapper easyblock (`#2746 `_) + * add more logging to install_pc_files method of OpenSSL wrapper easyblock (`#2752 `_) + * make WPS easyblock aware of (pre)buildopts (`#2754 `_) + * add Abseil system dependency for TensorFlow 2.9+ (`#2757 `_) + * disable altivec when building FFTW versions < 3.4 with single-precision with GCC on POWER (`#2758 `_) + +* various bug fixes, including: + + * make VEP easyblock compatible with --sanity-check-only (`#2743 `_) + * update Rosetta easyblock to take into account that $LD_LIBRARY_PATH, $CPATH, $PATH may not be defined (`#2744 `_) + * only load temporary module file during sanity check for pybind11 for stand-alone installations, so it can be installed as extension (`#2747 `_) + * make sure that CMakeMakeCp uses correct build dir (`#2748 `_) + * enhance Bazel easyblock to avoid writing to $HOME in sanity check (`#2756 `_) + +**easyconfigs** + +* added easyconfigs for foss/2022a, intel/2022a common toolchains (`#15755 `_) +* add easyconfig for gfbf/2022a toolchain (`#15653 `_, `#15755 `_) + + * see also https://docs.easybuild.io/en/latest/Common-toolchains.html + +* added example easyconfig files for 24 new software packages: + + * BLT (`#15624 `_), category_encoders (`#15638 `_), fio (`#10321 `_), FSON (`#15721 `_), G-PhoCS (`#7619 `_), GCTA (`#15649 `_), + Gibbs2 (`#15702 `_), InterProScan_data (`#15717 `_), Jorg (`#15346 `_), libopus (`#15682 `_), Minipolish (`#15713 `_), + mm-common (`#15764 `_), MONA (`#15696 `_), NetPyNE (`#15606 `_), pfind (`#15685 `_), regionmask (`#15786 `_), samplot (`#15686 `_), + SISSO (`#15766 `_), sklearn-pandas (`#15637 `_), STAR-CCM+ (`#7398 `_), SWIPE (`#6795 `_), topaz (`#15739 `_), + uncertainty-calibration (`#15612 `_), Virtuoso-opensource (`#14102 `_) + +* added additional easyconfigs for various supported software packages, including: + + * AlphaFold 2.2.2, Arriba 2.3.0, Arrow 8.0.0, Bracken 2.7, CellRanger 7.0.0, Clp 1.17.7, CoinUtils 2.11.6, + cppy 1.2.1, deal.II 9.3.3, double-conversion 3.2.0, Doxygen 1.9.4, FLAC 1.3.4, fmt 7.1.1, FSL 6.0.5.1, GDAL 3.5.0, + gdbm 1.21, geopandas 0.11.0, GEOS 3.10.3, Ghostscript 9.56.1, GLibmm 2.66.4, Groovy 4.0.3, GULP 6.1, h5py 3.7.0, + HDF5 1.13.1, hifiasm 0.16.1, IGMPlot 2.6.9b, ImageMagick 7.1.0-37, InterProScan 5.55-88.0, IRkernel 1.3, + jemalloc 5.3.0, JsonCpp 1.9.5, Julia 1.7.3, Leptonica 1.82.0, libgeotiff 1.7.1, libgit2 1.4.3, libiconv 1.17, + libRmath 4.2.0, libsigc++ 2.10.8, libsndfile 1.1.0, libxc 5.2.3, libxml++ 2.42.1, line_profiler 3.5.1, + LittleCMS 2.13.1, MaSuRCA 4.0.9, mayavi 4.7.4, MetaEuk 5, mold 1.3.0, NCCL 2.12.12, netCDF 4.9.0, nettle 3.8, + networkx 2.8.4, NEURON 7.8.2, NLopt 2.7.1, nodejs 16.15.1, NSPR 4.34, NSS 3.79, nsync 1.25.0, nvtop 2.0.2, + Osi 0.108.7, p4est 2.8, parasail 2.5, Pillow 9.1.1, PLUMED 2.8.0, PnetCDF 1.12.3, PRISMS-PF 2.2, PROJ 9.0.0, + protobuf 3.19.4, protobuf-python 3.19.4, pyfaidx 0.7.0, PyOpenGL 3.1.6, pyproj 3.3.1, PyTorch 1.11.0, Qhull 2020.2, + Qt5 5.15.5, QuantumESPRESSO 7.1, Qwt 6.2.0, R 4.2.1, rasterio 1.2.10, Ray-project 1.13.0, RE2 2022-06-01, + redis-py 4.3.3, ReFrame 3.11.2, rioxarray 0.11.1, RNA-SeQC 2.4.2, Schrodinger 2022-2, Shapely 1.8.2, Siesta 4.1.5, + SimpleITK 2.1.1.2, SpectrA 1.0.1, TensorFlow 2.7.1, Tk 8.6.12, Tkinter 3.10.4, Transformers 4.20.1, + UCX-CUDA 1.12.1, utf8proc 2.7.0, WhatsHap 1.4, WPS 3.9.1, Xvfb 21.1.3 + +* minor enhancements, including: + + * add extensions to R v4.2.0: hypergeo (`#15701 `_), rtdists (`#15734 `_), geeM (`#15810 `_) + * add patch for GCCcore 11.3.0 to support using -fuse-ld=mold (`#15715 `_) + * add patch for porefoam to fix hardcoded mpirun command and take into account $POREFOAM_MPIRUN_CMD (`#15730 `_) +* various bug fixes, including: + * switch to Rust 1.60.0 build dependency for bamtofastq, since build of fails with Rust 1.52.1 (`#15636 `_) + * avoid that pygmo v2.18.0 installs stuff in Python installation directory + add custom sanity check paths to pygmo easyconfigs (`#15657 `_) + * add patch for Mmg v5.6.0 to remove library CI tests that point to external sources (`#15691 `_) + * correct configopts in deal.II v9.1.1 easyconfig (`#15692 `_) + * add missing Python dependency for HPDBSCAN to fix unresolved %(pyshortver)s template (`#15694 `_) + +* other changes: + + * disable flaky GPU test for TensorFlow 2.6.0 (`#15824 `_) + + .. _release_notes_eb455: EasyBuild v4.5.5 (June 8th 2022) diff --git a/docs/conf.py b/docs/conf.py index ef73c784..e2d56add 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.5.5' # this is meant to reference the version of EasyBuild +version = '4.6.0' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20220608.0' # this is meant to reference the version of the documentation itself +release = '20220708.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From b3a6406453d9b419e95505a22a3ee47e81499bd8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Jul 2022 08:38:26 +0200 Subject: [PATCH 227/286] minor formatting changes for EasyBuild v4.6.0 release notes --- docs/Release_notes.rst | 43 +++++++++++++++++++++--------------------- 1 file changed, 22 insertions(+), 21 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index b8348d01..1703b707 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -20,24 +20,24 @@ feature release * various enhancements, including: - * allow searching for sources/patches in alternative location by specifying 'alt_location' in source/patch spec (`#3994 `_) + * allow searching for sources/patches in alternative location by specifying '``alt_location``' in source/patch spec (`#3994 `_) * show URLs used for download attempts in trace output (`#4026 `_) - * add support for setting environment variables via 'pushenv' with modextravars (`#4030 `_) - * add support for OneAPI compilers using toolchain option 'oneapi' (`#4031 `_, `#4032 `_, `#4039 `_) - * make check_linked_shared_libs more robust by taking into account that 'ldd' may fail (`#4033 `_) + * add support for setting environment variables via '``pushenv``' with ``modextravars`` (`#4030 `_) + * add support for OneAPI compilers using toolchain option '``oneapi``' (`#4031 `_, `#4032 `_, `#4039 `_) + * make ``check_linked_shared_libs`` more robust by taking into account that '``ldd``' may fail (`#4033 `_) * fall back to sequential extension install if parallel install is not implemented (`#4034 `_) * add support for using template values in name/version of extensions (`#4036 `_) * various bug fixes, including: - * make sure that ARCH constant has 'aarch64' (rather than 'arm64') as value on macOS ARM (`#4018 `_) - * tweak 'eb' wrapper script to correctly handle errors when python command being considered fails to run (`#4019 `_) - * tweak is_patch_for function to make it more robust (`#4028 `_) + * make sure that ``ARCH`` constant has '``aarch64``' (rather than '``arm64``') as value on macOS ARM (`#4018 `_) + * tweak '``eb``' wrapper script to correctly handle errors when python command being considered fails to run (`#4019 `_) + * tweak ``is_patch_for`` function to make it more robust (`#4028 `_) * other changes: * update Lmod used to run tests to version 8.7.6 (`#4027 `_, `#4030 `_) - * tweak apply_patch to not create .orig files (by default) when applying patch files (`#4038 `_) + * tweak ``apply_patch`` to not create ``.orig files`` (by default) when applying patch files (`#4038 `_) **easyblocks** @@ -45,30 +45,31 @@ feature release * minor enhancements and updates, including: - * update Siesta EasyBlock to support GCC 10+ by adding -fallow-argument-mismatch Fortran compiler option (`#2690 `_) + * update Siesta EasyBlock to support GCC 10+ by adding ``-fallow-argument-mismatch`` Fortran compiler option (`#2690 `_) * enable building of shared library for Libint 2.7+ (`#2738 `_) * allow some PyTorch tests to fail + print warning if one or more tests fail (`#2742 `_) * also support OpenSSL 3.0 in OpenSSL wrapper easyblock (`#2746 `_) - * add more logging to install_pc_files method of OpenSSL wrapper easyblock (`#2752 `_) - * make WPS easyblock aware of (pre)buildopts (`#2754 `_) + * add more logging to ``install_pc_files`` method of OpenSSL wrapper easyblock (`#2752 `_) + * make WPS easyblock aware of ``(pre)buildopts`` (`#2754 `_) * add Abseil system dependency for TensorFlow 2.9+ (`#2757 `_) * disable altivec when building FFTW versions < 3.4 with single-precision with GCC on POWER (`#2758 `_) * various bug fixes, including: - * make VEP easyblock compatible with --sanity-check-only (`#2743 `_) - * update Rosetta easyblock to take into account that $LD_LIBRARY_PATH, $CPATH, $PATH may not be defined (`#2744 `_) + * make VEP easyblock compatible with ``--sanity-check-only`` (`#2743 `_) + * update Rosetta easyblock to take into account that ``$LD_LIBRARY_PATH``, ``$CPATH``, ``$PATH`` may not be defined (`#2744 `_) * only load temporary module file during sanity check for pybind11 for stand-alone installations, so it can be installed as extension (`#2747 `_) - * make sure that CMakeMakeCp uses correct build dir (`#2748 `_) - * enhance Bazel easyblock to avoid writing to $HOME in sanity check (`#2756 `_) + * make sure that ``CMakeMakeCp`` uses correct build dir (`#2748 `_) + * enhance Bazel easyblock to avoid writing to ``$HOME`` in sanity check (`#2756 `_) **easyconfigs** -* added easyconfigs for foss/2022a, intel/2022a common toolchains (`#15755 `_) -* add easyconfig for gfbf/2022a toolchain (`#15653 `_, `#15755 `_) +* added easyconfigs for ``foss/2022a``, ``intel/2022a`` common toolchains (`#15755 `_) * see also https://docs.easybuild.io/en/latest/Common-toolchains.html +* add easyconfig for ``gfbf/2022a`` toolchain (`#15653 `_, `#15755 `_) + * added example easyconfig files for 24 new software packages: * BLT (`#15624 `_), category_encoders (`#15638 `_), fio (`#10321 `_), FSON (`#15721 `_), G-PhoCS (`#7619 `_), GCTA (`#15649 `_), @@ -97,14 +98,14 @@ feature release * minor enhancements, including: * add extensions to R v4.2.0: hypergeo (`#15701 `_), rtdists (`#15734 `_), geeM (`#15810 `_) - * add patch for GCCcore 11.3.0 to support using -fuse-ld=mold (`#15715 `_) - * add patch for porefoam to fix hardcoded mpirun command and take into account $POREFOAM_MPIRUN_CMD (`#15730 `_) + * add patch for GCCcore 11.3.0 to support using ``-fuse-ld=mold`` (`#15715 `_) + * add patch for porefoam to fix hardcoded ``mpirun`` command and take into account ``$POREFOAM_MPIRUN_CMD`` (`#15730 `_) * various bug fixes, including: - * switch to Rust 1.60.0 build dependency for bamtofastq, since build of fails with Rust 1.52.1 (`#15636 `_) + * switch to Rust 1.60.0 build dependency for bamtofastq, since build fails with Rust 1.52.1 (`#15636 `_) * avoid that pygmo v2.18.0 installs stuff in Python installation directory + add custom sanity check paths to pygmo easyconfigs (`#15657 `_) * add patch for Mmg v5.6.0 to remove library CI tests that point to external sources (`#15691 `_) * correct configopts in deal.II v9.1.1 easyconfig (`#15692 `_) - * add missing Python dependency for HPDBSCAN to fix unresolved %(pyshortver)s template (`#15694 `_) + * add missing Python dependency for HPDBSCAN to fix unresolved ``%(pyshortver)s`` template (`#15694 `_) * other changes: From 6ed09459ccbb64131d9245f2dc695b8751d77b11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Jul 2022 08:40:29 +0200 Subject: [PATCH 228/286] add missing empty lines to fix list formatting in EasyBuild v4.6.0 release notes --- docs/Release_notes.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 1703b707..d8adb1a8 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -69,7 +69,6 @@ feature release * see also https://docs.easybuild.io/en/latest/Common-toolchains.html * add easyconfig for ``gfbf/2022a`` toolchain (`#15653 `_, `#15755 `_) - * added example easyconfig files for 24 new software packages: * BLT (`#15624 `_), category_encoders (`#15638 `_), fio (`#10321 `_), FSON (`#15721 `_), G-PhoCS (`#7619 `_), GCTA (`#15649 `_), @@ -100,7 +99,9 @@ feature release * add extensions to R v4.2.0: hypergeo (`#15701 `_), rtdists (`#15734 `_), geeM (`#15810 `_) * add patch for GCCcore 11.3.0 to support using ``-fuse-ld=mold`` (`#15715 `_) * add patch for porefoam to fix hardcoded ``mpirun`` command and take into account ``$POREFOAM_MPIRUN_CMD`` (`#15730 `_) + * various bug fixes, including: + * switch to Rust 1.60.0 build dependency for bamtofastq, since build fails with Rust 1.52.1 (`#15636 `_) * avoid that pygmo v2.18.0 installs stuff in Python installation directory + add custom sanity check paths to pygmo easyconfigs (`#15657 `_) * add patch for Mmg v5.6.0 to remove library CI tests that point to external sources (`#15691 `_) From 96531e4595b4d8f08157c8cd3ae0e065f9be6087 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Jul 2022 10:08:04 +0200 Subject: [PATCH 229/286] bump version to 4.6.0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 1e1f973c..f93b4316 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.5.5' +VERSION = '4.6.0' # Utility function to read README file From 24fe67f459f1d9919cfab7eb98f01f581572afad Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sun, 21 Aug 2022 14:57:19 +0800 Subject: [PATCH 230/286] add Sebastian as release manager --- docs/Maintainers.rst | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/docs/Maintainers.rst b/docs/Maintainers.rst index b66351db..54b5d366 100644 --- a/docs/Maintainers.rst +++ b/docs/Maintainers.rst @@ -35,15 +35,19 @@ Roles .. _maintainers_release_manager: -Release manager -~~~~~~~~~~~~~~~ +Release managers +~~~~~~~~~~~~~~~~ -The release manager is responsible for releasing new stable EasyBuild versions on a regular basis, +The release managers are responsible for releasing new stable EasyBuild versions on a regular basis, with the help of the other EasyBuild maintainers. -Miguel & Kenneth are working together to get EasyBuild releases out the door on a regular basis +Sebastian, Miguel & Kenneth have been working together to get EasyBuild releases out the door on a regular basis (about once every 6 weeks, see https://pypi.org/project/easybuild/#history). +* **Sebastian Achilles** (`JSC `_) + + * GitHub: `@SebastianAchilles `_ - e-mail: ``s.achilles (at) fz-juelich.de`` - IRC/Slack: ``Sebastian Achilles`` + * **Miguel Dias Costa** (National University of Singapore) * GitHub: `@migueldiascosta `_ - e-mail: ``migueldiascosta (at) nus.edu.sg`` - IRC/Slack: ``migueldiascosta`` From a47d6fbe830ae600ddd19726f3d513597aab8312 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 22 Aug 2022 06:23:14 +0800 Subject: [PATCH 231/286] also fix some typos --- docs/Implementing-easyblocks.rst | 2 +- docs/Release_notes.rst | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Implementing-easyblocks.rst b/docs/Implementing-easyblocks.rst index 598de99c..2eca1b20 100644 --- a/docs/Implementing-easyblocks.rst +++ b/docs/Implementing-easyblocks.rst @@ -188,7 +188,7 @@ use ``--include-easyblocks`` to make EasyBuild use additional or customised easy Structure of an easyblock ------------------------- -The example below shows the overal structure of an easyblock: +The example below shows the overall structure of an easyblock: .. code:: python diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index d8adb1a8..a7863bb1 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -4828,7 +4828,7 @@ feature release - add expat dependency to Mesa v18.1.1 (`#6706 `_) - add missing ``--with-trio-flavor=netcdf`` flag to ABINIT 8.x easyconfigs (`#6711 `_) - remove useless definition of $TORCH_CUDA_ARCH_LIST in PyTorch easyconfig that doesn't use CUDA (`#6719 `_) - - fix builing GCCcore 6.3.0 on recent OSs by backporting patches from 6.4.0 (`#6727 `_) + - fix building GCCcore 6.3.0 on recent OSs by backporting patches from 6.4.0 (`#6727 `_) - fix ``source_urls`` in bzip2 easyconfigs (`#6728 `_) - specify location of dependencies in configure options for libgd (to avoid system libraries being used instead) (`#6731 `_) - also install docs/man pages in recent git easyconfigs (versions 2.1x.y) (`#6751 `_) From 5acbdb6c566cc41a9a55340e7c819fb5e24bd0c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 11 Sep 2022 23:20:08 +0200 Subject: [PATCH 232/286] fix release date for 2022a common toolchains --- docs/Common-toolchains.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Common-toolchains.rst b/docs/Common-toolchains.rst index d42441f4..9352a4e3 100644 --- a/docs/Common-toolchains.rst +++ b/docs/Common-toolchains.rst @@ -166,7 +166,7 @@ Component versions in ``foss`` toolchain +----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ | ``2021b`` | Oct '21 | 2.37 | 11.2.0 | 4.1.1 | 3.0.4 | 0.3.18 | (incl. with OpenBLAS) | 2.1.0 | 3.3.10 | +----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2022a`` | Jun '21 | 2.38 | 11.3.0 | 4.1.4 | 3.2.0 | 0.3.20 | (incl. with OpenBLAS) | 2.2.0 | 3.3.10 | +| ``2022a`` | Jun '22 | 2.38 | 11.3.0 | 4.1.4 | 3.2.0 | 0.3.20 | (incl. with OpenBLAS) | 2.2.0 | 3.3.10 | +----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ *(components marked with* * *were patched)* @@ -191,7 +191,7 @@ Component versions in ``intel`` toolchain +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ | ``2021b`` | Oct'21 | 2.37 | 11.2.0 | 2021.4.0 | 2021.4.0 | 2021.4.0 | +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2022a`` | Jun'21 | 2.38 | 11.3.0 | 2022.1.0 | 2021.6.0 | 2022.1.0 | +| ``2022a`` | Jun'22 | 2.38 | 11.3.0 | 2022.1.0 | 2021.6.0 | 2022.1.0 | +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ .. _common_toolchains_overview_deprecated: From 3b4427c300e7fee4e34c245fa81ab87851bc00ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 11 Sep 2022 23:40:35 +0200 Subject: [PATCH 233/286] auto-update docs for EasyBuild v4.6.1 --- docs/version-specific/Supported_software.rst | 2155 ++++++++++++------ docs/version-specific/generic_easyblocks.rst | 2 +- docs/version-specific/help.rst | 86 +- 3 files changed, 1505 insertions(+), 738 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 37fb551b..8a708757 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2736 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2773 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_Abseil_592` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_Albumentations_1478` - :ref:`list_software_alevin-fry_1021` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMD-uProf_779` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AMPtk_445` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_AMS_225` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_ANGEL_359` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_Arcade-Learning-Environment_2655` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_ArchR_464` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_arosics_756` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_atropos_776` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Austin_628` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock-GPU_1075` - :ref:`list_software_AutoDock-Vina_1237` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_Abseil_592` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_Albumentations_1478` - :ref:`list_software_alevin-fry_1021` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMD-uProf_779` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AMPtk_445` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_AMS_225` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_ANGEL_359` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_AptaSUITE_784` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_Arcade-Learning-Environment_2655` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_ArchR_464` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_arosics_756` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_atropos_776` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Austin_628` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock-GPU_1075` - :ref:`list_software_AutoDock-Vina_1237` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -342,11 +342,13 @@ The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists t *homepage*: https://www.olcf.ornl.gov/center-projects/adios/ -========== ================== ============== -version versionsuffix toolchain -========== ================== ============== -``1.13.1`` ``-Python-2.7.15`` ``foss/2019a`` -========== ================== ============== +============ ================== ============== +version versionsuffix toolchain +============ ================== ============== +``1.13.1`` ``-Python-2.7.15`` ``foss/2019a`` +``1.13.1`` ``-Python-3.8.2`` ``foss/2020a`` +``20210804`` ``-Python-3.8.2`` ``foss/2020a`` +============ ================== ============== .. _list_software_adjustText_1072: @@ -421,6 +423,7 @@ version toolchain ``2019_update5`` ``system`` ``2021.2.0`` ``system`` ``2021.4.0`` ``system`` +``2022.1.0`` ``system`` ================ ========== @@ -538,6 +541,7 @@ alevin-fry is an efficient and flexible tool for processing single-cell sequenci version toolchain ========= ================== ``0.4.3`` ``GCCcore/11.2.0`` +``0.6.0`` ``GCCcore/10.3.0`` ========= ================== @@ -782,14 +786,16 @@ AmberTools consists of several independently developed packages that work well b *homepage*: https://ambermd.org/ -======= ================== ================================ -version versionsuffix toolchain -======= ================== ================================ -``17`` ``intel/2017b``, ``intel/2018a`` -``17`` ``-Python-2.7.14`` ``foss/2018a`` -``20`` ``-Python-3.8.2`` ``intel/2020a`` -``21`` ``intel/2021b`` -======= ================== ================================ +========= ================== ================================ +version versionsuffix toolchain +========= ================== ================================ +``17`` ``intel/2017b``, ``intel/2018a`` +``17`` ``-Python-2.7.14`` ``foss/2018a`` +``20`` ``-Python-3.8.2`` ``intel/2020a`` +``21`` ``foss/2021a``, ``intel/2021b`` +``21.12`` ``foss/2021b`` +``22.3`` ``foss/2021b`` +========= ================== ================================ .. _list_software_AMD-LibM_611: @@ -1217,6 +1223,8 @@ version versionsuffix toolchain ``1.10.9`` ``-Java-11`` ``system`` ``1.10.11`` ``-Java-11`` ``system`` ``1.10.11`` ``-Java-13`` ``system`` +``1.10.12`` ``-Java-11`` ``system`` +``1.10.12`` ``-Java-17`` ``system`` =========== =================== ========== @@ -1247,16 +1255,16 @@ ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language to *homepage*: http://www.antlr2.org/ -========= ================== ===================================================================================================== -version versionsuffix toolchain -========= ================== ===================================================================================================== -``2.7.7`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b`` -``2.7.7`` ``-Java-11`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.7.7`` ``-Python-2.7.11`` ``foss/2016a`` -``2.7.7`` ``-Python-2.7.13`` ``intel/2017a`` -``2.7.7`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` -``2.7.7`` ``-Python-3.6.4`` ``intel/2018a`` -========= ================== ===================================================================================================== +========= ================== ==================================================================================================================== +version versionsuffix toolchain +========= ================== ==================================================================================================================== +``2.7.7`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b`` +``2.7.7`` ``-Java-11`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.7.7`` ``-Python-2.7.11`` ``foss/2016a`` +``2.7.7`` ``-Python-2.7.13`` ``intel/2017a`` +``2.7.7`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` +``2.7.7`` ``-Python-3.6.4`` ``intel/2018a`` +========= ================== ==================================================================================================================== .. _list_software_ANTs_342: @@ -1327,7 +1335,7 @@ version toolchain ``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``3.0.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``3.2.0`` ``GCCcore/11.2.0`` +``3.2.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ========================================================== @@ -1413,6 +1421,22 @@ version toolchain ========= ======================================================================================================================================================= +.. _list_software_AptaSUITE_784: + +*AptaSUITE* ++++++++++++ + +A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments + +*homepage*: https://drivenbyentropy.github.io/ + +========= ============= ========== +version versionsuffix toolchain +========= ============= ========== +``0.9.4`` ``-Java-11`` ``system`` +========= ============= ========== + + .. _list_software_ARAGORN_522: *ARAGORN* @@ -1594,6 +1618,7 @@ aria2 is a lightweight multi-protocol & multi-source command-line download utili version toolchain ========== ================== ``1.35.0`` ``GCCcore/10.3.0`` +``1.36.0`` ``GCCcore/11.3.0`` ========== ================== @@ -1748,7 +1773,7 @@ version versionsuffix toolchain ``0.17.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``6.0.0`` ``foss/2021a``, ``foss/2021b`` ``6.0.1`` ``foss/2021a`` -``8.0.0`` ``foss/2022.05`` +``8.0.0`` ``foss/2022.05``, ``foss/2022a`` ========== ================== =================================================== @@ -1768,6 +1793,7 @@ version versionsuffix toolchain ``6.0.0.2`` ``-R-4.1.0`` ``foss/2021a`` ``6.0.0.2`` ``-R-4.1.2`` ``foss/2021b`` ``6.0.0.2`` ``-R-4.2.0`` ``foss/2021b`` +``8.0.0`` ``-R-4.2.1`` ``foss/2022a`` =========== ============= ============== @@ -1931,6 +1957,7 @@ version versionsuffix toolchain ``3.21.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``3.21.1`` ``-Python-3.8.2`` ``foss/2020a`` ``3.22.0`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021a`` +``3.22.1`` ``foss/2022a`` ============== ================== ==================================================================================== @@ -2234,13 +2261,13 @@ Commands for Manipulating Filesystem Extended Attributes *homepage*: https://savannah.nongnu.org/projects/attr -========== ================== -version toolchain -========== ================== -``2.4.47`` ``GCCcore/8.2.0`` -``2.4.48`` ``GCCcore/9.3.0`` -``2.5.1`` ``GCCcore/10.3.0`` -========== ================== +========== ====================================== +version toolchain +========== ====================================== +``2.4.47`` ``GCCcore/8.2.0`` +``2.4.48`` ``GCCcore/9.3.0`` +``2.5.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ====================================== .. _list_software_attrdict_863: @@ -2284,18 +2311,18 @@ AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences *homepage*: https://bioinf.uni-greifswald.de/augustus/ -========= ================== ============================================== -version versionsuffix toolchain -========= ================== ============================================== -``3.2.3`` ``-Python-2.7.13`` ``intel/2017a`` -``3.3`` ``foss/2018a`` -``3.3.2`` ``intel/2019a`` -``3.3.2`` ``-Python-2.7.13`` ``intel/2017a`` -``3.3.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``3.3.2`` ``-Python-2.7.15`` ``intel/2018b`` -``3.3.3`` ``foss/2019b``, ``intel/2019b`` -``3.4.0`` ``foss/2020a``, ``foss/2020b``, ``foss/2021b`` -========= ================== ============================================== +========= ================== ============================================================== +version versionsuffix toolchain +========= ================== ============================================================== +``3.2.3`` ``-Python-2.7.13`` ``intel/2017a`` +``3.3`` ``foss/2018a`` +``3.3.2`` ``intel/2019a`` +``3.3.2`` ``-Python-2.7.13`` ``intel/2017a`` +``3.3.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``3.3.2`` ``-Python-2.7.15`` ``intel/2018b`` +``3.3.3`` ``foss/2019b``, ``intel/2019b`` +``3.4.0`` ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` +========= ================== ============================================================== .. _list_software_Austin_628: @@ -2554,7 +2581,7 @@ version versionsuffix toolchain --- -:ref:`list_software_BabelStream_1090` - :ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_Bambi_475` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_bamtofastq_1074` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_bcbio-gff_863` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biom-format_1117` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_Blosc2_549` - :ref:`list_software_BLT_226` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_boost_histogram_1620` - :ref:`list_software_boto3_487` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_Brotli-python_1339` - :ref:`list_software_Brunsli_735` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` +:ref:`list_software_BabelStream_1090` - :ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_Bambi_475` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_bamtofastq_1074` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_bcbio-gff_863` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BigDFT_496` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biom-format_1117` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_Blosc2_549` - :ref:`list_software_BLT_226` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_boost_histogram_1620` - :ref:`list_software_boto3_487` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_Brotli-python_1339` - :ref:`list_software_Brunsli_735` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` .. _list_software_BabelStream_1090: @@ -2752,7 +2779,7 @@ version toolchain ``2.4.1`` ``intel/2017a`` ``2.5.0`` ``foss/2016b``, ``intel/2017b`` ``2.5.1`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018b`` -``2.5.2`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``2.5.2`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` ========= ================================================================================================================================================================================================================================================ @@ -3044,6 +3071,8 @@ version versionsuffix toolchain ``38.79`` ``GCC/8.3.0`` ``38.87`` ``iccifort/2020.1.217`` ``38.90`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``38.96`` ``GCC/10.3.0`` +``38.98`` ``GCC/11.2.0`` ========== =================== =============================== @@ -3134,6 +3163,7 @@ version toolchain ``1.11`` ``GCC/10.2.0`` ``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` ``1.14`` ``GCC/11.2.0`` +``1.15.1`` ``GCC/11.3.0`` ========== ========================================================================================= @@ -3263,18 +3293,18 @@ Beautiful Soup is a Python library designed for quick turnaround projects like s *homepage*: https://www.crummy.com/software/BeautifulSoup -========== ================= ====================================== -version versionsuffix toolchain -========== ================= ====================================== -``4.6.0`` ``-Python-3.6.3`` ``intel/2017b`` -``4.6.3`` ``-Python-3.6.4`` ``intel/2018a`` -``4.7.1`` ``-Python-3.6.6`` ``intel/2018b`` -``4.8.0`` ``GCCcore/8.2.0`` -``4.9.1`` ``GCCcore/8.3.0`` -``4.9.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``4.9.3`` ``GCCcore/10.2.0`` -``4.10.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========== ================= ====================================== +========== ================= ========================================================== +version versionsuffix toolchain +========== ================= ========================================================== +``4.6.0`` ``-Python-3.6.3`` ``intel/2017b`` +``4.6.3`` ``-Python-3.6.4`` ``intel/2018a`` +``4.7.1`` ``-Python-3.6.6`` ``intel/2018b`` +``4.8.0`` ``GCCcore/8.2.0`` +``4.9.1`` ``GCCcore/8.3.0`` +``4.9.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``4.9.3`` ``GCCcore/10.2.0`` +``4.10.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========== ================= ========================================================== .. _list_software_BEDOPS_445: @@ -3308,16 +3338,16 @@ BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow *homepage*: https://bedtools.readthedocs.io/ -========== ==================================================================================== -version toolchain -========== ==================================================================================== -``2.25.0`` ``foss/2016a`` -``2.26.0`` ``GCCcore/6.4.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``2.27.1`` ``GCCcore/6.4.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` -``2.28.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2.29.2`` ``GCC/8.3.0``, ``GCC/9.3.0`` -``2.30.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304`` -========== ==================================================================================== +========== ======================================================================================= +version toolchain +========== ======================================================================================= +``2.25.0`` ``foss/2016a`` +``2.26.0`` ``GCCcore/6.4.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +``2.27.1`` ``GCCcore/6.4.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` +``2.28.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.29.2`` ``GCC/8.3.0``, ``GCC/9.3.0`` +``2.30.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``iccifort/2020.4.304`` +========== ======================================================================================= .. _list_software_BEEF_274: @@ -3472,6 +3502,22 @@ version versionsuffix toolchain ========= ================= =============== +.. _list_software_BigDFT_496: + +*BigDFT* +++++++++ + +BigDFT: electronic structure calculation based on Daubechies wavelets. bigdft-suite is a set of different packages to run bigdft. + +*homepage*: https://gitlab.com/l_sim/bigdft-suite + +========= ============== +version toolchain +========= ============== +``1.9.1`` ``foss/2021b`` +========= ============== + + .. _list_software_BinSanity_913: *BinSanity* @@ -3514,6 +3560,7 @@ version toolchain ``2.36.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/8.4.0``, ``GCCcore/9.4.0``, ``system`` ``2.37`` ``GCCcore/11.2.0``, ``system`` ``2.38`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.5.0``, ``system`` +``2.39`` ``GCCcore/12.2.0``, ``system`` ========== ======================================================================================================================================================================================== @@ -3719,30 +3766,30 @@ Biopython is a set of freely available tools for biological computation written *homepage*: https://www.biopython.org -======== ================== =================================================== -version versionsuffix toolchain -======== ================== =================================================== -``1.65`` ``-Python-2.7.11`` ``foss/2016a`` -``1.68`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.68`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``1.70`` ``-Python-2.7.13`` ``foss/2017a`` -``1.70`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``1.70`` ``-Python-3.6.1`` ``intel/2017a`` -``1.70`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.71`` ``-Python-2.7.14`` ``intel/2018a`` -``1.71`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.72`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``1.72`` ``-Python-3.6.6`` ``foss/2018b`` -``1.73`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` -``1.73`` ``-Python-3.6.6`` ``foss/2018b`` -``1.74`` ``foss/2019a`` -``1.75`` ``-Python-2.7.16`` ``foss/2019b`` -``1.75`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``1.76`` ``-Python-2.7.18`` ``foss/2020b`` -``1.78`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``1.78`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.79`` ``foss/2021a``, ``foss/2021b``, ``intel/2021b`` -======== ================== =================================================== +======== ================== =============================================================== +version versionsuffix toolchain +======== ================== =============================================================== +``1.65`` ``-Python-2.7.11`` ``foss/2016a`` +``1.68`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``1.68`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``1.70`` ``-Python-2.7.13`` ``foss/2017a`` +``1.70`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``1.70`` ``-Python-3.6.1`` ``intel/2017a`` +``1.70`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``1.71`` ``-Python-2.7.14`` ``intel/2018a`` +``1.71`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.72`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``1.72`` ``-Python-3.6.6`` ``foss/2018b`` +``1.73`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` +``1.73`` ``-Python-3.6.6`` ``foss/2018b`` +``1.74`` ``foss/2019a`` +``1.75`` ``-Python-2.7.16`` ``foss/2019b`` +``1.75`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``1.76`` ``-Python-2.7.18`` ``foss/2020b`` +``1.78`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``1.78`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.79`` ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``intel/2021b`` +======== ================== =============================================================== .. _list_software_BioServices_1118: @@ -3835,7 +3882,7 @@ version toolchain ``3.6.1`` ``GCCcore/10.1.0`` ``3.7.1`` ``GCCcore/10.2.0``, ``system`` ``3.7.6`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0``, ``system`` -``3.8.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.5.0``, ``system`` +``3.8.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0``, ``system`` ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -3952,6 +3999,7 @@ version versionsuffix toolchain ``2.10.1`` ``gompi/2020a``, ``iimpi/2020a`` ``2.11.0`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a`` ``2.12.0`` ``gompi/2021b`` +``2.13.0`` ``gompi/2022a`` ========== ================== =================================================================================== @@ -3990,6 +4038,7 @@ version versionsuffix toolchain ``2.81`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.0.0`` ``-linux-x64`` ``system`` ``3.1.2`` ``-linux-x64`` ``system`` +``3.2.2`` ``-linux-x64`` ``system`` ========= ============================= =============================== @@ -4027,12 +4076,12 @@ Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in *homepage*: https://github.com/blitzpp/blitz -========= ================================= -version toolchain -========= ================================= -``0.10`` ``GCCcore/6.4.0``, ``foss/2016a`` -``1.0.2`` ``GCCcore/9.3.0`` -========= ================================= +========= ========================================================= +version toolchain +========= ========================================================= +``0.10`` ``GCCcore/6.4.0``, ``foss/2016a`` +``1.0.2`` ``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +========= ========================================================= .. _list_software_BlobTools_912: @@ -4433,6 +4482,7 @@ version toolchain ``2.4.1`` ``GCC/9.3.0`` ``2.4.2`` ``GCC/10.2.0``, ``GCC/9.3.0`` ``2.4.4`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``2.4.5`` ``GCC/11.3.0`` =========== ====================================================================================================== @@ -4711,13 +4761,14 @@ This module sets a group of environment variables for compilers, linkers, maths *homepage*: None -=========== ================ ================================================================================================================================================================================================================================================================================================================================================================================= -version versionsuffix toolchain -=========== ================ ================================================================================================================================================================================================================================================================================================================================================================================= -``default`` ``FCC/4.5.0``, ``Fujitsu/21.05``, ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b`` -``default`` ``-CUDA-11.3.1`` ``foss/2021a`` -``default`` ``-CUDA-11.4.1`` ``foss/2021b`` -=========== ================ ================================================================================================================================================================================================================================================================================================================================================================================= +=========== ================ =================================================================================================================================================================================================================================================================================================================================================================================================================================== +version versionsuffix toolchain +=========== ================ =================================================================================================================================================================================================================================================================================================================================================================================================================================== +``default`` ``FCC/4.5.0``, ``Fujitsu/21.05``, ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b`` +``default`` ``-CUDA-11.3.1`` ``foss/2021a`` +``default`` ``-CUDA-11.4.1`` ``foss/2021b`` +``default`` ``-CUDA-11.7.0`` ``foss/2022a`` +=========== ================ =================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_Bullet_616: @@ -4755,6 +4806,8 @@ version versionsuffix toolchain ``4.0.6`` ``foss/2020b`` ``5.0.0`` ``foss/2020b`` ``5.1.2`` ``foss/2020b`` +``5.4.2`` ``foss/2021a`` +``5.4.3`` ``foss/2021b`` ========= ================== =============== @@ -4840,6 +4893,7 @@ version toolchain ========== ======================================================== ``1.9.13`` ``GCCcore/8.2.0`` ``1.9.14`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.9.15`` ``GCCcore/11.3.0`` ========== ======================================================== @@ -4956,7 +5010,7 @@ version toolchain --- -:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CASTEP_448` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_category_encoders_1808` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_CellTypist_1037` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMAverse_758` - :ref:`list_software_CmdStanR_764` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_CONN_302` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_Crumble_714` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CASTEP_448` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_category_encoders_1808` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_CellTypist_1037` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMAverse_758` - :ref:`list_software_CmdStanR_764` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_colossalai_1066` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_CONN_302` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_Crumble_714` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CrystFEL_748` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_c-ares_571: @@ -4968,12 +5022,12 @@ c-ares is a C library for asynchronous DNS requests (including name resolves) *homepage*: https://c-ares.org/ -========== ================== -version toolchain -========== ================== -``1.17.2`` ``GCCcore/10.3.0`` -``1.18.1`` ``GCCcore/11.2.0`` -========== ================== +========== ====================================== +version toolchain +========== ====================================== +``1.17.2`` ``GCCcore/10.3.0`` +``1.18.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========== ====================================== .. _list_software_C3D_186: @@ -5252,14 +5306,15 @@ Cap’n Proto is an insanely fast data interchange format and capability-based R *homepage*: https://capnproto.org -========= ========================================================== -version toolchain -========= ========================================================== -``0.6.1`` ``GCCcore/6.4.0`` -``0.7.0`` ``GCCcore/7.3.0`` -``0.8.0`` ``GCCcore/9.3.0`` -``0.9.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========= ========================================================== +========== ========================================================== +version toolchain +========== ========================================================== +``0.6.1`` ``GCCcore/6.4.0`` +``0.7.0`` ``GCCcore/7.3.0`` +``0.8.0`` ``GCCcore/9.3.0`` +``0.9.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``0.10.2`` ``GCCcore/11.3.0`` +========== ========================================================== .. _list_software_Cargo_492: @@ -5327,6 +5382,7 @@ version versionsuffix toolchain ``0.18.0`` ``-Python-3.8.2`` ``foss/2020a`` ``0.19.0.post1`` ``foss/2020b``, ``intel/2020b`` ``0.20.0`` ``foss/2021a`` +``0.20.3`` ``foss/2021b`` ================ ================= =============================== @@ -5537,16 +5593,17 @@ Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by cach *homepage*: https://ccache.dev/ -========== ============= ========== -version versionsuffix toolchain -========== ============= ========== -``3.2.5`` ``system`` -``3.3.1`` ``system`` -``3.3.3`` ``system`` -``3.3.4`` ``-f90`` ``system`` -``3.7.11`` ``system`` -``4.2.1`` ``system`` -========== ============= ========== +========== ============= ================== +version versionsuffix toolchain +========== ============= ================== +``3.2.5`` ``system`` +``3.3.1`` ``system`` +``3.3.3`` ``system`` +``3.3.4`` ``-f90`` ``system`` +``3.7.11`` ``system`` +``4.2.1`` ``system`` +``4.6.1`` ``GCCcore/11.2.0`` +========== ============= ================== .. _list_software_CCfits_572: @@ -5597,6 +5654,7 @@ version versionsuffix toolchain ========= ================= =============================== ``1.5`` ``-Python-3.5.2`` ``foss/2016b`` ``1.6.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.7.2`` ``foss/2021b`` ========= ================= =============================== @@ -5721,6 +5779,7 @@ version toolchain ``1.9.5`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``1.9.8`` ``intel/2019b`` ``1.9.10`` ``gompi/2019b``, ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2021b`` +``2.0.5`` ``gompi/2021b`` ========== ================================================================== @@ -5832,6 +5891,7 @@ version toolchain ========= ========== ``1.2.0`` ``system`` ``2.0.0`` ``system`` +``2.1.0`` ``system`` ========= ========== @@ -5910,11 +5970,11 @@ CESM is a fully-coupled, community, global climate model that provides state-of- *homepage*: https://www.cesm.ucar.edu/models/cesm2/ -======= ================================================ -version toolchain -======= ================================================ -``2`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -======= ================================================ +======= ================================================================ +version toolchain +======= ================================================================ +``2`` ``foss/2018b``, ``foss/2021b``, ``intel/2018b``, ``iomkl/2018b`` +======= ================================================================ .. _list_software_CFDEMcoupling_1216: @@ -5983,27 +6043,27 @@ The goal of the CGAL Open Source Project is to provide easy access to efficient *homepage*: https://www.cgal.org/ -========== ================== ================================ -version versionsuffix toolchain -========== ================== ================================ -``4.8`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``4.8.1`` ``foss/2016b``, ``intel/2016b`` -``4.8.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``4.9`` ``-Python-2.7.12`` ``intel/2016b`` -``4.9`` ``-Python-2.7.13`` ``intel/2017a`` -``4.11`` ``-Python-2.7.13`` ``intel/2017a`` -``4.11`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``4.11`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``4.11.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``4.11.1`` ``-Python-2.7.15`` ``foss/2018b`` -``4.11.1`` ``-Python-3.6.4`` ``foss/2018a`` -``4.11.1`` ``-Python-3.6.6`` ``foss/2018b`` -``4.14`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``4.14.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``4.14.3`` ``gompi/2021a``, ``gompi/2021b`` -``4.14.3`` ``-Python-3.8.2`` ``gompi/2020a``, ``iimpi/2020a`` -``5.2`` ``gompi/2020b`` -========== ================== ================================ +========== ================== ================================================= +version versionsuffix toolchain +========== ================== ================================================= +``4.8`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``4.8.1`` ``foss/2016b``, ``intel/2016b`` +``4.8.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``4.9`` ``-Python-2.7.12`` ``intel/2016b`` +``4.9`` ``-Python-2.7.13`` ``intel/2017a`` +``4.11`` ``-Python-2.7.13`` ``intel/2017a`` +``4.11`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``4.11`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``4.11.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``4.11.1`` ``-Python-2.7.15`` ``foss/2018b`` +``4.11.1`` ``-Python-3.6.4`` ``foss/2018a`` +``4.11.1`` ``-Python-3.6.6`` ``foss/2018b`` +``4.14`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``4.14.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``4.14.3`` ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a`` +``4.14.3`` ``-Python-3.8.2`` ``gompi/2020a``, ``iimpi/2020a`` +``5.2`` ``gompi/2020b`` +========== ================== ================================================= .. _list_software_cget_419: @@ -6295,6 +6355,7 @@ UCSF Chimera is a highly extensible program for interactive visualization and version versionsuffix toolchain ======== ================= ========== ``1.10`` ``-linux_x86_64`` ``system`` +``1.16`` ``-linux_x86_64`` ``system`` ======== ================= ========== @@ -6520,7 +6581,7 @@ version versionsuffix toolchain ``11.0.1`` ``GCCcore/10.2.0``, ``gcccuda/2020b`` ``12.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``12.0.1`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` -``13.0.1`` ``GCCcore/11.2.0`` +``13.0.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``13.0.1`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` ========== ================== ====================================== @@ -7015,6 +7076,22 @@ version toolchain ========== ================================== +.. _list_software_colossalai_1066: + +*colossalai* +++++++++++++ + +Colossal-AI: A Unified Deep Learning System for Big Model Era + +*homepage*: https://colossalai.org/ + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``0.1.8`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== + + .. _list_software_Commet_613: *Commet* @@ -7199,11 +7276,12 @@ Schrodinger-developed 2D Coordinate Generation *homepage*: https://github.com/schrodinger/coordgenlibs -========= ================================ -version toolchain -========= ================================ -``1.3.2`` ``gompi/2019a``, ``iimpi/2019a`` -========= ================================ +========= ================================================================== +version toolchain +========= ================================================================== +``1.3.2`` ``gompi/2019a``, ``iimpi/2019a`` +``3.0.1`` ``gompi/2019b``, ``gompi/2021a``, ``gompi/2022a``, ``iimpi/2020a`` +========= ================================================================== .. _list_software_Coot_405: @@ -7375,12 +7453,12 @@ CppUnit is the C++ port of the famous JUnit framework for unit testing. *homepage*: https://freedesktop.org/wiki/Software/cppunit/ -========== ======================================================== -version toolchain -========== ======================================================== -``1.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a`` -``1.15.1`` ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ======================================================== +========== ============================================================================ +version toolchain +========== ============================================================================ +``1.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a`` +``1.15.1`` ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ============================================================================ .. _list_software_cppy_444: @@ -7711,6 +7789,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_CrystFEL_748: + +*CrystFEL* +++++++++++ + +CrystFEL is a suite of programs for processing diffraction data acquired "serially" in a "snapshot" manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser source. + +*homepage*: http://www.desy.de/~twhite/crystfel/ + +========= =============================== +version toolchain +========= =============================== +``0.8.0`` ``foss/2019a``, ``intel/2019a`` +========= =============================== + + .. _list_software_CSB_216: *CSB* @@ -8027,11 +8121,11 @@ Automated testing framework for C. *homepage*: https://sourceforge.net/projects/cunit/ -========= ================= -version toolchain -========= ================= -``2.1-3`` ``GCCcore/6.4.0`` -========= ================= +========= ===================================== +version toolchain +========= ===================================== +``2.1-3`` ``GCCcore/11.2.0``, ``GCCcore/6.4.0`` +========= ===================================== .. _list_software_CuPy_385: @@ -8085,6 +8179,7 @@ version toolchain ``7.76.0`` ``GCCcore/10.3.0`` ``7.78.0`` ``GCCcore/11.2.0`` ``7.83.0`` ``GCCcore/11.3.0`` +``7.84.0`` ``GCCcore/12.1.0`` ========== =================================================================================== @@ -8151,6 +8246,7 @@ version versionsuffix toolchain =========== ================ ================= ``1.2.2.5`` ``gcccuda/2019b`` ``1.2.2.5`` ``-CUDA-11.1.1`` ``system`` +``1.6.0.3`` ``-CUDA-11.3.1`` ``system`` =========== ================ ================= @@ -8321,7 +8417,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_deepmedic_928` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detectron2_1018` - :ref:`list_software_detonate_852` - :ref:`list_software_Devito_619` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dlib_411` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dRep_395` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_DualSPHysics_1180` - :ref:`list_software_DUBStepR_713` - :ref:`list_software_dune-core_898` - :ref:`list_software_dune-fem_785` - :ref:`list_software_dxpy_453` - :ref:`list_software_DyMat_479` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dakota_596` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_deepmedic_928` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_Detectron2_986` - :ref:`list_software_detonate_852` - :ref:`list_software_Devito_619` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dlib_411` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dRep_395` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_DualSPHysics_1180` - :ref:`list_software_DUBStepR_713` - :ref:`list_software_dune-core_898` - :ref:`list_software_dune-fem_785` - :ref:`list_software_dxpy_453` - :ref:`list_software_DyMat_479` .. _list_software_dadi_402: @@ -8356,6 +8452,22 @@ version versionsuffix toolchain ========= ============= ============== +.. _list_software_Dakota_596: + +*Dakota* +++++++++ + +The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ. Broadly, the Dakota software's advanced parametric analyses enable design exploration, model calibration, risk analysis, and quantification of margins and uncertainty with computational models. + +*homepage*: https://dakota.sandia.gov/ + +========== ============== +version toolchain +========== ============== +``6.16.0`` ``foss/2021b`` +========== ============== + + .. _list_software_Dalton_610: *Dalton* @@ -8517,16 +8629,16 @@ Berkeley DB enables the development of custom data management solutions, withou *homepage*: http://www.oracle.com/technetwork/products/berkeleydb -=========== =================================================================================================================================== -version toolchain -=========== =================================================================================================================================== -``4.8.30`` ``intel/2016a`` -``6.2.23`` ``foss/2016a`` -``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` -``18.1.25`` ``GCCcore/7.3.0`` -``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``18.1.40`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -=========== =================================================================================================================================== +=========== ======================================================================================================================================================= +version toolchain +=========== ======================================================================================================================================================= +``4.8.30`` ``intel/2016a`` +``6.2.23`` ``foss/2016a`` +``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` +``18.1.25`` ``GCCcore/7.3.0`` +``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``18.1.40`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +=========== ======================================================================================================================================================= .. _list_software_DB_File_613: @@ -8622,7 +8734,7 @@ version toolchain D-Bus is a message bus system, a simple way for applications to talk to one another. -*homepage*: http://dbus.freedesktop.org/doc/dbus-glib +*homepage*: https://dbus.freedesktop.org/doc/dbus-glib ========= ======================================================================== version toolchain @@ -8630,6 +8742,7 @@ version toolchain ``0.106`` ``foss/2016a``, ``intel/2016a`` ``0.108`` ``intel/2016b``, ``intel/2017a`` ``0.110`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b`` +``0.112`` ``GCCcore/10.3.0`` ========= ======================================================================== @@ -8910,18 +9023,19 @@ version versionsuffix toolchain ========= ============= =============== -.. _list_software_detectron2_1018: +.. _list_software_Detectron2_986: -*detectron2* +*Detectron2* ++++++++++++ -Detectron2 is a platform for object detection, segmentation and other visual recognition tasks. +Detectron2 is Facebook AI Research's next generation library that provides state-of-the-art detection and segmentation algorithms. It is the successor of Detectron and maskrcnn-benchmark. It supports a number of computer vision research projects and production applications in Facebook. *homepage*: https://github.com/facebookresearch/detectron2 ======= ================ ============== version versionsuffix toolchain ======= ================ ============== +``0.6`` ``foss/2021a`` ``0.6`` ``-CUDA-11.3.1`` ``foss/2021a`` ======= ================ ============== @@ -9415,12 +9529,13 @@ version toolchain *homepage*: https://www.microsoft.com/net/ -========= ================== -version toolchain -========= ================== -``2.0.7`` ``GCCcore/6.4.0`` -``6.0.1`` ``GCCcore/11.2.0`` -========= ================== +========== ================== +version toolchain +========== ================== +``2.0.7`` ``GCCcore/6.4.0`` +``5.0.17`` ``GCCcore/10.3.0`` +``6.0.1`` ``GCCcore/11.2.0`` +========== ================== .. _list_software_dotNET-SDK_829: @@ -9923,6 +10038,7 @@ version toolchain ``4.5.3`` ``system`` ``4.5.4`` ``system`` ``4.5.5`` ``system`` +``4.6.0`` ``system`` ========== ========== @@ -10150,6 +10266,7 @@ Flexible and powerful tensor operations for readable and reliable code. Supports version toolchain ========= ================== ``0.3.2`` ``GCCcore/10.2.0`` +``0.4.1`` ``GCCcore/10.3.0`` ========= ================== @@ -10237,6 +10354,7 @@ version toolchain ``6.3.2`` ``intel/2019b`` ``7.0.12`` ``foss/2020b`` ``7.2.42`` ``foss/2021a`` +``8.5.2`` ``foss/2022a`` ========== =============== @@ -10261,7 +10379,7 @@ version toolchain ``2019.11.001`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a``, ``iomkl/2019b`` ``2020.05.001`` ``intel/2020a`` ``2020.11.001`` ``foss/2020b``, ``intel/2020b`` -``2021.05.001`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` +``2021.05.001`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a``, ``intel/2021b`` ``2021.05.002`` ``intel/2020b`` ``2021.11.001`` ``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` =================== ================================================================================= @@ -10355,6 +10473,7 @@ version versionsuffix toolchain ``26.3`` ``GCCcore/8.3.0`` ``27.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``27.2`` ``GCCcore/11.2.0`` +``28.1`` ``GCCcore/10.2.0`` ======== ============= ======================================================= @@ -10404,11 +10523,12 @@ Intel® Embree is a collection of high-performance ray tracing kernels, develope *homepage*: https://embree.github.io/ -========= ====================================== -version toolchain -========= ====================================== -``3.4.0`` ``iccifort/2018.1.163-GCC-6.4.0-2.28`` -========= ====================================== +========== ====================================== +version toolchain +========== ====================================== +``3.4.0`` ``iccifort/2018.1.163-GCC-6.4.0-2.28`` +``3.13.4`` ``system`` +========== ====================================== .. _list_software_emcee_511: @@ -10886,7 +11006,7 @@ version toolchain ``2.2.7`` ``GCCcore/8.3.0`` ``2.2.9`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``2.4.1`` ``GCCcore/11.2.0`` -``2.4.8`` ``GCCcore/11.3.0`` +``2.4.8`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0`` ========= ========================================================================================================================= @@ -10915,11 +11035,11 @@ This library implements expect tests (also known as "golden" tests). Expect test *homepage*: https://github.com/ezyang/expecttest -========= ====================================== -version toolchain -========= ====================================== -``0.1.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========= ====================================== +========= ========================================================== +version toolchain +========= ========================================================== +``0.1.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +========= ========================================================== .. _list_software_eXpress_746: @@ -10963,7 +11083,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_Fastaq_608` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_FFTW.MPI_587` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_fio_318` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMPy_348` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoBiS_435` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeBarcodes_1189` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FSON_310` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_Fastaq_608` - :ref:`list_software_FastFold_787` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastparquet_1200` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_FFTW.MPI_587` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_fio_318` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMPy_348` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoBiS_435` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FOX-Toolkit_1024` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeBarcodes_1189` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FSON_310` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -11164,6 +11284,22 @@ version toolchain ========== ============== +.. _list_software_FastFold_787: + +*FastFold* +++++++++++ + +Optimizing Protein Structure Prediction Model Training and Inference on GPU Clusters + +*homepage*: https://github.com/hpcaitech/FastFold + +============ ================ ============== +version versionsuffix toolchain +============ ================ ============== +``20220729`` ``-CUDA-11.3.1`` ``foss/2021a`` +============ ================ ============== + + .. _list_software_FastME_544: *FastME* @@ -11199,6 +11335,23 @@ version toolchain ========== ============================================================ +.. _list_software_fastparquet_1200: + +*fastparquet* ++++++++++++++ + +fastparquet is a python implementation of the parquet format, aiming to integrate into python-based big data work-flows. It is used implicitly by the projects Dask, Pandas and intake-parquet. + +*homepage*: https://fastparquet.readthedocs.io/ + +========= ============== +version toolchain +========= ============== +``0.7.2`` ``foss/2021a`` +``0.8.0`` ``foss/2021b`` +========= ============== + + .. _list_software_fastPHASE_799: *fastPHASE* @@ -11744,6 +11897,8 @@ version toolchain ``4.2.2`` ``GCCcore/9.3.0`` ``4.3.1`` ``GCCcore/10.2.0`` ``4.3.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``4.4.2`` ``GCCcore/11.3.0`` +``5.0.1`` ``GCCcore/11.3.0`` =========== =================================================== @@ -12105,6 +12260,7 @@ Flexible I/O tester version toolchain ======== ================== ``3.30`` ``GCCcore/10.3.0`` +``3.32`` ``GCCcore/11.3.0`` ======== ================== @@ -12310,6 +12466,7 @@ version versionsuffix toolchain ``1.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``1.1.4`` ``GCCcore/10.3.0`` ``2.0.2`` ``GCCcore/11.2.0`` +``2.2.2`` ``GCCcore/11.3.0`` ========= ================= ================== @@ -12373,17 +12530,17 @@ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, some *homepage*: http://flex.sourceforge.net/ -========== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain -========== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``2.5.35`` ``system`` -``2.5.38`` ``GCC/4.8.2`` -``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` -``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.6.2`` ``intel/2016b`` -``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` -``2.6.4`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``GCCcore/system``, ``system`` -========== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +========== ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +version toolchain +========== ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +``2.5.35`` ``system`` +``2.5.38`` ``GCC/4.8.2`` +``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` +``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +``2.6.2`` ``intel/2016b`` +``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` +``2.6.4`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``GCCcore/system``, ``system`` +========== ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_Flexbar_708: @@ -12549,6 +12706,7 @@ version versionsuffix toolchain ``2.8.2`` ``-Python-3.8.2`` ``foss/2020a`` ``2.8.3`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` ``2.9`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` +``2.9.1`` ``GCC/11.2.0`` ========= ================== ============================================ @@ -12635,6 +12793,7 @@ version toolchain ``6.2.1`` ``GCCcore/9.3.0`` ``7.0.3`` ``GCCcore/9.3.0`` ``7.1.1`` ``GCCcore/11.2.0`` +``9.1.0`` ``GCCcore/11.3.0`` ========= ==================================== @@ -12725,12 +12884,13 @@ FORD is an automatic documentation generator for modern Fortran programs *homepage*: https://github.com/Fortran-FOSS-Programmers/ford/wiki -========= ================== -version toolchain -========= ================== -``6.1.1`` ``GCCcore/10.2.0`` -``6.1.6`` ``GCCcore/10.3.0`` -========= ================== +========== ================== +version toolchain +========== ================== +``6.1.1`` ``GCCcore/10.2.0`` +``6.1.6`` ``GCCcore/10.3.0`` +``6.1.15`` ``GCCcore/11.3.0`` +========== ================== .. _list_software_foss_443: @@ -12805,6 +12965,22 @@ version toolchain ========= =============================================================== +.. _list_software_FOX-Toolkit_1024: + +*FOX-Toolkit* ++++++++++++++ + +FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively. It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation. FOX also implements icons, images, and user-convenience features such as status line help, and tooltips. + +*homepage*: https://www.fox-toolkit.org/ + +========== ===================================== +version toolchain +========== ===================================== +``1.6.57`` ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========== ===================================== + + .. _list_software_FPM_227: *FPM* @@ -13043,6 +13219,7 @@ version versionsuffix toolchain ``7.2.0`` ``-centos7_x86_64`` ``system`` ``7.2.0`` ``-centos8_x86_64`` ``system`` ``7.2.0`` ``-ubuntu18_amd64`` ``system`` +``7.3.2`` ``-centos8_x86_64`` ``system`` ========= =================== ========== @@ -13477,7 +13654,7 @@ version toolchain --- -:ref:`list_software_G-PhoCS_561` - :ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_gcloud_638` - :ref:`list_software_GConf_461` - :ref:`list_software_GCTA_287` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_genozip_764` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_gfbf_405` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_Gibbs2_537` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPy_272` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap_784` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gRPC_332` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-bad_1393` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_gsutil_664` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GTK4_282` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_G-PhoCS_561` - :ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_gcloud_638` - :ref:`list_software_GConf_461` - :ref:`list_software_GCTA_287` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_genozip_764` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_gfbf_405` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_Gibbs2_537` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GLM-AED_471` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPy_272` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap_784` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gRPC_332` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-bad_1393` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_gsutil_664` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GTK4_282` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_G-PhoCS_561: @@ -13718,6 +13895,7 @@ version versionsuffix toolchain ``8.2`` ``-Python-2.7.15`` ``foss/2018b`` ``9.0`` ``-Python-3.7.4`` ``foss/2019b`` ``9.1`` ``foss/2021b`` +``9.2`` ``foss/2021b`` =========== =============================== =============================== @@ -13770,6 +13948,7 @@ version versionsuffix toolchain ``4.2.0.0`` ``-Java-11`` ``GCCcore/10.2.0`` ``4.2.3.0`` ``-Java-11`` ``GCCcore/11.2.0`` ``4.2.5.0`` ``-Java-11`` ``GCCcore/11.2.0`` +``4.2.6.1`` ``-Java-11`` ``GCCcore/11.2.0`` ============ =================== ================== @@ -13799,12 +13978,12 @@ The awk utility interprets a special-purpose programming language that makes it *homepage*: https://www.gnu.org/software/gawk -========= ============== -version toolchain -========= ============== -``5.1.0`` ``GCC/10.2.0`` -``5.1.1`` ``GCC/10.3.0`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``5.1.0`` ``GCC/10.2.0`` +``5.1.1`` ``GCC/10.3.0``, ``GCC/11.3.0`` +========= ============================== .. _list_software_Gblocks_709: @@ -13967,6 +14146,7 @@ version versionsuffix toolchain ``11.2.0`` ``system`` ``11.3.0`` ``system`` ``12.1.0`` ``system`` +``12.2.0`` ``system`` ``system`` ``system`` ``system`` ``-2.29`` ``system`` ========== =================== ========== @@ -14015,6 +14195,7 @@ version toolchain ``11.2.0`` ``system`` ``11.3.0`` ``system`` ``12.1.0`` ``system`` +``12.2.0`` ``system`` ``system`` ``system`` ========== ========== @@ -14067,11 +14248,11 @@ GConf is a system for storing application preferences. It is intended for user *homepage*: https://projects.gnome.org/gconf/ -========= ======================================================================================================================================== -version toolchain -========= ======================================================================================================================================== -``3.2.6`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -========= ======================================================================================================================================== +========= ============================================================================================================================================================ +version toolchain +========= ============================================================================================================================================================ +``3.2.6`` ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +========= ============================================================================================================================================================ .. _list_software_GCTA_287: @@ -14194,6 +14375,7 @@ version versionsuffix toolchain ``10.2`` ``GCCcore/10.3.0`` ``10.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``11.1`` ``GCCcore/11.2.0`` +``12.1`` ``GCCcore/11.3.0`` ========== ================== =============================== @@ -14388,6 +14570,8 @@ version toolchain ``10.6.2`` ``foss/2020a`` ``10.7.1`` ``GCC/10.2.0``, ``GCC/11.2.0`` ``11.0.0`` ``GCC/11.2.0`` +``11.0.1`` ``GCC/11.2.0`` +``11.0.2`` ``GCC/11.2.0`` ============= ================================================================ @@ -14841,6 +15025,7 @@ version versionsuffix toolchain ``1.7.2`` ``-Python-3.8.2`` ``foss/2020a`` ``1.7.4-pre2`` ``foss/2020b`` ``1.7.5.3`` ``foss/2021b`` +``1.7.6.1`` ``foss/2021b`` ============== ================= ============== @@ -15076,11 +15261,12 @@ Gifsicle is a command-line tool for creating, editing, and getting information *homepage*: https://github.com/kohler/gifsicle -======== ================= -version toolchain -======== ================= -``1.92`` ``GCCcore/8.2.0`` -======== ================= +======== ================== +version toolchain +======== ================== +``1.92`` ``GCCcore/8.2.0`` +``1.93`` ``GCCcore/11.3.0`` +======== ================== .. _list_software_GIMIC_361: @@ -15273,7 +15459,7 @@ version toolchain *git-lfs* +++++++++ -Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com +Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com *homepage*: https://git-lfs.github.com @@ -15283,6 +15469,7 @@ version toolchain ``1.1.1`` ``system`` ``2.7.1`` ``system`` ``2.11.0`` ``system`` +``3.2.0`` ``system`` ========== ========== @@ -15414,6 +15601,7 @@ version toolchain ``3.3.2`` ``GCCcore/9.3.0`` ``3.3.3`` ``GCCcore/10.2.0`` ``3.3.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``3.3.8`` ``GCCcore/11.3.0`` ========= ====================================== @@ -15461,6 +15649,7 @@ Network extensions for GLib version toolchain ========== ================== ``2.68.1`` ``GCCcore/10.3.0`` +``2.72.1`` ``GCCcore/11.2.0`` ========== ================== @@ -15551,6 +15740,22 @@ version toolchain =========== ============================================================================= +.. _list_software_GLM-AED_471: + +*GLM-AED* ++++++++++ + +The General Lake Model (GLM) is a water balance and one-dimensional vertical stratification hydrodynamic model, which is dynamically coupled with the AED water quality modelling library. GLM-AED is suitable for simulating conditions in a wide range of natural and engineered lakes, including shallow (well-mixed) and deep (stratified) systems. The model has been successfully applied to systems from the scale of individual ponds and wetlands, to actively operated reservoirs, upto the scale of the Great Lakes. + +*homepage*: https://github.com/AquaticEcoDynamics/glm-aed + +=========== =============== +version toolchain +=========== =============== +``3.3.0a5`` ``gompi/2021b`` +=========== =============== + + .. _list_software_GlobalArrays_1219: *GlobalArrays* @@ -15580,11 +15785,14 @@ A Command Line Wrapper over the Globus SDK for Python, which provides an interfa *homepage*: https://docs.globus.org/cli/ -========== ================= -version toolchain -========== ================= -``1.11.0`` ``GCCcore/8.3.0`` -========== ================= +========== ================== +version toolchain +========== ================== +``1.11.0`` ``GCCcore/8.3.0`` +``3.1.1`` ``GCCcore/10.2.0`` +``3.2.0`` ``GCCcore/10.3.0`` +``3.6.0`` ``GCCcore/11.2.0`` +========== ================== .. _list_software_GlobusConnectPersonal_2170: @@ -15894,6 +16102,7 @@ version toolchain ``5.2.8`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``5.4.1`` ``GCCcore/10.2.0`` ``5.4.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``5.4.4`` ``GCCcore/11.3.0`` ========= ================================================================ @@ -16302,6 +16511,7 @@ version toolchain ``2.7.90`` ``GCCcore/8.3.0`` ``2.8`` ``GCCcore/9.3.0`` ``2.9.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.10`` ``GCCcore/11.3.0`` ========== ========================================================== @@ -16567,6 +16777,7 @@ version versionsuffix toolchain ``2.47.0`` ``-Java-11`` ``GCCcore/10.2.0`` ``2.47.2`` ``GCCcore/10.3.0`` ``2.50.0`` ``GCCcore/11.2.0`` +``5.0.0`` ``GCCcore/11.3.0`` ========== ========================= =============================== @@ -16731,11 +16942,11 @@ Groff (GNU troff) is a typesetting system that reads plain text mixed with forma *homepage*: https://www.gnu.org/software/groff -========== =================================================================================================================================== -version toolchain -========== =================================================================================================================================== -``1.22.4`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== =================================================================================================================================== +========== ======================================================================================================================================================= +version toolchain +========== ======================================================================================================================================================= +``1.22.4`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ======================================================================================================================================================= .. _list_software_GroIMP_526: @@ -16799,8 +17010,11 @@ version versionsuffix toolchain ``2021.3`` ``foss/2021a`` ``2021.3`` ``-CUDA-11.3.1`` ``foss/2021a`` ``2021.3`` ``-CUDA-11.3.1-PLUMED-2.7.2`` ``foss/2021a`` +``2021.3`` ``-PLUMED-2.7.2`` ``foss/2021a`` ``2021.5`` ``foss/2021b`` ``2021.5`` ``-CUDA-11.4.1`` ``foss/2021b`` +``2021.5`` ``-CUDA-11.4.1-PLUMED-2.8.0`` ``foss/2021b`` +``2021.5`` ``-PLUMED-2.8.0`` ``foss/2021b`` ========== ============================= ============================================================================================================ @@ -17090,13 +17304,13 @@ version toolchain The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. -*homepage*: https://developer.gnome.org/gtk+/stable/ +*homepage*: https://www.gtk.org -=========== ================== -version toolchain -=========== ================== -``2.24.33`` ``GCCcore/10.3.0`` -=========== ================== +=========== ====================================== +version toolchain +=========== ====================================== +``2.24.33`` ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +=========== ====================================== .. _list_software_GTK3_281: @@ -17175,12 +17389,12 @@ GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free *homepage*: http://gts.sourceforge.net/ -============ =================================================================================================================================================================================================================================== -version toolchain -============ =================================================================================================================================================================================================================================== -``0.7.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` -``20121130`` ``foss/2017b`` -============ =================================================================================================================================================================================================================================== +============ ======================================================================================================================================================================================================================================================= +version toolchain +============ ======================================================================================================================================================================================================================================================= +``0.7.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` +``20121130`` ``foss/2017b`` +============ ======================================================================================================================================================================================================================================================= .. _list_software_gubbins_746: @@ -17281,6 +17495,7 @@ version versionsuffix toolchain ``9.1.1`` ``GCCcore/10.2.0`` ``9.1.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``system`` ``9.5.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``9.5.2`` ``GCCcore/11.3.0`` ========= ================= ================================================== @@ -17309,7 +17524,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_hector_645` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_HIP_225` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_HISAT2_427` - :ref:`list_software_histolab_854` - :ref:`list_software_hivtrace_854` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hydra_504` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_hector_645` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_HIP_225` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_hiredis_744` - :ref:`list_software_HISAT2_427` - :ref:`list_software_histolab_854` - :ref:`list_software_hivtrace_854` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_how_are_we_stranded_here_2519` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hydra_504` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -17686,7 +17901,10 @@ version versionsuffix toolchain ``1.10.8`` ``gompi/2021b`` ``1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` ``1.12.1`` ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021b`` +``1.12.2`` ``gompi/2022a``, ``iimpi/2022a`` +``1.12.2`` ``-serial`` ``GCCcore/11.3.0`` ``1.13.1`` ``gompi/2022a``, ``iimpi/2022a`` +``1.13.1`` ``-serial`` ``GCCcore/11.3.0`` ================= ============= ================================================================================================================================================================================================================== @@ -17825,7 +18043,7 @@ version toolchain ``1.47.15`` ``GCCcore/10.1.0`` ``1.47.16`` ``GCCcore/10.2.0`` ``1.48.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0`` -``1.49.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.5.0`` +``1.49.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0`` =========== ================================================================================================================================================================================== @@ -17838,14 +18056,14 @@ The HH-suite is an open-source software package for sensitive protein sequence *homepage*: https://github.com/soedinglab/hh-suite -============== ================= ================================================================== -version versionsuffix toolchain -============== ================= ================================================================== -``3.0-beta.3`` ``intel/2018a`` -``3.2.0`` ``foss/2019b``, ``fosscuda/2019b`` -``3.3.0`` ``foss/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b`` -``3.3.0`` ``-Python-3.7.4`` ``gompic/2019b`` -============== ================= ================================================================== +============== ================= =================================================================================== +version versionsuffix toolchain +============== ================= =================================================================================== +``3.0-beta.3`` ``intel/2018a`` +``3.2.0`` ``foss/2019b``, ``fosscuda/2019b`` +``3.3.0`` ``foss/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b`` +``3.3.0`` ``-Python-3.7.4`` ``gompic/2019b`` +============== ================= =================================================================================== .. _list_software_HiC-Pro_594: @@ -17993,6 +18211,22 @@ version toolchain ========= ================================= +.. _list_software_hiredis_744: + +*hiredis* ++++++++++ + +Hiredis is a minimalistic C client library for the Redis database. It is minimalistic because it just adds minimal support for the protocol, but at the same time it uses a high level printf-alike API in order to make it much higher level than otherwise suggested by its minimal code base and the lack of explicit bindings for every Redis command. + +*homepage*: https://github.com/redis/hiredis + +========= ================== +version toolchain +========= ================== +``1.0.2`` ``GCCcore/11.2.0`` +========= ================== + + .. _list_software_HISAT2_427: *HISAT2* @@ -18197,6 +18431,22 @@ version versionsuffix toolchain ========= ================== =============================== +.. _list_software_how_are_we_stranded_here_2519: + +*how_are_we_stranded_here* +++++++++++++++++++++++++++ + +Python package for testing strandedness of RNA-Seq fastq files + +*homepage*: https://github.com/signalbash/how_are_we_stranded_here + +========= ============== +version toolchain +========= ============== +``1.0.1`` ``foss/2021b`` +========= ============== + + .. _list_software_HPCG_290: *HPCG* @@ -18335,6 +18585,7 @@ version versionsuffix toolchain ``1.11`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` ``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` ``1.14`` ``GCC/11.2.0`` +``1.15.1`` ``GCC/11.3.0`` ``20160107`` ``-PacBio`` ``intel/2017a`` ============ ============= =========================================================================================================================================================== @@ -18558,6 +18809,7 @@ version toolchain ``2.20.0`` ``foss/2020b``, ``intel/2020b`` ``2.21.0`` ``foss/2021a``, ``fosscuda/2020b`` ``2.24.0`` ``intel/2021b`` +``2.25.0`` ``foss/2022a`` ========== ================================================================ @@ -18567,7 +18819,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_i7z_282` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_InterProScan_data_1713` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intervaltree-python_2020` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_Iris_407` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_IsoNet_594` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_i7z_282` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_indicators_1072` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_InterProScan_data_1713` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intervaltree-python_2020` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_Iris_407` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_IsoNet_594` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -19556,6 +19808,22 @@ version toolchain ======== ============== +.. _list_software_indicators_1072: + +*indicators* +++++++++++++ + +- Thread-safe progress bars and spinners - Header-only library. Grab a copy of include/indicators. - Single-header version in single_include/indicators. + +*homepage*: https://github.com/p-ranav/indicators + +======= ================== +version toolchain +======= ================== +``2.2`` ``GCCcore/11.3.0`` +======= ================== + + .. _list_software_Inelastica_1021: *Inelastica* @@ -19682,6 +19950,7 @@ version toolchain ``2019_update5`` ``system`` ``2021.4.0`` ``system`` ``2022.0.0`` ``system`` +``2022.1.0`` ``system`` ================ ========== @@ -19939,12 +20208,12 @@ A mutable, self-balancing interval tree. Queries may be by point, by range over *homepage*: https://github.com/chaimleib/intervaltree -========= ================= ================== -version versionsuffix toolchain -========= ================= ================== -``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` -``3.1.0`` ``GCCcore/10.3.0`` -========= ================= ================== +========= ================= ====================================== +version versionsuffix toolchain +========= ================= ====================================== +``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` +``3.1.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ================= ====================================== .. _list_software_intltool_885: @@ -20340,7 +20609,7 @@ version toolchain ``0.16`` ``GCC/4.9.3-2.25`` ``0.17`` ``foss/2016a`` ``0.23`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``0.24`` ``GCCcore/11.2.0`` +``0.24`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ======== ========================================================= @@ -20417,6 +20686,7 @@ version toolchain ``2019.4.036`` ``system`` ``2021.2.0`` ``system`` ``2021.5.0`` ``system`` +``2021.6.0`` ``system`` ============== ========== @@ -20523,7 +20793,7 @@ version toolchain --- -:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_Jasmine_711` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_jax_323` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_Jorg_402` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_JSON-GLib_709` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyter-matlab-proxy_2080` - :ref:`list_software_jupyter-server-proxy_2118` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` - :ref:`list_software_jxrlib_651` +:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_Jasmine_711` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_JavaFX_544` - :ref:`list_software_jax_323` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_Jorg_402` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_json-fortran_1251` - :ref:`list_software_JSON-GLib_709` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyter-matlab-proxy_2080` - :ref:`list_software_jupyter-resource-usage_2282` - :ref:`list_software_jupyter-server-proxy_2118` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` - :ref:`list_software_jxrlib_651` .. _list_software_JAGS_293: @@ -20552,12 +20822,13 @@ Jansson is a C library for encoding, decoding and manipulating JSON data. Its m *homepage*: http://www.digip.org/jansson/ -========== ============== -version toolchain -========== ============== -``2.6`` ``GCC/4.8.3`` -``2.13.1`` ``GCC/10.2.0`` -========== ============== +========== ============================== +version toolchain +========== ============================== +``2.6`` ``GCC/4.8.3`` +``2.13.1`` ``GCC/10.2.0``, ``GCC/11.2.0`` +``2.14`` ``GCC/11.3.0`` +========== ============================== .. _list_software_Jasmine_711: @@ -20657,10 +20928,13 @@ version versionsuffix toolchain ``1.8_191`` ``-b26-OpenJDK`` ``system`` ``1.8_265`` ``-b01-OpenJDK-aarch64`` ``system`` ``1.9.0.4`` ``system`` +``8`` ``system`` +``8.345`` ``system`` ``11`` ``system`` ``11.0.2`` ``system`` ``11.0.6`` ``-ppc64le`` ``system`` ``11.0.8`` ``-aarch64`` ``system`` +``11.0.16`` ``system`` ``13`` ``system`` ``13.0.2`` ``system`` ``15`` ``system`` @@ -20670,9 +20944,26 @@ version versionsuffix toolchain ``17`` ``system`` ``17.0.1`` ``system`` ``17.0.2`` ``system`` +``17.0.4`` ``system`` ============= ======================== ========== +.. _list_software_JavaFX_544: + +*JavaFX* +++++++++ + +OpenJFX is an open source, next generation client application platform for desktop, mobile and embedded systems built on Java + +*homepage*: https://openjfx.io/ + +========== ====================== ========== +version versionsuffix toolchain +========== ====================== ========== +``11.0.2`` ``_linux-x64_bin-sdk`` ``system`` +========== ====================== ========== + + .. _list_software_jax_323: *jax* @@ -20691,6 +20982,7 @@ version versionsuffix toolchain ``0.2.24`` ``-CUDA-11.3.1`` ``foss/2021a`` ``0.3.9`` ``foss/2021a`` ``0.3.9`` ``-CUDA-11.3.1`` ``foss/2021a`` +``0.3.14`` ``-CUDA-11.7.0`` ``foss/2022a`` ========== ================ ================================== @@ -20885,6 +21177,22 @@ version toolchain ======== ========================================================== +.. _list_software_json-fortran_1251: + +*json-fortran* +++++++++++++++ + +JSON-Fortran: A Modern Fortran JSON API + +*homepage*: https://github.com/jacobwilliams/json-fortran + +========= ================== +version toolchain +========= ================== +``8.3.0`` ``GCCcore/11.2.0`` +========= ================== + + .. _list_software_JSON-GLib_709: *JSON-GLib* @@ -21038,6 +21346,22 @@ version toolchain ========= ================== +.. _list_software_jupyter-resource-usage_2282: + +*jupyter-resource-usage* +++++++++++++++++++++++++ + +Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU) + +*homepage*: https://github.com/jupyter-server/jupyter-resource-usage + +========= ================== +version toolchain +========= ================== +``0.6.1`` ``GCCcore/10.3.0`` +========= ================== + + .. _list_software_jupyter-server-proxy_2118: *jupyter-server-proxy* @@ -21183,6 +21507,7 @@ version toolchain ========= ====================================== ``2.0.4`` ``GCCcore/10.2.0`` ``3.3.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``3.3.2`` ``GCCcore/11.2.0`` ========= ====================================== @@ -21351,6 +21676,7 @@ version toolchain ``2.1.2`` ``foss/2019a``, ``intel/2019a`` ``2.1.3`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` ``2.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.3.0`` ``GCCcore/11.2.0`` ========= ================================================================ @@ -21603,7 +21929,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LBFGS++_452` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_LERC_294` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaec_608` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libavif_733` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libde265_669` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libexif_739` - :ref:`list_software_libfabric_926` - :ref:`list_software_libfdf_615` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgdiplus_1071` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libheif_723` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_LibLZF_515` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libmbd_618` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libnsl_644` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libopus_766` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpspio_866` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libSBML_613` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libtree_743` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_longread_umi_1270` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPeg_360` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LBFGS++_452` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_LERC_294` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaec_608` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libavif_733` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libde265_669` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libev_530` - :ref:`list_software_libevent_857` - :ref:`list_software_libexif_739` - :ref:`list_software_libfabric_926` - :ref:`list_software_libfdf_615` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgdiplus_1071` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libheif_723` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_LibLZF_515` - :ref:`list_software_libmad_617` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libmbd_618` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libnsl_644` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libopus_766` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libplinkio_1069` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpspio_866` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libSBML_613` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libtree_743` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_longread_umi_1270` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPeg_360` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_LuaJIT2-OpenResty_1553` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -21664,14 +21990,17 @@ LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale At *homepage*: https://lammps.sandia.gov/ -============ ============================= =============================== -version versionsuffix toolchain -============ ============================= =============================== -``3Mar2020`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` -``3Mar2020`` ``-Python-3.8.2-kokkos`` ``foss/2020a``, ``intel/2020a`` -``7Aug2019`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` -``7Aug2019`` ``-Python-3.7.4-kokkos-OCTP`` ``intel/2019b`` -============ ============================= =============================== +============= ============================= =============================== +version versionsuffix toolchain +============= ============================= =============================== +``3Mar2020`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` +``3Mar2020`` ``-Python-3.8.2-kokkos`` ``foss/2020a``, ``intel/2020a`` +``7Aug2019`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` +``7Aug2019`` ``-Python-3.7.4-kokkos-OCTP`` ``intel/2019b`` +``23Jun2022`` ``-kokkos`` ``foss/2021a``, ``foss/2021b`` +``23Jun2022`` ``-kokkos-CUDA-11.3.1`` ``foss/2021a`` +``23Jun2022`` ``-kokkos-CUDA-11.4.1`` ``foss/2021b`` +============= ============================= =============================== .. _list_software_lancet_631: @@ -21699,13 +22028,13 @@ LAPACK is written in Fortran90 and provides routines for solving systems of sim *homepage*: https://www.netlib.org/lapack/ -========== ================== -version toolchain -========== ================== -``3.8.0`` ``GCC/7.3.0-2.30`` -``3.9.1`` ``GCC/10.2.0`` -``3.10.1`` ``GCC/11.2.0`` -========== ================== +========== ============================== +version toolchain +========== ============================== +``3.8.0`` ``GCC/7.3.0-2.30`` +``3.9.1`` ``GCC/10.2.0`` +``3.10.1`` ``GCC/11.2.0``, ``GCC/11.3.0`` +========== ============================== .. _list_software_LAST_308: @@ -21974,11 +22303,11 @@ Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsig *homepage*: https://gitlab.dkrz.de/k202009/libaec -========= ================== -version toolchain -========= ================== -``1.0.6`` ``GCCcore/10.2.0`` -========= ================== +========= ========================================================== +version toolchain +========= ========================================================== +``1.0.6`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ========================================================== .. _list_software_libaio_624: @@ -22119,6 +22448,7 @@ version toolchain ``1.14`` ``GCCcore/10.2.0`` ``1.15`` ``GCCcore/10.3.0`` ``1.17`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.1`` ``GCCcore/11.3.0`` ======== ========================================================================================================= @@ -22371,6 +22701,7 @@ The DWARF Debugging Information Format is of interest to programmers working on ============ =================================================== version toolchain ============ =================================================== +``0.4.1`` ``GCCcore/11.3.0`` ``20140805`` ``GCC/4.9.2`` ``20150310`` ``GCC/4.9.2``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0`` ``20190529`` ``GCCcore/8.2.0`` @@ -22408,11 +22739,11 @@ libelf is a free ELF object file access library *homepage*: https://directory.fsf.org/wiki/Libelf -========== ==================================================================================================================================================================== -version toolchain -========== ==================================================================================================================================================================== -``0.8.13`` ``GCC/4.8.3``, ``GCC/4.9.2``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` -========== ==================================================================================================================================================================== +========== ======================================================================================================================================================================================== +version toolchain +========== ======================================================================================================================================================================================== +``0.8.13`` ``GCC/4.8.3``, ``GCC/4.9.2``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +========== ======================================================================================================================================================================================== .. _list_software_libepoxy_876: @@ -22435,6 +22766,22 @@ version toolchain ========== ======================================================== +.. _list_software_libev_530: + +*libev* ++++++++ + +A full-featured and high-performance (see benchmark) event loop that is loosely modelled after libevent, but without its limitations and bugs. It is used in GNU Virtual Private Ethernet, rxvt-unicode, auditd, the Deliantra MORPG Server and Client, and many other programs. + +*homepage*: http://software.schmorp.de/pkg/libev.html + +======== ============== +version toolchain +======== ============== +``4.33`` ``GCC/11.2.0`` +======== ============== + + .. _list_software_libevent_857: *libevent* @@ -22617,7 +22964,7 @@ version toolchain ``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b``, ``intel/2018a`` ``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``2.3.1`` ``GCCcore/10.3.0`` -``2.3.3`` ``GCCcore/11.2.0`` +``2.3.3`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ============================================================================================================ @@ -22830,11 +23177,11 @@ libHaru is a free, cross platform, open source library for generating PDF files. *homepage*: http://libharu.org/ -========= ================================================================================================================================================================================================= -version toolchain -========= ================================================================================================================================================================================================= -``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2021a``, ``foss/2021b``, ``intel/2017a``, ``intel/2018b`` -========= ================================================================================================================================================================================================= +========= ===================================================================================================================================================================================================================== +version toolchain +========= ===================================================================================================================================================================================================================== +``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2021a``, ``foss/2021b``, ``intel/2017a``, ``intel/2018b`` +========= ===================================================================================================================================================================================================================== .. _list_software_libheif_723: @@ -22975,6 +23322,7 @@ version versionsuffix toolchain ``2.4.2`` ``intel/2018a`` ``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` ``2.6.0`` ``-lmax-6-cp2k`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a``, ``iimpi/2021a`` +``2.7.2`` ``-lmax-6-cp2k`` ``GCC/11.3.0`` ========= ================ =================================================================================================================================================================================================================== @@ -23055,6 +23403,22 @@ version toolchain ======= ================== +.. _list_software_libmad_617: + +*libmad* +++++++++ + +MAD is a high-quality MPEG audio decoder. + +*homepage*: https://www.underbit.com/products/mad/ + +=========== ================== +version toolchain +=========== ================== +``0.15.1b`` ``GCCcore/11.3.0`` +=========== ================== + + .. _list_software_libmatheval_1161: *libmatheval* @@ -23285,6 +23649,22 @@ version toolchain ========== ==================================================================================================================== +.. _list_software_libplinkio_1069: + +*libplinkio* +++++++++++++ + +A small C and Python library for reading PLINK genotype files. + +*homepage*: https://github.com/mfranberg/libplinkio + +========= ================= +version toolchain +========= ================= +``0.9.8`` ``GCCcore/9.3.0`` +========= ================= + + .. _list_software_libpng_636: *libpng* @@ -23299,6 +23679,7 @@ version toolchain ========== ==================================================================================================================== ``1.2.58`` ``system`` ``1.2.59`` ``system`` +``1.5.30`` ``system`` ``1.6.21`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``1.6.23`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``1.6.24`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` @@ -23322,13 +23703,13 @@ C library for the Public Suffix List *homepage*: https://rockdaboot.github.io/libpsl -========== ====================================== -version toolchain -========== ====================================== -``0.20.2`` ``GCCcore/7.3.0`` -``0.21.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.21.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -========== ====================================== +========== ========================================================== +version toolchain +========== ========================================================== +``0.20.2`` ``GCCcore/7.3.0`` +``0.21.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.21.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========== ========================================================== .. _list_software_libPSML_627: @@ -23429,6 +23810,7 @@ version versionsuffix toolchain ``2.6.3`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` ``2.6.4`` ``intel/2016b`` ``2.7.1`` ``intel/2018a`` +``2.8.0`` ``GCCcore/10.3.0`` ========= ================ =============================================== @@ -23448,7 +23830,7 @@ version toolchain ``7.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``8.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ``8.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``8.1.2`` ``GCCcore/11.3.0`` +``8.1.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0`` ========= =================================================================================================================================================================================================================================================================================================================================================================================== @@ -23668,6 +24050,7 @@ version toolchain ``2.66.1`` ``GCCcore/8.2.0`` ``2.70.0`` ``GCCcore/8.3.0`` ``2.72.0`` ``GCCcore/10.2.0`` +``2.74.0`` ``GCCcore/10.3.0`` ========== ================== @@ -24501,15 +24884,15 @@ LibYAML is a YAML parser and emitter written in C. *homepage*: https://pyyaml.org/wiki/LibYAML -========= =================================================================== -version toolchain -========= =================================================================== -``0.1.6`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``0.1.7`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``system`` -``0.2.1`` ``GCCcore/7.3.0``, ``system`` -``0.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========= =================================================================== +========= ============================================================================== +version toolchain +========= ============================================================================== +``0.1.6`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``0.1.7`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``system`` +``0.2.1`` ``GCCcore/7.3.0``, ``system`` +``0.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ============================================================================== .. _list_software_libzeep_747: @@ -24542,6 +24925,7 @@ version toolchain ========= ========================================================== ``1.5.2`` ``GCCcore/8.2.0`` ``1.7.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.9.2`` ``GCCcore/11.3.0`` ========= ========================================================== @@ -25198,6 +25582,7 @@ version toolchain ``5.3.5`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ``5.4.2`` ``GCCcore/10.2.0`` ``5.4.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``5.4.4`` ``GCCcore/11.3.0`` =========== ======================================================================================= @@ -25217,6 +25602,22 @@ version toolchain ========= ============= +.. _list_software_LuaJIT2-OpenResty_1553: + +*LuaJIT2-OpenResty* ++++++++++++++++++++ + +openresty/luajit2 - OpenResty's maintained branch of LuaJIT. LuaJIT is a Just-In-Time Compiler (JIT) for the Lua programming language. Lua is a powerful, dynamic and light-weight programming language. It may be embedded or used as a general-purpose, stand-alone language. + +*homepage*: https://github.com/openresty/luajit2 + +================ ============= +version toolchain +================ ============= +``2.1-20220411`` ``GCC/9.3.0`` +================ ============= + + .. _list_software_Lucene-Geo-Gazetteer_1916: *Lucene-Geo-Gazetteer* @@ -25309,6 +25710,7 @@ version versionsuffix toolchain ``4.5.2`` ``GCCcore/9.3.0`` ``4.6.2`` ``GCCcore/10.2.0`` ``4.6.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``4.9.1`` ``GCCcore/11.3.0`` ========= ================== ====================================== @@ -25371,7 +25773,7 @@ version toolchain --- -:ref:`list_software_M1QN3_336` - :ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_MAGeCK_456` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_matplotlib-inline_1764` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_MEGAN_360` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_Minipolish_1052` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_mm-common_912` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MNE-Python_911` - :ref:`list_software_MOABS_370` - :ref:`list_software_ModelTest-NG_1107` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_MONA_299` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MuJoCo_557` - :ref:`list_software_mujoco-py_931` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M1QN3_336` - :ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_MAGeCK_456` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_matplotlib-inline_1764` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_MEGAN_360` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaMorpheus_1242` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mgltools_881` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_miniasm_750` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_Minipolish_1052` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_mm-common_912` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MNE-Python_911` - :ref:`list_software_MOABS_370` - :ref:`list_software_ModelTest-NG_1107` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_MONA_299` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MuJoCo_557` - :ref:`list_software_mujoco-py_931` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_muMerge_722` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M1QN3_336: @@ -25405,7 +25807,7 @@ version toolchain ``1.4.16`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.4.18`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` -``1.4.19`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``system`` +``1.4.19`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``system`` ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -25470,11 +25872,12 @@ maeparser is a parser for Schrodinger Maestro files. *homepage*: https://github.com/schrodinger/maeparser -========= ================================ -version toolchain -========= ================================ -``1.2.2`` ``gompi/2019a``, ``iimpi/2019a`` -========= ================================ +========= ================================================================== +version toolchain +========= ================================================================== +``1.2.2`` ``gompi/2019a``, ``iimpi/2019a`` +``1.3.0`` ``gompi/2019b``, ``gompi/2021a``, ``gompi/2022a``, ``iimpi/2020a`` +========= ================================================================== .. _list_software_MAFFT_366: @@ -25689,7 +26092,7 @@ version versionsuffix toolchain ======= ============= =========================================================================================== ``6.7`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``6.7`` ``-minimal`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``6.8`` ``GCCcore/11.2.0`` +``6.8`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ======= ============= =========================================================================================== @@ -26070,6 +26473,7 @@ version versionsuffix toolchain ``3.4.2`` ``foss/2021a``, ``intel/2021a`` ``3.4.3`` ``foss/2021b``, ``intel/2021b`` ``3.5.1`` ``foss/2020b``, ``intel/2020b`` +``3.5.2`` ``foss/2022a`` ========= ================================= =================================================================================== @@ -26096,13 +26500,14 @@ version toolchain MATSim is an open-source framework to implement large-scale agent-based transport simulations. -*homepage*: http://www.matsim.org/ +*homepage*: https://www.matsim.org/ -========= =================== =============== -version versionsuffix toolchain -========= =================== =============== -``0.8.1`` ``-Java-1.8.0_112`` ``intel/2016b`` -========= =================== =============== +========= =================== ============================== +version versionsuffix toolchain +========= =================== ============================== +``0.8.1`` ``-Java-1.8.0_112`` ``intel/2016b`` +``14.0`` ``-Java-11`` ``GCCcore/11.2.0``, ``system`` +========= =================== ============================== .. _list_software_Maude_492: @@ -26381,6 +26786,7 @@ version versionsuffix toolchain ``0.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``1.1.1`` ``foss/2020b`` ``2.0.0`` ``foss/2021b``, ``intel/2021b`` +``2.2.0`` ``foss/2022a`` ========== ================= =============================== @@ -26509,6 +26915,7 @@ version versionsuffix toolchain ``1.4.3`` ``foss/2020b`` ``1.4.3`` ``-Python-3.7.4`` ``foss/2019b`` ``1.5.0`` ``foss/2021a`` +``1.6.0`` ``foss/2021b`` ========== ================= ============== @@ -26629,11 +27036,13 @@ Megalodon is a research command line tool to extract high accuracy modified base *homepage*: https://github.com/nanoporetech/megalodon -========= ================================== -version toolchain -========= ================================== -``2.3.5`` ``foss/2020b``, ``fosscuda/2020b`` -========= ================================== +========= ================ ================================== +version versionsuffix toolchain +========= ================ ================================== +``2.3.5`` ``foss/2020b``, ``fosscuda/2020b`` +``2.5.0`` ``foss/2021a`` +``2.5.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ================================== .. _list_software_MEGAN_360: @@ -26786,6 +27195,7 @@ version versionsuffix toolchain ``5.7.1`` ``GCCcore/10.2.0`` ``5.7.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``5.8`` ``GCCcore/10.3.0`` +``6.2`` ``GCCcore/11.3.0`` ========= ================== ================== @@ -27014,6 +27424,7 @@ version toolchain ======= ============== ``4`` ``GCC/10.2.0`` ``5`` ``GCC/10.3.0`` +``6`` ``GCC/11.2.0`` ======= ============== @@ -27066,6 +27477,22 @@ version toolchain ============== ============== +.. _list_software_MetaMorpheus_1242: + +*MetaMorpheus* +++++++++++++++ + +MetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability. This program combines features of Morpheus and G-PTM-D in a single tool. + +*homepage*: https://github.com/smith-chem-wisc/MetaMorpheus + +=========== ================== +version toolchain +=========== ================== +``0.0.320`` ``GCCcore/10.3.0`` +=========== ================== + + .. _list_software_MetaPhlAn_858: *MetaPhlAn* @@ -27178,13 +27605,29 @@ METIS is a set of serial programs for partitioning graphs, partitioning finite e *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview -========= ============= ============================================================================================================================================================================================================================================================================================== -version versionsuffix toolchain -========= ============= ============================================================================================================================================================================================================================================================================================== -``5.0.2`` ``gimkl/2.11.5`` -``5.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``5.1.0`` ``-32bitIDX`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -========= ============= ============================================================================================================================================================================================================================================================================================== +========= ============= ================================================================================================================================================================================================================================================================================================================== +version versionsuffix toolchain +========= ============= ================================================================================================================================================================================================================================================================================================================== +``5.0.2`` ``gimkl/2.11.5`` +``5.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``5.1.0`` ``-32bitIDX`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +========= ============= ================================================================================================================================================================================================================================================================================================================== + + +.. _list_software_mgltools_881: + +*mgltools* +++++++++++ + +The MGLTools software suite can be used for visualization and analysis of molecular structures and comprises the Python Molecular Viewer (PMV, a general purpose molecular viewer), AutoDockTools (ADT, a set of PMV commands specifically developed to support AutoDock users) and Vision (a visual programming environment). + +*homepage*: https://ccsb.scripps.edu/mgltools/ + +========= ========== +version toolchain +========= ========== +``1.5.7`` ``system`` +========= ========== .. _list_software_mhcflurry_988: @@ -27343,12 +27786,30 @@ Mini-XML is a small XML parsing library that you can use to read XML data files *homepage*: https://www.msweet.org/mxml -======= ================== -version toolchain -======= ================== -``2.9`` ``GCCcore/8.2.0`` -``3.2`` ``GCCcore/10.3.0`` -======= ================== +========= ================== +version toolchain +========= ================== +``2.9`` ``GCCcore/8.2.0`` +``2.12`` ``GCCcore/9.3.0`` +``3.2`` ``GCCcore/10.3.0`` +``3.3.1`` ``GCCcore/11.2.0`` +========= ================== + + +.. _list_software_miniasm_750: + +*miniasm* ++++++++++ + +Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads. + +*homepage*: https://github.com/lh3/minimap2 + +================ ====================================== +version toolchain +================ ====================================== +``0.3-20191007`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +================ ====================================== .. _list_software_minibar_738: @@ -27984,9 +28445,9 @@ version toolchain *Molekel* +++++++++ -Molekel is an open-source multi-platform molecular visualization program. +Molekel is an open-source multi-platform molecular visualization program. -*homepage*: http://molekel.cscs.ch/ +*homepage*: http://ugovaretto.github.io/molekel/wiki/pmwiki.php/Main/HomePage.html ========= ================= ========== version versionsuffix toolchain @@ -28004,21 +28465,21 @@ MolMod is a Python library with many compoments that are useful to write molecul *homepage*: https://molmod.github.io/molmod/ -========= ================== =============================== -version versionsuffix toolchain -========= ================== =============================== -``1.1`` ``-Python-2.7.11`` ``intel/2016a`` -``1.1`` ``-Python-2.7.12`` ``intel/2016b`` -``1.1`` ``-Python-2.7.13`` ``intel/2017a`` -``1.4.3`` ``-Python-2.7.14`` ``intel/2017b`` -``1.4.3`` ``-Python-3.6.3`` ``intel/2017b`` -``1.4.4`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``1.4.4`` ``-Python-2.7.15`` ``intel/2018b`` -``1.4.4`` ``-Python-3.7.2`` ``intel/2019a`` -``1.4.5`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.4.5`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.4.8`` ``foss/2020b``, ``foss/2021a`` -========= ================== =============================== +========= ================== ============================================== +version versionsuffix toolchain +========= ================== ============================================== +``1.1`` ``-Python-2.7.11`` ``intel/2016a`` +``1.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.1`` ``-Python-2.7.13`` ``intel/2017a`` +``1.4.3`` ``-Python-2.7.14`` ``intel/2017b`` +``1.4.3`` ``-Python-3.6.3`` ``intel/2017b`` +``1.4.4`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``1.4.4`` ``-Python-2.7.15`` ``intel/2018b`` +``1.4.4`` ``-Python-3.7.2`` ``intel/2019a`` +``1.4.5`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.4.5`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.4.8`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` +========= ================== ============================================== .. _list_software_Molpro_633: @@ -28295,14 +28756,14 @@ Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily h *homepage*: http://www.multiprecision.org/ -========= =============== ========================================================== -version versionsuffix toolchain -========= =============== ========================================================== -``1.0.3`` ``intel/2017a`` -``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` -``1.1.0`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/9.3.0`` -``1.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========= =============== ========================================================== +========= =============== ============================================================================== +version versionsuffix toolchain +========= =============== ============================================================================== +``1.0.3`` ``intel/2017a`` +``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` +``1.1.0`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/9.3.0`` +``1.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= =============== ============================================================================== .. _list_software_MPFR_309: @@ -28752,12 +29213,28 @@ version toolchain ========= ================================ +.. _list_software_muMerge_722: + +*muMerge* ++++++++++ + +muMerge is a tool for combining bed regions from multiple bed files that overlap. + +*homepage*: https://github.com/Dowell-Lab/mumerge + +========= ============== +version toolchain +========= ============== +``1.1.0`` ``foss/2022a`` +========= ============== + + .. _list_software_MUMmer_563: *MUMmer* ++++++++ -MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. +MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. *homepage*: http://mummer.sourceforge.net/ @@ -28766,6 +29243,7 @@ version toolchain ============== ========================================================================= ``3.23`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``foss/2016b`` ``4.0.0beta2`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``foss/2018b`` +``4.0.0rc1`` ``GCCcore/11.2.0`` ============== ========================================================================= @@ -28788,6 +29266,7 @@ version versionsuffix toolchain ``5.4.0`` ``-metis`` ``foss/2021a`` ``5.4.1`` ``-metis`` ``foss/2021b``, ``intel/2021b`` ``5.5.0`` ``-metis`` ``foss/2021a`` +``5.5.1`` ``-metis`` ``foss/2022a`` ========= ============== ================================================================================================================= @@ -29153,7 +29632,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_namedlist_961` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_NetPyNE_643` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_num2words_945` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numdiff_745` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_namedlist_961` - :ref:`list_software_nano_428` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_NetPyNE_643` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_nghttp3_712` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_num2words_945` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numdiff_745` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -29227,6 +29706,22 @@ version toolchain ======= ================== +.. _list_software_nano_428: + +*nano* +++++++ + +a simple editor, inspired by Pico + +*homepage*: https://www.nano-editor.org/ + +======= ================== +version toolchain +======= ================== +``6.4`` ``GCCcore/11.3.0`` +======= ================== + + .. _list_software_NanoComp_795: *NanoComp* @@ -29708,7 +30203,7 @@ version toolchain ``6.0`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``6.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` ``6.2`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``system`` -``6.3`` ``GCCcore/11.3.0`` +``6.3`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``system`` ======= ============================================================================================================================================================================================================================================================================================================================================================================= @@ -29725,7 +30220,7 @@ Ncview is a visual browser for netCDF format files. Typically you would use ncv version toolchain ========= ====================================================================================================================================================================================== ``2.1.7`` ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``gompi/2019a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b``, ``iomkl/2018b`` -``2.1.8`` ``gompi/2020a``, ``gompi/2021a``, ``gompi/2021b`` +``2.1.8`` ``gompi/2020a``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a`` ========= ====================================================================================================================================================================================== @@ -29917,14 +30412,14 @@ NetCDF (network Common Data Form) is a set of software libraries and machine-in *homepage*: https://www.unidata.ucar.edu/software/netcdf/ -========= ================ ======================================================================================================================================================================== -version versionsuffix toolchain -========= ================ ======================================================================================================================================================================== -``4.3.0`` ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``4.3.0`` ``-HDF5-1.8.18`` ``intel/2017a`` -``4.3.0`` ``-HDF5-1.8.19`` ``intel/2017b`` -``4.3.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b`` -========= ================ ======================================================================================================================================================================== +========= ================ ========================================================================================================================================================================================= +version versionsuffix toolchain +========= ================ ========================================================================================================================================================================================= +``4.3.0`` ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +``4.3.0`` ``-HDF5-1.8.18`` ``intel/2017a`` +``4.3.0`` ``-HDF5-1.8.19`` ``intel/2017b`` +``4.3.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b`` +========= ================ ========================================================================================================================================================================================= .. _list_software_netCDF-Fortran_1309: @@ -29948,6 +30443,7 @@ version versionsuffix toolchain ``4.4.5`` ``gompi/2019a``, ``iimpi/2019a`` ``4.5.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` ``4.5.3`` ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b`` +``4.6.0`` ``gompi/2022a`` ========= ================ ==================================================================================================================================================================================================================================================================================================================================== @@ -30279,6 +30775,22 @@ version toolchain ========= ============================================== +.. _list_software_nghttp3_712: + +*nghttp3* ++++++++++ + +nghttp3 is an implementation of RFC 9114 HTTP/3 mapping over QUIC and RFC 9204 QPACK in C. It does not depend on any particular QUIC transport implementation. + +*homepage*: https://github.com/ngtcp2/nghttp3 + +========= ================== +version toolchain +========= ================== +``0.6.0`` ``GCCcore/11.2.0`` +========= ================== + + .. _list_software_NGLess_556: *NGLess* @@ -30385,6 +30897,7 @@ NGSpeciesID is a tool for clustering and consensus forming of targeted ONT reads version versionsuffix toolchain =========== ================= ============== ``0.1.1.1`` ``-Python-3.7.4`` ``foss/2019b`` +``0.1.2.1`` ``foss/2021b`` =========== ================= ============== @@ -31196,7 +31709,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OGDF_288` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ONNX_323` - :ref:`list_software_ONNX-Runtime_1108` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_ont-remora_1028` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCensus-python_1746` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFace_769` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSceneGraph_1394` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_Optuna_631` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OGDF_288` - :ref:`list_software_olaFlow_724` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ONNX_323` - :ref:`list_software_ONNX-Runtime_1108` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_ont-remora_1028` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCensus-python_1746` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFace_769` - :ref:`list_software_OpenFAST_704` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenFold_791` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSceneGraph_1394` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_Optuna_631` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -31355,6 +31868,22 @@ version toolchain ================== ============== +.. _list_software_olaFlow_724: + +*olaFlow* ++++++++++ + +olaFlow CFD Suite is a free and open source project committed to bringing the latest advances for the simulation of wave dynamics to the OpenFOAM® and FOAM-extend communities. + +*homepage*: https://olaflow.github.io/ + +============ ============== +version toolchain +============ ============== +``20210820`` ``foss/2021b`` +============ ============== + + .. _list_software_OMA_221: *OMA* @@ -31453,6 +31982,8 @@ version versionsuffix toolchain ========= ================ ============== ``0.1.2`` ``foss/2021a`` ``0.1.2`` ``-CUDA-11.3.1`` ``foss/2021a`` +``1.0.0`` ``foss/2021a`` +``1.0.0`` ``-CUDA-11.3.1`` ``foss/2021a`` ========= ================ ============== @@ -31532,18 +32063,19 @@ Open Babel is a chemical toolbox designed to speak the many languages of chemic *homepage*: https://openbabel.org -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``2.3.2`` ``-Python-2.7.11`` ``foss/2016a`` -``2.4.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.4.1`` ``-Python-2.7.15`` ``intel/2018b`` -``2.4.1`` ``-Python-3.6.6`` ``intel/2018b`` -``2.4.1`` ``-Python-3.7.2`` ``intel/2019a`` -``3.0.0`` ``-Python-3.7.4`` ``gompi/2019b`` -``3.1.1`` ``gompi/2021a`` -``3.1.1`` ``-Python-3.7.4`` ``gompi/2019b`` -========= ================== =============== +========= ================== ================================ +version versionsuffix toolchain +========= ================== ================================ +``2.3.2`` ``-Python-2.7.11`` ``foss/2016a`` +``2.4.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.4.1`` ``-Python-2.7.15`` ``intel/2018b`` +``2.4.1`` ``-Python-3.6.6`` ``intel/2018b`` +``2.4.1`` ``-Python-3.7.2`` ``intel/2019a`` +``3.0.0`` ``-Python-3.7.4`` ``gompi/2019b`` +``3.1.1`` ``gompi/2021a``, ``gompi/2022a`` +``3.1.1`` ``-Python-3.7.4`` ``gompi/2019b`` +``3.1.1`` ``-Python-3.8.2`` ``iimpi/2020a`` +========= ================== ================================ .. _list_software_OpenBLAS_692: @@ -31729,6 +32261,22 @@ version versionsuffix toolchain ========= ================ ============== +.. _list_software_OpenFAST_704: + +*OpenFAST* +++++++++++ + +OpenFAST is a wind turbine simulation tool which builds on FAST v8. FAST.Farm extends the capability of OpenFAST to simulate multi-turbine wind farms + +*homepage*: http://openfast.readthedocs.io/ + +========= ============== +version toolchain +========= ============== +``3.0.0`` ``foss/2021b`` +========= ============== + + .. _list_software_OpenFOAM_693: *OpenFOAM* @@ -31769,6 +32317,7 @@ version versionsuffix toolchain ``v2012`` ``foss/2020a`` ``v2106`` ``foss/2021a`` ``v2112`` ``foss/2021b`` +``v2206`` ``foss/2022a`` ================ ============= ================================================= @@ -31793,6 +32342,22 @@ version versionsuffix toolchain ================ ================== ================================= +.. _list_software_OpenFold_791: + +*OpenFold* +++++++++++ + +A faithful PyTorch reproduction of DeepMind's AlphaFold 2 + +*homepage*: https://github.com/aqlaboratory/openfold + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``1.0.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== + + .. _list_software_OpenForceField_1381: *OpenForceField* @@ -31891,16 +32456,17 @@ OpenMM is a toolkit for molecular simulation. *homepage*: https://openmm.org -========= ================= =================================================== -version versionsuffix toolchain -========= ================= =================================================== -``7.1.1`` ``-Python-3.6.3`` ``intel/2017b`` -``7.4.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``7.4.2`` ``-Python-3.8.2`` ``intel/2020a`` -``7.5.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``7.5.0`` ``-Python-3.8.2`` ``fosscuda/2020a``, ``intel/2020a`` -``7.5.1`` ``foss/2020b``, ``fosscuda/2020b`` -========= ================= =================================================== +========= =================== =================================================== +version versionsuffix toolchain +========= =================== =================================================== +``7.1.1`` ``-Python-3.6.3`` ``intel/2017b`` +``7.4.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``7.4.2`` ``-Python-3.8.2`` ``intel/2020a`` +``7.5.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``7.5.0`` ``-Python-3.8.2`` ``fosscuda/2020a``, ``intel/2020a`` +``7.5.1`` ``foss/2020b``, ``fosscuda/2020b`` +``7.5.1`` ``-DeepMind-patch`` ``foss/2021a`` +========= =================== =================================================== .. _list_software_OpenMM-PLUMED_1056: @@ -32004,7 +32570,7 @@ version versionsuffix toolchain ``4.0.7`` ``GCC/10.3.0`` ``4.1.0`` ``GCC/10.2.0`` ``4.1.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0`` -``4.1.2`` ``GCC/11.2.0`` +``4.1.2`` ``GCC/10.2.0``, ``GCC/11.2.0`` ``4.1.4`` ``GCC/11.3.0`` ``system`` ``GCC/system-2.29`` ========== ================ ==================================================================================================================== @@ -32481,6 +33047,8 @@ version versionsuffix toolchain ``5.8`` ``iimpi/2021b`` ``5.9`` ``gompi/2022.05``, ``gompi/2022a`` ``5.9`` ``-CUDA-11.3.1`` ``gompi/2021a`` +``5.9`` ``-CUDA-11.4.1`` ``gompi/2021b`` +``5.9`` ``-CUDA-11.7.0`` ``gompi/2022a`` ========= ================ ============================================================================================================================================================================================= @@ -32499,6 +33067,7 @@ version toolchain ``2.0`` ``foss/2016a``, ``foss/2017a`` ``2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``3.0`` ``GCCcore/11.3.0`` ======= ======================================================= @@ -32541,7 +33110,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_panito_651` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parameterized_1389` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patch_528` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pfind_529` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_porefoam_857` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_presto_669` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_purge_dups_1086` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyEVTK_515` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_PyFrag_585` - :ref:`list_software_pygccxml_871` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_pyradiomics_1188` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch-Lightning_1690` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_panito_651` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parameterized_1389` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patch_528` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pfind_529` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_Phantompeakqualtools_2140` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_porefoam_857` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_presto_669` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_purge_dups_1086` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyEVTK_515` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_PyFrag_585` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGenomeTracks_1452` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_pyradiomics_1188` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch-Lightning_1690` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -32628,7 +33197,7 @@ version toolchain ``9.38.1`` ``GCC/4.9.2``, ``system`` ``16.02`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2018a`` ``17.03`` ``GCCcore/10.2.0`` -``17.04`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``17.04`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== =========================================================================== @@ -32660,12 +33229,12 @@ pagmo is a C++ scientific library for massively parallel optimization. *homepage*: https://esa.github.io/pagmo2 -========== ============== -version toolchain -========== ============== -``2.17.0`` ``foss/2020b`` -``2.18.0`` ``foss/2021a`` -========== ============== +========== ============================== +version toolchain +========== ============================== +``2.17.0`` ``foss/2020b`` +``2.18.0`` ``foss/2021a``, ``foss/2021b`` +========== ============================== .. _list_software_PAL2NAL_490: @@ -32928,6 +33497,7 @@ version toolchain ``20210322`` ``GCCcore/10.2.0`` ``20210622`` ``GCCcore/10.3.0`` ``20210722`` ``GCCcore/11.2.0`` +``20220722`` ``GCCcore/11.3.0`` ============ =============================== @@ -33028,21 +33598,22 @@ ParaView is a scientific parallel visualizer. *homepage*: https://www.paraview.org -========= ====================== ================================================================================================= -version versionsuffix toolchain -========= ====================== ================================================================================================= -``4.4.0`` ``foss/2016a``, ``intel/2016a`` -``4.4.0`` ``-mpi`` ``gimkl/2.11.5`` -``5.1.2`` ``-mpi`` ``foss/2016b``, ``intel/2016b`` -``5.2.0`` ``-mpi`` ``foss/2016b``, ``intel/2017a`` -``5.3.0`` ``-mpi`` ``foss/2016b`` -``5.4.1`` ``-mpi`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``5.5.2`` ``-Python-2.7.15-mpi`` ``foss/2018b`` -``5.6.2`` ``-Python-3.7.4-mpi`` ``foss/2019b``, ``intel/2019b`` -``5.8.0`` ``-Python-3.8.2-mpi`` ``foss/2020a``, ``intel/2020a`` -``5.8.1`` ``-mpi`` ``foss/2020b`` -``5.9.1`` ``-mpi`` ``foss/2021a``, ``foss/2021b`` -========= ====================== ================================================================================================= +========== ====================== ================================================================================================= +version versionsuffix toolchain +========== ====================== ================================================================================================= +``4.4.0`` ``foss/2016a``, ``intel/2016a`` +``4.4.0`` ``-mpi`` ``gimkl/2.11.5`` +``5.1.2`` ``-mpi`` ``foss/2016b``, ``intel/2016b`` +``5.2.0`` ``-mpi`` ``foss/2016b``, ``intel/2017a`` +``5.3.0`` ``-mpi`` ``foss/2016b`` +``5.4.1`` ``-mpi`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +``5.5.2`` ``-Python-2.7.15-mpi`` ``foss/2018b`` +``5.6.2`` ``-Python-3.7.4-mpi`` ``foss/2019b``, ``intel/2019b`` +``5.8.0`` ``-Python-3.8.2-mpi`` ``foss/2020a``, ``intel/2020a`` +``5.8.1`` ``-mpi`` ``foss/2020b`` +``5.9.1`` ``-mpi`` ``foss/2021a``, ``foss/2021b`` +``5.10.1`` ``-mpi`` ``foss/2022a`` +========== ====================== ================================================================================================= .. _list_software_PARI-GP_496: @@ -33184,15 +33755,16 @@ PatchELF is a small utility to modify the dynamic linker and RPATH of ELF execut *homepage*: http://nixos.org/patchelf.html -======== ========================================================= -version toolchain -======== ========================================================= -``0.8`` ``GNU/4.9.3-2.25`` -``0.9`` ``GCCcore/6.4.0``, ``foss/2016a`` -``0.10`` ``GCCcore/7.2.0``, ``GCCcore/8.3.0`` -``0.12`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``0.13`` ``GCCcore/11.2.0`` -======== ========================================================= +========== ========================================================= +version toolchain +========== ========================================================= +``0.8`` ``GNU/4.9.3-2.25`` +``0.9`` ``GCCcore/6.4.0``, ``foss/2016a`` +``0.10`` ``GCCcore/7.2.0``, ``GCCcore/8.3.0`` +``0.12`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``0.13`` ``GCCcore/11.2.0`` +``0.15.0`` ``GCCcore/11.3.0`` +========== ========================================================= .. _list_software_path.py_708: @@ -33603,6 +34175,7 @@ version versionsuffix toolchain ``5.34.0`` ``-minimal`` ``GCCcore/11.2.0`` ``5.34.1`` ``GCCcore/11.3.0`` ``5.34.1`` ``-minimal`` ``GCCcore/11.3.0`` +``5.36.0`` ``GCCcore/12.1.0`` ========== ============= ========================================================================================= @@ -33729,6 +34302,7 @@ A suite of tools to build and search generalized profiles (protein and DNA). version toolchain ============ ================================== ``3.2.11`` ``GCCcore/10.3.0``, ``foss/2021a`` +``3.2.12`` ``GCCcore/11.2.0`` ``20160324`` ``foss/2016a`` ============ ================================== @@ -33817,6 +34391,22 @@ version toolchain ============ ============== +.. _list_software_Phantompeakqualtools_2140: + +*Phantompeakqualtools* +++++++++++++++++++++++ + +It computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. + +*homepage*: https://github.com/kundajelab/phantompeakqualtools + +========= ============== +version toolchain +========= ============== +``1.2.2`` ``foss/2021b`` +========= ============== + + .. _list_software_PHASE_369: *PHASE* @@ -34493,14 +35083,14 @@ pkg-config is a helper tool used when compiling applications and libraries. It *homepage*: http://www.freedesktop.org/wiki/Software/pkg-config/ -========== ============================================================================================================================================================================================================================ -version toolchain -========== ============================================================================================================================================================================================================================ -``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` -``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``0.29.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a``, ``system`` -========== ============================================================================================================================================================================================================================ +========== ================================================================================================================================================================================================================================================ +version toolchain +========== ================================================================================================================================================================================================================================================ +``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` +``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``0.29.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a``, ``system`` +========== ================================================================================================================================================================================================================================================ .. _list_software_pkgconf_744: @@ -34689,6 +35279,7 @@ version toolchain ``2.00a2.3`` ``GCC/10.3.0``, ``GCC/11.2.0`` ``2.00a2.3_x86_64`` ``system`` ``2.00a3.1`` ``GCC/11.2.0`` +``2.00a3.6`` ``GCC/11.3.0`` =========================== ============================== @@ -34925,7 +35516,7 @@ version toolchain ``1.10.0`` ``foss/2018b``, ``intel/2018b`` ``1.12.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2020a`` ``1.12.2`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2021a`` -``1.12.3`` ``gompi/2021b`` +``1.12.3`` ``gompi/2021b``, ``gompi/2022a`` ========== ===================================================================================== @@ -35079,13 +35670,14 @@ Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. *homepage*: https://github.com/rrwick/Porechop -========= ================= =============== -version versionsuffix toolchain -========= ================= =============== -``0.2.3`` ``-Python-3.5.2`` ``foss/2016b`` -``0.2.4`` ``-Python-3.6.6`` ``foss/2018b`` -``0.2.4`` ``-Python-3.7.4`` ``intel/2019b`` -========= ================= =============== +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``0.2.3`` ``-Python-3.5.2`` ``foss/2016b`` +``0.2.4`` ``GCCcore/11.2.0`` +``0.2.4`` ``-Python-3.6.6`` ``foss/2018b`` +``0.2.4`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= ================== .. _list_software_porefoam_857: @@ -35403,12 +35995,13 @@ PyYAML-based python module to produce pretty and readable YAML-serialized data. *homepage*: https://github.com/mk-fg/pretty-yaml -=========== ================= -version toolchain -=========== ================= -``19.12.0`` ``GCCcore/8.3.0`` -``20.4.0`` ``GCCcore/9.3.0`` -=========== ================= +=========== ================== +version toolchain +=========== ================== +``19.12.0`` ``GCCcore/8.3.0`` +``20.4.0`` ``GCCcore/9.3.0`` +``21.10.1`` ``GCCcore/10.3.0`` +=========== ================== .. _list_software_Primer3_674: @@ -35771,6 +36364,7 @@ version toolchain ``2.2.12`` ``GCCcore/8.3.0`` ``2.3.1`` ``GCCcore/9.3.0`` ``2.3.3`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``2.3.5`` ``GCCcore/11.3.0`` ========== ===================================== @@ -36065,6 +36659,7 @@ pugixml is a light-weight C++ XML processing library version toolchain ========== ================== ``1.11.4`` ``GCCcore/10.3.0`` +``1.12.1`` ``GCCcore/11.2.0`` ========== ================== @@ -36849,6 +37444,22 @@ version versionsuffix toolchain ============ ================== ============== +.. _list_software_pyGenomeTracks_1452: + +*pyGenomeTracks* +++++++++++++++++ + +pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. + +*homepage*: https://pygenometracks.readthedocs.io + +======= ============== +version toolchain +======= ============== +``3.7`` ``foss/2021b`` +======= ============== + + .. _list_software_PyGEOS_503: *PyGEOS* @@ -36910,12 +37521,12 @@ pygmo is a scientific Python library for massively parallel optimization. *homepage*: https://esa.github.io/pygmo2 -========== ============== -version toolchain -========== ============== -``2.16.1`` ``foss/2020b`` -``2.18.0`` ``foss/2021a`` -========== ============== +========== ============================== +version toolchain +========== ============================== +``2.16.1`` ``foss/2020b`` +``2.18.0`` ``foss/2021a``, ``foss/2021b`` +========== ============================== .. _list_software_PyGObject_871: @@ -37285,6 +37896,7 @@ version versionsuffix toolchain ``5.5.0`` ``-Python-2.7.15`` ``foss/2018b`` ``5.5.0`` ``-Python-3.6.6`` ``foss/2018b`` ``6.0.1`` ``foss/2020b``, ``foss/2021a`` +``6.4.2`` ``foss/2022a`` ========= ================== ============================== @@ -37297,12 +37909,13 @@ PyOpenCL lets you access GPUs and other massively parallel compute devices from *homepage*: https://mathema.tician.de/software/pyopencl/ -============ ================= =================================================== -version versionsuffix toolchain -============ ================= =================================================== -``2020.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``2021.1.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -============ ================= =================================================== +============= ================= =================================================== +version versionsuffix toolchain +============= ================= =================================================== +``2020.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2021.1.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``2021.2.13`` ``foss/2021b`` +============= ================= =================================================== .. _list_software_PyOpenGL_750: @@ -37663,6 +38276,7 @@ version versionsuffix toolchain ``0.16.0.1`` ``-Python-2.7.18`` ``GCC/10.2.0`` ``0.17.0`` ``GCC/11.2.0`` ``0.18.0`` ``GCC/11.2.0`` +``0.19.1`` ``GCC/11.3.0`` ============ ================== ============================================================================================================== @@ -37874,12 +38488,13 @@ Python interface to Stan, a package for Bayesian inference using the No-U-Turn *homepage*: https://github.com/stan-dev/pystan -============ ================= =============== -version versionsuffix toolchain -============ ================= =============== -``2.19.0.0`` ``-Python-3.6.4`` ``intel/2018a`` -``2.19.1.1`` ``intel/2020b`` -============ ================= =============== +============ ================= =============================== +version versionsuffix toolchain +============ ================= =============================== +``2.19.0.0`` ``-Python-3.6.4`` ``intel/2018a`` +``2.19.1.1`` ``foss/2020b``, ``intel/2020b`` +``3.5.0`` ``foss/2021b`` +============ ================= =============================== .. _list_software_pystran_785: @@ -37987,7 +38602,7 @@ version toolchain ========= ====================================== ``2.1.0`` ``GCCcore/10.2.0`` ``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.5.0`` ``GCCcore/11.2.0`` +``2.5.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ====================================== @@ -38353,6 +38968,7 @@ version versionsuffix toolchain ``5.3`` ``GCCcore/9.3.0`` ``5.3.1`` ``GCCcore/10.2.0`` ``5.4.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``6.0`` ``GCCcore/11.3.0`` ========= ================== ==================================================================================== @@ -38391,7 +39007,7 @@ version versionsuffix toolchain --- -:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcat_425` - :ref:`list_software_QCG-PilotJob_1067` - :ref:`list_software_qcint_543` - :ref:`list_software_QCxMS_428` - :ref:`list_software_QD_149` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_Qtconsole_952` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_QtPy_398` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` +:ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcat_425` - :ref:`list_software_QCG-PilotJob_1067` - :ref:`list_software_qcint_543` - :ref:`list_software_QCxMS_428` - :ref:`list_software_QD_149` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_Qtconsole_952` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_QtPy_398` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_QuickPIC_729` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` .. _list_software_Q6_135: @@ -38690,11 +39306,11 @@ qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions *homepage*: https://sourceforge.net/projects/qrupdate/ -========= ===================================================================================================================================================================================================== -version toolchain -========= ===================================================================================================================================================================================================== -``1.1.2`` ``GCC/5.4.0-2.26``, ``GCC/8.2.0-2.31.1``, ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -========= ===================================================================================================================================================================================================== +========= ========================================================================================================================================================================================================================= +version toolchain +========= ========================================================================================================================================================================================================================= +``1.1.2`` ``GCC/5.4.0-2.26``, ``GCC/8.2.0-2.31.1``, ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +========= ========================================================================================================================================================================================================================= .. _list_software_QScintilla_1012: @@ -38924,6 +39540,7 @@ version versionsuffix toolchain ``6.6`` ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2019b`` ``6.7`` ``foss/2019b``, ``foss/2020b``, ``foss/2021a``, ``intel/2019b``, ``intel/2021a``, ``iomkl/2019b`` ``6.8`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` +``7.0`` ``foss/2021b``, ``intel/2021b`` ``7.1`` ``foss/2022a``, ``intel/2022a`` ========= ============= ================================================================================================= @@ -38986,6 +39603,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_QuickPIC_729: + +*QuickPIC* +++++++++++ + +QuickPIC is a 3D parallel (MPI & OpenMP Hybrid) Quasi-Static PIC code, which is developed based on the framework UPIC. QuickPIC can efficiently simulate plasma based accelerator problems. This is the UCLA Plasma Simulation Group's official open-source repository for QuickPIC. + +*homepage*: https://github.com/UCLA-Plasma-Simulation-Group/QuickPIC-OpenSource + +============ =============== +version toolchain +============ =============== +``20210224`` ``gompi/2021b`` +============ =============== + + .. _list_software_Quip_415: *Quip* @@ -39077,7 +39710,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_RaGOO_408` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_RAPSearch2_875` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redis_503` - :ref:`list_software_redis-py_813` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_regionmask_1072` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rising_652` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_ruamel.yaml_1127` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_RaGOO_408` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_RAPSearch2_875` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redis_503` - :ref:`list_software_redis-py_813` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_regionmask_1072` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_RheoTool_812` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rising_652` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_ruamel.yaml_1127` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -39148,6 +39781,7 @@ version versionsuffix toolchain ``3.13`` ``-R-4.1.0`` ``foss/2021a`` ``3.14`` ``-R-4.1.2`` ``foss/2021b`` ``3.15`` ``-R-4.2.0`` ``foss/2021b`` +``3.15`` ``-R-4.2.1`` ``foss/2022a`` ======== ============= =============================== @@ -39548,17 +40182,18 @@ version toolchain *Ray-project* +++++++++++++ -Ray is a fast and simple framework for building and running distributed applications. +Ray is an open source project that makes it simple to scale any compute-intensive Python workload — from deep learning to production model serving. With a rich set of libraries and integrations built on a flexible distributed execution framework, Ray makes distributed computing easy and accessible to every engineer. -*homepage*: https://docs.ray.io/en/latest/ +*homepage*: https://www.ray.io/ -========== ================= ================== -version versionsuffix toolchain -========== ================= ================== -``0.8.4`` ``-Python-3.7.4`` ``foss/2019b`` -``1.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``1.13.0`` ``foss/2021b`` -========== ================= ================== +========== ================= ============================== +version versionsuffix toolchain +========== ================= ============================== +``0.8.4`` ``-Python-3.7.4`` ``foss/2019b`` +``1.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.9.2`` ``foss/2021b`` +``1.13.0`` ``foss/2021a``, ``foss/2021b`` +========== ================= ============================== .. _list_software_Raysect_731: @@ -39697,6 +40332,7 @@ version versionsuffix toolchain ``2020.03.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``2020.09.3`` ``-Python-3.7.4`` ``foss/2019b`` ``2021.03.4`` ``foss/2021a`` +``2022.03.5`` ``foss/2021b`` ============= ================= =============================== @@ -40255,6 +40891,22 @@ version versionsuffix toolchain ========== ============= =============== +.. _list_software_RheoTool_812: + +*RheoTool* +++++++++++ + +RheoTool is an open-source toolbox based on OpenFOAM to simulate Generalized Newtonian Fluids (GNF) and viscoelastic fluids under pressure-driven and/or electrically-driven flows. + +*homepage*: https://github.com/fppimenta/rheoTool + +======= ============== +version toolchain +======= ============== +``5.0`` ``foss/2019b`` +======= ============== + + .. _list_software_rickflow_865: *rickflow* @@ -40428,13 +41080,13 @@ Fast, efficient RNA-Seq metrics for quality control and process optimization *homepage*: https://github.com/getzlab/rnaseqc -========= =================== ============== -version versionsuffix toolchain -========= =================== ============== -``1.1.8`` ``-Java-1.8`` ``foss/2018b`` -``1.1.8`` ``-Java-1.8.0_121`` ``foss/2016b`` -``2.4.2`` ``foss/2021a`` -========= =================== ============== +========= =================== ============================== +version versionsuffix toolchain +========= =================== ============================== +``1.1.8`` ``-Java-1.8`` ``foss/2018b`` +``1.1.8`` ``-Java-1.8.0_121`` ``foss/2016b`` +``2.4.2`` ``foss/2021a``, ``foss/2021b`` +========= =================== ============================== .. _list_software_RNAclust_780: @@ -41064,7 +41716,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_samplot_768` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_SCGid_426` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_SCopeLoomR_963` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_scPred_609` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_ShengBTE_720` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_SHTns_464` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SISSO_401` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-pandas_1428` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_skorch_650` - :ref:`list_software_SlamDunk_799` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_slow5tools_1067` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_smooth-topk_1157` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SoXt_398` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_SPM_240` - :ref:`list_software_spoa_435` - :ref:`list_software_SPOTPY_495` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-CCM+_613` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_STRique_685` - :ref:`list_software_Structure_977` - :ref:`list_software_STRUMPACK_698` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SURVIVOR_656` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_SWIPE_392` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_samplot_768` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_Satsuma2_784` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_SCGid_426` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_SCopeLoomR_963` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_scPred_609` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_ShengBTE_720` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_SHTns_464` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SISSO_401` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-pandas_1428` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_skorch_650` - :ref:`list_software_SlamDunk_799` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_slow5tools_1067` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_SMC++_313` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_smooth-topk_1157` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SoXt_398` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_SPM_240` - :ref:`list_software_spoa_435` - :ref:`list_software_SPOTPY_495` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-CCM+_613` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_stripy_683` - :ref:`list_software_STRique_685` - :ref:`list_software_Structure_977` - :ref:`list_software_STRUMPACK_698` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SURVIVOR_656` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_SWIPE_392` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -41308,7 +41960,7 @@ version versionsuffix toolchain ``1.13`` ``GCC/10.3.0`` ``1.14`` ``GCC/11.2.0`` ``1.15`` ``GCC/11.2.0`` -``1.15.1`` ``GCC/11.2.0`` +``1.15.1`` ``GCC/11.2.0``, ``GCC/11.3.0`` ========== ================= ======================================================================================================================================= @@ -41344,6 +41996,22 @@ version toolchain ======= ========== +.. _list_software_Satsuma2_784: + +*Satsuma2* +++++++++++ + +Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and complex DNA sequences providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accommodate the billions of base pairs in vertebrate genomes). + +*homepage*: https://github.com/bioinfologics/satsuma2 + +============ ============== +version toolchain +============ ============== +``20220304`` ``GCC/11.3.0`` +============ ============== + + .. _list_software_savvy_569: *savvy* @@ -41575,7 +42243,9 @@ version toolchain ========== ========== ``2020-4`` ``system`` ``2021-4`` ``system`` +``2022-1`` ``system`` ``2022-2`` ``system`` +``2022-3`` ``system`` ========== ========== @@ -41643,6 +42313,7 @@ scikit-bio is an open-source, BSD-licensed Python 3 package providing data struc version versionsuffix toolchain ========= ================= ============== ``0.5.6`` ``-Python-3.8.2`` ``foss/2020a`` +``0.5.7`` ``foss/2021b`` ========= ================= ============== @@ -41661,6 +42332,7 @@ version versionsuffix toolchain ``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``0.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` ``0.11.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +``0.15.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ================= ================================================================================================================ @@ -41753,6 +42425,8 @@ version versionsuffix toolchain ``0.23.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` ``0.24.2`` ``foss/2021a``, ``intel/2021a`` ``1.0.1`` ``foss/2021b``, ``intel/2021b`` +``1.0.2`` ``foss/2021b`` +``1.1.2`` ``foss/2022a`` ========== ================================= ======================================================================== @@ -41787,6 +42461,7 @@ version versionsuffix toolchain ``0.5.2`` ``-Python-3.6.6`` ``intel/2018b`` ``0.7.4`` ``-Python-3.7.4`` ``foss/2019b`` ``0.8.1`` ``-Python-3.8.2`` ``foss/2020a`` +``0.9.0`` ``foss/2021a`` ========= ================= =============== @@ -41995,7 +42670,7 @@ version toolchain Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. -*homepage*: https://gforge.inria.fr/projects/scotch/ +*homepage*: https://www.labri.fr/perso/pelegrin/scotch/ =================== ============= ===================================================================================================================================================== version versionsuffix toolchain @@ -42007,6 +42682,7 @@ version versionsuffix toolchain ``6.0.9`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` ``6.1.0`` ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2020b`` ``6.1.2`` ``gompi/2021b``, ``iimpi/2021b`` +``7.0.1`` ``gompi/2022a`` =================== ============= ===================================================================================================================================================== @@ -43194,6 +43870,7 @@ version versionsuffix toolchain ``1.7.1`` ``-tools`` ``foss/2017a`` ``1.7.4`` ``-tools`` ``GCCcore/8.2.0`` ``1.7.6`` ``-tools`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.7.7`` ``-tools`` ``GCCcore/11.3.0`` ========= ============= ============================================================================ @@ -43229,11 +43906,12 @@ A data-driven method combining symbolic regression and compressed sensing toward *homepage*: https://github.com/rouyang2017/SISSO -========= =============== -version toolchain -========= =============== -``3.0.2`` ``iimpi/2021b`` -========= =============== +================ =============== +version toolchain +================ =============== +``3.0.2`` ``iimpi/2021b`` +``3.1-20220324`` ``iimpi/2021b`` +================ =============== .. _list_software_SKESA_375: @@ -43521,6 +44199,22 @@ version toolchain ============ ============== +.. _list_software_SMC++_313: + +*SMC++* ++++++++ + +SMC++ is a program for estimating the size history of populations from whole genome sequence data. + +*homepage*: https://github.com/popgenmethods/smcpp + +========== ============== +version toolchain +========== ============== +``1.15.4`` ``foss/2022a`` +========== ============== + + .. _list_software_smithwaterman_1412: *smithwaterman* @@ -43970,15 +44664,15 @@ version toolchain *SoX* +++++ -SoX is the Swiss Army Knife of sound processing utilities. It can convert audio files to other popular audio file types and also apply sound effects and filters during the conversion. +Sound eXchange, the Swiss Army knife of audio manipulation -*homepage*: https://sourceforge.net/projects/sox +*homepage*: http://sox.sourceforge.net/ -========== ============= -version toolchain -========== ============= -``14.4.2`` ``GCC/8.3.0`` -========== ============= +========== ================================= +version toolchain +========== ================================= +``14.4.2`` ``GCC/8.3.0``, ``GCCcore/11.3.0`` +========== ================================= .. _list_software_SoXt_398: @@ -44053,7 +44747,7 @@ version versionsuffix toolchain ``3.10.1`` ``foss/2016b``, ``foss/2017a`` ``3.11.1`` ``foss/2017b``, ``foss/2018a`` ``3.12.0`` ``foss/2016b``, ``foss/2018a``, ``foss/2018b`` -``3.13.0`` ``foss/2018b`` +``3.13.0`` ``GCC/10.3.0``, ``foss/2018b`` ``3.13.1`` ``GCC/8.2.0-2.31.1`` ``3.14.0`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` ``3.14.0`` ``-Python-3.7.4`` ``GCC/8.3.0`` @@ -44258,6 +44952,7 @@ version versionsuffix toolchain ``1.16.0`` ``-Python-3.7.4`` ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` ``1.16.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``1.16.1`` ``foss/2021a``, ``intel/2021a`` +``2.0.0`` ``foss/2022a`` ================ ================== ======================================================== @@ -44413,6 +45108,7 @@ SPM (Statistical Parametric Mapping) refers to the construction and assessment version versionsuffix toolchain ============== ================= ========== ``12.5_r7771`` ``-MATLAB-2021a`` ``system`` +``12.5_r7771`` ``-MATLAB-2021b`` ``system`` ============== ================= ========== @@ -44729,6 +45425,7 @@ version toolchain ``2.41`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.53`` ``foss/2019b``, ``iccifort/2019.5.281`` ``2.54`` ``foss/2020a`` +``2.62`` ``foss/2022a`` ============== ============================================================================== @@ -44791,29 +45488,30 @@ STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays *homepage*: https://github.com/alexdobin/STAR -========== ============================================================== -version toolchain -========== ============================================================== -``2.4.2a`` ``foss/2018b`` -``2.5.0a`` ``GNU/4.9.3-2.25`` -``2.5.2a`` ``foss/2016a`` -``2.5.2b`` ``intel/2016b`` -``2.5.3a`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``intel/2017a``, ``intel/2017b`` -``2.5.4b`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` -``2.6.0c`` ``foss/2018a``, ``intel/2018a`` -``2.6.1c`` ``foss/2018b`` -``2.7.0d`` ``foss/2018b`` -``2.7.0f`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` -``2.7.1a`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` -``2.7.2b`` ``GCC/8.3.0`` -``2.7.3a`` ``GCC/8.3.0``, ``GCC/9.3.0`` -``2.7.4a`` ``GCC/9.3.0`` -``2.7.5b`` ``GCC/9.3.0`` -``2.7.6a`` ``GCC/10.2.0``, ``GCC/9.3.0`` -``2.7.7a`` ``GCC/10.2.0``, ``GCC/9.3.0`` -``2.7.8a`` ``GCC/10.2.0`` -``2.7.9a`` ``GCC/10.3.0``, ``GCC/11.2.0`` -========== ============================================================== +======================== ============================================================== +version toolchain +======================== ============================================================== +``2.4.2a`` ``foss/2018b`` +``2.5.0a`` ``GNU/4.9.3-2.25`` +``2.5.2a`` ``foss/2016a`` +``2.5.2b`` ``intel/2016b`` +``2.5.3a`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``intel/2017a``, ``intel/2017b`` +``2.5.4b`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` +``2.6.0c`` ``foss/2018a``, ``intel/2018a`` +``2.6.1c`` ``foss/2018b`` +``2.7.0d`` ``foss/2018b`` +``2.7.0f`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` +``2.7.1a`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` +``2.7.2b`` ``GCC/8.3.0`` +``2.7.3a`` ``GCC/8.3.0``, ``GCC/9.3.0`` +``2.7.4a`` ``GCC/9.3.0`` +``2.7.5b`` ``GCC/9.3.0`` +``2.7.6a`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``2.7.7a`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``2.7.8a`` ``GCC/10.2.0`` +``2.7.9a`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``2.7.10a_alpha_220601`` ``GCC/10.3.0`` +======================== ============================================================== .. _list_software_STAR-CCM+_613: @@ -44821,15 +45519,19 @@ version toolchain *STAR-CCM+* +++++++++++ -STAR-CCM+ is a complete multidisciplinary platform for the simulation of products and designs operating under real-world conditions. +STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products operating under real-world conditions. *homepage*: https://mdx.plm.automation.siemens.com/star-ccm-plus -============= ========== -version toolchain -============= ========== -``13.04.011`` ``system`` -============= ========== +============= ============= ========== +version versionsuffix toolchain +============= ============= ========== +``13.04.011`` ``system`` +``17.02.008`` ``system`` +``17.02.008`` ``-r8`` ``system`` +``17.04.008`` ``system`` +``17.04.008`` ``-r8`` ``system`` +============= ============= ========== .. _list_software_STAR-Fusion_987: @@ -44880,6 +45582,7 @@ version versionsuffix toolchain ======= ============= ========== ``15`` ``system`` ``16`` ``-legacy`` ``system`` +``17`` ``system`` ======= ============= ========== @@ -45038,6 +45741,22 @@ version toolchain ========== ================================== +.. _list_software_stripy_683: + +*stripy* +++++++++ + +A Python interface to TRIPACK and STRIPACK Fortran code for (constrained) triangulation in Cartesian coordinates and on a sphere. Stripy is an object-oriented package and includes routines from SRFPACK and SSRFPACK for interpolation (nearest neighbor, linear and hermite cubic) and to evaluate derivatives (Renka 1996a,b and 1997a,b). + +*homepage*: https://github.com/underworldcode/stripy + +========= ============== +version toolchain +========= ============== +``2.1.0`` ``foss/2021a`` +========= ============== + + .. _list_software_STRique_685: *STRique* @@ -45227,9 +45946,9 @@ version toolchain *SUMO* ++++++ -"Simulation of Urban MObility" (SUMO) is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a large set of tools for scenario creation. +Simulation of Urban MObility" (SUMO) is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a large set of tools for scenario creation. -*homepage*: https://sumo.dlr.de/ +*homepage*: https://www.eclipse.org/sumo/ ========== ================= ================= version versionsuffix toolchain @@ -45237,6 +45956,7 @@ version versionsuffix toolchain ``1.3.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``1.7.0`` ``-Python-3.8.2`` ``foss/2020a`` ``1.12.0`` ``foss/2021b`` +``1.14.1`` ``foss/2021b`` ========== ================= ================= @@ -45483,28 +46203,28 @@ SWIG is a software development tool that connects programs written in C and C++ *homepage*: http://www.swig.org/ -========== ============================ ================================================================ -version versionsuffix toolchain -========== ============================ ================================================================ -``3.0.8`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``3.0.8`` ``-Python-3.5.1`` ``foss/2016a`` -``3.0.10`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.0.10`` ``-Python-2.7.12-PCRE-8.39`` ``intel/2016b`` -``3.0.11`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.0.12`` ``-Python-2.7.13`` ``intel/2017a`` -``3.0.12`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``3.0.12`` ``-Python-2.7.14-bare`` ``GCCcore/6.4.0`` -``3.0.12`` ``-Python-2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``intel/2018b`` -``3.0.12`` ``-Python-3.6.1`` ``intel/2017a`` -``3.0.12`` ``-Python-3.6.2`` ``foss/2017b``, ``intel/2018.00`` -``3.0.12`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.01`` -``3.0.12`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` -``3.0.12`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.0.12`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``4.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.0.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========== ============================ ================================================================ +========== ============================ ============================================================================== +version versionsuffix toolchain +========== ============================ ============================================================================== +``3.0.8`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``3.0.8`` ``-Python-3.5.1`` ``foss/2016a`` +``3.0.10`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.0.10`` ``-Python-2.7.12-PCRE-8.39`` ``intel/2016b`` +``3.0.11`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.0.12`` ``-Python-2.7.13`` ``intel/2017a`` +``3.0.12`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``3.0.12`` ``-Python-2.7.14-bare`` ``GCCcore/6.4.0`` +``3.0.12`` ``-Python-2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``intel/2018b`` +``3.0.12`` ``-Python-3.6.1`` ``intel/2017a`` +``3.0.12`` ``-Python-3.6.2`` ``foss/2017b``, ``intel/2018.00`` +``3.0.12`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.01`` +``3.0.12`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` +``3.0.12`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.0.12`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``4.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.0.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========== ============================ ============================================================================== .. _list_software_SWIPE_392: @@ -45851,6 +46571,7 @@ version toolchain ``2020.2`` ``GCCcore/8.3.0`` ``2020.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``2021.4.0`` ``GCCcore/11.2.0`` +``2021.5.0`` ``GCCcore/11.3.0`` ============== ========================================================== @@ -46735,11 +47456,11 @@ A Tcl/Tk widget for OpenGL rendering. *homepage*: https://sourceforge.net/projects/togl/ -======= ===================================== -version toolchain -======= ===================================== -``2.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` -======= ===================================== +======= ========================================================= +version toolchain +======= ========================================================= +``2.0`` ``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` +======= ========================================================= .. _list_software_Tombo_513: @@ -46891,6 +47612,7 @@ version versionsuffix toolchain ``0.11.1`` ``foss/2021a`` ``0.11.1`` ``-CUDA-11.3.1`` ``foss/2021a`` ``0.11.3`` ``foss/2021a`` +``0.11.3`` ``-CUDA-11.3.1`` ``foss/2021a`` ========== ==================================== ================================== @@ -46937,6 +47659,7 @@ version versionsuffix toolchain ``4.61.1`` ``GCCcore/10.3.0`` ``4.61.2`` ``GCCcore/10.3.0`` ``4.62.3`` ``GCCcore/11.2.0`` +``4.64.0`` ``GCCcore/11.3.0`` ========== ================== =============================== @@ -47002,6 +47725,7 @@ version versionsuffix toolchain ========== ================= ============== ``4.2.1`` ``-Python-3.8.2`` ``foss/2020a`` ``4.20.1`` ``foss/2021a`` +``4.21.1`` ``foss/2021b`` ========== ================= ============== @@ -47361,6 +48085,7 @@ version versionsuffix toolchain ========= ================= ============== ``0.3.3`` ``-Python-3.8.2`` ``foss/2020a`` ``0.5.2`` ``foss/2021a`` +``0.5.3`` ``foss/2021b`` ========= ================= ============== @@ -47522,7 +48247,7 @@ version versionsuffix toolchain --- -:ref:`list_software_UCC_219` - :ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_UCX-CUDA_570` - :ref:`list_software_ucx-py_614` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_uncertainty-calibration_2411` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_unimap_650` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_UShER_423` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` +:ref:`list_software_UCC_219` - :ref:`list_software_UCC-CUDA_549` - :ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_UCX-CUDA_570` - :ref:`list_software_ucx-py_614` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_uncertainty-calibration_2411` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_unimap_650` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_UShER_423` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` .. _list_software_UCC_219: @@ -47541,6 +48266,22 @@ version toolchain ========= ================== +.. _list_software_UCC-CUDA_549: + +*UCC-CUDA* +++++++++++ + +UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. This module adds the UCC CUDA support. + +*homepage*: https://www.openucx.org/ + +========= ================ ================== +version versionsuffix toolchain +========= ================ ================== +``1.0.0`` ``-CUDA-11.7.0`` ``GCCcore/11.3.0`` +========= ================ ================== + + .. _list_software_UCLUST_480: *UCLUST* @@ -47788,6 +48529,7 @@ version versionsuffix toolchain ``0.4.7`` ``-Python-3.7.2`` ``foss/2019a`` ``0.4.8`` ``-Python-3.8.2`` ``gompi/2020a`` ``0.4.9`` ``gompi/2021a`` +``0.5.0`` ``gompi/2021b`` ========= ================= =============== @@ -48015,7 +48757,7 @@ version toolchain --- -:ref:`list_software_V8_142` - :ref:`list_software_Vala_388` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_Vampire_724` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_vawk_441` - :ref:`list_software_VBZ-Compression_1457` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcflib_630` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_Virtuoso-opensource_2011` - :ref:`list_software_VisPy_507` - :ref:`list_software_VMD_231` - :ref:`list_software_VMTK_322` - :ref:`list_software_voltools_898` - :ref:`list_software_vorbis-tools_1267` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` +:ref:`list_software_V8_142` - :ref:`list_software_Vala_388` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_Vampire_724` - :ref:`list_software_VarDict_685` - :ref:`list_software_variant_tools_1413` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_vawk_441` - :ref:`list_software_VBZ-Compression_1457` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcflib_630` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_velocyto_885` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_VESTA_387` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_Virtuoso-opensource_2011` - :ref:`list_software_VisPy_507` - :ref:`list_software_VMD_231` - :ref:`list_software_VMTK_322` - :ref:`list_software_voltools_898` - :ref:`list_software_vorbis-tools_1267` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` .. _list_software_V8_142: @@ -48071,6 +48813,7 @@ version toolchain ``3.16.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020a`` ``3.17.0`` ``gompi/2021a`` ``3.18.1`` ``gompi/2021b``, ``iimpi/2021b`` +``3.19.0`` ``gompi/2022a`` ========== ================================================================================= @@ -48313,16 +49056,16 @@ The aim of VCFtools is to provide easily accessible methods for working with c *homepage*: https://vcftools.github.io -========== ================ ===================================================================================================== -version versionsuffix toolchain -========== ================ ===================================================================================================== -``0.1.14`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` -``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` -``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` -``0.1.16`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` -``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` -========== ================ ===================================================================================================== +========== ================ ===================================================================================================================== +version versionsuffix toolchain +========== ================ ===================================================================================================================== +``0.1.14`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` +``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` +``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` +``0.1.16`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` +``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` +========== ================ ===================================================================================================================== .. _list_software_VEGAS_374: @@ -48429,6 +49172,22 @@ version toolchain ========= ============== +.. _list_software_VESTA_387: + +*VESTA* ++++++++ + +VESTA is a 3D visualization program for structured models, volumetric data such as electron/nuclear densities, and crystal morphologies. + +*homepage*: http://www.jp-minerals.org/vesta + +========= ============= ========== +version versionsuffix toolchain +========= ============= ========== +``3.5.8`` ``-gtk3`` ``system`` +========= ============= ========== + + .. _list_software_ViennaRNA_834: *ViennaRNA* @@ -48448,6 +49207,7 @@ version versionsuffix toolchain ``2.4.11`` ``-Python-3.6.6`` ``foss/2018b`` ``2.4.14`` ``-Python-3.6.6`` ``foss/2018b`` ``2.5.0`` ``foss/2021b`` +``2.5.1`` ``foss/2021b`` ========== ================== =============================== @@ -48612,11 +49372,11 @@ Voro++ is a software library for carrying out three-dimensional computations of *homepage*: http://math.lbl.gov/voro++/ -========= ============================================================================================================================================== -version toolchain -========= ============================================================================================================================================== -``0.4.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/6.4.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2019b``, ``intel/2016a``, ``intel/2019b`` -========= ============================================================================================================================================== +========= ================================================================================================================================================================== +version toolchain +========= ================================================================================================================================================================== +``0.4.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2019b``, ``intel/2016a``, ``intel/2019b`` +========= ================================================================================================================================================================== .. _list_software_vsc-base_788: @@ -48791,28 +49551,29 @@ The Visualization Toolkit (VTK) is an open-source, freely available software sys *homepage*: https://www.vtk.org -========= ================== =================================================== -version versionsuffix toolchain -========= ================== =================================================== -``6.3.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``6.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``7.0.0`` ``-Python-2.7.12`` ``intel/2016b`` -``7.1.0`` ``-Python-2.7.12`` ``intel/2016b`` -``7.1.1`` ``-Python-2.7.13`` ``intel/2017a`` -``8.0.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``8.1.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``8.1.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` -``8.1.1`` ``-Python-2.7.15`` ``foss/2018b`` -``8.1.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``8.2.0`` ``foss/2021a`` -``8.2.0`` ``-Python-2.7.15`` ``foss/2019a`` -``8.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``8.2.0`` ``-Python-3.7.4`` ``foss/2019b`` -``8.2.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` -``9.0.1`` ``foss/2020b``, ``foss/2021a`` -``9.1.0`` ``foss/2021b`` -========= ================== =================================================== +============= ================== =================================================== +version versionsuffix toolchain +============= ================== =================================================== +``6.3.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``6.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``7.0.0`` ``-Python-2.7.12`` ``intel/2016b`` +``7.1.0`` ``-Python-2.7.12`` ``intel/2016b`` +``7.1.1`` ``-Python-2.7.13`` ``intel/2017a`` +``8.0.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``8.1.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``8.1.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` +``8.1.1`` ``-Python-2.7.15`` ``foss/2018b`` +``8.1.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``8.2.0`` ``foss/2021a`` +``8.2.0`` ``-Python-2.7.15`` ``foss/2019a`` +``8.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``8.2.0`` ``-Python-3.7.4`` ``foss/2019b`` +``8.2.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` +``9.0.1`` ``foss/2020b``, ``foss/2021a`` +``9.1.0`` ``foss/2021b`` +``9.2.0.rc2`` ``foss/2022a`` +============= ================== =================================================== .. _list_software_VTune_498: @@ -48849,6 +49610,7 @@ version toolchain ``2021.9.0`` ``system`` ``2022.0.0`` ``system`` ``2022.2.0`` ``system`` +``2022.3.0`` ``system`` ================= ========== @@ -48918,16 +49680,16 @@ A tool for obtaining maximally-localised Wannier functions *homepage*: http://www.wannier.org -=========== ============= ================================================================================================================== -version versionsuffix toolchain -=========== ============= ================================================================================================================== -``1.2`` ``intel/2016.02-GCC-4.9`` -``2.0.1`` ``intel/2016.02-GCC-4.9``, ``intel/2016a`` -``2.0.1.1`` ``-abinit`` ``intel/2018b`` -``2.1.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``3.0.0`` ``intel/2018b`` -``3.1.0`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` -=========== ============= ================================================================================================================== +=========== ============= =================================================================================================================================================== +version versionsuffix toolchain +=========== ============= =================================================================================================================================================== +``1.2`` ``intel/2016.02-GCC-4.9`` +``2.0.1`` ``intel/2016.02-GCC-4.9``, ``intel/2016a`` +``2.0.1.1`` ``-abinit`` ``intel/2018b`` +``2.1.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``3.0.0`` ``intel/2018b`` +``3.1.0`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``gomkl/2021a``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` +=========== ============= =================================================================================================================================================== .. _list_software_WannierTools_1253: @@ -49023,12 +49785,12 @@ WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for *homepage*: https://webkitgtk.org/ -========== ==================== -version toolchain -========== ==================== -``2.24.1`` ``GCC/8.2.0-2.31.1`` -``2.27.4`` ``GCC/8.3.0`` -========== ==================== +========== ============================= +version toolchain +========== ============================= +``2.24.1`` ``GCC/8.2.0-2.31.1`` +``2.27.4`` ``GCC/10.3.0``, ``GCC/8.3.0`` +========== ============================= .. _list_software_WebSocket++_989: @@ -49403,9 +50165,9 @@ version toolchain *wxPython* ++++++++++ -wxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. It is implemented as a Python extension module (native code) that wraps the popular wxWidgets cross platform GUI library, which is written in C++. +Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel and requiring very little (if any) platform specific code. -*homepage*: https://www.wxpython.org +*homepage*: https://www.wxpython.org/ =============== ================== =============================== version versionsuffix toolchain @@ -49418,6 +50180,7 @@ version versionsuffix toolchain ``4.0.4`` ``-Python-2.7.15`` ``GCC/8.2.0-2.31.1`` ``4.0.4`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` ``4.0.7.post2`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``4.1.1`` ``foss/2021a`` =============== ================== =============================== @@ -49506,6 +50269,7 @@ version toolchain ``20201026`` ``GCCcore/10.2.0`` ``20210414`` ``GCCcore/10.3.0`` ``20210613`` ``GCCcore/11.2.0`` +``20220620`` ``GCCcore/11.3.0`` ============ ================================= @@ -49518,19 +50282,19 @@ x265 is a free software library and application for encoding video streams into *homepage*: https://x265.org/ -======= ====================================== -version toolchain -======= ====================================== -``2.4`` ``foss/2016b`` -``2.5`` ``intel/2017a`` -``2.6`` ``GCCcore/6.4.0``, ``intel/2017b`` -``2.7`` ``GCCcore/6.4.0`` -``2.9`` ``GCCcore/7.3.0`` -``3.0`` ``GCCcore/8.2.0`` -``3.2`` ``GCCcore/8.3.0`` -``3.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.5`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -======= ====================================== +======= ========================================================== +version toolchain +======= ========================================================== +``2.4`` ``foss/2016b`` +``2.5`` ``intel/2017a`` +``2.6`` ``GCCcore/6.4.0``, ``intel/2017b`` +``2.7`` ``GCCcore/6.4.0`` +``2.9`` ``GCCcore/7.3.0`` +``3.0`` ``GCCcore/8.2.0`` +``3.2`` ``GCCcore/8.3.0`` +``3.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.5`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +======= ========================================================== .. _list_software_XALT_313: @@ -49733,16 +50497,16 @@ version versionsuffix toolchain *XCrySDen* ++++++++++ -XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. +XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It also possesses some tools for analysis of properties in reciprocal space such as interactive selection of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces. *homepage*: http://www.xcrysden.org/ -========== =============================================== -version toolchain -========== =============================================== -``1.5.60`` ``intel/2019a`` -``1.6.2`` ``foss/2019b``, ``foss/2020b``, ``intel/2019b`` -========== =============================================== +========== ================================================================================ +version toolchain +========== ================================================================================ +``1.5.60`` ``intel/2019a`` +``1.6.2`` ``foss/2019b``, ``foss/2020b``, ``foss/2022a``, ``intel/2019b``, ``intel/2022a`` +========== ================================================================================ .. _list_software_Xerces-C++_816: @@ -49995,6 +50759,7 @@ version versionsuffix toolchain ``2.44_01`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` ``2.44_01`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` ``2.46`` ``-Perl-5.32.1`` ``GCCcore/10.3.0`` +``2.46`` ``-Perl-5.34.1`` ``GCCcore/11.3.0`` =========== ================ ====================================================================================== @@ -50177,13 +50942,13 @@ Semiempirical Extended Tight-Binding Program Package. *homepage*: https://xtb-docs.readthedocs.io -================ ================= =============== -version versionsuffix toolchain -================ ================= =============== -``6.2.2-hotfix`` ``-Python-3.6.3`` ``intel/2017b`` -``6.2.3`` ``foss/2019b`` -``6.4.1`` ``intel/2021a`` -================ ================= =============== +================ ================= =============================== +version versionsuffix toolchain +================ ================= =============================== +``6.2.2-hotfix`` ``-Python-3.6.3`` ``intel/2017b`` +``6.2.3`` ``foss/2019b`` +``6.4.1`` ``foss/2021b``, ``intel/2021a`` +================ ================= =============================== .. _list_software_xtensor_787: @@ -50438,11 +51203,11 @@ Yasm: Complete rewrite of the NASM assembler with BSD license *homepage*: http://www.tortall.net/projects/yasm/ -========= =============================================================================================================================================================================================================================================================================================== -version toolchain -========= =============================================================================================================================================================================================================================================================================================== -``1.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -========= =============================================================================================================================================================================================================================================================================================== +========= =================================================================================================================================================================================================================================================================================================================== +version toolchain +========= =================================================================================================================================================================================================================================================================================================================== +``1.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +========= =================================================================================================================================================================================================================================================================================================================== .. _list_software_YAXT_326: @@ -50509,6 +51274,7 @@ version toolchain ``4.8.11`` ``GCCcore/10.3.0`` ``4.8.12`` ``GCCcore/11.2.0`` ``4.8.16`` ``GCCcore/11.3.0`` +``4.10.2`` ``GCCcore/11.3.0`` ========== ==================================== @@ -50567,6 +51333,7 @@ zfp is a compressed format for representing multidimensional floating-point and version toolchain ========= ================== ``0.5.5`` ``GCCcore/10.2.0`` +``1.0.0`` ``GCCcore/9.3.0`` ========= ================== @@ -50634,7 +51401,7 @@ version toolchain ``1.2.8`` ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.2.10`` ``system`` ``1.2.11`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` -``1.2.12`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.5.0``, ``system`` +``1.2.12`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0``, ``system`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index 1335df5f..a05715a9 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -1190,7 +1190,7 @@ easyconfig parameter description ``serial_number`` Serial number for the product ``None`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` ``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` -``use_gold_linker`` Configure GCC to use GOLD as default linker (default: True for GCC < 11.3.0) ``None`` +``use_gold_linker`` Configure GCC to use GOLD as default linker (default: enable automatically for GCC < 11.3.0, except on RISC-V) ``None`` ``usetmppath`` Use temporary path for installation ``False`` ``withamdgcn`` Build GCC with AMD GCN offload support ``False`` ``withcloog`` Build GCC with CLooG support ``False`` diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index 7ac56ffa..309526a9 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -76,49 +76,49 @@ Option flag Option description Configuration options --------------------- -================================================================= ================================================================================================================================================================================================================================================================================= -Option flag Option description -================================================================= ================================================================================================================================================================================================================================================================================= -``--avail-module-naming-schemes`` Show all supported module naming schemes (default: False) -``--avail-modules-tools`` Show all supported module tools (default: False) -``--avail-repositories`` Show all repository types (incl. non-usable) (default: False) -``--buildpath=BUILDPATH`` Temporary build path (default: /home/example/.local/easybuild/build) -``--containerpath=CONTAINERPATH`` Location where container recipe & image will be stored (default: /home/example/.local/easybuild/containers) -``--envvars-user-modules=ENVVARS-USER-MODULES`` List of environment variables that hold the base paths for which user-specific modules will be installed relative to (type comma-separated list; default: HOME) -``--external-modules-metadata=EXTERNAL-MODULES-METADATA`` List of (glob patterns for) paths to files specifying metadata for external modules (INI format) (type comma-separated list) -``--hooks=HOOKS`` Location of Python module with hook implementations (type str) -``--ignore-dirs=IGNORE-DIRS`` Directory names to ignore when searching for files/dirs (type comma-separated list; default: .git,.svn) -``--include-easyblocks=INCLUDE-EASYBLOCKS`` Location(s) of extra or customized easyblocks (type comma-separated list; default: ) -``--include-module-naming-schemes=INCLUDE-MODULE-NAMING-SCHEMES`` Location(s) of extra or customized module naming schemes (type comma-separated list; default: ) -``--include-toolchains=INCLUDE-TOOLCHAINS`` Location(s) of extra or customized toolchains or toolchain components (type comma-separated list; default: ) -``--installpath=INSTALLPATH`` Install path for software and modules (default: /home/example/.local/easybuild) -``--installpath-modules=INSTALLPATH-MODULES`` Install path for modules (if None, combine --installpath and --subdir-modules) -``--installpath-software=INSTALLPATH-SOFTWARE`` Install path for software (if None, combine --installpath and --subdir-software) -``--job-backend=JOB-BACKEND`` Backend to use for submitting jobs (type choice; default: GC3Pie) (choices: GC3Pie, PbsPython, Slurm) -``--logfile-format=DIR,FORMAT`` Directory name and format of the log file (type comma-separated tuple; default: easybuild,easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log) -``--module-depends-on`` Use depends_on (Lmod 7.6.1+) for dependencies in all generated modules (implies recursive unloading of modules). (default: False) -``--module-extensions`` Include 'extensions' statement in generated module file (Lua syntax only) (default: False) -``--module-naming-scheme=MODULE-NAMING-SCHEME`` Module naming scheme to use (default: EasyBuildMNS) -``--module-syntax=MODULE-SYNTAX`` Syntax to be used for module files (type choice; default: Lua) (choices: Lua, Tcl) -``--moduleclasses=MODULECLASSES`` Extend supported module classes (For more info on the default classes, use --show-default-moduleclasses) (type comma-separated list; default: base,astro,bio,cae,chem,compiler,data,debugger,devel,geo,ide,lang,lib,math,mpi,numlib,perf,quantum,phys,system,toolchain,tools,vis) -``--modules-footer=PATH`` Path to file containing footer to be added to all generated module files -``--modules-header=PATH`` Path to file containing header to be added to all generated module files -``--modules-tool=MODULES-TOOL`` Modules tool to use (type choice; default: Lmod) (choices: EnvironmentModules, EnvironmentModulesC, EnvironmentModulesTcl, Lmod) -``--package-naming-scheme=PACKAGE-NAMING-SCHEME`` Packaging naming scheme choice (type choice; default: EasyBuildPNS) (choices: EasyBuildPNS) -``--packagepath=PACKAGEPATH`` The destination path for the packages built by package-tool (default: /home/example/.local/easybuild/packages) -``--prefix=PREFIX`` Change prefix for buildpath, installpath, sourcepath and repositorypath (used prefix for defaults /home/example/.local/easybuild) -``--recursive-module-unload`` Enable generating of modules that unload recursively. (default: False) -``--repository=REPOSITORY`` Repository type, using repositorypath (type choice; default: FileRepository) (choices: FileRepository, GitRepository, HgRepository) -``--repositorypath=REPOSITORYPATH`` Repository path, used by repository (is passed as list of arguments to create the repository instance). For more info, use --avail-repositories. (type comma-separated list; default: /home/example/.local/easybuild/ebfiles_repo) -``--sourcepath=SOURCEPATH`` Path(s) to where sources should be downloaded (string, colon-separated) (default: /home/example/.local/easybuild/sources) -``--subdir-modules=SUBDIR-MODULES`` Installpath subdir for modules (default: modules) -``--subdir-software=SUBDIR-SOFTWARE`` Installpath subdir for software (default: software) -``--subdir-user-modules=SUBDIR-USER-MODULES`` Base path of user-specific modules relative to --envvars-user-modules -``--suffix-modules-path=SUFFIX-MODULES-PATH`` Suffix for module files install path (default: all) -``--testoutput=TESTOUTPUT`` Path to where a job should place the output (to be set within jobscript) -``--tmp-logdir=TMP-LOGDIR`` Log directory where temporary log files are stored -``--tmpdir=TMPDIR`` Directory to use for temporary storage -================================================================= ================================================================================================================================================================================================================================================================================= +================================================================= ==================================================================================================================================================================================================================================================================================== +Option flag Option description +================================================================= ==================================================================================================================================================================================================================================================================================== +``--avail-module-naming-schemes`` Show all supported module naming schemes (default: False) +``--avail-modules-tools`` Show all supported module tools (default: False) +``--avail-repositories`` Show all repository types (incl. non-usable) (default: False) +``--buildpath=BUILDPATH`` Temporary build path (default: /home/example/.local/easybuild/build) +``--containerpath=CONTAINERPATH`` Location where container recipe & image will be stored (default: /home/example/.local/easybuild/containers) +``--envvars-user-modules=ENVVARS-USER-MODULES`` List of environment variables that hold the base paths for which user-specific modules will be installed relative to (type comma-separated list; default: HOME) +``--external-modules-metadata=EXTERNAL-MODULES-METADATA`` List of (glob patterns for) paths to files specifying metadata for external modules (INI format) (type comma-separated list) +``--hooks=HOOKS`` Location of Python module with hook implementations (type str) +``--ignore-dirs=IGNORE-DIRS`` Directory names to ignore when searching for files/dirs (type comma-separated list; default: .git,.svn) +``--include-easyblocks=INCLUDE-EASYBLOCKS`` Location(s) of extra or customized easyblocks (type comma-separated list; default: ) +``--include-module-naming-schemes=INCLUDE-MODULE-NAMING-SCHEMES`` Location(s) of extra or customized module naming schemes (type comma-separated list; default: ) +``--include-toolchains=INCLUDE-TOOLCHAINS`` Location(s) of extra or customized toolchains or toolchain components (type comma-separated list; default: ) +``--installpath=INSTALLPATH`` Install path for software and modules (default: /home/example/.local/easybuild) +``--installpath-modules=INSTALLPATH-MODULES`` Install path for modules (if None, combine --installpath and --subdir-modules) +``--installpath-software=INSTALLPATH-SOFTWARE`` Install path for software (if None, combine --installpath and --subdir-software) +``--job-backend=JOB-BACKEND`` Backend to use for submitting jobs (type choice; default: GC3Pie) (choices: GC3Pie, PbsPython, Slurm) +``--logfile-format=DIR,FORMAT`` Directory name and format of the log file (type comma-separated tuple; default: easybuild,easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log) +``--module-depends-on`` Use depends_on (Lmod 7.6.1+) for dependencies in all generated modules (implies recursive unloading of modules). (default: False) +``--module-extensions`` Include 'extensions' statement in generated module file (Lua syntax only) (default: False) +``--module-naming-scheme=MODULE-NAMING-SCHEME`` Module naming scheme to use (default: EasyBuildMNS) +``--module-syntax=MODULE-SYNTAX`` Syntax to be used for module files (type choice; default: Lua) (choices: Lua, Tcl) +``--moduleclasses=MODULECLASSES`` Extend supported module classes (For more info on the default classes, use --show-default-moduleclasses) (type comma-separated list; default: base,ai,astro,bio,cae,chem,compiler,data,debugger,devel,geo,ide,lang,lib,math,mpi,numlib,perf,quantum,phys,system,toolchain,tools,vis) +``--modules-footer=PATH`` Path to file containing footer to be added to all generated module files +``--modules-header=PATH`` Path to file containing header to be added to all generated module files +``--modules-tool=MODULES-TOOL`` Modules tool to use (type choice; default: Lmod) (choices: EnvironmentModules, EnvironmentModulesC, EnvironmentModulesTcl, Lmod) +``--package-naming-scheme=PACKAGE-NAMING-SCHEME`` Packaging naming scheme choice (type choice; default: EasyBuildPNS) (choices: EasyBuildPNS) +``--packagepath=PACKAGEPATH`` The destination path for the packages built by package-tool (default: /home/example/.local/easybuild/packages) +``--prefix=PREFIX`` Change prefix for buildpath, installpath, sourcepath and repositorypath (used prefix for defaults /home/example/.local/easybuild) +``--recursive-module-unload`` Enable generating of modules that unload recursively. (default: False) +``--repository=REPOSITORY`` Repository type, using repositorypath (type choice; default: FileRepository) (choices: FileRepository) +``--repositorypath=REPOSITORYPATH`` Repository path, used by repository (is passed as list of arguments to create the repository instance). For more info, use --avail-repositories. (type comma-separated list; default: /home/example/.local/easybuild/ebfiles_repo) +``--sourcepath=SOURCEPATH`` Path(s) to where sources should be downloaded (string, colon-separated) (default: /home/example/.local/easybuild/sources) +``--subdir-modules=SUBDIR-MODULES`` Installpath subdir for modules (default: modules) +``--subdir-software=SUBDIR-SOFTWARE`` Installpath subdir for software (default: software) +``--subdir-user-modules=SUBDIR-USER-MODULES`` Base path of user-specific modules relative to --envvars-user-modules +``--suffix-modules-path=SUFFIX-MODULES-PATH`` Suffix for module files install path (default: all) +``--testoutput=TESTOUTPUT`` Path to where a job should place the output (to be set within jobscript) +``--tmp-logdir=TMP-LOGDIR`` Log directory where temporary log files are stored +``--tmpdir=TMPDIR`` Directory to use for temporary storage +================================================================= ==================================================================================================================================================================================================================================================================================== Container options From 53dac84c7bb6267417fa4786e1ea4c2d40c32a5e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 12 Sep 2022 06:24:45 +0800 Subject: [PATCH 234/286] update release notes and changelog for EasyBuild v4.6.1 + bump version to 4.6.1 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 161 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 162 insertions(+), 4 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index b3c53c4f..f6c6285a 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20220912.01** (`Sep 12th 2022`): update release notes for EasyBuild v4.6.1 (see :ref:`release_notes_eb461`) * **release 20220708.01** (`Jul 8th 2022`): update release notes for EasyBuild v4.6.0 (see :ref:`release_notes_eb460`) * **release 20220608.01** (`Jun 8th 2022`): update release notes for EasyBuild v4.5.5 (see :ref:`release_notes_eb455`) * **release 20220331.01** (`Mar 31st 2022`): update release notes for EasyBuild v4.5.4 (see :ref:`release_notes_eb454`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index a7863bb1..cbe3eb11 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,169 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,736** different software packages, +The latest version of EasyBuild provides support for building and installing **2,773** different software packages, including 37 different (compiler) toolchains. It contains 246 software-specific easyblocks and 37 generic easyblocks, -alongside 15,020 easyconfig files. +alongside 15,332 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb461: + +EasyBuild v4.6.1 (September 12th 2022) +-------------------------------------- + +bugfix/update release + +**framework** + +* various enhancements, including: + + * add script to find dependencies of Python packages (`#3839 `_) + * add ``ai`` default module class (`#4053 `_) + +* various bug fixes, including: + + * fix code style issues reported by recent flake8 linter (`#4049 `_) + * stick to autopep8 < 1.7.0 with Python 2.7 (`#4055 `_) + * ensure we call ``EasyBlock.patch_step`` for ``postinstallpatches`` (`#4063 `_) + * fix leaked handles in ``set_columns``, ``complete_cmd``, ``run_cmd_qa``, ``det_terminal_size functions`` + tests (`#4066 `_) + * fix ``quote_str`` when string with both ``'`` and ``"`` ends with a double quote (`#4068 `_) + * fix type-checking of patches to allow dict values + correctly handle patches specified as dict values in ``--new-pr`` (`#4070 `_) + * relax toolchain test by accepting both ``-march=native`` (x86_64) and ``-mcpu=native`` (aarch64) (`#4071 `_) + +* other changes: + + * run python in the same process as ``eb`` wrapper script by using ``exec`` (`#4048 `_) + * add ``get_linked_libs_raw`` function, and use it from both ``check_linked_shared_libs`` and ``sanity_check_rpath`` (`#4051 `_) + * update CI workflows (except container tests) to use Ubuntu 20.04, since Ubuntu 18.04 is deprecated (`#4064 `_) + * use ``SYSTEM`` constant for dependency that uses system toolchain in dumped easyconfig (`#4069 `_) + +**easyblocks** + +* minor enhancements and updates, including: + + * update LAMMPS easyblock for LAMMPS/23Jun22 (`#2213 `_) + * reduce the number of command line options for ``cmake`` command in CMakeMake generic easyblock (`#2514 `_) + * update libQGLViewer easyblock to take into account changes in the shared library names depending on Qt versions they are compiled with (`#2730 `_) + * improve PLUMED detection in GROMACS easyblock (`#2749 `_) + * make ``$LD_LIBRARY_PATH`` detection more robust for LAMMPS (`#2765 `_) + * enhance NVHPC easyblock to avoid superfluous warning (`#2767 `_) + * enhance PyTorch easyblock to also capture tests failing with signal (`#2768 `_) + * enhance PythonPackage easyblock to make sure all test command output makes it to the EasyBuild log, also when ``return_output_ec=True`` (`#2770 `_) + * set ``$NVHPC_CUDA_HOME`` for NVHPC 22.7+ (`#2776 `_) + +* various bug fixes, including: + + * make Amber easyblock aware of FlexiBLAS (`#2720 `_) + * update PyTorch easyblock to configure without breakpad support on POWER (`#2763 `_) + * use ``lib*`` in ``post_install`` step of FFTW.MPI easyblock to fix paths not being found on Linux distros favouring lib64 (like Suse/SLES) (`#2771 `_) + * use ``det_cmake_version`` function to determine CMake version in CMakeMake generic easyblock (`#2772 `_) + * don't enable building of ``ld.gold`` when installing binutils on a RISC-V system + don't configure GCC to use gold as default linker on a RISC-V system (`#2780 `_) + * tweak Amber(Tools) easyblock to run tests from top-level directory (`#2781 `_) + * fix version check for NVPTX library in sanity check of Clang easyblock (`#2783 `_) + +* other changes: + + * update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is deprecated) (`#2779 `_) + +**easyconfigs** + +* added example easyconfig files for 37 new software packages: + + * AptaSUITE (`#8583 `_), BigDFT (`#15860 `_), colossalai (`#15971 `_), CrystFEL (`#8407 `_), Dakota (`#15883 `_, `#16210 `_), + FastFold (`#15972 `_), fastparquet (`#15020 `_), FOX-Toolkit (`#15986 `_), GLM-AED (`#15879 `_), hiredis (`#16071 `_), + how_are_we_stranded_here (`#16220 `_, `#16227 `_), indicators (`#16209 `_), JavaFX (`#8583 `_), json-fortran (`#15979 `_), + jupyter-resource-usage (`#15834 `_), libev (`#16086 `_), libmad (`#16067 `_), libplinkio (`#13040 `_), LuaJIT2-OpenResty (`#16047 `_), + MetaMorpheus (`#15825 `_), mgltools (`#16226 `_), miniasm (`#15858 `_), muMerge (`#16115 `_), nano (`#16198 `_), nghttp3 (`#16097 `_), + olaFlow (`#16021 `_), OpenFAST (`#15983 `_, `#15983 `_), OpenFold (`#15971 `_), Phantompeakqualtools (`#15871 `_), + pyGenomeTracks (`#16143 `_), QuickPIC (`#15978 `_), RheoTool (`#16077 `_), Satsuma2 (`#16068 `_), SMC++ (`#16017 `_), stripy (`#15866 `_), + UCC-CUDA (`#15956 `_), VESTA (`#16217 `_) + +* added additional easyconfigs for various supported software packages, including: + + * alevin-fry 0.6.0, AmberTools 22.3, arrow-R 8.0.0, ASE 3.22.1, BBMap 38.98, BCFtools 1.15.1, binutils 2.39, + BLAST+ 2.13.0, Bowtie2 2.4.5, BUSCO 5.4.3, CapnProto 0.10.2, Cartopy 0.20.3, ccache 4.6.1, cclib 1.7.2, CDO 2.0.5, + CellRanger-ATAC 2.1.0, CoordgenLibs 3.0.1, cURL 7.84.0, cuTENSOR 1.6.0.3, einops 0.4.1, Elk 8.5.2, Emacs 28.1, + Embree 3.13.4, FFmpeg 4.4.2 + 5.0.1, fio 3.32, Flask 2.2.2, Flye 2.9.1, fmt 9.1.0, FORD 6.1.15, FreeSurfer 7.3.2, + GATE 9.2, GATK 4.2.6.1, GCC(core) 12.2.0, GDB 12.1, Geant4 11.0.2, GetOrganelle 1.7.6.1, gifsicle 1.93, GLFW 3.3.8, + glib-networking 2.72.1, Globus-CLI 3.6.0, gnuplot 5.4.4, gperftools 2.10, Graphviz 5.0.0, Gurobi 9.5.2, HDF5 1.12.2, + HTSlib 1.15.1, Hypre 2.25.0, Jansson 2.14, jax 0.3.14, Kalign 3.3.2, kim-api 2.3.0, LAMMPS 23Jun2022, libcerf 2.1, + libdwarf 0.4.1, Libint 2.7.2, libQGLViewer 2.8.0, LibSoup 2.74.0, libzip 1.9.2, Lua 5.4.4, lxml 4.9.1, + maeparser 1.3.0, matplotlib 3.5.2, MATSim 14.0, MDAnalysis 2.2.0, medaka 1.6.0, Megalodon 2.5.0, Mercurial 6.2, + MetaEuk 6, Mini-XML-3.3.1, MUMmer 4.0.0rc1, MUMPS 5.5.1, netCDF-Fortran 4.6.0, NGSpeciesID 0.1.2.1, + ont-remora 1.0.0, OpenFOAM v2206, OTF2 3.0, parallel 20220722, ParaView 5.10.1, patchelf 0.15.0, Perl 5.36.0, + pftoolsV3 3.2.12, PLINK 2.00a3.6, pretty-yaml 21.10.1, PRSice 2.3.5, pugixml 1.12.1, Pyomo 6.4.2, + PyOpenCL 2021.2.13, Pysam 0.19.1, PyStan 3.5.0, PyYAML 6.0, RDKit 2022.03.5, scikit-bio 0.5.7, scikit-build 0.15.0, + scikit-learn 1.1.2, scikit-optimize 0.9.0, SCOTCH 7.0.1, SIONlib 1.7.7, SISSO 3.1, spglib-python 2.0.0, Stacks 2.62, + Stata 17, SUMO 1.14.1, tbb 2021.5.0, tqdm 4.64.0, Transformers 4.21.1, Trycycler 0.5.3, Unicycler 0.5.0, + Valgrind 3.19.0, ViennaRNA 2.5.1, VTune 2022.3.0.eb, wxPython 4.1.1, x264 20220620, Z3 4.10.2, zfp 1.0.0 + +* minor enhancements, including: + + * add alternate download URL for Voro++ (`#15898 `_) + * add extra symlinks and sanity checks for libtinfo in ncurses (`#15903 `_) + * include some easyconfig constants in flake8 configuration file (`#16040 `_) + * add pigz dependency for cutadapt v3.4 + v3.5 (`#16056 `_) + * add sanity check commands for recent gettext versions (>= 0.20.x) (`#16091 `_) + +* various bug fixes, including: + + * use correct Matlab Runtime Compiler (v8.4) for FreeSurfer v7.1.1 (`#13375 `_) + * fix set-alias statements for MaxQuant v2.0.3.0 (`#15743 `_) + * add Autotools build dependency to R 4.2.0 w/ foss 2021b (`#15822 `_) + * add patch for BLIS to fix auto-detection of POWER (`#15826 `_) + * downgrade SPAdes dependency to v3.13.1 for Unicycler 0.4.9 since v3.15.3 is too new (`#15840 `_) + * explicitly enable HDF5 from kallisto v0.46.2 onwards (`#15843 `_) + * add CVE patch for XZ 5.2.5 + attempt to fix symbol patch for all OSs (`#15856 `_) + * use build environment set by EasyBuild and add missing dependency on zlib to minimap2 (`#15859 `_) + * add missing dependencies and execute tests on Trycycler v0.5.2 (`#15864 `_) + * add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9 (`#15874 `_) + * exclude (flaky) ``fault_tolerance_test`` and fix non-x86 build for TensorFlow 2.7.1 (`#15882 `_) + * work around miscompilation of OpenBLAS on POWER by compiling with ``-fstack-protector-strong`` (`#15885 `_) + * fix tests on POWER9 for BLIS 0.9.0 + fix auto-detect for POWER10 for BLIS (AMD) v2.0 + v3.0 (`#15889 `_) + * add and fix patches for PyTorch 1.9.0 on POWER (`#15919 `_) + * exclude Binary, PackedBinary and JAR easyblocks from binutils build requirements (`#15932 `_) + * consistently add libffi + elfutils dependencies to recent Clang easyconfigs (`#15935 `_, `#16225 `_) + * add patch to fix broken test on POWER for numpy in SciPy-bundle 2022.05 (`#15968 `_) + * refactor checksum test for extensions to use ``collect_exts_file_info`` (`#15973 `_) + * fix dependency on FOX Toolkit in SUMO (`#15986 `_) + * add missing SciPy-bundle dependency for rMATS-turbo (`#15988 `_) + * explicitly download wannier90 source tarball from wannier90 GitHub repository in QuantumESPRESSO 7.1 easyconfigs (`#15993 `_) + * restore ploteig in EIGENSOFT 7.2.1 (`#15996 `_) + * add alternative checksum for plot3Drgl extension in R v4.1.x + v4.2.0 easyconfigs (`#16011 `_) + * add patch to fix missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2020 (`#16027 `_) and 2021 (`#16026 `_) + * exclude failing test in TensorFlow 2.4.1 (`#16042 `_) + * skip NASA performance and remote server tests in netCDF v4.9.0 (`#16050 `_, `#16158 `_) + * use versioned symbols in ncurses built with system toolchain (by adding ``--with-versioned-syms`` configure option) (`#16064 `_) + * add patch to fix pkgconfig file for Blitz++ v1.0.2 (`#16102 `_) + * add missing BCFtools dependency for recent medaka versions (`#16107 `_) + * add GTK2 v2.24.33 as a dependency for Ghostscript v9.56.1 (`#16112 `_) + * fix checksum for Stacks v2.62 (due to silent re-release without version bump) (`#16134 `_) + * fix libsanitzer for glibc 2.36 to build GCCcore 11.3.0 (`#16145 `_) + * fix top level Makefile for AmberTools 20 and enable tests (`#16150 `_) + * add missing patches + enable running tests for AmberTools 21 with intel/2021a (`#16151 `_) and intel/2021b (`#16152 `_) + * replace HDF5 v1.13.1 with v1.12.1 as dependency, since we shouldn't use odd minor versions of HDF5 which are not stable releases (`#16153 `_) + * remove modextrapaths to add top-level install directory to ``$PATH ``for recent InterProScan easyconfigs (now done by default by Binary easyblock) (`#16167 `_) + * fix sources + source URL + homepage for Molekel v5.4.0 (`#16219 `_) + * consistently add maeparser + CoordgenLibs dependencies to OpenBabel 3.1.1 easyconfigs (`#16231 `_) + * fix checksum for CUDA 11.4.1 aarch64 installer (`#16234 `_) + * remove incorrect comment for Boost dependency in OpenBabel 3.1.1 easyconfigs (`#16238 `_) + * add direct Pango dependency in recent ImageMagick easyconfigs (`#16237 `_) + +* other changes: + + * remove superfluous ``-DCMAKE_BUILD_TYPE=Release``, use of ``build_type = Release``, or enabling ``separate_build_dir`` from easyconfigs using CMakeMake easyblock (`#13384 `_) + * synchronize ncurses easyconfigs using system toolchain (`#15903 `_) + * stick to Java/11 as dependency for Bazel 5.1.1 (which is available for x86_64, aarch64, ppc64le) (`#15906 `_) + * speed up OpenMPI 4.1.4 configure by not running ``autogen.pl --force``, but only running required Autotools commands (`#15957 `_) + * replace sed commands by upstreamed patches for BLIS built with intel-compilers toolchain (`#15958 `_) + * simplify AlphaFold foss/2021a easyconfigs by using a fleshed out patched OpenMM dependency (`#15981 `_) + * update Java/11 to 11.0.16 and Java/17 to 17.0.4 (`#16001 `_) + * remove unnecessary patch in recent JupyterLab (`#16030 `_) + * update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is deprecated) (`#16070 `_) + * make check for toolchain value in dependency spec in easyconfigs test suite aware that dumped easyconfig uses ``SYSTEM`` constant (`#16126 `_) + + .. _release_notes_eb460: EasyBuild v4.6.0 (July 8th 2022) diff --git a/docs/conf.py b/docs/conf.py index e2d56add..e2e63af6 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.6.0' # this is meant to reference the version of EasyBuild +version = '4.6.1' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20220708.0' # this is meant to reference the version of the documentation itself +release = '20220912.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 00c92db1fc764aea61997f014a4c948f104a5073 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 12 Sep 2022 13:42:10 +0800 Subject: [PATCH 235/286] bump version to 4.6.1 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index f93b4316..00e12ed4 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.6.0' +VERSION = '4.6.1' # Utility function to read README file From 3c11ca4328d308085212b8406e93495849f5263e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 27 Sep 2022 13:16:17 +0200 Subject: [PATCH 236/286] Improve the description of using a tuple in `patches` Clarify that the level must be an integer and describe the alternative to use a string to specify the starting directory. Also some minor rewording. --- docs/Writing_easyconfig_files.rst | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index 0b714dd9..d4f38dd3 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -163,18 +163,21 @@ Patches Patches can be provided via the ``patches`` easyconfig parameter (list). A patch can be defined as: * a ``string``, -* a ``tuple``, or +* a ``tuple`` of 2 elements, or * a ``dict`` The most straight-forward use-case is ``string``, which contains the name of the patch file (and must have ``.patch`` extension). -A ``tuple`` adds the possibility to specify the patch level which is used in patch command. -This is mostly needed if patch file adds new files or generally it is not possible to determine -the starting directory. +A ``tuple`` adds the possibility to specify where patch should be applied. +This is mostly needed if a patch file adds new files or it is generally not possible to determine +the starting directory. +The first element is the patch file and the second is +either the patch level (as an integer) which is used in the patch command (``patch -p``) +or a directory relative to the unpacked source dir. .. note:: ``tuple`` also has a special use case if the patch file has any other extension than ``.patch``. - In this case, the first tuple argument is a file which should be copied to unpacked source + In this case, the first tuple argument is a file which should be copied to the unpacked source dir and the second tuple argument is the target path, where the files should be copied to (relative to the unpacked source dir). See below for an example of this use case. @@ -193,9 +196,12 @@ Example: # a simple patch file 'name-versions-fix.patch', - # when creating only new files by patch file, you need to specify level: + # when creating only new files by patch file, you need to specify the level: ('name-versions-fix.patch', 1), + # apply the patch in a (sub-)subdirectory inside the source tree + ('name-versions-fix.patch', 'src/subfolder'), + # copy file to target_path folder ('Makefile', 'target_path'), From 2db140dcfa5b228ed52d1dec87ef47f462d288f3 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 12 Oct 2022 15:39:01 +0100 Subject: [PATCH 237/286] update docs to reflect easybuilders/easybuild-easyconfigs/#16330 --- docs/Wrapping_dependencies.rst | 2 +- docs/Writing_easyconfig_files.rst | 10 +++------- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/docs/Wrapping_dependencies.rst b/docs/Wrapping_dependencies.rst index 369cec75..f7ecd0b8 100644 --- a/docs/Wrapping_dependencies.rst +++ b/docs/Wrapping_dependencies.rst @@ -27,7 +27,7 @@ depending on a specific version (e.g., ``Java/1.8.0_181``): .. code:: # specify dependency on Java/1.8 "wrapper", rather than a specific Java version - dependencies = [('Java', '1.8', '', True)] + dependencies = [('Java', '1.8', '', SYSTEM)] This has a couple of advantages: diff --git a/docs/Writing_easyconfig_files.rst b/docs/Writing_easyconfig_files.rst index d4f38dd3..f8ab10eb 100644 --- a/docs/Writing_easyconfig_files.rst +++ b/docs/Writing_easyconfig_files.rst @@ -579,16 +579,12 @@ versions prior to v4.0, see :ref:`system_toolchain_motivation_deprecating_dummy` Specifying dependencies using ``system`` toolchain ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -To make EasyBuild resolve a dependency using the ``system`` toolchain, either specify '``system``' as toolchain name -in the tuple representing the dependency specification, or simply use ``True`` as 4th value in the tuple. +To make EasyBuild resolve a dependency using the ``system`` toolchain, simply use the ``SYSTEM`` template constant as +the 4th value in the tuple representing the dependency specification. For example, to specify PnMPI version 1.2.0 built with the ``system`` toolchain as a (runtime) dependency:: - dependencies = [('PnMPI', '1.2.0', '', ('system', ''))] - -which is equivalent to:: - - dependencies = [('PnMPI', '1.2.0', '', True)] + dependencies = [('PnMPI', '1.2.0', '', SYSTEM)] Using external modules as dependencies From a1594ff05928d75436e8b5953c867beee8edbefc Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 17 Oct 2022 14:02:15 +0200 Subject: [PATCH 238/286] Document GITHUB_RELEASE & GITHUB_LOWER_RELEASE --- docs/version-specific/easyconfig_templates.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/version-specific/easyconfig_templates.rst b/docs/version-specific/easyconfig_templates.rst index d9452410..cdbf4155 100644 --- a/docs/version-specific/easyconfig_templates.rst +++ b/docs/version-specific/easyconfig_templates.rst @@ -98,6 +98,8 @@ Constant Template value ``FTPGNOME_SOURCE`` http download for gnome ftp server ``https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s`` ``GITHUB_SOURCE`` GitHub source URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(name)s/archive`` ``GITHUB_LOWER_SOURCE`` GitHub source URL (lowercase name, namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(namelower)s/archive`` +``GITHUB_RELEASE`` GitHub release URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(name)s/releases/download/v%(version)s`` +``GITHUB_LOWER_RELEASE`` GitHub release URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s`` ``GNU_SAVANNAH_SOURCE`` download.savannah.gnu.org source url ``https://download-mirror.savannah.gnu.org/releases/%(namelower)s`` ``GNU_SOURCE`` gnu.org source url ``https://ftpmirror.gnu.org/gnu/%(namelower)s`` ``GOOGLECODE_SOURCE`` googlecode.com source url ``http://%(namelower)s.googlecode.com/files`` From 4b79f83a3c6172438e370bff7eb84e420f3380e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Oct 2022 09:55:35 +0200 Subject: [PATCH 239/286] auto-update docs for EasyBuild v4.6.2 --- docs/version-specific/Supported_software.rst | 1264 ++++++++++++----- docs/version-specific/easyblocks.rst | 8 + .../version-specific/easyconfig_templates.rst | 115 +- docs/version-specific/generic_easyblocks.rst | 56 +- 4 files changed, 977 insertions(+), 466 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index 8a708757..bd3bc1fa 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2773 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2798 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_Abseil_592` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_Albumentations_1478` - :ref:`list_software_alevin-fry_1021` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMD-uProf_779` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AMPtk_445` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_AMS_225` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_ANGEL_359` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_AptaSUITE_784` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_Arcade-Learning-Environment_2655` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_ArchR_464` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_arosics_756` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_atropos_776` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Austin_628` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock-GPU_1075` - :ref:`list_software_AutoDock-Vina_1237` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_Abseil_592` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGAT_285` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_Albumentations_1478` - :ref:`list_software_alevin-fry_1021` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_AMAPVox_604` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMD-uProf_779` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AMPtk_445` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_AMS_225` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_ANGEL_359` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_AptaSUITE_784` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_Arcade-Learning-Environment_2655` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_ArchR_464` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_arosics_756` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_atropos_776` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Austin_628` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock-GPU_1075` - :ref:`list_software_AutoDock-Vina_1237` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_Avogadro2_869` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -89,6 +89,7 @@ version versionsuffix toolchain ``2021`` ``-hotfix-2132`` ``system`` ``2022`` ``system`` ``2022`` ``-hotfix-2214`` ``system`` +``2022`` ``-hotfix-2223`` ``system`` ========== ================= ========== @@ -255,11 +256,11 @@ ACTC converts independent triangles into triangle strips or fans. *homepage*: https://sourceforge.net/projects/actc -======= =============================================================================================================== -version toolchain -======= =============================================================================================================== -``1.1`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2016b`` -======= =============================================================================================================== +======= =================================================================================================================================== +version toolchain +======= =================================================================================================================================== +``1.1`` ``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2016b`` +======= =================================================================================================================================== .. _list_software_ada_294: @@ -446,6 +447,22 @@ version versionsuffix toolchain ============ ================== =============================== +.. _list_software_AGAT_285: + +*AGAT* +++++++ + +AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations in any GTF/GFF format. + +*homepage*: https://agat.readthedocs.io/en/latest/ + +========= ============== +version toolchain +========= ============== +``0.9.2`` ``GCC/11.2.0`` +========= ============== + + .. _list_software_AGFusion_764: *AGFusion* @@ -702,6 +719,22 @@ version toolchain ========= ================= +.. _list_software_AMAPVox_604: + +*AMAPVox* ++++++++++ + +LiDAR data voxelisation software + +*homepage*: https://amap-dev.cirad.fr/projects/amapvox + +========= ============= ========== +version versionsuffix toolchain +========= ============= ========== +``1.9.4`` ``-Java-11`` ``system`` +========= ============= ========== + + .. _list_software_Amara_482: *Amara* @@ -742,7 +775,7 @@ version toolchain Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. -*homepage*: http://ambermd.org/amber.html +*homepage*: https://ambermd.org/amber.html ========= ================================================= ======================================================================== version versionsuffix toolchain @@ -758,6 +791,7 @@ version versionsuffix toolchain ``18`` ``-AmberTools-19-patchlevel-12-17-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b`` ``20.11`` ``-AmberTools-20.15-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` ``20.11`` ``-AmberTools-21.3`` ``foss/2020b``, ``fosscuda/2020b`` +``22.0`` ``-AmberTools-22.3`` ``foss/2021b`` ========= ================================================= ======================================================================== @@ -975,6 +1009,7 @@ The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for c version versionsuffix toolchain ============ ============= =============== ``2020.102`` ``-intelmpi`` ``iimpi/2020b`` +``2022.102`` ``-intelmpi`` ``iimpi/2021b`` ============ ============= =============== @@ -1530,11 +1565,11 @@ Provide an interface to ZIP archive files. *homepage*: https://metacpan.org/pod/Archive::Zip -======== ========================================================== -version toolchain -======== ========================================================== -``1.68`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -======== ========================================================== +======== ============================================================================== +version toolchain +======== ============================================================================== +``1.68`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +======== ============================================================================== .. _list_software_ArchR_464: @@ -1957,7 +1992,7 @@ version versionsuffix toolchain ``3.21.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``3.21.1`` ``-Python-3.8.2`` ``foss/2020a`` ``3.22.0`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021a`` -``3.22.1`` ``foss/2022a`` +``3.22.1`` ``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` ============== ================== ==================================================================================== @@ -2215,6 +2250,7 @@ version versionsuffix toolchain ``1.4.2`` ``-Python-2.7.12`` ``intel/2016b`` ``1.4.6`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` ``1.4.8`` ``-Python-2.7.18`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.5.1`` ``GCCcore/11.2.0`` ========= ================== ====================================== @@ -2371,7 +2407,7 @@ version toolchain ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= ``2.68`` ``foss/2016b`` ``2.69`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.71`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` +``2.71`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= @@ -2434,12 +2470,12 @@ AutoDock Vina is an open-source program for doing molecular docking. *homepage*: https://vina.scripps.edu/ -========= ============== ============== -version versionsuffix toolchain -========= ============== ============== -``1.1.2`` ``-linux_x86`` ``system`` -``1.2.3`` ``foss/2021a`` -========= ============== ============== +========= ============== ============================== +version versionsuffix toolchain +========= ============== ============================== +``1.1.2`` ``-linux_x86`` ``system`` +``1.2.3`` ``foss/2021a``, ``foss/2021b`` +========= ============== ============================== .. _list_software_AutoGeneS_875: @@ -2495,7 +2531,7 @@ version toolchain ``1.16.2`` ``GCCcore/10.2.0`` ``1.16.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` ``1.16.4`` ``GCCcore/11.2.0`` -``1.16.5`` ``GCCcore/11.3.0`` +``1.16.5`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -2550,10 +2586,26 @@ version toolchain ``20200321`` ``GCCcore/10.2.0`` ``20210128`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` ``20210726`` ``GCCcore/11.2.0`` -``20220317`` ``GCCcore/11.3.0`` +``20220317`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +.. _list_software_Avogadro2_869: + +*Avogadro2* ++++++++++++ + +Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. + +*homepage*: https://two.avogadro.cc/index.html + +========== ================= ========== +version versionsuffix toolchain +========== ================= ========== +``1.97.0`` ``-linux-x86_64`` ``system`` +========== ================= ========== + + .. _list_software_awscli_643: *awscli* @@ -2581,7 +2633,7 @@ version versionsuffix toolchain --- -:ref:`list_software_BabelStream_1090` - :ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_Bambi_475` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_bamtofastq_1074` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_bcbio-gff_863` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BigDFT_496` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biom-format_1117` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_Blosc2_549` - :ref:`list_software_BLT_226` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_boost_histogram_1620` - :ref:`list_software_boto3_487` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_Brotli-python_1339` - :ref:`list_software_Brunsli_735` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` +:ref:`list_software_BabelStream_1090` - :ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_Bambi_475` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_bamtofastq_1074` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_bcbio-gff_863` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BigDFT_496` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biom-format_1117` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_Blosc2_549` - :ref:`list_software_BLT_226` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_boost_histogram_1620` - :ref:`list_software_boto3_487` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_Brotli-python_1339` - :ref:`list_software_Brunsli_735` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_buildingspy_1194` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` .. _list_software_BabelStream_1090: @@ -3248,15 +3300,15 @@ beagle-lib is a high-performance library that can perform the core calculations *homepage*: https://github.com/beagle-dev/beagle-lib -========= ================ ================================================================================================================ -version versionsuffix toolchain -========= ================ ================================================================================================================ -``2.1.2`` ``foss/2016a``, ``foss/2017a`` -``3.0.1`` ``foss/2018a``, ``intel/2018a`` -``3.0.2`` ``foss/2018b`` -``3.0.2`` ``-CUDA-9.2.88`` ``foss/2018b`` -``3.1.2`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0``, ``gcccuda/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -========= ================ ================================================================================================================ +========= ================ ================================================================================================================================ +version versionsuffix toolchain +========= ================ ================================================================================================================================ +``2.1.2`` ``foss/2016a``, ``foss/2017a`` +``3.0.1`` ``foss/2018a``, ``intel/2018a`` +``3.0.2`` ``foss/2018b`` +``3.0.2`` ``-CUDA-9.2.88`` ``foss/2018b`` +``3.1.2`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0``, ``gcccuda/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +========= ================ ================================================================================================================================ .. _list_software_Beast_495: @@ -3281,6 +3333,7 @@ version toolchain ``2.5.2`` ``GCC/8.2.0-2.31.1`` ``2.6.3`` ``gcccuda/2019b`` ``2.6.4`` ``GCC/10.2.0`` +``2.6.7`` ``GCC/10.3.0`` ========== ==================================== @@ -3573,15 +3626,15 @@ Read files using HTSlib including BAM/CRAM, Tabix and BCF database files *homepage*: https://metacpan.org/release/Bio-DB-HTS -======== ================ =============================== -version versionsuffix toolchain -======== ================ =============================== -``2.11`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``2.11`` ``-Perl-5.26.1`` ``intel/2018a`` -``2.11`` ``-Perl-5.28.0`` ``foss/2018b`` -``3.01`` ``GCC/10.2.0``, ``GCC/11.2.0`` -``3.01`` ``-Perl-5.28.1`` ``GCC/8.2.0-2.31.1`` -======== ================ =============================== +======== ================ ============================================== +version versionsuffix toolchain +======== ================ ============================================== +``2.11`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``2.11`` ``-Perl-5.26.1`` ``intel/2018a`` +``2.11`` ``-Perl-5.28.0`` ``foss/2018b`` +``3.01`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +``3.01`` ``-Perl-5.28.1`` ``GCC/8.2.0-2.31.1`` +======== ================ ============================================== .. _list_software_Bio-EUtilities_1352: @@ -3673,12 +3726,13 @@ Biogeme is a open source Python package designed for the maximum likelihood esti *homepage*: https://pypi.python.org/pypi/biogeme -========= ============== -version toolchain -========= ============== -``3.1.2`` ``foss/2021a`` -``3.2.8`` ``foss/2021a`` -========= ============== +========== ============== +version toolchain +========== ============== +``3.1.2`` ``foss/2021a`` +``3.2.8`` ``foss/2021a`` +``3.2.10`` ``foss/2022a`` +========== ============== .. _list_software_biom-format_1117: @@ -3723,22 +3777,22 @@ Bioperl is the product of a community effort to produce Perl code which is usefu *homepage*: https://bioperl.org/ -=========== ================ ========================================================== -version versionsuffix toolchain -=========== ================ ========================================================== -``1.6.924`` ``-Perl-5.20.3`` ``intel/2016a`` -``1.6.924`` ``-Perl-5.22.1`` ``foss/2016a`` -``1.7.0`` ``-Perl-5.24.0`` ``foss/2016b`` -``1.7.1`` ``-Perl-5.24.0`` ``intel/2016b`` -``1.7.1`` ``-Perl-5.24.1`` ``intel/2017a`` -``1.7.2`` ``GCCcore/8.3.0`` -``1.7.2`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``1.7.2`` ``-Perl-5.26.1`` ``intel/2018a`` -``1.7.2`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` -``1.7.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -``1.7.7`` ``GCCcore/9.3.0`` -``1.7.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -=========== ================ ========================================================== +=========== ================ ============================================================================== +version versionsuffix toolchain +=========== ================ ============================================================================== +``1.6.924`` ``-Perl-5.20.3`` ``intel/2016a`` +``1.6.924`` ``-Perl-5.22.1`` ``foss/2016a`` +``1.7.0`` ``-Perl-5.24.0`` ``foss/2016b`` +``1.7.1`` ``-Perl-5.24.0`` ``intel/2016b`` +``1.7.1`` ``-Perl-5.24.1`` ``intel/2017a`` +``1.7.2`` ``GCCcore/8.3.0`` +``1.7.2`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``1.7.2`` ``-Perl-5.26.1`` ``intel/2018a`` +``1.7.2`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` +``1.7.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``1.7.7`` ``GCCcore/9.3.0`` +``1.7.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +=========== ================ ============================================================================== .. _list_software_BioPP_442: @@ -4385,6 +4439,7 @@ version versionsuffix toolchain ``1.74.0`` ``GCC/10.2.0`` ``1.76.0`` ``GCC/10.3.0`` ``1.77.0`` ``GCC/11.2.0`` +``1.79.0`` ``GCC/11.3.0`` ========== ================== ==================================================================== @@ -4771,6 +4826,22 @@ version versionsuffix toolchain =========== ================ =================================================================================================================================================================================================================================================================================================================================================================================================================================== +.. _list_software_buildingspy_1194: + +*buildingspy* ++++++++++++++ + +Python modules for automating Modelica simulations and for running unit test for the Buildings library + +*homepage*: https://simulationresearch.lbl.gov/modelica/buildingspy + +========= ============== +version toolchain +========= ============== +``4.0.0`` ``foss/2022a`` +========= ============== + + .. _list_software_Bullet_616: *Bullet* @@ -5010,7 +5081,7 @@ version toolchain --- -:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CASTEP_448` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_category_encoders_1808` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_CellTypist_1037` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMAverse_758` - :ref:`list_software_CmdStanR_764` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_colossalai_1066` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_CONN_302` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_Crumble_714` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CrystFEL_748` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CASTEP_448` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_category_encoders_1808` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_CDBtools_762` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_CellTypist_1037` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMAverse_758` - :ref:`list_software_CmdStanR_764` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_colossalai_1066` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_Compress-Raw-Zlib_1633` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_CONN_302` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_Crumble_714` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CrystFEL_748` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcompat_929` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_CWIPI_380` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_c-ares_571: @@ -5603,6 +5674,7 @@ version versionsuffix toolchain ``3.7.11`` ``system`` ``4.2.1`` ``system`` ``4.6.1`` ``GCCcore/11.2.0`` +``4.6.3`` ``system`` ========== ============= ================== @@ -5725,6 +5797,22 @@ version toolchain ======== ================================================================================ +.. _list_software_CDBtools_762: + +*CDBtools* +++++++++++ + +CDB (Constant DataBase) indexing and retrieval tools for FASTA files + +*homepage*: http://compbio.dfci.harvard.edu/tgi + +======== ============== +version toolchain +======== ============== +``0.99`` ``GCC/10.2.0`` +======== ============== + + .. _list_software_cddlib_610: *cddlib* @@ -6611,13 +6699,13 @@ Python bindings for libclang *homepage*: https://clang.llvm.org -========== ================== ================== -version versionsuffix toolchain -========== ================== ================== -``8.0.0`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` -``10.0.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``13.0.1`` ``GCCcore/11.2.0`` -========== ================== ================== +========== ================== ====================================== +version versionsuffix toolchain +========== ================== ====================================== +``8.0.0`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``10.0.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``13.0.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========== ================== ====================================== .. _list_software_CLAPACK_495: @@ -7125,6 +7213,22 @@ version versionsuffix toolchain ========== ================== ============== +.. _list_software_Compress-Raw-Zlib_1633: + +*Compress-Raw-Zlib* ++++++++++++++++++++ + +Low-Level Interface to zlib or zlib-ng compression library + +*homepage*: https://metacpan.org/pod/Compress::Raw::Zlib + +========= ================== +version toolchain +========= ================== +``2.202`` ``GCCcore/11.3.0`` +========= ================== + + .. _list_software_COMSOL_461: *COMSOL* @@ -8028,6 +8132,26 @@ version toolchain ================= ========================================================================== +.. _list_software_CUDAcompat_929: + +*CUDAcompat* +++++++++++++ + +Using the CUDA Forward Compatibility package, system administrators can run applications built using a newer toolkit even when an older driver that does not satisfy the minimum required driver version is installed on the system. This forward compatibility allows the CUDA deployments in data centers and enterprises to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit. + +*homepage*: https://docs.nvidia.com/deploy/cuda-compatibility/index.html + +======== ============== ========== +version versionsuffix toolchain +======== ============== ========== +``11`` ``system`` +``11.6`` ``system`` +``11.6`` ``-510.85.02`` ``system`` +``11.7`` ``system`` +``11.7`` ``-515.65.01`` ``system`` +======== ============== ========== + + .. _list_software_CUDAcore_710: *CUDAcore* @@ -8304,6 +8428,22 @@ version versionsuffix toolchain ========== ================= ============== +.. _list_software_CWIPI_380: + +*CWIPI* ++++++++ + +CWIPI (Coupling With Interpolation Parallel Interface) library helps in chaining and coupling codes. Provides exchanges of interpolated fields through a non-compliant geometric interface and allows control of the coupling algorithm using control parameters. CWIPI takes advantage of the distribution of the definition of the coupling algorithm in the different codes. + +*homepage*: https://w3.onera.fr/cwipi/ + +========== =============== +version toolchain +========== =============== +``0.12.0`` ``gompi/2021a`` +========== =============== + + .. _list_software_cxxopts_793: *cxxopts* @@ -8629,16 +8769,16 @@ Berkeley DB enables the development of custom data management solutions, withou *homepage*: http://www.oracle.com/technetwork/products/berkeleydb -=========== ======================================================================================================================================================= -version toolchain -=========== ======================================================================================================================================================= -``4.8.30`` ``intel/2016a`` -``6.2.23`` ``foss/2016a`` -``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` -``18.1.25`` ``GCCcore/7.3.0`` -``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``18.1.40`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -=========== ======================================================================================================================================================= +=========== =========================================================================================================================================================================== +version toolchain +=========== =========================================================================================================================================================================== +``4.8.30`` ``intel/2016a`` +``6.2.23`` ``foss/2016a`` +``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` +``18.1.25`` ``GCCcore/7.3.0`` +``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``18.1.40`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +=========== =========================================================================================================================================================================== .. _list_software_DB_File_613: @@ -8659,6 +8799,7 @@ version versionsuffix toolchain ``1.855`` ``GCCcore/10.2.0`` ``1.856`` ``GCCcore/10.3.0`` ``1.857`` ``GCCcore/11.2.0`` +``1.858`` ``GCCcore/11.3.0`` ========= ================ ================== @@ -8671,18 +8812,18 @@ Perl binding for MySQL *homepage*: https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm -========= ================ =============================== -version versionsuffix toolchain -========= ================ =============================== -``4.032`` ``-Perl-5.22.2`` ``intel/2016a`` -``4.033`` ``-Perl-5.24.0`` ``intel/2016b`` -``4.042`` ``-Perl-5.24.1`` ``intel/2017a`` -``4.046`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``4.046`` ``-Perl-5.26.1`` ``intel/2018a`` -``4.048`` ``-Perl-5.28.0`` ``foss/2018b`` -``4.050`` ``GCC/10.2.0``, ``GCC/11.2.0`` -``4.050`` ``-Perl-5.28.1`` ``foss/2019a`` -========= ================ =============================== +========= ================ ============================================== +version versionsuffix toolchain +========= ================ ============================================== +``4.032`` ``-Perl-5.22.2`` ``intel/2016a`` +``4.033`` ``-Perl-5.24.0`` ``intel/2016b`` +``4.042`` ``-Perl-5.24.1`` ``intel/2017a`` +``4.046`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``4.046`` ``-Perl-5.26.1`` ``intel/2018a`` +``4.048`` ``-Perl-5.28.0`` ``foss/2018b`` +``4.050`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +``4.050`` ``-Perl-5.28.1`` ``foss/2019a`` +========= ================ ============================================== .. _list_software_DBG2OLC_477: @@ -8742,7 +8883,7 @@ version toolchain ``0.106`` ``foss/2016a``, ``intel/2016a`` ``0.108`` ``intel/2016b``, ``intel/2017a`` ``0.110`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b`` -``0.112`` ``GCCcore/10.3.0`` +``0.112`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ======================================================================== @@ -8809,12 +8950,12 @@ deal.II is a C++ program library targeted at the computational solution of part *homepage*: https://www.dealii.org -========= =============== -version toolchain -========= =============== -``9.1.1`` ``intel/2019a`` -``9.3.3`` ``foss/2021a`` -========= =============== +========= =============================== +version toolchain +========= =============================== +``9.1.1`` ``foss/2019a``, ``intel/2019a`` +``9.3.3`` ``foss/2021a`` +========= =============================== .. _list_software_deap_410: @@ -8969,6 +9110,7 @@ version versionsuffix toolchain ========= ================= =============== ``0.7.8`` ``-linux_x86_64`` ``system`` ``0.8.7`` ``gompi/2020b`` +``1.1.5`` ``GCC/11.3.0`` ========= ================= =============== @@ -9884,7 +10026,7 @@ version versionsuffix toolchain --- -:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_eht-imaging_1098` - :ref:`list_software_Eigen_488` - :ref:`list_software_EigenExa_774` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_einops_654` - :ref:`list_software_elastix_762` - :ref:`list_software_elbencho_832` - :ref:`list_software_ELFIO_367` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_elprep_648` - :ref:`list_software_ELSI_301` - :ref:`list_software_ELSI-RCI_568` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_Embree_592` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_epiScanpy_940` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESL-Bundle_875` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExaML_439` - :ref:`list_software_Excel-Writer-XLSX_1559` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_expecttest_1097` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_eht-imaging_1098` - :ref:`list_software_Eigen_488` - :ref:`list_software_EigenExa_774` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_einops_654` - :ref:`list_software_elastix_762` - :ref:`list_software_elbencho_832` - :ref:`list_software_ELFIO_367` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_elprep_648` - :ref:`list_software_ELSI_301` - :ref:`list_software_ELSI-RCI_568` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_Embree_592` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_enchant-2_832` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_epiScanpy_940` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESL-Bundle_875` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExaML_439` - :ref:`list_software_Excel-Writer-XLSX_1559` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_expecttest_1097` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_E-ANTIC_481: @@ -10039,6 +10181,7 @@ version toolchain ``4.5.4`` ``system`` ``4.5.5`` ``system`` ``4.6.0`` ``system`` +``4.6.1`` ``system`` ========== ========== @@ -10598,6 +10741,22 @@ version toolchain ========= =============== +.. _list_software_enchant-2_832: + +*enchant-2* ++++++++++++ + +Enchant aims to provide a simple but comprehensive abstraction for dealing with different spell checking libraries in a consistent way. A client, such as a text editor or word processor, need not know anything about a specific spell-checker, and since all back-ends are plugins, new spell-checkers can be added without needing any change to the program using Enchant. + +*homepage*: https://github.com/AbiWord/enchant + +========= ================== +version toolchain +========= ================== +``2.3.3`` ``GCCcore/11.2.0`` +========= ================== + + .. _list_software_EnsEMBLCoreAPI_1193: *EnsEMBLCoreAPI* @@ -10734,6 +10893,7 @@ version versionsuffix toolchain ``8.0.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` ``8.1.1`` ``foss/2021a``, ``intel/2021a`` ``8.2.0`` ``foss/2021b``, ``intel/2021b`` +``8.3.0`` ``foss/2022a`` ============ ================ ================================================================================= @@ -10990,7 +11150,7 @@ version toolchain *expat* +++++++ -Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) +Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags). *homepage*: https://libexpat.github.io @@ -11007,6 +11167,7 @@ version toolchain ``2.2.9`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ``2.4.1`` ``GCCcore/11.2.0`` ``2.4.8`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0`` +``2.4.9`` ``GCCcore/12.2.0`` ========= ========================================================================================================================= @@ -11035,11 +11196,11 @@ This library implements expect tests (also known as "golden" tests). Expect test *homepage*: https://github.com/ezyang/expecttest -========= ========================================================== -version toolchain -========= ========================================================== -``0.1.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` -========= ========================================================== +========= ============================================================================== +version toolchain +========= ============================================================================== +``0.1.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ============================================================================== .. _list_software_eXpress_746: @@ -11083,7 +11244,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_Fastaq_608` - :ref:`list_software_FastFold_787` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastparquet_1200` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_FFTW.MPI_587` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_fio_318` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMPy_348` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoBiS_435` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FOX-Toolkit_1024` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeBarcodes_1189` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FSON_310` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_f90wrap_649` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_Fastaq_608` - :ref:`list_software_FastFold_787` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastparquet_1200` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_FFTW.MPI_587` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_fio_318` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMPy_348` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoBiS_435` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FOX-Toolkit_1024` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeBarcodes_1189` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FSON_310` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -11102,6 +11263,22 @@ version toolchain ======== ========== +.. _list_software_f90wrap_649: + +*f90wrap* ++++++++++ + +f90wrap is a tool to automatically generate Python extension modules which interface to Fortran code that makes use of derived types. It builds on the capabilities of the popular f2py utility by generating a simpler Fortran 90 interface to the original Fortran code which is then suitable for wrapping with f2py, together with a higher-level Pythonic wrapper that makes the existance of an additional layer transparent to the final user. + +*homepage*: https://github.com/jameskermode/f90wrap + +========= ============== +version toolchain +========= ============== +``0.2.8`` ``foss/2021a`` +========= ============== + + .. _list_software_Faber_480: *Faber* @@ -11697,6 +11874,7 @@ version versionsuffix toolchain ``6.7.5`` ``intel/2020a`` ``6.7.6`` ``intel/2020b`` ``6.7.7`` ``intel/2021b`` +``6.7.9`` ``intel/2022a`` ========= ============= ================================ @@ -11973,7 +12151,7 @@ version versionsuffix toolchain ``3.3.8`` ``-amd`` ``gompi/2020a`` ``3.3.8`` ``-serial`` ``GCC/9.3.0`` ``3.3.9`` ``gompi/2021a``, ``intel/2021a`` -``3.3.10`` ``GCC/11.3.0``, ``gompi/2021b``, ``iimpi/2021b`` +``3.3.10`` ``GCC/11.3.0``, ``gompi/2021b``, ``iimpi/2021b``, ``iimpi/2022a`` ========== ============= ======================================================================================================================================================================================================================================================================================================================= @@ -12131,6 +12309,7 @@ version toolchain ``5.39`` ``GCCcore/10.2.0`` ``5.40`` ``GCCcore/10.3.0`` ``5.41`` ``GCCcore/11.2.0`` +``5.43`` ``GCCcore/11.3.0`` ======== ==================================== @@ -12660,6 +12839,7 @@ version toolchain ``1.3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``1.3.6`` ``GCCcore/10.3.0`` ``1.3.7`` ``GCCcore/11.2.0`` +``1.3.8`` ``GCCcore/11.3.0`` ========= =================================================================================================================================================================================================== @@ -13456,12 +13636,13 @@ version toolchain FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications. -*homepage*: http://ftgl.sourceforge.net/docs/html/ +*homepage*: https://github.com/frankheckenbach/ftgl ============= ========================================================================================================== version toolchain ============= ========================================================================================================== ``2.1.3-rc5`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2018b``, ``intel/2017b`` +``2.4.0`` ``GCCcore/11.3.0`` ============= ========================================================================================================== @@ -13978,12 +14159,12 @@ The awk utility interprets a special-purpose programming language that makes it *homepage*: https://www.gnu.org/software/gawk -========= ============================== -version toolchain -========= ============================== -``5.1.0`` ``GCC/10.2.0`` -``5.1.1`` ``GCC/10.3.0``, ``GCC/11.3.0`` -========= ============================== +========= ============================================== +version toolchain +========= ============================================== +``5.1.0`` ``GCC/10.2.0`` +``5.1.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +========= ============================================== .. _list_software_Gblocks_709: @@ -14053,6 +14234,7 @@ version toolchain ``7.6.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``8.0.4`` ``GCCcore/10.3.0`` ``8.2.0`` ``GCCcore/11.2.0`` +``8.2.2`` ``GCCcore/11.3.0`` ========== ==================================== @@ -14248,11 +14430,11 @@ GConf is a system for storing application preferences. It is intended for user *homepage*: https://projects.gnome.org/gconf/ -========= ============================================================================================================================================================ -version toolchain -========= ============================================================================================================================================================ -``3.2.6`` ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -========= ============================================================================================================================================================ +========= ================================================================================================================================================================================ +version toolchain +========= ================================================================================================================================================================================ +``3.2.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +========= ================================================================================================================================================================================ .. _list_software_GCTA_287: @@ -15493,6 +15675,7 @@ version versionsuffix toolchain ``3.1.14`` ``GCCcore/10.2.0`` ``3.1.18`` ``GCCcore/10.3.0`` ``3.1.24`` ``GCCcore/11.2.0`` +``3.1.27`` ``GCCcore/11.3.0`` ========== ================= =============================== @@ -15982,7 +16165,7 @@ version versionsuffix toolchain ``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``2.1.0b4`` ``GCC/8.3.0`` ``2.1.0b5`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` -``2.1.2`` ``GCC/11.2.0`` +``2.1.2`` ``GCC/11.2.0``, ``GCC/11.3.0`` =========== ================== ====================================================================== @@ -16154,6 +16337,7 @@ version toolchain ``1.17.3`` ``system`` ``1.17.6`` ``system`` ``1.18.1`` ``system`` +``1.18.3`` ``system`` ========== ================= @@ -16443,19 +16627,20 @@ GPAW is a density-functional theory (DFT) Python code based on the projector-aug *homepage*: https://wiki.fysik.dtu.dk/gpaw/ -=========== ============================ =============================== -version versionsuffix toolchain -=========== ============================ =============================== -``1.4.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``19.8.1`` ``-ASE-3.18.0-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``19.8.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``20.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``20.10.0`` ``foss/2020b``, ``intel/2020b`` -``20.10.0`` ``-ASE-3.20.1-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``21.1.0`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` -``21.6.0`` ``foss/2021a`` -``21.6.0`` ``-ASE-3.22.0`` ``foss/2020b``, ``intel/2020b`` -=========== ============================ =============================== +=========== ============================ ================================================================ +version versionsuffix toolchain +=========== ============================ ================================================================ +``1.4.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``19.8.1`` ``-ASE-3.18.0-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``19.8.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``20.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``20.10.0`` ``foss/2020b``, ``intel/2020b`` +``20.10.0`` ``-ASE-3.20.1-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``21.1.0`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` +``21.6.0`` ``foss/2021a`` +``21.6.0`` ``-ASE-3.22.0`` ``foss/2020b``, ``intel/2020b`` +``22.8.0`` ``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` +=========== ============================ ================================================================ .. _list_software_GPAW-setups_1024: @@ -16942,11 +17127,11 @@ Groff (GNU troff) is a typesetting system that reads plain text mixed with forma *homepage*: https://www.gnu.org/software/groff -========== ======================================================================================================================================================= -version toolchain -========== ======================================================================================================================================================= -``1.22.4`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ======================================================================================================================================================= +========== =========================================================================================================================================================================== +version toolchain +========== =========================================================================================================================================================================== +``1.22.4`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== =========================================================================================================================================================================== .. _list_software_GroIMP_526: @@ -17447,6 +17632,7 @@ version toolchain ``2.2.4`` ``GCCcore/7.3.0``, ``GCCcore/9.3.0`` ``2.2.7`` ``GCCcore/10.3.0`` ``3.0.7`` ``GCCcore/11.2.0`` +``3.0.8`` ``GCCcore/11.3.0`` ========== ====================================================================================================================================================================================================================== @@ -18216,15 +18402,15 @@ version toolchain *hiredis* +++++++++ -Hiredis is a minimalistic C client library for the Redis database. It is minimalistic because it just adds minimal support for the protocol, but at the same time it uses a high level printf-alike API in order to make it much higher level than otherwise suggested by its minimal code base and the lack of explicit bindings for every Redis command. +Hiredis is a minimalistic C client library for the Redis database. It is minimalistic because it just adds minimal support for the protocol, but at the same time it uses a high level printf-alike API in order to make it much higher level than otherwise suggested by its minimal code base and the lack of explicit bindings for every Redis command. *homepage*: https://github.com/redis/hiredis -========= ================== -version toolchain -========= ================== -``1.0.2`` ``GCCcore/11.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.0.2`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ====================================== .. _list_software_HISAT2_427: @@ -18511,7 +18697,7 @@ version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intel/2022.09``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -18522,13 +18708,14 @@ version toolchain An interactive process viewer for Unix -*homepage*: http://hisham.hm/htop/ +*homepage*: https://htop.dev ========= ========== version toolchain ========= ========== ``2.0.0`` ``system`` ``2.0.1`` ``system`` +``3.2.1`` ``system`` ========= ========== @@ -18611,16 +18798,17 @@ version versionsuffix toolchain *hunspell* ++++++++++ -Hunspell is a spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding. +Hunspell is a spell checker and morphological analyzer library and program designed for languageswith rich morphology and complex word compounding or character encoding. *homepage*: http://hunspell.github.io/ -========= ================= -version toolchain -========= ================= -``1.6.1`` ``intel/2017a`` -``1.7.0`` ``GCCcore/8.2.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``1.6.1`` ``intel/2017a`` +``1.7.0`` ``GCCcore/8.2.0`` +``1.7.1`` ``GCCcore/11.2.0`` +========= ================== .. _list_software_hwloc_541: @@ -18819,7 +19007,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_i7z_282` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_indicators_1072` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_InterProScan_data_1713` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intervaltree-python_2020` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_Iris_407` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_IsoNet_594` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_i7z_282` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_Imath_499` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_indicators_1072` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_InterProScan_data_1713` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intervaltree-python_2020` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_Iris_407` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_IsoNet_594` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -19363,6 +19551,7 @@ version versionsuffix toolchain ``2021b`` ``system`` ``2022.00`` ``system`` ``2022.05`` ``system`` +``2022.09`` ``system`` ``2022a`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ===================== ==================== ========== @@ -19548,6 +19737,22 @@ version toolchain ========= ========================================================== +.. _list_software_Imath_499: + +*Imath* ++++++++ + +Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics + +*homepage*: https://imath.readthedocs.io/en/latest/ + +========= ================== +version toolchain +========= ================== +``3.1.5`` ``GCCcore/11.3.0`` +========= ================== + + .. _list_software_IMB_216: *IMB* @@ -19596,14 +19801,15 @@ This python library helps you with augmenting images for your machine learning p *homepage*: https://imgaug.readthedocs.io/en/latest/ -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``0.2.8`` ``-Python-3.6.6`` ``foss/2018b`` -``0.4.0`` ``foss/2021b`` -``0.4.0`` ``-CUDA-11.3.1`` ``foss/2021a`` -``0.4.0`` ``-Python-3.7.4`` ``foss/2019b`` -========= ================= ============== +========= ================= ============================== +version versionsuffix toolchain +========= ================= ============================== +``0.2.8`` ``-Python-3.6.6`` ``foss/2018b`` +``0.4.0`` ``foss/2021a``, ``foss/2021b`` +``0.4.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``0.4.0`` ``-CUDA-11.4.1`` ``foss/2021b`` +``0.4.0`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============================== .. _list_software_imkl_429: @@ -19648,6 +19854,7 @@ version versionsuffix toolchain ``2021.4.0`` ``system`` ``2022.0.1`` ``system`` ``2022.1.0`` ``system`` +``2022.2.0`` ``system`` ============== ============= ====================================================================================================================================================================================================================================================================== @@ -19666,6 +19873,7 @@ version toolchain ``2021.4.0`` ``gompi/2021b``, ``iimpi/2021b`` ``2022.0.1`` ``iimpi/2022.00`` ``2022.1.0`` ``iimpi/2022.05``, ``iimpi/2022a`` +``2022.2.0`` ``iimpi/2022.09`` ============ ================================== @@ -19769,6 +19977,7 @@ version versionsuffix toolchain ``2021.4.0`` ``intel-compilers/2021.4.0`` ``2021.5.0`` ``intel-compilers/2022.0.1`` ``2021.6.0`` ``intel-compilers/2022.1.0`` +``2021.7.0`` ``intel-compilers/2022.2.0`` ``system`` ``iccifort/system-GCC-system-2.29`` =============== ============= ================================================================================================================================================================================================================================ @@ -20050,6 +20259,7 @@ version versionsuffix toolchain ``2021b`` ``system`` ``2022.00`` ``system`` ``2022.05`` ``system`` +``2022.09`` ``system`` ``2022a`` ``system`` ===================== ============= ========== @@ -20073,6 +20283,7 @@ version toolchain ``2022.0.1`` ``system`` ``2022.0.2`` ``system`` ``2022.1.0`` ``system`` +``2022.2.0`` ``system`` ============ ========== @@ -20499,6 +20710,7 @@ version versionsuffix toolchain ``7.18.1`` ``GCCcore/10.2.0`` ``7.25.0`` ``GCCcore/10.3.0`` ``7.26.0`` ``GCCcore/11.2.0`` +``8.5.0`` ``GCCcore/11.3.0`` ========== ================== ======================================================================================= @@ -21153,11 +21365,12 @@ jq is a lightweight and flexible command-line JSON processor. *homepage*: https://stedolan.github.io/jq/ -======= ================= -version toolchain -======= ================= -``1.5`` ``GCCcore/6.4.0`` -======= ================= +======= ========================================================== +version toolchain +======= ========================================================== +``1.5`` ``GCCcore/6.4.0`` +``1.6`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +======= ========================================================== .. _list_software_json-c_586: @@ -21258,11 +21471,11 @@ A C library that implements a dynamic array. *homepage*: http://judy.sourceforge.net/ -========= ================================================================================================ -version toolchain -========= ================================================================================================ -``1.0.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -========= ================================================================================================ +========= ==================================================================================================================== +version toolchain +========= ==================================================================================================================== +``1.0.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +========= ==================================================================================================================== .. _list_software_Julia_501: @@ -21290,10 +21503,13 @@ version versionsuffix toolchain ``1.6.4`` ``-linux-x86_64`` ``system`` ``1.6.5`` ``-linux-x86_64`` ``system`` ``1.6.6`` ``-linux-x86_64`` ``system`` +``1.6.7`` ``-linux-x86_64`` ``system`` ``1.7.0`` ``-linux-x86_64`` ``system`` ``1.7.1`` ``-linux-x86_64`` ``system`` ``1.7.2`` ``-linux-x86_64`` ``system`` ``1.7.3`` ``-linux-x86_64`` ``system`` +``1.8.0`` ``-linux-x86_64`` ``system`` +``1.8.2`` ``-linux-x86_64`` ``system`` ========= ================= ========== @@ -22136,8 +22352,10 @@ The LLVM-based D Compiler version versionsuffix toolchain ========== ============= ================== ``0.17.6`` ``-x86_64`` ``system`` +``1.24.0`` ``-x86_64`` ``system`` ``1.25.1`` ``GCCcore/10.2.0`` ``1.26.0`` ``GCCcore/10.3.0`` +``1.30.0`` ``GCCcore/11.3.0`` ========== ============= ================== @@ -22319,12 +22537,12 @@ Asynchronous input/output library that uses the kernels native interface. *homepage*: https://pagure.io/libaio -=========== ========================================================== -version toolchain -=========== ========================================================== -``0.3.111`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.3.112`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -=========== ========================================================== +=========== ============================================================================== +version toolchain +=========== ============================================================================== +``0.3.111`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.3.112`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +=========== ============================================================================== .. _list_software_libarchive_1049: @@ -22465,6 +22683,7 @@ libcint is an open source library for analytical Gaussian integrals. version toolchain ========= ============================== ``4.4.0`` ``foss/2020b``, ``foss/2021a`` +``5.1.6`` ``foss/2022a`` ========= ============================== @@ -22510,13 +22729,14 @@ Libconfig is a simple library for processing structured configuration files *homepage*: https://hyperrealm.github.io/libconfig -========= ================= -version toolchain -========= ================= -``1.5`` ``intel/2016b`` -``1.7.1`` ``GCCcore/6.4.0`` -``1.7.2`` ``GCCcore/7.3.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``1.5`` ``intel/2016b`` +``1.7.1`` ``GCCcore/6.4.0`` +``1.7.2`` ``GCCcore/7.3.0`` +``1.7.3`` ``GCCcore/10.3.0`` +========= ================== .. _list_software_libcpuset_971: @@ -23831,6 +24051,7 @@ version toolchain ``8.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ``8.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ``8.1.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0`` +``8.2`` ``GCCcore/12.2.0`` ========= =================================================================================================================================================================================================================================================================================================================================================================================== @@ -24021,18 +24242,18 @@ Sodium is a modern, easy-to-use software library for encryption, decryption, sig *homepage*: https://doc.libsodium.org/ -========== ================================================================================================ -version toolchain -========== ================================================================================================ -``1.0.6`` ``intel/2016a`` -``1.0.8`` ``foss/2016a`` -``1.0.11`` ``foss/2016b``, ``intel/2016b`` -``1.0.12`` ``GCCcore/6.4.0``, ``intel/2017a`` -``1.0.13`` ``GCCcore/6.4.0``, ``foss/2017a`` -``1.0.16`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.0.17`` ``GCCcore/8.2.0`` -``1.0.18`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ================================================================================================ +========== ==================================================================================================================== +version toolchain +========== ==================================================================================================================== +``1.0.6`` ``intel/2016a`` +``1.0.8`` ``foss/2016a`` +``1.0.11`` ``foss/2016b``, ``intel/2016b`` +``1.0.12`` ``GCCcore/6.4.0``, ``intel/2017a`` +``1.0.13`` ``GCCcore/6.4.0``, ``foss/2017a`` +``1.0.16`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.0.17`` ``GCCcore/8.2.0`` +``1.0.18`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ==================================================================================================================== .. _list_software_LibSoup_702: @@ -24051,6 +24272,7 @@ version toolchain ``2.70.0`` ``GCCcore/8.3.0`` ``2.72.0`` ``GCCcore/10.2.0`` ``2.74.0`` ``GCCcore/10.3.0`` +``3.0.7`` ``GCC/11.2.0`` ========== ================== @@ -24138,6 +24360,7 @@ version toolchain ``3.23`` ``foss/2018b``, ``intel/2018b`` ``3.24`` ``GCCcore/9.3.0`` ``3.25`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``3.30`` ``GCCcore/11.3.0`` ======== ========================================================== @@ -24251,7 +24474,7 @@ version toolchain ``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` ``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` ``2.4.6`` ``FCC/4.5.0``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.4.7`` ``GCCcore/11.3.0`` +``2.4.7`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` ========= ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -24288,7 +24511,7 @@ version toolchain ``0.9.6`` ``GCCcore/5.4.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016b`` ``0.9.7`` ``GCCcore/6.4.0`` ``0.9.10`` ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.0`` ``GCCcore/11.2.0`` +``1.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ============================================================================================== @@ -24370,12 +24593,12 @@ libvdwxc is a general library for evaluating energy and potential for exchange-c *homepage*: https://libvdwxc.org -========= ================================================================================================================================================= -version toolchain -========= ================================================================================================================================================= -``0.3.2`` ``foss/2018b`` -``0.4.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` -========= ================================================================================================================================================= +========= ================================================================================================================================================================= +version toolchain +========= ================================================================================================================================================================= +``0.3.2`` ``foss/2018b`` +``0.4.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` +========= ================================================================================================================================================================= .. _list_software_libvorbis_972: @@ -24410,6 +24633,7 @@ version toolchain ``1.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.2.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.2.4`` ``GCCcore/11.3.0`` ========= ======================================================== @@ -25015,6 +25239,7 @@ version toolchain ``5.1.0`` ``GCCcore/9.3.0`` ``5.2.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0`` ``5.2.1`` ``GCC/11.2.0`` +``5.2.2`` ``GCC/11.3.0`` ========= ===================================================================================================== @@ -25187,16 +25412,16 @@ Lmfit provides a high-level interface to non-linear optimization and curve fitti *homepage*: https://lmfit.github.io/lmfit-py -========== ================== =============================== -version versionsuffix toolchain -========== ================== =============================== -``0.9.9`` ``-Python-3.6.4`` ``intel/2018a`` -``0.9.14`` ``-Python-2.7.15`` ``intel/2018b`` -``1.0.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.0.1`` ``-Python-3.8.2`` ``foss/2020a`` -``1.0.2`` ``foss/2020b``, ``intel/2020b`` -``1.0.3`` ``foss/2021a`` -========== ================== =============================== +========== ================== =============================================== +version versionsuffix toolchain +========== ================== =============================================== +``0.9.9`` ``-Python-3.6.4`` ``intel/2018a`` +``0.9.14`` ``-Python-2.7.15`` ``intel/2018b`` +``1.0.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.0.1`` ``-Python-3.8.2`` ``foss/2020a`` +``1.0.2`` ``foss/2020b``, ``intel/2020b`` +``1.0.3`` ``foss/2021a``, ``foss/2022a``, ``intel/2022a`` +========== ================== =============================================== .. _list_software_Lmod_396: @@ -25759,12 +25984,12 @@ Portable lossless data compression library *homepage*: http://www.oberhumer.com/opensource/lzo/ -======== ============================================================================================================================================================================================================================================================================== -version toolchain -======== ============================================================================================================================================================================================================================================================================== -``2.09`` ``intel/2016b``, ``intel/2017b`` -``2.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` -======== ============================================================================================================================================================================================================================================================================== +======== ================================================================================================================================================================================================================================================================================================== +version toolchain +======== ================================================================================================================================================================================================================================================================================================== +``2.09`` ``intel/2016b``, ``intel/2017b`` +``2.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` +======== ================================================================================================================================================================================================================================================================================================== .. _list_software_letter_m: @@ -25773,7 +25998,7 @@ version toolchain --- -:ref:`list_software_M1QN3_336` - :ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_MAGeCK_456` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_matplotlib-inline_1764` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_MEGAN_360` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaMorpheus_1242` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mgltools_881` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_miniasm_750` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_Minipolish_1052` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_mm-common_912` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MNE-Python_911` - :ref:`list_software_MOABS_370` - :ref:`list_software_ModelTest-NG_1107` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_MONA_299` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MuJoCo_557` - :ref:`list_software_mujoco-py_931` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_muMerge_722` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M1QN3_336` - :ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_MAGeCK_456` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_Mamba_478` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_matplotlib-inline_1764` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_MEGAN_360` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaMorpheus_1242` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mgltools_881` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_Miller_613` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_miniasm_750` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_Minipolish_1052` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_mm-common_912` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MNE-Python_911` - :ref:`list_software_MOABS_370` - :ref:`list_software_ModelTest-NG_1107` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_MONA_299` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MuJoCo_557` - :ref:`list_software_mujoco-py_931` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_muMerge_722` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M1QN3_336: @@ -25975,6 +26200,7 @@ version versionsuffix toolchain ``2.5.4`` ``fosscuda/2019a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intelcuda/2019b``, ``intelcuda/2020b`` ``2.6.1`` ``-CUDA-11.3.1`` ``foss/2021a`` ``2.6.2`` ``-CUDA-11.4.1`` ``foss/2021b`` +``2.6.2`` ``-CUDA-11.7.0`` ``foss/2022a`` ========= ================ ======================================================================================================================== @@ -26123,6 +26349,22 @@ version versionsuffix toolchain ========= ================== ================================================================================================================================================================= +.. _list_software_Mamba_478: + +*Mamba* ++++++++ + +Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux (ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda's commands. + +*homepage*: https://mamba.readthedocs.io/ + +============ ========== +version toolchain +============ ========== +``4.14.0-0`` ``system`` +============ ========== + + .. _list_software_manta_529: *manta* @@ -26234,6 +26476,7 @@ version toolchain ``10.4.13`` ``gompi/2019b`` ``10.5.8`` ``GCC/10.2.0`` ``10.6.4`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``10.9.3`` ``GCC/11.3.0`` =========== =============================== @@ -26473,7 +26716,7 @@ version versionsuffix toolchain ``3.4.2`` ``foss/2021a``, ``intel/2021a`` ``3.4.3`` ``foss/2021b``, ``intel/2021b`` ``3.5.1`` ``foss/2020b``, ``intel/2020b`` -``3.5.2`` ``foss/2022a`` +``3.5.2`` ``foss/2022a``, ``intel/2022a`` ========= ================================= =================================================================================== @@ -26882,16 +27125,16 @@ Read, write and analyze MD trajectories with only a few lines of Python code. *homepage*: https://mdtraj.org -========= ================= =================================================== -version versionsuffix toolchain -========= ================= =================================================== -``1.9.1`` ``-Python-3.6.3`` ``intel/2017b`` -``1.9.2`` ``-Python-3.6.6`` ``intel/2018b`` -``1.9.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.9.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.9.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``1.9.7`` ``intel/2021b`` -========= ================= =================================================== +========= ================= ================================================================ +version versionsuffix toolchain +========= ================= ================================================================ +``1.9.1`` ``-Python-3.6.3`` ``intel/2017b`` +``1.9.2`` ``-Python-3.6.6`` ``intel/2018b`` +``1.9.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.9.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.9.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``1.9.7`` ``foss/2021a``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` +========= ================= ================================================================ .. _list_software_medaka_611: @@ -27729,6 +27972,22 @@ version toolchain ========== ============== +.. _list_software_Miller_613: + +*Miller* +++++++++ + +Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON + +*homepage*: https://miller.readthedocs.io/ + +========= ========== +version toolchain +========= ========== +``6.4.0`` ``system`` +========= ========== + + .. _list_software_mimalloc_846: *mimalloc* @@ -28252,16 +28511,16 @@ version toolchain *Mmg* +++++ -Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries +Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries. *homepage*: https://www.mmgtools.org/ -========= =============== -version toolchain -========= =============== -``5.3.9`` ``foss/2017b`` -``5.6.0`` ``gompi/2021b`` -========= =============== +========= ================================ +version toolchain +========= ================================ +``5.3.9`` ``foss/2017b`` +``5.6.0`` ``gompi/2021a``, ``gompi/2021b`` +========= ================================ .. _list_software_MMSEQ_387: @@ -28289,18 +28548,18 @@ MMseqs2: ultra fast and sensitive search and clustering suite *homepage*: https://mmseqs.com -===================== ================================ -version toolchain -===================== ================================ -``1-c7a89`` ``foss/2016b`` -``5-9375b`` ``intel/2018a`` -``8-fac81`` ``intel/2018b`` -``10-6d92c`` ``gompi/2019b``, ``iimpi/2019b`` -``11-e1a1c`` ``iimpi/2019b`` -``13-45111`` ``gompi/2020b``, ``gompi/2021b`` -``13-45111-20211006`` ``gompi/2020b`` -``13-45111-20211019`` ``gompi/2020b`` -===================== ================================ +===================== ================================================= +version toolchain +===================== ================================================= +``1-c7a89`` ``foss/2016b`` +``5-9375b`` ``intel/2018a`` +``8-fac81`` ``intel/2018b`` +``10-6d92c`` ``gompi/2019b``, ``iimpi/2019b`` +``11-e1a1c`` ``iimpi/2019b`` +``13-45111`` ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b`` +``13-45111-20211006`` ``gompi/2020b`` +``13-45111-20211019`` ``gompi/2020b`` +===================== ================================================= .. _list_software_mmtf-cpp_804: @@ -29632,7 +29891,7 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_namedlist_961` - :ref:`list_software_nano_428` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_NetPyNE_643` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_nghttp3_712` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_num2words_945` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numdiff_745` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_namedlist_961` - :ref:`list_software_nano_428` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_NetPyNE_643` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_nghttp2_711` - :ref:`list_software_nghttp3_712` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_ngtcp2_590` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_num2words_945` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numdiff_745` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_NVSHMEM_542` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: @@ -30089,6 +30348,7 @@ version toolchain ``1.14`` ``GCCcore/7.3.0`` ``1.15.1`` ``GCCcore/9.3.0`` ``1.16`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``1.17`` ``GCC/11.3.0`` ========== ============================== @@ -30203,7 +30463,7 @@ version toolchain ``6.0`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``6.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` ``6.2`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``system`` -``6.3`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``system`` +``6.3`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``system`` ======= ============================================================================================================================================================================================================================================================================================================================================================================= @@ -30474,6 +30734,7 @@ version versionsuffix toolchain ``1.5.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``1.5.5.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.5.7`` ``foss/2021a``, ``foss/2021b``, ``intel/2021b`` +``1.6.1`` ``foss/2022a`` =========== ============================= =================================================== @@ -30738,6 +30999,7 @@ version toolchain ``21.08.0`` ``system`` ``21.10.6`` ``system`` ``22.04.0`` ``system`` +``22.10.0`` ``system`` =========== ========== @@ -30772,9 +31034,26 @@ version toolchain ``3.1.3`` ``foss/2020b``, ``fosscuda/2020b`` ``3.5.1`` ``foss/2018b``, ``foss/2019a`` ``3.5.2`` ``foss/2020a``, ``foss/2021a``, ``foss/2021b`` +``3.5.3`` ``foss/2022a`` ========= ============================================== +.. _list_software_nghttp2_711: + +*nghttp2* ++++++++++ + +This is an implementation of the Hypertext Transfer Protocol version 2 in C. The framing layer of HTTP/2 is implemented as a reusable C library. On top of that, we have implemented an HTTP/2 client, server and proxy. We have also developed load test and benchmarking tools for HTTP/2. An HPACK encoder and decoder are available as a public API. + +*homepage*: https://github.com/nghttp2/nghttp2 + +========== ============== +version toolchain +========== ============== +``1.48.0`` ``GCC/11.2.0`` +========== ============== + + .. _list_software_nghttp3_712: *nghttp3* @@ -30917,6 +31196,22 @@ version toolchain ======= ============== +.. _list_software_ngtcp2_590: + +*ngtcp2* +++++++++ + +'Call it TCP/2. One More Time.' ngtcp2 project is an effort to implement RFC9000 QUIC protocol. + +*homepage*: https://github.com/ngtcp2/ngtcp2 + +========= ============== +version toolchain +========= ============== +``0.7.0`` ``GCC/11.2.0`` +========= ============== + + .. _list_software_NiBabel_653: *NiBabel* @@ -31069,6 +31364,7 @@ version versionsuffix toolchain ``1.0.2`` ``-Python-3.6.4`` ``intel/2018a`` ``1.1.3`` ``-Python-3.6.6`` ``foss/2018b`` ``1.4.2`` ``-Python-3.7.4`` ``intel/2019b`` +``1.8.5`` ``foss/2021a`` ========= ================= =============== @@ -31518,6 +31814,7 @@ version toolchain ``2.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.0.13`` ``GCCcore/10.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` ``2.0.14`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.0.16`` ``GCCcore/12.2.0`` ========== ============================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -31646,6 +31943,22 @@ version toolchain ========= ========== +.. _list_software_NVSHMEM_542: + +*NVSHMEM* ++++++++++ + +NVSHMEM is a parallel programming interface based on OpenSHMEM that provides efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a global address space for data that spans the memory of multiple GPUs and can be accessed with fine-grained GPU-initiated operations, CPU-initiated operations, and operations on CUDA streams. + +*homepage*: https://developer.nvidia.com/nvshmem + +========= ================ =============== +version versionsuffix toolchain +========= ================ =============== +``2.5.0`` ``-CUDA-11.7.0`` ``gompi/2022a`` +========= ================ =============== + + .. _list_software_nvtop_567: *nvtop* @@ -31913,6 +32226,7 @@ A free Microsoft OneDrive Client which supports OneDrive Personal, OneDrive for version toolchain ========== ================== ``2.4.11`` ``GCCcore/10.2.0`` +``2.4.21`` ``GCCcore/11.3.0`` ========== ================== @@ -32218,7 +32532,9 @@ version versionsuffix toolchain ``4.5.1`` ``-contrib`` ``foss/2020b``, ``fosscuda/2020b`` ``4.5.3`` ``-CUDA-11.3.1-contrib`` ``foss/2021a`` ``4.5.3`` ``-contrib`` ``foss/2021a`` +``4.5.5`` ``-CUDA-11.4.1-contrib`` ``foss/2021b`` ``4.5.5`` ``-contrib`` ``foss/2021b`` +``4.6.0`` ``-contrib`` ``foss/2022a`` ========== ========================= ================================================================ @@ -32241,6 +32557,7 @@ version toolchain ``2.5.5`` ``GCCcore/10.2.0`` ``3.0.1`` ``GCCcore/10.3.0`` ``3.1.1`` ``GCCcore/11.2.0`` +``3.1.5`` ``GCCcore/11.3.0`` ========= ================================ @@ -32410,6 +32727,7 @@ version toolchain ``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.4.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``2.5.0`` ``GCCcore/11.3.0`` ========= ============================================================================= @@ -32466,6 +32784,8 @@ version versionsuffix toolchain ``7.5.0`` ``-Python-3.8.2`` ``fosscuda/2020a``, ``intel/2020a`` ``7.5.1`` ``foss/2020b``, ``fosscuda/2020b`` ``7.5.1`` ``-DeepMind-patch`` ``foss/2021a`` +``7.7.0`` ``foss/2021a``, ``foss/2022a`` +``7.7.0`` ``-CUDA-11.3.1`` ``foss/2021a`` ========= =================== =================================================== @@ -32617,11 +32937,11 @@ OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM *homepage*: http://code.google.com/p/openpgm/ -=========== ============================================================================================================================================================================================================================================================ -version toolchain -=========== ============================================================================================================================================================================================================================================================ -``5.2.122`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -=========== ============================================================================================================================================================================================================================================================ +=========== ================================================================================================================================================================================================================================================================================ +version toolchain +=========== ================================================================================================================================================================================================================================================================================ +``5.2.122`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +=========== ================================================================================================================================================================================================================================================================================ .. _list_software_OpenPIV_641: @@ -32772,6 +33092,7 @@ version toolchain ``1.1.1h`` ``GCCcore/10.2.0`` ``1.1.1k`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``1.1.1n`` ``GCCcore/11.3.0`` +``1.1.1q`` ``GCCcore/10.3.0`` ========== ===================================================================== @@ -33110,7 +33431,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_panito_651` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parameterized_1389` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patch_528` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pfind_529` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_Phantompeakqualtools_2140` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_porefoam_857` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_presto_669` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_purge_dups_1086` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyEVTK_515` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_PyFrag_585` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGenomeTracks_1452` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_pyradiomics_1188` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch-Lightning_1690` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_pairsnp_765` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_paladin_729` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_panito_651` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parameterized_1389` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patch_528` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pfind_529` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_Phantompeakqualtools_2140` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_porefoam_857` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_presto_669` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_purge_dups_1086` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyEVTK_515` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_PyFrag_585` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGenomeTracks_1452` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyMOL_433` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_pyradiomics_1188` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-irodsclient_1903` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch-Lightning_1690` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -33156,12 +33477,12 @@ p4est is a C library to manage a collection (a forest) of multiple connected ada *homepage*: https://www.p4est.org -======= =============== -version toolchain -======= =============== -``2.2`` ``intel/2019a`` -``2.8`` ``foss/2021a`` -======= =============== +======= =============================== +version toolchain +======= =============================== +``2.2`` ``foss/2019a``, ``intel/2019a`` +``2.8`` ``foss/2021a`` +======= =============================== .. _list_software_p4vasp_606: @@ -33237,6 +33558,22 @@ version toolchain ========== ============================== +.. _list_software_pairsnp_765: + +*pairsnp* ++++++++++ + +A set of scripts for very quickly obtaining pairwise SNP distance matrices from multiple sequence alignments using sparse matrix libraries to improve performance. + +*homepage*: https://github.com/gtonkinhill/pairsnp + +========= ============== +version toolchain +========= ============== +``0.0.7`` ``foss/2021a`` +========= ============== + + .. _list_software_PAL2NAL_490: *PAL2NAL* @@ -33253,6 +33590,22 @@ version toolchain ======= ====================================== +.. _list_software_paladin_729: + +*paladin* ++++++++++ + +Protein ALignment And Detection INterface PALADIN is a protein sequence alignment tool designed for the accurate functional characterization of metagenomes. + +*homepage*: https://github.com/ToniWestbrook/paladin + +========= ====================================== +version toolchain +========= ====================================== +``1.4.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== + + .. _list_software_PAML_298: *PAML* @@ -34175,7 +34528,7 @@ version versionsuffix toolchain ``5.34.0`` ``-minimal`` ``GCCcore/11.2.0`` ``5.34.1`` ``GCCcore/11.3.0`` ``5.34.1`` ``-minimal`` ``GCCcore/11.3.0`` -``5.36.0`` ``GCCcore/12.1.0`` +``5.36.0`` ``GCCcore/12.1.0``, ``GCCcore/12.2.0`` ========== ============= ========================================================================================= @@ -34853,6 +35206,7 @@ version versionsuffix toolchain ``8.2.0`` ``GCCcore/10.3.0`` ``8.3.1`` ``GCCcore/11.2.0`` ``8.3.2`` ``GCCcore/11.2.0`` +``9.2.0`` ``GCCcore/11.3.0`` =============== ================= =================================================== @@ -35106,6 +35460,7 @@ pkgconf is a program which helps to configure compiler and linker flags for deve version toolchain ========= ================================================== ``1.8.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` +``1.9.3`` ``GCCcore/12.2.0`` ========= ================================================== @@ -35537,7 +35892,7 @@ version toolchain ``1.4`` ``GCC/8.3.0``, ``gcccuda/2019b`` ``1.5`` ``GCC/9.3.0`` ``1.6`` ``GCC/10.2.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` -``1.8`` ``GCC/11.2.0`` +``1.8`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` ======= ========================================================== @@ -35769,6 +36124,7 @@ version versionsuffix toolchain ``13.2`` ``GCCcore/10.2.0`` ``13.3`` ``GCCcore/10.3.0`` ``13.4`` ``GCCcore/11.2.0`` +``14.4`` ``GCCcore/11.3.0`` ========= ================== ================================================================ @@ -35797,13 +36153,14 @@ The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which *homepage*: https://www.povray.org/ -=========== ================================================================================= -version toolchain -=========== ================================================================================= -``3.7.0.0`` ``intel/2016b`` -``3.7.0.7`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``3.7.0.8`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -=========== ================================================================================= +============ ================================================================================= +version toolchain +============ ================================================================================= +``3.7.0.0`` ``intel/2016b`` +``3.7.0.7`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``3.7.0.8`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``3.7.0.10`` ``GCC/11.3.0`` +============ ================================================================================= .. _list_software_PPanGGOLiN_847: @@ -36065,12 +36422,12 @@ PRISMS-PF is a powerful, massively parallel finite element code for conducting p *homepage*: https://prisms-center.github.io/phaseField -========= =============== -version toolchain -========= =============== -``2.1.1`` ``intel/2019a`` -``2.2`` ``foss/2021a`` -========= =============== +========= =============================== +version toolchain +========= =============================== +``2.1.1`` ``foss/2019a``, ``intel/2019a`` +``2.2`` ``foss/2021a`` +========= =============================== .. _list_software_ProbABEL_679: @@ -36963,6 +37320,7 @@ version toolchain ``2017.2.3`` ``system`` ``2019.3.1`` ``system`` ``2021.1.1`` ``system`` +``2022.2.2`` ``system`` ============ ========== @@ -37831,6 +38189,22 @@ version versionsuffix toolchain ========= ================= =============================== +.. _list_software_PyMOL_433: + +*PyMOL* ++++++++ + +PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone! + +*homepage*: https://github.com/schrodinger/pymol-open-source + +========= ============== +version toolchain +========= ============== +``2.5.0`` ``foss/2020b`` +========= ============== + + .. _list_software_PyNAST_511: *PyNAST* @@ -38036,11 +38410,12 @@ QSTEM is a program for quantitative image simulation in electron microscopy, inc *homepage*: https://github.com/jacobjma/PyQSTEM -========= ================= =============================== -version versionsuffix toolchain -========= ================= =============================== -``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -========= ================= =============================== +========= ================= ================================== +version versionsuffix toolchain +========= ================= ================================== +``1.0.3`` ``-ASE-3.22.0`` ``foss/2020b``, ``fosscuda/2020b`` +``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +========= ================= ================================== .. _list_software_PyQt_398: @@ -38727,6 +39102,22 @@ version versionsuffix toolchain =============== ================== ================================== +.. _list_software_python-irodsclient_1903: + +*python-irodsclient* +++++++++++++++++++++ + +A python API for iRODS + +*homepage*: https://github.com/irods/python-irodsclient + +========= ====================================== +version toolchain +========= ====================================== +``1.1.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== + + .. _list_software_python-isal_1144: *python-isal* @@ -38850,6 +39241,8 @@ version versionsuffix toolchain ``1.10.0`` ``foss/2021a``, ``fosscuda/2020b`` ``1.10.0`` ``-CUDA-11.3.1`` ``foss/2021a`` ``1.11.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``1.12.0`` ``foss/2022a`` +``1.12.0`` ``-CUDA-11.7.0`` ``foss/2022a`` ========== ============================= ================================== @@ -38887,6 +39280,8 @@ version versionsuffix toolchain ========= ================ ============== ``1.5.9`` ``foss/2021a`` ``1.5.9`` ``-CUDA-11.3.1`` ``foss/2021a`` +``1.7.7`` ``foss/2022a`` +``1.7.7`` ``-CUDA-11.7.0`` ``foss/2022a`` ========= ================ ============== @@ -39710,7 +40105,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_RaGOO_408` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_RAPSearch2_875` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redis_503` - :ref:`list_software_redis-py_813` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_regionmask_1072` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_RheoTool_812` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rising_652` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_ruamel.yaml_1127` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_RaGOO_408` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_RAPSearch2_875` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redis_503` - :ref:`list_software_redis-py_813` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_regionmask_1072` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_RheoTool_812` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rising_652` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_ruamel.yaml_1127` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_ruffus_667` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -40312,6 +40707,7 @@ version toolchain ========= ================================= ``4.2.2`` ``GCCcore/8.3.0``, ``foss/2019a`` ``5.0.0`` ``GCCcore/10.2.0`` +``6.2.0`` ``GCCcore/10.3.0`` ========= ================================= @@ -41630,11 +42026,11 @@ ruamel.yaml is a YAML 1.2 loader/dumper package for Python. *homepage*: https://sourceforge.net/projects/ruamel-yaml -=========== ================== -version toolchain -=========== ================== -``0.17.21`` ``GCCcore/11.2.0`` -=========== ================== +=========== ====================================== +version toolchain +=========== ====================================== +``0.17.21`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +=========== ====================================== .. _list_software_Ruby_418: @@ -41680,6 +42076,22 @@ version versionsuffix toolchain ========= =============== =============================== +.. _list_software_ruffus_667: + +*ruffus* +++++++++ + +Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, and widely used in science and bioinformatics. + +*homepage*: http://www.ruffus.org.uk/ + +========= ============== +version toolchain +========= ============== +``2.8.4`` ``foss/2021b`` +========= ============== + + .. _list_software_Rust_430: *Rust* @@ -41961,6 +42373,7 @@ version versionsuffix toolchain ``1.14`` ``GCC/11.2.0`` ``1.15`` ``GCC/11.2.0`` ``1.15.1`` ``GCC/11.2.0``, ``GCC/11.3.0`` +``1.16.1`` ``GCC/11.2.0``, ``GCC/11.3.0`` ========== ================= ======================================================================================================================================= @@ -42426,7 +42839,7 @@ version versionsuffix toolchain ``0.24.2`` ``foss/2021a``, ``intel/2021a`` ``1.0.1`` ``foss/2021b``, ``intel/2021b`` ``1.0.2`` ``foss/2021b`` -``1.1.2`` ``foss/2022a`` +``1.1.2`` ``foss/2022a``, ``intel/2022a`` ========== ================================= ======================================================================== @@ -42654,13 +43067,14 @@ The Score-P measurement infrastructure is a highly scalable and easy-to-use too *homepage*: https://www.score-p.org -========= ================================================== -version toolchain -========= ================================================== -``2.0.1`` ``foss/2016a`` -``6.0`` ``gompi/2019a``, ``gompi/2020a``, ``gompic/2019b`` -``7.0`` ``gompi/2021a``, ``gompic/2020b`` -========= ================================================== +========= ================ ================================================== +version versionsuffix toolchain +========= ================ ================================================== +``2.0.1`` ``foss/2016a`` +``6.0`` ``gompi/2019a``, ``gompi/2020a``, ``gompic/2019b`` +``7.0`` ``gompi/2021a``, ``gompic/2020b`` +``7.1`` ``-CUDA-11.3.1`` ``gompi/2021a`` +========= ================ ================================================== .. _list_software_SCOTCH_452: @@ -42819,6 +43233,7 @@ version toolchain ``2.0.10`` ``GCCcore/8.3.0`` ``2.0.14`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``2.0.20`` ``GCCcore/11.2.0`` +``2.0.22`` ``GCCcore/11.3.0`` ========== ====================================================================== @@ -44772,6 +45187,7 @@ version toolchain ========== ======================================== ``2.3.3c`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.4.03`` ``iccifort/2019.5.281`` +``2.4.12`` ``GCC/10.2.0`` ========== ======================================== @@ -44952,7 +45368,8 @@ version versionsuffix toolchain ``1.16.0`` ``-Python-3.7.4`` ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` ``1.16.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``1.16.1`` ``foss/2021a``, ``intel/2021a`` -``2.0.0`` ``foss/2022a`` +``1.16.3`` ``foss/2021b``, ``intel/2021b`` +``2.0.0`` ``foss/2022a``, ``intel/2022a`` ================ ================== ======================================================== @@ -45241,7 +45658,7 @@ version versionsuffix toolchain The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format -*homepage*: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software +*homepage*: https://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software =========== =================== =============== version versionsuffix toolchain @@ -45258,6 +45675,7 @@ version versionsuffix toolchain ``2.10.5`` ``-centos_linux64`` ``system`` ``2.10.8`` ``gompi/2020a`` ``2.10.9`` ``gompi/2020b`` +``3.0.0`` ``-centos_linux64`` ``system`` =========== =================== =============== @@ -45906,6 +46324,7 @@ version versionsuffix toolchain ``5.8.1`` ``-METIS-5.1.0`` ``foss/2020b``, ``intel/2020b`` ``5.10.1`` ``-METIS-5.1.0`` ``foss/2021a``, ``foss/2021b`` ``5.10.1`` ``-METIS-5.1.0-CUDA-11.3.1`` ``foss/2021a`` +``5.13.0`` ``-METIS-5.1.0`` ``foss/2022a`` ========== ============================ ================================================================================================= @@ -45976,6 +46395,7 @@ version toolchain ``2.7.0`` ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``5.1.0`` ``foss/2019b``, ``intel/2019b`` ``5.7.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``6.3.0`` ``foss/2021b``, ``foss/2022a`` ========= ================================================================================================================================== @@ -46004,14 +46424,14 @@ SuperLU is a general purpose library for the direct solution of large, sparse, *homepage*: https://crd-legacy.lbl.gov/~xiaoye/SuperLU/ -========= =============================== -version toolchain -========= =============================== -``5.1.1`` ``foss/2016a``, ``intel/2016a`` -``5.2.1`` ``foss/2017b``, ``intel/2017b`` -``5.2.2`` ``foss/2020a``, ``intel/2020a`` -``5.3.0`` ``foss/2021a`` -========= =============================== +========= ================================================================================ +version toolchain +========= ================================================================================ +``5.1.1`` ``foss/2016a``, ``intel/2016a`` +``5.2.1`` ``foss/2017b``, ``intel/2017b`` +``5.2.2`` ``foss/2020a``, ``intel/2020a`` +``5.3.0`` ``foss/2020b``, ``foss/2021a``, ``foss/2022a``, ``intel/2020b``, ``intel/2022a`` +========= ================================================================================ .. _list_software_SuperLU_DIST_1091: @@ -46318,21 +46738,23 @@ SymPy is a Python library for symbolic mathematics. It aims to become a full-fe *homepage*: https://sympy.org/ -========= ================== =============================== -version versionsuffix toolchain -========= ================== =============================== -``1.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``1.3`` ``-Python-2.7.14`` ``intel/2018a`` -``1.3`` ``-Python-2.7.15`` ``foss/2018b`` -``1.3`` ``-Python-3.6.4`` ``intel/2018a`` -``1.3`` ``-Python-3.6.6`` ``foss/2018b`` -``1.4`` ``foss/2019a``, ``intel/2019a`` -``1.5.1`` ``-Python-3.7.4`` ``foss/2019b`` -``1.6.2`` ``-Python-3.8.2`` ``foss/2020a`` -``1.7.1`` ``foss/2020b``, ``intel/2020b`` -``1.8`` ``foss/2021a`` -``1.9`` ``foss/2021b`` -========= ================== =============================== +========== ================== =============================== +version versionsuffix toolchain +========== ================== =============================== +``1.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``1.3`` ``-Python-2.7.14`` ``intel/2018a`` +``1.3`` ``-Python-2.7.15`` ``foss/2018b`` +``1.3`` ``-Python-3.6.4`` ``intel/2018a`` +``1.3`` ``-Python-3.6.6`` ``foss/2018b`` +``1.4`` ``foss/2019a``, ``intel/2019a`` +``1.5.1`` ``-Python-3.7.4`` ``foss/2019b`` +``1.6.2`` ``-Python-3.8.2`` ``foss/2020a`` +``1.7.1`` ``foss/2020b``, ``intel/2020b`` +``1.8`` ``foss/2021a`` +``1.9`` ``foss/2021b`` +``1.10.1`` ``foss/2022a`` +``1.11.1`` ``foss/2022a`` +========== ================== =============================== .. _list_software_SyRI_359: @@ -46374,7 +46796,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TALYS_397` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboard_1187` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_termcolor_983` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_ThemisPy_819` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmap_434` - :ref:`list_software_tmux_462` - :ref:`list_software_TN93_270` - :ref:`list_software_TOBIAS_450` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_topaz_558` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` +:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TALYS_397` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_TELEMAC-MASCARET_1144` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboard_1187` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_termcolor_983` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_ThemisPy_819` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmap_434` - :ref:`list_software_tmux_462` - :ref:`list_software_TN93_270` - :ref:`list_software_TOBIAS_450` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_topaz_558` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchdata_954` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` .. _list_software_tabix_536: @@ -46691,6 +47113,22 @@ version toolchain =========== ========== +.. _list_software_TELEMAC-MASCARET_1144: + +*TELEMAC-MASCARET* +++++++++++++++++++ + +TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free-surface flow. Having been used in the context of many studies throughout the world, it has become one of the major standards in its field. + +*homepage*: http://www.opentelemac.org + +========= ============== +version toolchain +========= ============== +``8p3r1`` ``foss/2021b`` +========= ============== + + .. _list_software_Telescope_932: *Telescope* @@ -46732,11 +47170,12 @@ TensorBoard is a suite of web applications for inspecting and understanding your *homepage*: https://github.com/tensorflow/tensorboard -========= ============== -version toolchain -========= ============== -``2.8.0`` ``foss/2021a`` -========= ============== +========== ============== +version toolchain +========== ============== +``2.8.0`` ``foss/2021a`` +``2.10.0`` ``foss/2022a`` +========== ============== .. _list_software_tensorboardX_1275: @@ -47547,6 +47986,22 @@ version versionsuffix toolchain ========= =============================== ================================== +.. _list_software_torchdata_954: + +*torchdata* ++++++++++++ + +TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines." + +*homepage*: https://github.com/pytorch/data + +========= =============================== ============== +version versionsuffix toolchain +========= =============================== ============== +``0.3.0`` ``-PyTorch-1.11.0-CUDA-11.3.1`` ``foss/2021a`` +========= =============================== ============== + + .. _list_software_torchinfo_972: *torchinfo* @@ -47613,6 +48068,8 @@ version versionsuffix toolchain ``0.11.1`` ``-CUDA-11.3.1`` ``foss/2021a`` ``0.11.3`` ``foss/2021a`` ``0.11.3`` ``-CUDA-11.3.1`` ``foss/2021a`` +``0.12.0`` ``-PyTorch-1.11.0-CUDA-11.3.1`` ``foss/2021a`` +``0.13.1`` ``-CUDA-11.7.0`` ``foss/2022a`` ========== ==================================== ================================== @@ -47984,6 +48441,7 @@ version versionsuffix toolchain ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ``2.2.1`` ``-Python-2.7.15`` ``foss/2019a`` ``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` +``3.1.1`` ``foss/2022a`` ========= ================== ============== @@ -48001,6 +48459,7 @@ version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` +``3.1.0`` ``foss/2022a`` ========= ================== ============== @@ -48018,6 +48477,7 @@ version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` +``3.1.0`` ``foss/2022a`` ========= ================== ============== @@ -48035,6 +48495,7 @@ version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` +``3.1.1`` ``foss/2022a`` ========= ================== ============== @@ -48068,6 +48529,7 @@ version toolchain =========== ============== ``1.0.5.1`` ``system`` ``1.0.6`` ``GCC/11.2.0`` +``1.0.7`` ``GCC/11.3.0`` =========== ============== @@ -48114,11 +48576,12 @@ TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to pro *homepage*: https://www.turbovnc.org -========= ================= -version toolchain -========= ================= -``2.2.3`` ``GCCcore/8.2.0`` -========= ================= +========= ================== +version toolchain +========= ================== +``2.2.3`` ``GCCcore/8.2.0`` +``3.0.1`` ``GCCcore/11.3.0`` +========= ================== .. _list_software_TVB_236: @@ -48238,6 +48701,7 @@ version versionsuffix toolchain ``3.7.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``3.10.0.0`` ``GCCcore/10.3.0`` ``3.10.0.2`` ``GCCcore/11.2.0`` +``4.3.0`` ``GCCcore/11.3.0`` ============ ================= ================== @@ -48324,6 +48788,7 @@ version versionsuffix toolchain ``1.11.0`` ``GCCcore/11.2.0`` ``1.11.2`` ``GCCcore/11.2.0`` ``1.12.1`` ``GCCcore/11.3.0`` +``1.13.1`` ``GCCcore/12.2.0`` ============ ================ ======================================================= @@ -48421,14 +48886,15 @@ version versionsuffix toolchain *umap-learn* ++++++++++++ -Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction. +Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction. -*homepage*: https://pypi.org/project/umap-learn/ +*homepage*: https://umap-learn.readthedocs.io/en/latest/ ========= ================== version toolchain ========= ================== ``0.4.6`` ``fosscuda/2020b`` +``0.5.3`` ``foss/2021a`` ========= ================== @@ -49137,6 +49603,7 @@ version versionsuffix toolchain ``96.0`` ``-Perl-5.28.1`` ``foss/2019a`` ``103.1`` ``GCC/10.2.0`` ``105`` ``GCC/11.2.0`` +``107`` ``GCC/11.3.0`` ========= ================ =============================== @@ -49312,6 +49779,7 @@ version versionsuffix toolchain ``1.9.3`` ``-Python-2.7.15`` ``intel/2018b`` ``1.9.4a43`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``1.9.4a51`` ``foss/2020b``, ``fosscuda/2020b`` +``1.9.4a57`` ``foss/2022a`` ============ ================== ================================== @@ -49652,7 +50120,7 @@ version toolchain --- -:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_Wayland_720` - :ref:`list_software_WCT_238` - :ref:`list_software_wcwidth_762` - :ref:`list_software_webin-cli_890` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wgsim_551` - :ref:`list_software_WHAM_301` - :ref:`list_software_WhatsHap_800` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` +:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_Wayland_720` - :ref:`list_software_Waylandpp_944` - :ref:`list_software_WCT_238` - :ref:`list_software_wcwidth_762` - :ref:`list_software_webin-cli_890` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wgsim_551` - :ref:`list_software_WHAM_301` - :ref:`list_software_WhatsHap_800` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` .. _list_software_wandb_524: @@ -49680,16 +50148,16 @@ A tool for obtaining maximally-localised Wannier functions *homepage*: http://www.wannier.org -=========== ============= =================================================================================================================================================== -version versionsuffix toolchain -=========== ============= =================================================================================================================================================== -``1.2`` ``intel/2016.02-GCC-4.9`` -``2.0.1`` ``intel/2016.02-GCC-4.9``, ``intel/2016a`` -``2.0.1.1`` ``-abinit`` ``intel/2018b`` -``2.1.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``3.0.0`` ``intel/2018b`` -``3.1.0`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``gomkl/2021a``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` -=========== ============= =================================================================================================================================================== +=========== ============= ==================================================================================================================================================================== +version versionsuffix toolchain +=========== ============= ==================================================================================================================================================================== +``1.2`` ``intel/2016.02-GCC-4.9`` +``2.0.1`` ``intel/2016.02-GCC-4.9``, ``intel/2016a`` +``2.0.1.1`` ``-abinit`` ``intel/2018b`` +``2.1.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``3.0.0`` ``intel/2018b`` +``3.1.0`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``gomkl/2021a``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a`` +=========== ============= ==================================================================================================================================================================== .. _list_software_WannierTools_1253: @@ -49722,9 +50190,26 @@ Wayland is a project to define a protocol for a compositor to talk to its clien version toolchain ========== ================== ``1.20.0`` ``GCCcore/11.3.0`` +``1.21.0`` ``GCCcore/11.2.0`` ========== ================== +.. _list_software_Waylandpp_944: + +*Waylandpp* ++++++++++++ + +Wayland is an object oriented display protocol, which features request and events. Requests can be seen as method calls on certain objects, whereas events can be seen as signals of an object. This makes the Wayland protocol a perfect candidate for a C++ binding. The goal of this library is to create such a C++ binding for Wayland using the most modern C++ technology currently available, providing an easy to use C++ API to Wayland. + +*homepage*: https://github.com/NilsBrause/waylandpp + +========= ================== +version toolchain +========= ================== +``1.0.0`` ``GCCcore/11.2.0`` +========= ================== + + .. _list_software_WCT_238: *WCT* @@ -50201,6 +50686,7 @@ version toolchain ``3.1.3`` ``GCC/8.3.0`` ``3.1.4`` ``GCC/10.2.0`` ``3.1.5`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``3.2.1`` ``GCC/11.3.0`` ========= ============================== @@ -50210,7 +50696,7 @@ version toolchain --- -:ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_XGrafix_697` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-Compile_999` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_XPLOR-NIH_673` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtensor_787` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_xxd_340` - :ref:`list_software_xxHash_628` - :ref:`list_software_XZ_178` +:ref:`list_software_X11_186` - :ref:`list_software_x13as_432` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_XGrafix_697` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-Compile_999` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_XPLOR-NIH_673` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtensor_787` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_xxd_340` - :ref:`list_software_xxHash_628` - :ref:`list_software_XZ_178` .. _list_software_X11_186: @@ -50241,6 +50727,22 @@ version toolchain ============ ================================================== +.. _list_software_x13as_432: + +*x13as* ++++++++ + +X-13ARIMA-SEATS is seasonal adjustment software produced, distributed, and maintained by the Census Bureau. Features of X-13ARIMA-SEATS include: - Extensive time series modeling and model selection capabilities for linear regression models with ARIMA errors (regARIMA models); - The capability to generate ARIMA model-based seasonal adjustment using a version of the SEATS software originally developed by Victor Gómez and Agustín Maravall at the Bank of Spain, as well as nonparametric adjustments from the X-11 procedure; - Diagnostics of the quality and stability of the adjustments achieved under the options selected; - The ability to efficiently process many series at once. + +*homepage*: https://www.census.gov/data/software/x13as.About_X-13.html + +=========== ====================================== +version toolchain +=========== ====================================== +``1-1-b59`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` +=========== ====================================== + + .. _list_software_x264_276: *x264* @@ -50723,20 +51225,20 @@ Perl binding for libxml2 *homepage*: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod -========== ================ ====================================== -version versionsuffix toolchain -========== ================ ====================================== -``2.0132`` ``-Perl-5.24.0`` ``foss/2016b``, ``intel/2016b`` -``2.0132`` ``-Perl-5.24.1`` ``intel/2017a`` -``2.0132`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``2.0132`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``2.0132`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -``2.0200`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -``2.0201`` ``GCCcore/8.3.0`` -``2.0205`` ``GCCcore/9.3.0`` -``2.0206`` ``GCCcore/10.2.0`` -``2.0207`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========== ================ ====================================== +========== ================ ========================================================== +version versionsuffix toolchain +========== ================ ========================================================== +``2.0132`` ``-Perl-5.24.0`` ``foss/2016b``, ``intel/2016b`` +``2.0132`` ``-Perl-5.24.1`` ``intel/2017a`` +``2.0132`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``2.0132`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``2.0132`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``2.0200`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``2.0201`` ``GCCcore/8.3.0`` +``2.0205`` ``GCCcore/9.3.0`` +``2.0206`` ``GCCcore/10.2.0`` +``2.0207`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========== ================ ========================================================== .. _list_software_XML-Parser_907: @@ -50879,7 +51381,7 @@ version versionsuffix toolchain ``1.2.2`` ``-X11-20180131`` ``GCCcore/6.4.0`` ``1.2.3`` ``GCCcore/7.3.0`` ``1.2.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ================= ======================================================================================================================= @@ -50892,13 +51394,13 @@ X protocol and ancillary headers *homepage*: https://www.freedesktop.org/wiki/Software/xlibs -========== ========================================================================================================================================================= -version toolchain -========== ========================================================================================================================================================= -``7.0.28`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``7.0.29`` ``intel/2016a`` -``7.0.31`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== ========================================================================================================================================================= +========== ============================================================================================================================================================================= +version toolchain +========== ============================================================================================================================================================================= +``7.0.28`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``7.0.29`` ``intel/2016a`` +``7.0.31`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ============================================================================================================================================================================= .. _list_software_XSD_239: @@ -50976,11 +51478,11 @@ xtrans includes a number of routines to make X implementations transport-indepen *homepage*: http://www.freedesktop.org/wiki/Software/xlibs -========= ================================================= -version toolchain -========= ================================================= -``1.3.5`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -========= ================================================= +========= ===================================================================== +version toolchain +========= ===================================================================== +``1.3.5`` ``GCCcore/11.3.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +========= ===================================================================== .. _list_software_Xvfb_406: @@ -51316,7 +51818,7 @@ version toolchain ``4.2.5`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` ``4.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.3.3`` ``GCCcore/10.2.0`` -``4.3.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``4.3.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ========================================================================================================= diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index f535af5b..fb54297c 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -8,10 +8,18 @@ * EB_ABAQUS * EB_Allinea * EB_Anaconda + + * EB_Mamba + + * EB_Anaconda + + * EB_Mamba + * EB_AOMP * EB_CPLEX * EB_CRISPR_minus_DAV * EB_CUDA + * EB_CUDAcompat * EB_EPD * EB_IMOD * EB_Maple diff --git a/docs/version-specific/easyconfig_templates.rst b/docs/version-specific/easyconfig_templates.rst index cdbf4155..841b377f 100644 --- a/docs/version-specific/easyconfig_templates.rst +++ b/docs/version-specific/easyconfig_templates.rst @@ -79,6 +79,7 @@ Template name Template value ``%(arch)s`` System architecture (e.g. x86_64, aarch64, ppc64le, ...) ``%(mpi_cmd_prefix)s`` Prefix command for running MPI programs (with default number of ranks) ``%(cuda_compute_capabilities)s`` Comma-separated list of CUDA compute capabilities, as specified via --cuda-compute-capabilities configuration option or via cuda_compute_capabilities easyconfig parameter +``%(cuda_cc_cmake)s`` List of CUDA compute capabilities suitable for use with $CUDAARCHS in CMake 3.18+ ``%(cuda_cc_space_sep)s`` Space-separated list of CUDA compute capabilities ``%(cuda_cc_semicolon_sep)s`` Semicolon-separated list of CUDA compute capabilities ``%(cuda_sm_comma_sep)s`` Comma-separated list of sm_* values that correspond with CUDA compute capabilities @@ -88,61 +89,61 @@ Template name Template value Template constants that can be used in easyconfigs -------------------------------------------------- -======================= ============================================================================================================= ======================================================================================== -Constant Template value Template name -======================= ============================================================================================================= ======================================================================================== -``APACHE_SOURCE`` apache.org source url ``https://archive.apache.org/dist/%(namelower)s`` -``BITBUCKET_SOURCE`` bitbucket.org source url (namelower is used if bitbucket_account easyconfig parameter is not specified) ``https://bitbucket.org/%(bitbucket_account)s/%(namelower)s/get`` -``BITBUCKET_DOWNLOADS`` bitbucket.org downloads url (namelower is used if bitbucket_account easyconfig parameter is not specified) ``https://bitbucket.org/%(bitbucket_account)s/%(namelower)s/downloads`` -``CRAN_SOURCE`` CRAN (contrib) source url ``https://cran.r-project.org/src/contrib`` -``FTPGNOME_SOURCE`` http download for gnome ftp server ``https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s`` -``GITHUB_SOURCE`` GitHub source URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(name)s/archive`` -``GITHUB_LOWER_SOURCE`` GitHub source URL (lowercase name, namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(namelower)s/archive`` -``GITHUB_RELEASE`` GitHub release URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(name)s/releases/download/v%(version)s`` -``GITHUB_LOWER_RELEASE`` GitHub release URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s`` -``GNU_SAVANNAH_SOURCE`` download.savannah.gnu.org source url ``https://download-mirror.savannah.gnu.org/releases/%(namelower)s`` -``GNU_SOURCE`` gnu.org source url ``https://ftpmirror.gnu.org/gnu/%(namelower)s`` -``GOOGLECODE_SOURCE`` googlecode.com source url ``http://%(namelower)s.googlecode.com/files`` -``LAUNCHPAD_SOURCE`` launchpad.net source url ``https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/%(version)s/+download/`` -``PYPI_SOURCE`` pypi source url ``https://pypi.python.org/packages/source/%(nameletter)s/%(name)s`` -``PYPI_LOWER_SOURCE`` pypi source url (lowercase name) ``https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s`` -``R_SOURCE`` cran.r-project.org (base) source url ``https://cran.r-project.org/src/base/R-%(version_major)s`` -``SOURCEFORGE_SOURCE`` sourceforge.net source url ``https://download.sourceforge.net/%(namelower)s`` -``XORG_DATA_SOURCE`` xorg data source url ``https://xorg.freedesktop.org/archive/individual/data/`` -``XORG_LIB_SOURCE`` xorg lib source url ``https://xorg.freedesktop.org/archive/individual/lib/`` -``XORG_PROTO_SOURCE`` xorg proto source url ``https://xorg.freedesktop.org/archive/individual/proto/`` -``XORG_UTIL_SOURCE`` xorg util source url ``https://xorg.freedesktop.org/archive/individual/util/`` -``XORG_XCB_SOURCE`` xorg xcb source url ``https://xorg.freedesktop.org/archive/individual/xcb/`` -``SHLIB_EXT`` extension for shared libraries ``dylib`` -``SOURCE_TAR_GZ`` Source .tar.gz bundle ``%(name)s-%(version)s.tar.gz`` -``SOURCELOWER_TAR_GZ`` Source .tar.gz bundle with lowercase name ``%(namelower)s-%(version)s.tar.gz`` -``SOURCE_TAR_XZ`` Source .tar.xz bundle ``%(name)s-%(version)s.tar.xz`` -``SOURCELOWER_TAR_XZ`` Source .tar.xz bundle with lowercase name ``%(namelower)s-%(version)s.tar.xz`` -``SOURCE_TAR_BZ2`` Source .tar.bz2 bundle ``%(name)s-%(version)s.tar.bz2`` -``SOURCELOWER_TAR_BZ2`` Source .tar.bz2 bundle with lowercase name ``%(namelower)s-%(version)s.tar.bz2`` -``SOURCE_TGZ`` Source .tgz bundle ``%(name)s-%(version)s.tgz`` -``SOURCELOWER_TGZ`` Source .tgz bundle with lowercase name ``%(namelower)s-%(version)s.tgz`` -``SOURCE_TXZ`` Source .txz bundle ``%(name)s-%(version)s.txz`` -``SOURCELOWER_TXZ`` Source .txz bundle with lowercase name ``%(namelower)s-%(version)s.txz`` -``SOURCE_TBZ2`` Source .tbz2 bundle ``%(name)s-%(version)s.tbz2`` -``SOURCELOWER_TBZ2`` Source .tbz2 bundle with lowercase name ``%(namelower)s-%(version)s.tbz2`` -``SOURCE_TB2`` Source .tb2 bundle ``%(name)s-%(version)s.tb2`` -``SOURCELOWER_TB2`` Source .tb2 bundle with lowercase name ``%(namelower)s-%(version)s.tb2`` -``SOURCE_GTGZ`` Source .gtgz bundle ``%(name)s-%(version)s.gtgz`` -``SOURCELOWER_GTGZ`` Source .gtgz bundle with lowercase name ``%(namelower)s-%(version)s.gtgz`` -``SOURCE_ZIP`` Source .zip bundle ``%(name)s-%(version)s.zip`` -``SOURCELOWER_ZIP`` Source .zip bundle with lowercase name ``%(namelower)s-%(version)s.zip`` -``SOURCE_TAR`` Source .tar bundle ``%(name)s-%(version)s.tar`` -``SOURCELOWER_TAR`` Source .tar bundle with lowercase name ``%(namelower)s-%(version)s.tar`` -``SOURCE_XZ`` Source .xz bundle ``%(name)s-%(version)s.xz`` -``SOURCELOWER_XZ`` Source .xz bundle with lowercase name ``%(namelower)s-%(version)s.xz`` -``SOURCE_TAR_Z`` Source .tar.Z bundle ``%(name)s-%(version)s.tar.Z`` -``SOURCELOWER_TAR_Z`` Source .tar.Z bundle with lowercase name ``%(namelower)s-%(version)s.tar.Z`` -``SOURCE_WHL`` Generic (non-compiled) Python 2 & Python 3 wheel package ``%(name)s-%(version)s-py2.py3-none-any.whl`` -``SOURCELOWER_WHL`` Generic (non-compiled) Python 2 & Python 3 wheel package with lowercase name ``%(namelower)s-%(version)s-py2.py3-none-any.whl`` -``SOURCE_PY2_WHL`` Generic (non-compiled) Python 2 wheel package ``%(name)s-%(version)s-py2-none-any.whl`` -``SOURCELOWER_PY2_WHL`` Generic (non-compiled) Python 2 wheel package with lowercase name ``%(namelower)s-%(version)s-py2-none-any.whl`` -``SOURCE_PY3_WHL`` Generic (non-compiled) Python 3 wheel package ``%(name)s-%(version)s-py3-none-any.whl`` -``SOURCELOWER_PY3_WHL`` Generic (non-compiled) Python 3 wheel package with lowercase name ``%(namelower)s-%(version)s-py3-none-any.whl`` -======================= ============================================================================================================= ======================================================================================== +======================== ============================================================================================================= ======================================================================================== +Constant Template value Template name +======================== ============================================================================================================= ======================================================================================== +``APACHE_SOURCE`` apache.org source url ``https://archive.apache.org/dist/%(namelower)s`` +``BITBUCKET_SOURCE`` bitbucket.org source url (namelower is used if bitbucket_account easyconfig parameter is not specified) ``https://bitbucket.org/%(bitbucket_account)s/%(namelower)s/get`` +``BITBUCKET_DOWNLOADS`` bitbucket.org downloads url (namelower is used if bitbucket_account easyconfig parameter is not specified) ``https://bitbucket.org/%(bitbucket_account)s/%(namelower)s/downloads`` +``CRAN_SOURCE`` CRAN (contrib) source url ``https://cran.r-project.org/src/contrib`` +``FTPGNOME_SOURCE`` http download for gnome ftp server ``https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s`` +``GITHUB_SOURCE`` GitHub source URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(name)s/archive`` +``GITHUB_LOWER_SOURCE`` GitHub source URL (lowercase name, namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(namelower)s/archive`` +``GITHUB_RELEASE`` GitHub release URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(name)s/releases/download/v%(version)s`` +``GITHUB_LOWER_RELEASE`` GitHub release URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s`` +``GNU_SAVANNAH_SOURCE`` download.savannah.gnu.org source url ``https://download-mirror.savannah.gnu.org/releases/%(namelower)s`` +``GNU_SOURCE`` gnu.org source url ``https://ftpmirror.gnu.org/gnu/%(namelower)s`` +``GOOGLECODE_SOURCE`` googlecode.com source url ``http://%(namelower)s.googlecode.com/files`` +``LAUNCHPAD_SOURCE`` launchpad.net source url ``https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/%(version)s/+download/`` +``PYPI_SOURCE`` pypi source url ``https://pypi.python.org/packages/source/%(nameletter)s/%(name)s`` +``PYPI_LOWER_SOURCE`` pypi source url (lowercase name) ``https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s`` +``R_SOURCE`` cran.r-project.org (base) source url ``https://cran.r-project.org/src/base/R-%(version_major)s`` +``SOURCEFORGE_SOURCE`` sourceforge.net source url ``https://download.sourceforge.net/%(namelower)s`` +``XORG_DATA_SOURCE`` xorg data source url ``https://xorg.freedesktop.org/archive/individual/data/`` +``XORG_LIB_SOURCE`` xorg lib source url ``https://xorg.freedesktop.org/archive/individual/lib/`` +``XORG_PROTO_SOURCE`` xorg proto source url ``https://xorg.freedesktop.org/archive/individual/proto/`` +``XORG_UTIL_SOURCE`` xorg util source url ``https://xorg.freedesktop.org/archive/individual/util/`` +``XORG_XCB_SOURCE`` xorg xcb source url ``https://xorg.freedesktop.org/archive/individual/xcb/`` +``SHLIB_EXT`` extension for shared libraries ``dylib`` +``SOURCE_TAR_GZ`` Source .tar.gz bundle ``%(name)s-%(version)s.tar.gz`` +``SOURCELOWER_TAR_GZ`` Source .tar.gz bundle with lowercase name ``%(namelower)s-%(version)s.tar.gz`` +``SOURCE_TAR_XZ`` Source .tar.xz bundle ``%(name)s-%(version)s.tar.xz`` +``SOURCELOWER_TAR_XZ`` Source .tar.xz bundle with lowercase name ``%(namelower)s-%(version)s.tar.xz`` +``SOURCE_TAR_BZ2`` Source .tar.bz2 bundle ``%(name)s-%(version)s.tar.bz2`` +``SOURCELOWER_TAR_BZ2`` Source .tar.bz2 bundle with lowercase name ``%(namelower)s-%(version)s.tar.bz2`` +``SOURCE_TGZ`` Source .tgz bundle ``%(name)s-%(version)s.tgz`` +``SOURCELOWER_TGZ`` Source .tgz bundle with lowercase name ``%(namelower)s-%(version)s.tgz`` +``SOURCE_TXZ`` Source .txz bundle ``%(name)s-%(version)s.txz`` +``SOURCELOWER_TXZ`` Source .txz bundle with lowercase name ``%(namelower)s-%(version)s.txz`` +``SOURCE_TBZ2`` Source .tbz2 bundle ``%(name)s-%(version)s.tbz2`` +``SOURCELOWER_TBZ2`` Source .tbz2 bundle with lowercase name ``%(namelower)s-%(version)s.tbz2`` +``SOURCE_TB2`` Source .tb2 bundle ``%(name)s-%(version)s.tb2`` +``SOURCELOWER_TB2`` Source .tb2 bundle with lowercase name ``%(namelower)s-%(version)s.tb2`` +``SOURCE_GTGZ`` Source .gtgz bundle ``%(name)s-%(version)s.gtgz`` +``SOURCELOWER_GTGZ`` Source .gtgz bundle with lowercase name ``%(namelower)s-%(version)s.gtgz`` +``SOURCE_ZIP`` Source .zip bundle ``%(name)s-%(version)s.zip`` +``SOURCELOWER_ZIP`` Source .zip bundle with lowercase name ``%(namelower)s-%(version)s.zip`` +``SOURCE_TAR`` Source .tar bundle ``%(name)s-%(version)s.tar`` +``SOURCELOWER_TAR`` Source .tar bundle with lowercase name ``%(namelower)s-%(version)s.tar`` +``SOURCE_XZ`` Source .xz bundle ``%(name)s-%(version)s.xz`` +``SOURCELOWER_XZ`` Source .xz bundle with lowercase name ``%(namelower)s-%(version)s.xz`` +``SOURCE_TAR_Z`` Source .tar.Z bundle ``%(name)s-%(version)s.tar.Z`` +``SOURCELOWER_TAR_Z`` Source .tar.Z bundle with lowercase name ``%(namelower)s-%(version)s.tar.Z`` +``SOURCE_WHL`` Generic (non-compiled) Python 2 & Python 3 wheel package ``%(name)s-%(version)s-py2.py3-none-any.whl`` +``SOURCELOWER_WHL`` Generic (non-compiled) Python 2 & Python 3 wheel package with lowercase name ``%(namelower)s-%(version)s-py2.py3-none-any.whl`` +``SOURCE_PY2_WHL`` Generic (non-compiled) Python 2 wheel package ``%(name)s-%(version)s-py2-none-any.whl`` +``SOURCELOWER_PY2_WHL`` Generic (non-compiled) Python 2 wheel package with lowercase name ``%(namelower)s-%(version)s-py2-none-any.whl`` +``SOURCE_PY3_WHL`` Generic (non-compiled) Python 3 wheel package ``%(name)s-%(version)s-py3-none-any.whl`` +``SOURCELOWER_PY3_WHL`` Generic (non-compiled) Python 3 wheel package with lowercase name ``%(namelower)s-%(version)s-py3-none-any.whl`` +======================== ============================================================================================================= ======================================================================================== diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index a05715a9..de762df2 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -374,7 +374,7 @@ easyconfig parameter description ``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` ``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` ``runtest`` Run unit tests. ``None`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``separate_build_dir`` Perform build in a separate directory ``True`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` ``srcdir`` Source directory location to provide to cmake command ``None`` @@ -382,11 +382,11 @@ easyconfig parameter description ``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` ``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` ``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``zipped_egg`` Install as a zipped eggs ``False`` ========================= ======================================================================================================================================================================================================================================================================================================================== ======================================================================= @@ -574,17 +574,17 @@ easyconfig parameter description ``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` ``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` ``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` ``tar_config_opts`` Override tar settings as determined by configure. ``False`` ``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` ``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` ``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``zipped_egg`` Install as a zipped eggs ``False`` ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= @@ -680,15 +680,15 @@ easyconfig parameter description ``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` ``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` ``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` ``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` ``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``zipped_egg`` Install as a zipped eggs ``False`` ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= @@ -978,15 +978,15 @@ easyconfig parameter description ``runtest`` Run unit tests. ``True`` ``sanity_check_all_components`` Enable sanity checks for all components ``False`` ``sanity_check_components`` List of components for which to run sanity checks ``[]`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` ``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` ``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``zipped_egg`` Install as a zipped eggs ``False`` =============================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= @@ -1016,15 +1016,15 @@ easyconfig parameter description ``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` ``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` ``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` ``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` ``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``zipped_egg`` Install as a zipped eggs ``False`` ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= @@ -1331,15 +1331,15 @@ easyconfig parameter description ``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` ``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` ``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` ``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` ``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``zipped_egg`` Install as a zipped eggs ``False`` ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= @@ -1369,15 +1369,15 @@ easyconfig parameter description ``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` ``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` ``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` ``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` ``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` ``use_pip_editable`` Install using 'pip install --editable' ``False`` ``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using 'pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` ``zipped_egg`` Install as a zipped eggs ``False`` ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= From 5a94339027a97fd2f7e777a9fa65cdf2b3a247d4 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 21 Oct 2022 15:55:18 +0800 Subject: [PATCH 240/286] update release notes and changelog for EasyBuild v4.6.2 + bump version to 4.6.2 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 130 ++++++++++++++++++++++++++++++++++++++++- docs/conf.py | 4 +- 3 files changed, 130 insertions(+), 5 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index f6c6285a..e3c517ea 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20221021.01** (`Oct 21st 2022`): update release notes for EasyBuild v4.6.2 (see :ref:`release_notes_eb462`) * **release 20220912.01** (`Sep 12th 2022`): update release notes for EasyBuild v4.6.1 (see :ref:`release_notes_eb461`) * **release 20220708.01** (`Jul 8th 2022`): update release notes for EasyBuild v4.6.0 (see :ref:`release_notes_eb460`) * **release 20220608.01** (`Jun 8th 2022`): update release notes for EasyBuild v4.5.5 (see :ref:`release_notes_eb455`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index cbe3eb11..c3ed0e46 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,12 +3,136 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,773** different software packages, -including 37 different (compiler) toolchains. It contains 246 software-specific easyblocks and 37 generic easyblocks, -alongside 15,332 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,798** different software packages, +including 37 different (compiler) toolchains. It contains 248 software-specific easyblocks and 37 generic easyblocks, +alongside 15,535 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. +.. _release_notes_eb462: + +EasyBuild v4.6.2 (October 21st 2022) +------------------------------------ + +bugfix/update release + +**framework** + +* various enhancements, including: + + * add support for easystack file that contains easyconfig filenames + implement parsing of configuration options (`#4021 `_) + * skip over unset ``$EB_PYTHON``/``$EB_INSTALLPYTHON`` in eb wrapper script (`#4080 `_) + * add ``GITHUB_RELEASE`` and ``GITHUB_LOWER_RELEASE`` templates (`#4084 `_) + * add ``%(cuda_cc_cmake)s`` template (`#4087 `_) + +* various bug fixes, including: + + * make ``check_sha256_checksums`` verify all checksums if they're specified as a dict value (`#4076 `_) + * replace use of symlink with copied files in ``alt_location`` tests to fix failing EasyBuild installation on BeeGFS (`#4083 `_) + * fix trying to generate RPATH wrappers for Clang (`#4088 `_) + * make sure that GitPython version is a proper version before checking minimal required version (`#4090 `_, `#4091 `_) + * first look for patch in ``alt_location`` when it is specified (`#4093 `_) + +* other changes: + + * make scripts executable (`#4081 `_) + * make ``--inject-checksums`` inject dictionary value for checksums which maps filename to SHA256 checksum (`#4085 `_) + * update to v3 of actions/checkout and actions/setup-python in CI workflows (`#4089 `_) + * use ``SYSTEM`` template constant in dependencies instead of ``True`` in framework tests (`#4094 `_) + +**easyblocks** + +* 2 new software-specific easyblock: + + * CUDA compatibility libraries (`#2764 `_) and mamba (`#2808 `_) + +* minor enhancements and updates, including: + + * update OpenFOAM easyblock to support OpenFOAM 10 + clean up variant/version checks (`#2766 `_) + * added support for ESMPy in ESMF (`#2789 `_) + * enhance OpenBLAS easyblock to support running LAPACK test suite + checking how many tests fail (`#2801 `_) + * make numexpr easyblock aware of toolchain with GCC + imkl (`#2810 `_) + * add sanity check commands for netCDF (`#2811 `_) + +* various bug fixes, including: + + * handle problems copying symlink that points to CUDA folder that is not created for non CUDA builds of SuiteSparse (`#2790 `_) + * don't install docs (to avoid trouble with Java) + add Rocky support for ABAQUS (`#2792 `_) + * correctly count the number of failing tests (not failing test suites) in PyTorch builds (`#2794 `_, `#2803 `_) + * fix docstring for PyTorch easyblock (`#2795 `_) + * handle iterative builds with MakeCp easyblock (`#2798 `_) + * accept both ``None`` and empty value for optarch to let OpenCV detect host CPU (`#2804 `_) + * enhance EasyBuildMeta easyblock: auto-enable installing with pip + fix setup.py of easyconfigs package so installation with setuptools >= 61.0 works (`#2805 `_) + * use ``python -m pip`` instead of ``pip`` in PythonPackage easyblock (`#2807 `_) + +* other changes: + + * make the test output from PythonPackage less verbose by disabling default search for error patterns done by ``run_cmd`` (`#2797 `_) + +**easyconfigs** + +* add easyconfig for intel/2022.09 toolchain (`#16435 `_) + +* added example easyconfig files for 25 new software packages: + + * AGAT (`#16261 `_), AMAPVox (`#16438 `_), Avogadro2 (`#16257 `_), buildingspy (`#16308 `_), CDBtools (`#16436 `_), + Compress-Raw-Zlib (`#16307 `_), CUDAcompat (`#15892 `_), CWIPI (`#16342 `_), enchant-2 (`#16082 `_, `#16319 `_), f90wrap (`#16346 `_), + Imath (`#16276 `_), Mamba (`#16432 `_), Miller (`#16221 `_), nghttp2 (`#16096 `_), ngtcp2 (`#16098 `_), NVSHMEM (`#16254 `_), + pairsnp (`#16331 `_), paladin (`#16320 `_), PyMOL (`#16394 `_), python-irodsclient (`#16328 `_), ruffus (`#16428 `_), + TELEMAC-MASCARET (`#16274 `_), torchdata (`#16344 `_), Waylandpp (`#16092 `_), x13as (`#16163 `_) + +* added additional easyconfigs for various supported software packages, including: + + * Amber 22.0, AMS 2022.102, ASE 3.22.1, atools 1.5.1, Beast 2.6.7, biogeme 3.2.10, Boost.Python 1.79.0, ccache 4.6.3, + dbus-glib 0.112, Delly 1.1.5, ESMF 8.3.0, expat 2.4.9, FDS 6.7.9, file 5.43, FLTK 1.3.8, FTGL 2.4.0, gc 8.2.2, + GitPython 3.1.27, Go 1.18.3, GPAW 22.8.0, Guile 3.0.8, htop 3.2.1, hunspell 1.7.1, IPython 8.5.0, jq 1.6, + Julia 1.8.2, LDC 1.30.0, libcint 5.1.6, libconfig 1.7.3, libreadline 8.2, LibSoup 3.0.7, LIBSVM 3.30, + libwebp 1.2.4, likwid 5.2.2, MariaDB 10.9.3, matplotlib 3.5.2, ncdu 1.17, netcdf4-python 1.6.1, Nextflow 22.10.0, + NFFT 3.5.3, Nipype 1.8.5, numactl 2.0.16, onedrive 2.4.21, OpenCV 4.6.0, OpenEXR 3.1.5, OpenJPEG 2.5.0, + OpenMM 7.7.0, OpenPGM 5.2.122, OpenSSL 1.1.1q, Perl 5.36.0, Pillow-SIMD 9.2.0, pkgconf 1.9.3, PostgreSQL 14.4, + PyCharm 2022.2.2, PyTorch 1.12.0, PyTorch 1.12.0, PyTorch-Lightning 1.7.7, RDFlib 6.2.0, SAMtools 1.16.1, + scikit-learn 1.1.2, Score-P 7.1, SDL2 2.0.22, spaln 2.4.12, spglib-python 2.0.0, SuiteSparse 5.13.0, SUNDIALS 6.3.0, + sympy 1.11.1, tensorboard 2.10.0, torchvision 0.13.1, TRIQS 3.1.1, TRIQS-cthyb 3.1.0, TRIQS-dft_tools 3.1.0, + TRIQS-tprf 3.1.1, TRUST4 1.0.7, TurboVNC 3.0.1, typing-extensions 4.3.0, UCX 1.13.1, umap-learn 0.5.3, VEP 107, + VMD 1.9.4a57, Wayland 1.21.0, wxWidgets 3.2.1, xprop 1.2.5 + +* minor enhancements, including: + + * configure recent pocl versions with ``-DLLC_HOST_CPU=native`` to avoid CPU auto-detection (`#16246 `_) + * add multi-dep exception to easyconfigs test suite for ncbi-vdb-3.0.0 which requires HDF5 1.10.x (`#16316 `_) + * enable running of LAPACK tests for recent OpenBLAS easyconfigs + add patch to fix failing LAPACK tests due to use of ``-ftree-vectorize`` (`#16406 `_) + * add ``GITHUB_(LOWER_)RELEASE`` to known constants in ``setup.cfg`` (`#16422 `_) + * add AMAPVox extension to R v4.2.1 (`#16439 `_) + * add OpenEXR dependency to POV-Ray 3.7.0.10 (`#16408 `_) + +* various bug fixes, including: + + * add patch for OpenBLAS 0.3.7-0.3.12 to fix miscomputation on POWER (`#16199 `_) + * skip flaky test in PyTorch 1.9.0 (`#16258 `_) + * add ``--with-versioned-syms`` to ncurses 6.2 and 6.3 (`#16270 `_) + * add missing pkg-config build dependency to Guile (`#16317 `_) + * add patches to fix incompatibilites between ASE and other packages in 2022a toolchain (`#16332 `_) + * add patches to fix PyTorch 1.11 on POWER (`#16339 `_) + * add patches for Ambertools 21 to Amber 20.11 to work with updated Amber easyblock (`#16343 `_) + * use Intel MPI from EasyBuild toolchain in AMS (`#16363 `_) + * fix execution permissions for ``bin/ngm*`` for NextGenMap v0.5.5 (`#16383 `_) + * fix using provided Qhull and freetype dependencies for matplotlib 3.5.2 by creating ``mplsetup.cfg`` rather than ``setup.cfg`` (`#16396 `_) + * fix GitHub download link in for libpsl 0.21.1 (`#16397 `_) + * stick to http in source URL for ``stride.tar.gz`` in VMD 1.9.4a51 easyconfigs due to problems with SSL certificate (`#16403 `_) + * add patch to detect available cores and remove unneeded deps for Unicycler 0.5.0 (`#16407 `_) + * add missing ICU + libunistring dependencies for libpsl 0.21.1 w/ GCCcore/10.3.0 (`#16410 `_) + * add patch to GCC 11.x + 12.x to fix vectorizer bug (`#16411 `_) + * fix checksum for GULP 6.1 (`#16423 `_) + * add bzip2 and libxml2 as dependencies for netCDF 4.9.0 (`#16450 `_) + +* other changes: + + * drop Java dep from ABAQUS 2022 (`#16314 `_) + * deprecate use of ``True`` in favour of ``SYSTEM`` for system-toolchain dependencies in easyconfigs using a recent toolchain version (>2019b) (`#16384 `_) + * update easyconfigs to use ``SYSTEM`` template constant instead of ``True`` in dependencies (`#16386 `_, `#16418 `_) + * update libxml2 + libxslt easyconfigs to use ``gnome.org`` source URL (`#16429 `_) + + .. _release_notes_eb461: EasyBuild v4.6.1 (September 12th 2022) diff --git a/docs/conf.py b/docs/conf.py index e2e63af6..f465205a 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.6.1' # this is meant to reference the version of EasyBuild +version = '4.6.2' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20220912.0' # this is meant to reference the version of the documentation itself +release = '20221021.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 6583f2802f3885d95e15f42300bb7c3ebc76d279 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 21 Oct 2022 18:30:44 +0800 Subject: [PATCH 241/286] bump version to 4.6.2 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 00e12ed4..c320f220 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.6.1' +VERSION = '4.6.2' # Utility function to read README file From 5efce9637cf8d874f407e97a537ae0e4bcf959b8 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 21 Oct 2022 18:49:46 +0200 Subject: [PATCH 242/286] Updated documentation in accordance with https://github.com/easybuilders/easybuild-framework/pull/4057 --- docs/Easystack-files.rst | 154 ++++++++++++++++++++++++--------------- 1 file changed, 97 insertions(+), 57 deletions(-) diff --git a/docs/Easystack-files.rst b/docs/Easystack-files.rst index 9c46e611..73ad4444 100644 --- a/docs/Easystack-files.rst +++ b/docs/Easystack-files.rst @@ -39,82 +39,122 @@ Structure of an easystack file Easystack files are written in `YAML syntax `_. -General options, which should be applied to each software (for example ``robot``), are defined at the top of the file. +Essentially, easystack files list the EasyConfigs you want to install. These are listed under the 'easyconfigs:' key: -Afterwards, particular software specifications follow. +.. code:: yaml -It is mandatory to specify basic software-related keywords: *software name*, *toolchains* and *versions*. + easyconfigs: + - PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb + - OpenFOAM-v2206-foss-2022a.eb -- *software name*: Name of the software. -- *toolchains*: Names and versions of compiler :ref:`toolchains`. -- *versions*: Versions of software. If multiple entries are provided, EasyBuild will install all of them. -Can be in form of a list or consecutive line entries (see example). +(note the use of the ``-`` to list the items). -**General structure of YAML-formatted easystack:** +In addition, you can specify additional options that will only apply to the installation of that EasyConfig: .. code:: yaml - software: - : - toolchains: - : - : - versionsuffix: '<-example>' + easyconfigs: + - PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb: + options: { + 'from-pr': 15924, + 'debug': True + } + - Hypre-2.25.0-foss-2022a.eb: + - OpenFOAM-v2206-foss-2022a.eb: + options: { + 'installpath': '/my/custom/installpath' + } + +The same command line arguments and options that are valid for the ``eb`` command can be used here, but any prefixed single or double dashes that are commonly used on the command line are ommitted in easystack files. + +Running the easystack file above would be equivalent to running: + +.. code:: -**Example of YAML-formatted easystack:** + eb PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb --from-pr 15924 --debug + eb Hypre-2.25.0-foss-2022a.eb + eb OpenFOAM-v2206-foss-2022a.eb --installpath /my/custom/installpath + +Note that whenever options are *not* specified (as is the case for ``Hyper`` in the above easystack file), you are +still allowed to use ``:`` the EasyConfig name: there is no difference in behaviour in ending with or without ``:``. + +Specifying short options in an easystack file, e.g. .. code:: yaml - software: - Bioconductor: - toolchains: - foss-2020a: - versions: - 3.11: - EasyBuild: - toolchains: - SYSTEM: - versions: [4.3.1] - GROMACS: - toolchains: - foss-2020a: - versions: - 2020.1: - 2020.3: - fosscuda-2020a: - versions: [2020.1] - OpenFOAM: - toolchains: - foss-2020a: - versions: [8, v2006] - R: - toolchains: - foss-2020a: - versions: [4.0.0] - -To install the software specified in this *easystack file* named '``myeasystack.yaml``', run: + easyconfigs: + - OpenFOAM-v2206-foss-2022a.eb: + options: { + 'D': True + } + +is allowed, but not recommended as they are more difficult to interpret by humans. + +.. _easystack_combining_options: + +Combining command line options with options in an easystack file +------------------------------ + +When building software with an easystack file, you can still add additional options on the command line as well. +These apply to *all* items in the easystack file. For example, if you have an easystack file named +``my_easystack.yaml`` + +.. code:: yaml + + easyconfigs: + - PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb: + options: { + 'from-pr': 15924, + 'debug': True + } + - OpenFOAM-v2206-foss-2022a.eb: + +and you run with .. code:: - eb --easystack myeasystack.yaml + eb --experimental --easystack my_easystack.yaml -D -This is equivalent to running: +this will have the same effect as running .. code:: - eb Bioconductor-3.11-foss-2020a.eb EasyBuild-4.3.1-SYSTEM.eb GROMACS-2020.1-foss-2020a.eb GROMACS-2020.3-foss-2020a.eb GROMACS-2020.1-fosscuda-2020a.eb OpenFOAM-8-foss-2020a.eb OpenFOAM-v2006-foss-2020a.eb R-4.0.0-foss-2020a.eb + eb PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb -D --from-pr 15924 --debug + eb OpenFOAM-v2206-foss-2022a.eb -D --installpath /my/custom/installpath + +Note that options specified on the command line are placed *before* the EasyConfig-specific options in the easystack file. EasyBuild will always respect the argument that was put *last*, for example: + +.. code:: + + eb PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb --dry-run --disable-dry-run + +will effectively run with ``--disabe-dry-run``. Since EasyConfig-specific options in from the easystack file are put *last*, this implies that they take priority over the the ones on the command line, if the same option is specified in both. For example, running + +.. code:: + + eb --experimental --easystack my_easystack.yaml --disable-debug + +will effectively cause the build of ``PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb`` to be build with ``--debug``, while ``OpenFOAM-v2206-foss-2022a.eb`` is effectively build with ``--disable-debug``. + To be developed --------------- -Optionally, more advanced keywords can be specified: *easybuild_version*, *robot*, *from_pr*, *versionsuffix*, *include-labels*, *exclude-labels*. - -- *easybuild_version:* if present, EasyBuild will check if the easystack file was intended for the current version of EasyBuild. -- *robot:* enables dependency resolution; see :ref:`Using_the_EasyBuild_command_line` for more details. -- *from_pr:* easyconfig files that are added or modified by a - particular pull request to the easybuild-easyconfigs GitHub repository - can be used (regardless of whether the pull request is merged or not). - (see :ref:`Integration_with_GitHub` for more details). -- *versionsuffix:* additional suffix for software version (placed after toolchain name) -- *include-labels:* only include this software when EasyBuild is configured with one of the specified labels -- *exclude-labels:* **do not** include this software when EasyBuild is configured with one of the specified labels +In the future, we are planning to support additional also global options specified in the easystack file. For example: + +.. code:: yaml + + options: { + robot: True + } + easyconfigs: + - PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb + - OpenFOAM-v2206-foss-2022a.eb + +would build both ``PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb`` and ``OpenFOAM-v2206-foss-2022a.eb`` with ``--robot`` (see https://github.com/easybuilders/easybuild-framework/issues/4105). + +Additionally, we plan to support specifying for which easybuild version an easystack file was intended, which can be helpful in more accurately recreating a certain software stack (see https://github.com/easybuilders/easybuild-framework/issues/4106). + +In the future, the need for specifying ``--easystack`` specifically will probably be dropped (see https://github.com/easybuilders/easybuild-framework/issues/4104). + +Finally, we plan to support specifying labels, which would make it more easy to build only a certain subset of the items in the easystack file. For example, by labelling all GPU-capable software with one specific label, one could easily choose to *not* build anything labeled ``gpu`` on a CPU node. (see https://github.com/easybuilders/easybuild-framework/issues/3512) From d4072b64868c82550f93edf493052983c54ad203 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 21 Oct 2022 18:53:21 +0200 Subject: [PATCH 243/286] Replace the word 'dashes' by the symbol --- docs/Easystack-files.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Easystack-files.rst b/docs/Easystack-files.rst index 73ad4444..d53c206e 100644 --- a/docs/Easystack-files.rst +++ b/docs/Easystack-files.rst @@ -65,7 +65,7 @@ In addition, you can specify additional options that will only apply to the inst 'installpath': '/my/custom/installpath' } -The same command line arguments and options that are valid for the ``eb`` command can be used here, but any prefixed single or double dashes that are commonly used on the command line are ommitted in easystack files. +The same command line arguments and options that are valid for the ``eb`` command can be used here, but any prefixed ``-`` or ``--`` that are commonly used on the command line are ommitted in easystack files. Running the easystack file above would be equivalent to running: From 61c41070ce0abac0576eaf2584bce10beb9fa12d Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 21 Oct 2022 18:53:53 +0200 Subject: [PATCH 244/286] Corrected typo --- docs/Easystack-files.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Easystack-files.rst b/docs/Easystack-files.rst index d53c206e..040bac68 100644 --- a/docs/Easystack-files.rst +++ b/docs/Easystack-files.rst @@ -75,7 +75,7 @@ Running the easystack file above would be equivalent to running: eb Hypre-2.25.0-foss-2022a.eb eb OpenFOAM-v2206-foss-2022a.eb --installpath /my/custom/installpath -Note that whenever options are *not* specified (as is the case for ``Hyper`` in the above easystack file), you are +Note that whenever options are *not* specified (as is the case for ``Hypre`` in the above easystack file), you are still allowed to use ``:`` the EasyConfig name: there is no difference in behaviour in ending with or without ``:``. Specifying short options in an easystack file, e.g. From 4452ab33de7e7a650b31280647934e9c4c6a9061 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 21 Oct 2022 18:55:27 +0200 Subject: [PATCH 245/286] Replaced e.g. by for example --- docs/Easystack-files.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Easystack-files.rst b/docs/Easystack-files.rst index 040bac68..ec766240 100644 --- a/docs/Easystack-files.rst +++ b/docs/Easystack-files.rst @@ -78,7 +78,7 @@ Running the easystack file above would be equivalent to running: Note that whenever options are *not* specified (as is the case for ``Hypre`` in the above easystack file), you are still allowed to use ``:`` the EasyConfig name: there is no difference in behaviour in ending with or without ``:``. -Specifying short options in an easystack file, e.g. +Specifying short options in an easystack file, for example .. code:: yaml From adadbad839c58d5529e9bef9cabb0b9af11c9aef Mon Sep 17 00:00:00 2001 From: casparl Date: Sun, 23 Oct 2022 18:15:57 +0200 Subject: [PATCH 246/286] Corrected spelling --- docs/Easystack-files.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Easystack-files.rst b/docs/Easystack-files.rst index ec766240..620d8168 100644 --- a/docs/Easystack-files.rst +++ b/docs/Easystack-files.rst @@ -65,7 +65,7 @@ In addition, you can specify additional options that will only apply to the inst 'installpath': '/my/custom/installpath' } -The same command line arguments and options that are valid for the ``eb`` command can be used here, but any prefixed ``-`` or ``--`` that are commonly used on the command line are ommitted in easystack files. +The same command line arguments and options that are valid for the ``eb`` command can be used here, but any prefixed ``-`` or ``--`` that are commonly used on the command line are omitted in easystack files. Running the easystack file above would be equivalent to running: From 21c9592649c179c9437d7f0a4d7b61c5b87cec64 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2022 19:49:54 +0100 Subject: [PATCH 247/286] add EasyBuild logos, old and new --- logo/old_logo_2012-2022/easybuild_logo.pdf | Bin 0 -> 53188 bytes logo/old_logo_2012-2022/easybuild_logo.png | Bin 0 -> 616872 bytes .../easybuild_logo_alpha.png | Bin 0 -> 638367 bytes .../easybuild_logo_blocks.png | Bin 0 -> 83027 bytes .../easybuild_logo_white.png | Bin 0 -> 134769 bytes .../easybuild_tech_talks.png | Bin 0 -> 414934 bytes .../easybuild_logo_2022_horizontal_dark_bg.pdf | Bin 0 -> 67689 bytes ...easybuild_logo_2022_horizontal_light_bg.pdf | Bin 0 -> 67687 bytes ..._logo_2022_horizontal_no_slogal_dark_bg.pdf | Bin 0 -> 59293 bytes ...logo_2022_horizontal_no_slogal_light_bg.pdf | Bin 0 -> 59362 bytes .../easybuild_logo_2022_vertical_dark_bg.pdf | Bin 0 -> 67655 bytes .../easybuild_logo_2022_vertical_light_bg.pdf | Bin 0 -> 67647 bytes ...ld_logo_2022_vertical_no_slogal_dark_bg.pdf | Bin 0 -> 59281 bytes ...d_logo_2022_vertical_no_slogal_light_bg.pdf | Bin 0 -> 59273 bytes .../easybuild_logo_2022_horizontal_dark_bg.png | Bin 0 -> 80908 bytes ...ogo_2022_horizontal_dark_bg_transparent.png | Bin 0 -> 68645 bytes ...easybuild_logo_2022_horizontal_light_bg.png | Bin 0 -> 80347 bytes ...go_2022_horizontal_light_bg_transparent.png | Bin 0 -> 68522 bytes ..._logo_2022_horizontal_no_slogan_dark_bg.png | Bin 0 -> 60571 bytes ...orizontal_no_slogan_dark_bg_transparent.png | Bin 0 -> 52699 bytes ...logo_2022_horizontal_no_slogan_light_bg.png | Bin 0 -> 59876 bytes ...rizontal_no_slogan_light_bg_transparent.png | Bin 0 -> 52675 bytes .../easybuild_logo_2022_vertical_dark_bg.png | Bin 0 -> 80064 bytes ..._logo_2022_vertical_dark_bg_transparent.png | Bin 0 -> 68250 bytes .../easybuild_logo_2022_vertical_light_bg.png | Bin 0 -> 79470 bytes ...logo_2022_vertical_light_bg_transparent.png | Bin 0 -> 67997 bytes ...ld_logo_2022_vertical_no_slogan_dark_bg.png | Bin 0 -> 228221 bytes ..._vertical_no_slogan_dark_bg_transparent.png | Bin 0 -> 62148 bytes ...d_logo_2022_vertical_no_slogan_light_bg.png | Bin 0 -> 70761 bytes ...vertical_no_slogan_light_bg_transparent.png | Bin 0 -> 61718 bytes 30 files changed, 0 insertions(+), 0 deletions(-) create mode 100755 logo/old_logo_2012-2022/easybuild_logo.pdf create mode 100644 logo/old_logo_2012-2022/easybuild_logo.png create mode 100644 logo/old_logo_2012-2022/easybuild_logo_alpha.png create mode 100644 logo/old_logo_2012-2022/easybuild_logo_blocks.png create mode 100644 logo/old_logo_2012-2022/easybuild_logo_white.png create mode 100644 logo/old_logo_2012-2022/easybuild_tech_talks.png create mode 100644 logo/pdf/easybuild_logo_2022_horizontal_dark_bg.pdf create mode 100644 logo/pdf/easybuild_logo_2022_horizontal_light_bg.pdf create mode 100644 logo/pdf/easybuild_logo_2022_horizontal_no_slogal_dark_bg.pdf create mode 100644 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z9Mb&umrT=$4u(x}#ae{X-9hBe3`A)F-PrNasfw*6@2HiGT`QL7eH$3oFsBZ_{4eq- zN>U5Ik-0W(?aDb{Tx#?vZT%d1)rjPQyp>K%hI0pBTs_2mG1*47%X;Ix-0^a9cfwP_ z#17T`$?~ZCn!YiG@E!5p@yytGU9oKutcIHO{P*69;=`2@KQh|NkPKA_)SKNujxnR% znG1RI_!yMX+vM&F3HDA!KeAZ(U+^Mu2XVarIh3O#j>6o%e~wMh@1HZ}|NV&}=wiS@ z{`U|#zA57WoEi%t@bS-a;=k31H@^}8-`^7wN7&In$EL^l&)Kgg!7ssrU+P2rWhB3# z;1?8tUr+#kK>_#$1^@q0z>cUPSU{fEq*b_KYyHuWD5`w?f2icIv;VNzUvl{`ou|{v Yx%G#tO1FgjIw9YkF|{%&K7ot+KQP_5ng9R* literal 0 HcmV?d00001 From b52a1eec9b750e5b25a7ec03158cf3859438a45c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2022 19:53:54 +0100 Subject: [PATCH 248/286] skip checking of logo/ subdir with codespell --- .github/workflows/check_with_codespell.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check_with_codespell.sh b/.github/workflows/check_with_codespell.sh index ef1f9122..4fa83aeb 100644 --- a/.github/workflows/check_with_codespell.sh +++ b/.github/workflows/check_with_codespell.sh @@ -1 +1 @@ -codespell --skip='.git,version-specific,scripts' --ignore-words-list=atleast,ninjs,simpy,proovread,namd,precice --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!'; else $(exit $retVal); fi; +codespell --skip='.git,version-specific,scripts,logo' --ignore-words-list=atleast,ninjs,simpy,proovread,namd,precice --quiet-level=2; retVal=$?; if [ $retVal -eq 1 ]; then echo 'Got one expected warning, so success!'; else $(exit $retVal); fi; From 94f88d2615fd9a360de6301d9e3f7db971e49ad8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2022 20:16:28 +0100 Subject: [PATCH 249/286] use new EasyBuild logo in README --- README.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 62687619..0f5ababf 100644 --- a/README.rst +++ b/README.rst @@ -1,5 +1,6 @@ -.. image:: https://easybuilders.github.io/easybuild/images/easybuild_logo_small.png +.. image:: 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These are listed under the 'easyconfigs:' key: +Essentially, an easystack file lists the easyconfig files you want to install, which are specified under the +`easyconfigs` key. + +For example: .. code:: yaml @@ -47,27 +58,35 @@ Essentially, easystack files list the EasyConfigs you want to install. These are - PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb - OpenFOAM-v2206-foss-2022a.eb -(note the use of the ``-`` to list the items). +.. note:: + You must use '``-``' to list the easyconfigs in an easystack file. + +In addition, you can specify additional configuration options via the ``options`` subkey +which will only apply to the installation of a particular easyconfig file. -In addition, you can specify additional options that will only apply to the installation of that EasyConfig: +For example: .. code:: yaml easyconfigs: - PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb: - options: { - 'from-pr': 15924, - 'debug': True - } + options: + from-pr: 15924 + debug: True - Hypre-2.25.0-foss-2022a.eb: - OpenFOAM-v2206-foss-2022a.eb: - options: { - 'installpath': '/my/custom/installpath' - } + options: + installpath: /my/custom/installpath + +.. note:: + You need to take care with some values in YAML, especially integers, booleans, etc. + To avoid that the YAML parser assumes that a value is of a particular type, + use quotes (``'...'``) to force a string value. -The same command line arguments and options that are valid for the ``eb`` command can be used here, but any prefixed ``-`` or ``--`` that are commonly used on the command line are omitted in easystack files. +The configuration options that are valid for the ``eb`` command can be used (see ``eb --help``), +but the ``-`` or ``--`` prefixes that are commonly used on the command line are omitted in easystack files. -Running the easystack file above would be equivalent to running: +Using the example easystack file above would be equivalent to running: .. code:: @@ -75,25 +94,25 @@ Running the easystack file above would be equivalent to running: eb Hypre-2.25.0-foss-2022a.eb eb OpenFOAM-v2206-foss-2022a.eb --installpath /my/custom/installpath -Note that whenever options are *not* specified (as is the case for ``Hypre`` in the above easystack file), you are -still allowed to use ``:`` the EasyConfig name: there is no difference in behaviour in ending with or without ``:``. +Note that whenever configuration options are *not* specified (as is the case for ``Hypre`` in the example easystack file above), +you are still allowed to use '``:``' after the easyconfig filename: there is no difference in behaviour in ending with or without '``:``'. -Specifying short options in an easystack file, for example +Specifying short options in an easystack file is allowed, for example: .. code:: yaml easyconfigs: - OpenFOAM-v2206-foss-2022a.eb: - options: { - 'D': True - } + options: + D: True + +This is not recommended however, as short options are more difficult to interpret by humans. -is allowed, but not recommended as they are more difficult to interpret by humans. .. _easystack_combining_options: Combining command line options with options in an easystack file ------------------------------- +---------------------------------------------------------------- When building software with an easystack file, you can still add additional options on the command line as well. These apply to *all* items in the easystack file. For example, if you have an easystack file named @@ -103,38 +122,46 @@ These apply to *all* items in the easystack file. For example, if you have an ea easyconfigs: - PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb: - options: { - 'from-pr': 15924, - 'debug': True - } + options: + from-pr: 15924 + debug: True - OpenFOAM-v2206-foss-2022a.eb: and you run with .. code:: - eb --experimental --easystack my_easystack.yaml -D + eb --experimental --easystack my_easystack.yaml --dry-run this will have the same effect as running .. code:: - eb PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb -D --from-pr 15924 --debug - eb OpenFOAM-v2206-foss-2022a.eb -D --installpath /my/custom/installpath + eb PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb --dry-run --from-pr 15924 --debug + eb OpenFOAM-v2206-foss-2022a.eb --dry-run --installpath /my/custom/installpath + +Note that options specified on the command line are placed *before* the easyconfig-specific options in the easystack file. +EasyBuild will always respect the argument that was put *last*. -Note that options specified on the command line are placed *before* the EasyConfig-specific options in the easystack file. EasyBuild will always respect the argument that was put *last*, for example: +For example: .. code:: eb PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb --dry-run --disable-dry-run -will effectively run with ``--disabe-dry-run``. Since EasyConfig-specific options in from the easystack file are put *last*, this implies that they take priority over the the ones on the command line, if the same option is specified in both. For example, running +will effectively run *without* enabling dry run mode, since ``--disable-dry-run`` is specified after ``--dry-run``. + +Since easyconfig-specific configuration options specified in the easystack file are put *last*, +they take priority over the the ones on the command line, if the same configuration option is specified in both. + +For example, running: .. code:: eb --experimental --easystack my_easystack.yaml --disable-debug -will effectively cause the build of ``PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb`` to be build with ``--debug``, while ``OpenFOAM-v2206-foss-2022a.eb`` is effectively build with ``--disable-debug``. +will effectively cause ``PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb`` to be installed with debug logging enabled, +while ``OpenFOAM-v2206-foss-2022a.eb`` will be effectively installed *without* debug logging. To be developed @@ -144,17 +171,24 @@ In the future, we are planning to support additional also global options specifi .. code:: yaml - options: { - robot: True - } + options: + robot: True + easyconfigs: - PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb - OpenFOAM-v2206-foss-2022a.eb -would build both ``PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb`` and ``OpenFOAM-v2206-foss-2022a.eb`` with ``--robot`` (see https://github.com/easybuilders/easybuild-framework/issues/4105). +would installed both ``PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb`` and ``OpenFOAM-v2206-foss-2022a.eb`` using ``--robot`` +(see `issue #4105 `_). -Additionally, we plan to support specifying for which easybuild version an easystack file was intended, which can be helpful in more accurately recreating a certain software stack (see https://github.com/easybuilders/easybuild-framework/issues/4106). +Additionally, we plan to support specifying for which EasyBuild version an easystack file was intended, +which can be helpful in more accurately recreating a certain software stack +(see `issue #4106 `_). -In the future, the need for specifying ``--easystack`` specifically will probably be dropped (see https://github.com/easybuilders/easybuild-framework/issues/4104). +In the future, the ``--easystack`` option will probably be dropped, and EasyBuild will automatically detect +the use of easystack files (see `issue #4104 `_). -Finally, we plan to support specifying labels, which would make it more easy to build only a certain subset of the items in the easystack file. For example, by labelling all GPU-capable software with one specific label, one could easily choose to *not* build anything labeled ``gpu`` on a CPU node. (see https://github.com/easybuilders/easybuild-framework/issues/3512) +Finally, we plan to support specifying *labels*, which would make it more easy to install only a certain subset of +the items listed in an easystack file. For example, by labelling all GPU-capable software with a ``gpu`` label, +one could easily choose to *not* build anything labeled ``gpu`` on a CPU node +(see `issue #3512 `_). From bbbc62464dc5b83f9d73bca35167eea93edcd483 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 10:41:06 +0100 Subject: [PATCH 252/286] clarify note on when to use quotes to force string values in easystack files --- docs/Easystack-files.rst | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/docs/Easystack-files.rst b/docs/Easystack-files.rst index d8759432..fc1a30e8 100644 --- a/docs/Easystack-files.rst +++ b/docs/Easystack-files.rst @@ -80,8 +80,12 @@ For example: .. note:: You need to take care with some values in YAML, especially integers, booleans, etc. - To avoid that the YAML parser assumes that a value is of a particular type, - use quotes (``'...'``) to force a string value. + + If the specified value definitely must be a string value, you should use quotes (``'...'``) to avoid + that the YAML parser automatically converts the value to be of a specific type. + + In other cases, the automatic conversion is useful, like for the ``True`` used above, + since ``debug`` is a boolean configuration option. The configuration options that are valid for the ``eb`` command can be used (see ``eb --help``), but the ``-`` or ``--`` prefixes that are commonly used on the command line are omitted in easystack files. @@ -94,8 +98,9 @@ Using the example easystack file above would be equivalent to running: eb Hypre-2.25.0-foss-2022a.eb eb OpenFOAM-v2206-foss-2022a.eb --installpath /my/custom/installpath -Note that whenever configuration options are *not* specified (as is the case for ``Hypre`` in the example easystack file above), -you are still allowed to use '``:``' after the easyconfig filename: there is no difference in behaviour in ending with or without '``:``'. +.. note:: + Whenever configuration options are *not* specified (as is the case for ``Hypre`` in the example easystack file above), + you are still allowed to use '``:``' after the easyconfig filename: there is no difference in behaviour in ending with or without '``:``'. Specifying short options in an easystack file is allowed, for example: From a602d0976bc497cc31115b486ee53a7f85ddc389 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 25 Nov 2022 14:38:36 +0000 Subject: [PATCH 253/286] fix typo --- docs/Python-2-3-compatibility.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Python-2-3-compatibility.rst b/docs/Python-2-3-compatibility.rst index e00667a1..c6e69686 100644 --- a/docs/Python-2-3-compatibility.rst +++ b/docs/Python-2-3-compatibility.rst @@ -226,7 +226,7 @@ Function to raise an error with specified message and traceback, implemented in ------------- * Python 2: corresponds to ``urllib.urlencode`` function -* Python 2: corresponds to ``urllib.parse.urlencode`` function +* Python 3: corresponds to ``urllib.parse.urlencode`` function .. _py2vs3_URLError: From ca3369f7183702ed8a80fbb92c797c1259e86e9a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Nov 2022 14:23:39 +0100 Subject: [PATCH 254/286] Cancel old GithubAction runs --- .github/workflows/doc_build.yml | 4 ++++ .github/workflows/linting.yml | 5 +++++ .github/workflows/scripts.yml | 5 +++++ 3 files changed, 14 insertions(+) diff --git a/.github/workflows/doc_build.yml b/.github/workflows/doc_build.yml index b039f279..19f45a3e 100644 --- a/.github/workflows/doc_build.yml +++ b/.github/workflows/doc_build.yml @@ -2,6 +2,10 @@ name: Docs build and installation end-to-end tests on: [push, pull_request] +concurrency: + group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}} + cancel-in-progress: true + jobs: docs: runs-on: ubuntu-latest diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 09493c87..6cda4340 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,5 +1,10 @@ name: Static Analysis on: [push, pull_request] + +concurrency: + group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}} + cancel-in-progress: true + jobs: python-linting: runs-on: ubuntu-18.04 diff --git a/.github/workflows/scripts.yml b/.github/workflows/scripts.yml index affae66a..725b45ea 100644 --- a/.github/workflows/scripts.yml +++ b/.github/workflows/scripts.yml @@ -1,5 +1,10 @@ name: Tests for scripts on: [push, pull_request] + +concurrency: + group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}} + cancel-in-progress: true + jobs: scripts: runs-on: ubuntu-latest From 88ad55c82bf7876aa5ee818b270281449a69d248 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 25 Nov 2022 14:38:36 +0000 Subject: [PATCH 255/286] fix typo --- docs/Python-2-3-compatibility.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Python-2-3-compatibility.rst b/docs/Python-2-3-compatibility.rst index e00667a1..c6e69686 100644 --- a/docs/Python-2-3-compatibility.rst +++ b/docs/Python-2-3-compatibility.rst @@ -226,7 +226,7 @@ Function to raise an error with specified message and traceback, implemented in ------------- * Python 2: corresponds to ``urllib.urlencode`` function -* Python 2: corresponds to ``urllib.parse.urlencode`` function +* Python 3: corresponds to ``urllib.parse.urlencode`` function .. _py2vs3_URLError: From 3449813894923cecab88bb198e4470afbff9aa51 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 11 Dec 2022 11:22:22 +0100 Subject: [PATCH 256/286] add Python 3.11 to classifiers in setup.py --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index c320f220..71ca46d3 100644 --- a/setup.py +++ b/setup.py @@ -76,6 +76,7 @@ def read(fname): "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", "Topic :: Scientific/Engineering", "Topic :: Software Development :: Build Tools", ], From b9c18f664194dc3b2c89afb0903756061f949a36 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 8 Jan 2023 15:45:37 +0100 Subject: [PATCH 257/286] update overview of common toolchains with foss/2022b and intel/2022b --- docs/Common-toolchains.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/Common-toolchains.rst b/docs/Common-toolchains.rst index 9352a4e3..d2e988b6 100644 --- a/docs/Common-toolchains.rst +++ b/docs/Common-toolchains.rst @@ -168,6 +168,8 @@ Component versions in ``foss`` toolchain +----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ | ``2022a`` | Jun '22 | 2.38 | 11.3.0 | 4.1.4 | 3.2.0 | 0.3.20 | (incl. with OpenBLAS) | 2.2.0 | 3.3.10 | +----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ +| ``2022b`` | Dec '22 | 2.39 | 12.2.0 | 4.1.4 | 3.2.1 | 0.3.21 | (incl. with OpenBLAS) | 2.2.0 | 3.3.10 | ++----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ *(components marked with* * *were patched)* @@ -193,6 +195,8 @@ Component versions in ``intel`` toolchain +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ | ``2022a`` | Jun'22 | 2.38 | 11.3.0 | 2022.1.0 | 2021.6.0 | 2022.1.0 | +----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ +| ``2022b`` | Dec'22 | 2.39 | 12.2.0 | 2022.2.1 | 2021.7.1 | 2022.2.1 | ++----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ .. _common_toolchains_overview_deprecated: From 84e571b6de5834437e2fddb499b3c92752a2a03e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Jan 2023 13:50:05 +0100 Subject: [PATCH 258/286] auto-update docs for EasyBuild v4.7.0 --- docs/version-specific/Supported_software.rst | 19373 +++++++++------- .../config_file_constants.rst | 11 +- docs/version-specific/easyblocks.rst | 3 + .../version-specific/easyconfig_constants.rst | 34 +- .../easyconfig_license_constants.rst | 10 +- .../easyconfig_parameters.rst | 205 +- .../version-specific/easyconfig_templates.rst | 168 +- docs/version-specific/generic_easyblocks.rst | 995 +- docs/version-specific/help.rst | 563 +- docs/version-specific/toolchain_opts.rst | 2351 +- docs/version-specific/toolchains.rst | 87 +- 11 files changed, 12980 insertions(+), 10820 deletions(-) diff --git a/docs/version-specific/Supported_software.rst b/docs/version-specific/Supported_software.rst index bd3bc1fa..01147263 100644 --- a/docs/version-specific/Supported_software.rst +++ b/docs/version-specific/Supported_software.rst @@ -3,7 +3,7 @@ List of supported software ========================== -EasyBuild |version| supports 2798 different software packages (incl. toolchains, bundles): +EasyBuild |version| supports 2906 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` @@ -27,10 +27,10 @@ lib3to2 is a set of fixers that are intended to backport code written for Python *homepage*: https://pypi.python.org/pypi/3to2 ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== ``1.1.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.1.1`` ``-Python-2.7.13`` ``intel/2017a`` +``1.1.1`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============================== @@ -53,7 +53,7 @@ A software package for algebraic, geometric and combinatorial problems on linear *homepage*: https://4ti2.github.io/ ========= ===================================== -version toolchain +version toolchain ========= ===================================== ``1.6.9`` ``GCC/8.2.0-2.31.1``, ``intel/2018b`` ========= ===================================== @@ -65,7 +65,7 @@ version toolchain --- -:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_Abseil_592` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGAT_285` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_Albumentations_1478` - :ref:`list_software_alevin-fry_1021` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_AMAPVox_604` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMD-uProf_779` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AMPtk_445` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_AMS_225` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_ANGEL_359` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_AptaSUITE_784` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_Arcade-Learning-Environment_2655` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_ArchR_464` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_arosics_756` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_atropos_776` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Austin_628` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock-GPU_1075` - :ref:`list_software_AutoDock-Vina_1237` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_Avogadro2_869` - :ref:`list_software_awscli_643` +:ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABRA2_328` - :ref:`list_software_ABRicate_731` - :ref:`list_software_Abseil_592` - :ref:`list_software_abTEM_425` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_ADIOS_368` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGAT_285` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_Albumentations_1478` - :ref:`list_software_alevin-fry_1021` - :ref:`list_software_ALFA_276` - :ref:`list_software_Alfred_590` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_almosthere_1076` - :ref:`list_software_Alpha_486` - :ref:`list_software_AlphaFold_875` - :ref:`list_software_ALPS_304` - :ref:`list_software_alsa-lib_773` - :ref:`list_software_AMAPVox_604` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMD-uProf_779` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPHORA2_570` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_amplimap_849` - :ref:`list_software_AMPtk_445` - :ref:`list_software_AmrPlusPlus_1128` - :ref:`list_software_AMS_225` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_aNCI_315` - :ref:`list_software_andi_412` - :ref:`list_software_ANGEL_359` - :ref:`list_software_angsd_525` - :ref:`list_software_ANIcalculator_1282` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_antiSMASH_808` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_any2fasta_905` - :ref:`list_software_AOCC_278` - :ref:`list_software_AOMP_301` - :ref:`list_software_APBS_294` - :ref:`list_software_apex_430` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_AptaSUITE_784` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_Arcade-Learning-Environment_2655` - :ref:`list_software_arcasHLA_735` - :ref:`list_software_ARCH_286` - :ref:`list_software_Archive-Zip_1058` - :ref:`list_software_ArchR_464` - :ref:`list_software_archspec_841` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_aria2_463` - :ref:`list_software_Arlequin_833` - :ref:`list_software_Armadillo_917` - :ref:`list_software_arosics_756` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_arrow-R_682` - :ref:`list_software_ART_231` - :ref:`list_software_artic-ncov2019_1218` - :ref:`list_software_ARTS_314` - :ref:`list_software_ArviZ_492` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP_293` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_assimp_653` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_atropos_776` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_attrdict_863` - :ref:`list_software_attrdict3_914` - :ref:`list_software_augur_548` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Austin_628` - :ref:`list_software_AUTO-07p_573` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock-GPU_1075` - :ref:`list_software_AutoDock-Vina_1237` - :ref:`list_software_AutoGeneS_875` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_AutoMap_695` - :ref:`list_software_autopep8_822` - :ref:`list_software_Autotools_970` - :ref:`list_software_Avogadro2_869` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: @@ -78,7 +78,7 @@ Finite Element Analysis software for modeling, visualization and best-in-class i *homepage*: http://www.simulia.com/products/abaqus_fea.html ========== ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ========== ``6.12.1`` ``-linux-x86_64`` ``system`` ``6.13.5`` ``-linux-x86_64`` ``system`` @@ -102,26 +102,26 @@ ABINIT is a package whose main program allows one to find the total energy, char *homepage*: https://www.abinit.org/ -========== ======================== ================================================ -version versionsuffix toolchain -========== ======================== ================================================ -``7.0.3`` ``-x86_64_linux_gnu4.5`` ``system`` -``7.0.5`` ``-x86_64_linux_gnu4.5`` ``system`` -``7.2.1`` ``-x86_64_linux_gnu4.5`` ``system`` -``7.10.5`` ``intel/2016.02-GCC-4.9`` -``7.10.5`` ``-libxc`` ``intel/2016.02-GCC-4.9`` -``8.0.8`` ``intel/2016a`` -``8.0.8b`` ``foss/2016b``, ``intel/2016b`` -``8.2.2`` ``foss/2016b``, ``intel/2016b`` -``8.4.4`` ``intel/2017b`` -``8.6.3`` ``intel/2018a`` -``8.10.2`` ``intel/2018b`` -``8.10.3`` ``intel/2018b`` -``9.2.1`` ``intel/2020a`` +========== ======================== ================================================================= +version versionsuffix toolchain +========== ======================== ================================================================= +``7.0.3`` ``-x86_64_linux_gnu4.5`` ``system`` +``7.0.5`` ``-x86_64_linux_gnu4.5`` ``system`` +``7.2.1`` ``-x86_64_linux_gnu4.5`` ``system`` +``7.10.5`` ``intel/2016.02-GCC-4.9`` +``7.10.5`` ``-libxc`` ``intel/2016.02-GCC-4.9`` +``8.0.8`` ``intel/2016a`` +``8.0.8b`` ``foss/2016b``, ``intel/2016b`` +``8.2.2`` ``foss/2016b``, ``intel/2016b`` +``8.4.4`` ``intel/2017b`` +``8.6.3`` ``intel/2018a`` +``8.10.2`` ``intel/2018b`` +``8.10.3`` ``intel/2018b`` +``9.2.1`` ``intel/2020a`` ``9.4.1`` ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` -``9.4.2`` ``foss/2021a``, ``intel/2021a`` -``9.6.2`` ``intel/2021a``, ``intel/2021b`` -========== ======================== ================================================ +``9.4.2`` ``foss/2021a``, ``intel/2021a`` +``9.6.2`` ``foss/2022a``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a`` +========== ======================== ================================================================= .. _list_software_ABRA2_328: @@ -134,9 +134,9 @@ Assembly Based ReAligner *homepage*: https://github.com/mozack/abra2 ======== ============================= -version toolchain +version toolchain ======== ============================= -``2.22`` ``iccifort/2019.5.281`` +``2.22`` ``iccifort/2019.5.281`` ``2.23`` ``GCC/10.2.0``, ``GCC/9.3.0`` ======== ============================= @@ -151,7 +151,7 @@ Mass screening of contigs for antimicrobial and virulence genes *homepage*: https://github.com/tseemann/abricate ========= ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =============== ``0.9.9`` ``gompi/2019b`` ``0.9.9`` ``-Perl-5.28.1`` ``gompi/2019a`` @@ -169,7 +169,7 @@ Abseil is an open-source collection of C++ library code designed to augment the *homepage*: https://abseil.io/ ============== ================== -version toolchain +version toolchain ============== ================== ``20210324.2`` ``GCCcore/11.2.0`` ============== ================== @@ -185,9 +185,9 @@ abTEM provides a Python API for running simulations of Transmission Electron Mic *homepage*: https://github.com/jacobjma/abTEM ============ =============== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ============ =============== ================================== -``1.0.0b24`` ``-ASE-3.22.0`` ``fosscuda/2020b`` +``1.0.0b24`` ``-ASE-3.22.0`` ``fosscuda/2020b`` ``1.0.0b26`` ``-ASE-3.22.0`` ``foss/2020b``, ``fosscuda/2020b`` ============ =============== ================================== @@ -202,13 +202,13 @@ Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler *homepage*: https://www.bcgsc.ca/platform/bioinfo/software/abyss ========= ================================================================ -version toolchain +version toolchain ========= ================================================================ -``1.9.0`` ``foss/2016a`` +``1.9.0`` ``foss/2016a`` ``2.0.2`` ``foss/2016b``, ``foss/2018a``, ``gompi/2019a``, ``intel/2016b`` -``2.0.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.5`` ``foss/2019b`` -``2.2.5`` ``foss/2020b`` +``2.0.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.5`` ``foss/2019b`` +``2.2.5`` ``foss/2020b`` ========= ================================================================ @@ -222,9 +222,9 @@ ack is a tool like grep, optimized for programmers *homepage*: https://beyondgrep.com ========= ================== -version toolchain +version toolchain ========= ================== -``2.14`` ``system`` +``2.14`` ``system`` ``3.4.0`` ``GCCcore/10.2.0`` ``3.5.0`` ``GCCcore/10.3.0`` ========= ================== @@ -240,7 +240,7 @@ ACT is a Java application for displaying pairwise comparisons between two or mor *homepage*: https://sanger-pathogens.github.io/Artemis/ACT/ ========== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ========== ``18.0.2`` ``-Java-11`` ``system`` ``18.0.3`` ``-Java-11`` ``system`` @@ -257,7 +257,7 @@ ACTC converts independent triangles into triangle strips or fans. *homepage*: https://sourceforge.net/projects/actc ======= =================================================================================================================================== -version toolchain +version toolchain ======= =================================================================================================================================== ``1.1`` ``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2016b`` ======= =================================================================================================================================== @@ -273,7 +273,7 @@ Performs discrete, real, and gentle boost under both exponential and logistic lo *homepage*: https://cran.r-project.org/web/packages/ada/index.html ========= ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= =============== ``2.0-5`` ``-R-3.4.0`` ``intel/2017a`` ========= ============= =============== @@ -289,12 +289,13 @@ AdapterRemoval searches for and removes remnant adapter sequences from High-Thr *homepage*: https://github.com/MikkelSchubert/adapterremoval ========= ============================================== -version toolchain +version toolchain ========= ============================================== -``2.2.0`` ``foss/2016b`` -``2.2.2`` ``foss/2018b`` -``2.3.1`` ``foss/2018b`` +``2.2.0`` ``foss/2016b`` +``2.2.2`` ``foss/2018b`` +``2.3.1`` ``foss/2018b`` ``2.3.2`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0`` +``2.3.3`` ``GCC/11.3.0`` ========= ============================================== @@ -308,7 +309,7 @@ ADDA is an open-source parallel implementation of the discrete dipole approximat *homepage*: https://github.com/adda-team/adda/wiki ========= ============== -version toolchain +version toolchain ========= ============== ``1.3b4`` ``foss/2019a`` ========= ============== @@ -324,13 +325,13 @@ ADF is an accurate, parallelized, powerful computational chemistry program to un *homepage*: https://www.scm.com/ADF/ ================================ ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ================================ ============= =============== -``2009.01a.pc64_linux.intelmpi`` ``system`` -``2014.02`` ``system`` +``2009.01a.pc64_linux.intelmpi`` ``system`` +``2014.02`` ``system`` ``2014.11.r48287`` ``intel/2016a`` -``2016.101`` ``system`` -``2019.303`` ``-intelmpi`` ``system`` +``2016.101`` ``system`` +``2019.303`` ``-intelmpi`` ``system`` ================================ ============= =============== @@ -344,7 +345,7 @@ The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists t *homepage*: https://www.olcf.ornl.gov/center-projects/adios/ ============ ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ============== ``1.13.1`` ``-Python-2.7.15`` ``foss/2019a`` ``1.13.1`` ``-Python-3.8.2`` ``foss/2020a`` @@ -362,10 +363,10 @@ A small library for automatically adjustment of text position in matplotlib plot *homepage*: https://github.com/Phlya/adjustText ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== -``0.7.3`` ``foss/2021b`` -``0.7.3`` ``-Python-3.6.6`` ``foss/2018b`` +``0.7.3`` ``foss/2021b`` +``0.7.3`` ``-Python-3.6.6`` ``foss/2018b`` ``0.7.3`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================= =============== @@ -380,7 +381,7 @@ ADMIXTURE is a software tool for maximum likelihood estimation of individual anc *homepage*: https://dalexander.github.io/admixture/ ========= ========== -version toolchain +version toolchain ========= ========== ``1.3.0`` ``system`` ========= ========== @@ -396,7 +397,7 @@ The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitates *homepage*: https://projects.coin-or.org/ADOL-C ========= =============== -version toolchain +version toolchain ========= =============== ``2.7.0`` ``gompi/2019a`` ``2.7.2`` ``gompi/2020a`` @@ -413,7 +414,7 @@ Vectorization Optimization and Thread Prototyping - Vectorize & thread code or *homepage*: https://software.intel.com/intel-advisor-xe ================ ========== -version toolchain +version toolchain ================ ========== ``2016_update2`` ``system`` ``2017_update1`` ``system`` @@ -438,12 +439,12 @@ AFNI is a set of C programs for processing, analyzing, and displaying functional *homepage*: http://afni.nimh.nih.gov/ ============ ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============================== -``18.1.09`` ``-Python-3.6.4`` ``intel/2018a`` -``18.3.00`` ``-Python-3.6.6`` ``foss/2018b`` +``18.1.09`` ``-Python-3.6.4`` ``intel/2018a`` +``18.3.00`` ``-Python-3.6.6`` ``foss/2018b`` ``19.0.01`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``20160329`` ``-Python-2.7.11`` ``intel/2016a`` +``20160329`` ``-Python-2.7.11`` ``intel/2016a`` ============ ================== =============================== @@ -457,7 +458,7 @@ AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotation *homepage*: https://agat.readthedocs.io/en/latest/ ========= ============== -version toolchain +version toolchain ========= ============== ``0.9.2`` ``GCC/11.2.0`` ========= ============== @@ -473,7 +474,7 @@ AGFusion is a python package for annotating gene fusions from the human or mous *homepage*: https://github.com/murphycj/AGFusion ======= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= ============== ``1.2`` ``-Python-3.7.2`` ``foss/2019a`` ======= ================= ============== @@ -489,10 +490,11 @@ Asynchronous HTTP client/server framework for asyncio and Python. *homepage*: https://github.com/aio-libs/aiohttp ========= ================= ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ====================================== -``3.5.4`` ``-Python-3.6.6`` ``foss/2018b`` +``3.5.4`` ``-Python-3.6.6`` ``foss/2018b`` ``3.8.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``3.8.3`` ``GCCcore/11.3.0`` ========= ================= ====================================== @@ -506,7 +508,7 @@ ALADIN was entirely built on the notion of compatibility with its mother system, *homepage*: http://www.cnrm.meteo.fr/aladin/ =============== =============== -version toolchain +version toolchain =============== =============== ``36t1_op2bf1`` ``intel/2016a`` =============== =============== @@ -522,7 +524,7 @@ Albacore is a software project that provides an entry point to the Oxford Nanopo *homepage*: https://community.nanoporetech.com/protocols/albacore-offline-basecalli/v/abec_2003_v1_revz_29nov2016 ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``2.0.2`` ``-Python-3.6.1`` ``intel/2017a`` ========= ================= =============== @@ -538,10 +540,12 @@ Albumentations is a Python library for fast and flexible image augmentations *homepage*: https://albumentations.ai ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``1.1.0`` ``foss/2021b`` ``1.1.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``1.3.0`` ``foss/2022a`` +``1.3.0`` ``-CUDA-11.7.0`` ``foss/2022a`` ========= ================ ============== @@ -555,7 +559,7 @@ alevin-fry is an efficient and flexible tool for processing single-cell sequenci *homepage*: https://github.com/COMBINE-lab/alevin-fry ========= ================== -version toolchain +version toolchain ========= ================== ``0.4.3`` ``GCCcore/11.2.0`` ``0.6.0`` ``GCCcore/10.3.0`` @@ -572,12 +576,28 @@ ALFA provides a global overview of features distribution composing NGS dataset(s *homepage*: https://github.com/biocompibens/ALFA ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.1.1`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= ============== +.. _list_software_Alfred_590: + +*Alfred* +++++++++ + +Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Alfred supports read counting, feature annotation and haplotype-resolved consensus computation using multiple sequence alignments. + +*homepage*: https://www.gear-genomics.com/alfred/ + +========= ============== +version toolchain +========= ============== +``0.2.6`` ``GCC/11.2.0`` +========= ============== + + .. _list_software_alleleCount_1144: *alleleCount* @@ -588,7 +608,7 @@ The alleleCount package primarily exists to prevent code duplication between som *homepage*: http://cancerit.github.io/alleleCount/ ========= ================= -version toolchain +version toolchain ========= ================= ``4.0.0`` ``GCCcore/6.4.0`` ========= ================= @@ -604,7 +624,7 @@ The Allinea environment is an essential toolkit for developers and computational *homepage*: http://www.allinea.com =============================== ========== -version toolchain +version toolchain =============================== ========== ``4.1-32834-Redhat-5.7-x86_64`` ``system`` ``4.1-32834-Redhat-6.0-x86_64`` ``system`` @@ -622,7 +642,7 @@ ALLPATHS-LG, the new short read genome assembler. *homepage*: http://www.broadinstitute.org/software/allpaths-lg/blog/ ========= ============== -version toolchain +version toolchain ========= ============== ``52488`` ``foss/2016a`` ========= ============== @@ -638,10 +658,10 @@ Progress indicator C library. ATHR is a simple yet powerful progress indicator l *homepage*: https://github.com/horta/almosthere ========== ================== -version toolchain +version toolchain ========== ================== -``1.0.1`` ``GCCcore/7.3.0`` -``1.0.10`` ``GCCcore/9.3.0`` +``1.0.1`` ``GCCcore/7.3.0`` +``1.0.10`` ``GCCcore/9.3.0`` ``2.0.2`` ``GCCcore/10.2.0`` ========== ================== @@ -656,7 +676,7 @@ Alpha is a tool designed for detailed comparative study of bacteriophage genomes *homepage*: https://www.lirmm.fr/~swenson/alpha/alpha.htm ============ ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ============== ``20200430`` ``-Python-2.7.16`` ``foss/2019b`` ============ ================== ============== @@ -672,16 +692,16 @@ AlphaFold can predict protein structures with atomic accuracy even where no simi *homepage*: https://deepmind.com/research/case-studies/alphafold ========= ===================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ===================== ================================== ``2.0.0`` ``foss/2020b``, ``fosscuda/2020b`` ``2.0.1`` ``foss/2020b``, ``fosscuda/2020b`` -``2.1.1`` ``fosscuda/2020b`` -``2.1.2`` ``foss/2021a`` -``2.1.2`` ``-CUDA-11.3.1`` ``foss/2021a`` +``2.1.1`` ``fosscuda/2020b`` +``2.1.2`` ``foss/2021a`` +``2.1.2`` ``-CUDA-11.3.1`` ``foss/2021a`` ``2.1.2`` ``-TensorFlow-2.5.0`` ``foss/2020b``, ``fosscuda/2020b`` -``2.2.2`` ``foss/2021a`` -``2.2.2`` ``-CUDA-11.3.1`` ``foss/2021a`` +``2.2.2`` ``foss/2021a`` +``2.2.2`` ``-CUDA-11.3.1`` ``foss/2021a`` ========= ===================== ================================== @@ -695,11 +715,11 @@ The ALPS project (Algorithms and Libraries for Physics Simulations) is an open s *homepage*: http://alps.comp-phys.org/ ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``2.2.b4`` ``-Python-2.7.11`` ``intel/2016a`` -``2.3.0`` ``-Python-2.7.12`` ``foss/2016b`` -``2.3.0`` ``-Python-3.5.2`` ``foss/2016b`` +``2.3.0`` ``-Python-2.7.12`` ``foss/2016b`` +``2.3.0`` ``-Python-3.5.2`` ``foss/2016b`` ========== ================== =============== @@ -712,11 +732,12 @@ The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionali *homepage*: https://www.alsa-project.org -========= ================= -version toolchain -========= ================= +========= ====================================== +version toolchain +========= ====================================== ``1.2.4`` ``GCCcore/9.3.0`` -========= ================= +``1.2.8`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ====================================== .. _list_software_AMAPVox_604: @@ -729,7 +750,7 @@ LiDAR data voxelisation software *homepage*: https://amap-dev.cirad.fr/projects/amapvox ========= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========== ``1.9.4`` ``-Java-11`` ``system`` ========= ============= ========== @@ -745,7 +766,7 @@ Library for XML processing in Python, designed to balance the native idioms of P *homepage*: https://pypi.org/project/Amara =========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== =============================== ``1.2.0.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` =========== ================== =============================== @@ -761,7 +782,7 @@ amask is a set of tools to to determine the affinity of MPI processes and OpenMP *homepage*: https://github.com/TACC/amask ============ ============== -version toolchain +version toolchain ============ ============== ``20171106`` ``foss/2018a`` ``20190404`` ``foss/2018b`` @@ -778,20 +799,21 @@ Amber (originally Assisted Model Building with Energy Refinement) is software fo *homepage*: https://ambermd.org/amber.html ========= ================================================= ======================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================================================= ======================================================================== -``14`` ``-AmberTools-15-patchlevel-13-13`` ``intel/2016a`` -``16`` ``-AmberTools-16-patchlevel-5-14`` ``iomkl/2016.07`` -``16`` ``-AmberTools-16-patchlevel-5-14-CUDA`` ``iomkl/2016.09-GCC-4.9.3-2.25`` -``16`` ``-AmberTools-16-patchlevel-5-14-serial`` ``iomkl/2016.07`` -``16`` ``-AmberTools-17-patchlevel-10-15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``14`` ``-AmberTools-15-patchlevel-13-13`` ``intel/2016a`` +``16`` ``-AmberTools-16-patchlevel-5-14`` ``iomkl/2016.07`` +``16`` ``-AmberTools-16-patchlevel-5-14-CUDA`` ``iomkl/2016.09-GCC-4.9.3-2.25`` +``16`` ``-AmberTools-16-patchlevel-5-14-serial`` ``iomkl/2016.07`` +``16`` ``-AmberTools-17-patchlevel-10-15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``16`` ``-AmberTools-17-patchlevel-10-15-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``16`` ``-AmberTools-17-patchlevel-8-12`` ``intel/2017b`` -``18`` ``-AmberTools-18-patchlevel-10-8`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017b`` -``18`` ``-AmberTools-19-patchlevel-12-17-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b`` -``20.11`` ``-AmberTools-20.15-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` -``20.11`` ``-AmberTools-21.3`` ``foss/2020b``, ``fosscuda/2020b`` -``22.0`` ``-AmberTools-22.3`` ``foss/2021b`` +``16`` ``-AmberTools-17-patchlevel-8-12`` ``intel/2017b`` +``18`` ``-AmberTools-18-patchlevel-10-8`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017b`` +``18`` ``-AmberTools-19-patchlevel-12-17-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b`` +``20.11`` ``-AmberTools-20.15-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``20.11`` ``-AmberTools-21.3`` ``foss/2020b``, ``fosscuda/2020b`` +``22.0`` ``-AmberTools-22.3`` ``foss/2021b`` +``22.0`` ``-AmberTools-22.3-CUDA-11.4.1`` ``foss/2021b`` ========= ================================================= ======================================================================== @@ -805,7 +827,7 @@ A stripped-down set of just antechamber, sqm, and tleap. *homepage*: https://github.com/choderalab/ambermini =========== ================================ -version toolchain +version toolchain =========== ================================ ``16.16.0`` ``intel/2017b``, ``intel/2020a`` =========== ================================ @@ -821,14 +843,14 @@ AmberTools consists of several independently developed packages that work well b *homepage*: https://ambermd.org/ ========= ================== ================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================================ ``17`` ``intel/2017b``, ``intel/2018a`` -``17`` ``-Python-2.7.14`` ``foss/2018a`` -``20`` ``-Python-3.8.2`` ``intel/2020a`` -``21`` ``foss/2021a``, ``intel/2021b`` -``21.12`` ``foss/2021b`` -``22.3`` ``foss/2021b`` +``17`` ``-Python-2.7.14`` ``foss/2018a`` +``20`` ``-Python-3.8.2`` ``intel/2020a`` +``21`` ``foss/2021a``, ``intel/2021b`` +``21.12`` ``foss/2021b`` +``22.3`` ``foss/2021b`` ========= ================== ================================ @@ -842,10 +864,10 @@ AMD LibM is a software library containing a collection of basic math functions o *homepage*: https://developer.amd.com/amd-cpu-libraries/amd-math-library-libm/ =========== ================== -version toolchain +version toolchain =========== ================== ``3.2.2`` ``GCC/7.3.0-2.30`` -``3.6.0-4`` ``GCC/9.3.0`` +``3.6.0-4`` ``GCC/9.3.0`` =========== ================== @@ -859,10 +881,10 @@ AMD Random Number Generator Library is a pseudorandom number generator library. *homepage*: https://developer.amd.com/amd-cpu-libraries/rng-library/ ========= ================== -version toolchain +version toolchain ========= ================== ``1.0`` ``GCC/7.3.0-2.30`` -``2.2-4`` ``GCC/9.3.0`` +``2.2-4`` ``GCC/9.3.0`` ========= ================== @@ -876,10 +898,10 @@ The AMD Secure Random Number Generator (RNG) is a library that provides APIs to *homepage*: https://developer.amd.com/amd-cpu-libraries/rng-library/ ========= ================== -version toolchain +version toolchain ========= ================== ``1.0`` ``GCC/7.3.0-2.30`` -``2.2-4`` ``GCC/9.3.0`` +``2.2-4`` ``GCC/9.3.0`` ========= ================== @@ -893,7 +915,7 @@ AMD uProf is a performance analysis tool for applications running on Windows, Li *homepage*: https://developer.amd.com/amd-uprof/ =========== ========== -version toolchain +version toolchain =========== ========== ``3.4.502`` ``system`` ``3.5.671`` ``system`` @@ -910,7 +932,7 @@ The AMOS consortium is committed to the development of open-source whole genome *homepage*: http://amos.sourceforge.net ========= ============================== -version toolchain +version toolchain ========= ============================== ``3.1.0`` ``foss/2018b``, ``foss/2021b`` ========= ============================== @@ -926,7 +948,7 @@ An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequence *homepage*: https://github.com/wu-lab-uva/AMPHORA2 ============ ========================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ========================== =============== ``20190730`` ``-Java-13-pthreads-avx2`` ``gompi/2020b`` ============ ========================== =============== @@ -942,7 +964,7 @@ An open-source library for mathematical programming. *homepage*: https://github.com/ampl/mp ========= ================= -version toolchain +version toolchain ========= ================= ``3.1.0`` ``GCCcore/6.4.0`` ========= ================= @@ -958,7 +980,7 @@ amplimap is a command-line tool to automate the processing and analysis of data *homepage*: https://amplimap.readthedocs.io/en/latest/ ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.4.16`` ``-Python-3.6.6`` ``foss/2018b`` ========== ================= ============== @@ -974,7 +996,7 @@ AMPtk is a series of scripts to process NGS amplicon data using USEARCH and VSEA *homepage*: https://amptk.readthedocs.io ========= ============== -version toolchain +version toolchain ========= ============== ``1.5.4`` ``foss/2021b`` ========= ============== @@ -990,7 +1012,7 @@ AmrPlusPlus v2.0 can process the raw data from the sequencer, identify the fragm *homepage*: https://megares.meglab.org/amrplusplus/latest/html/v2 ================ ============= -version toolchain +version toolchain ================ ============= ``2.0-20200114`` ``GCC/8.3.0`` ================ ============= @@ -1006,7 +1028,7 @@ The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for c *homepage*: https://www.scm.com/amsterdam-modeling-suite/ ============ ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= =============== ``2020.102`` ``-intelmpi`` ``iimpi/2020b`` ``2022.102`` ``-intelmpi`` ``iimpi/2021b`` @@ -1023,7 +1045,7 @@ Built to complement the rich, open source Python community, the Anaconda platfor *homepage*: https://www.anaconda.com =========== ========== -version toolchain +version toolchain =========== ========== ``4.0.0`` ``system`` ``4.2.0`` ``system`` @@ -1048,7 +1070,7 @@ Built to complement the rich, open source Python community, the Anaconda platfor *homepage*: https://www.anaconda.com =========== ========== -version toolchain +version toolchain =========== ========== ``4.0.0`` ``system`` ``4.2.0`` ``system`` @@ -1079,7 +1101,7 @@ Non-covalent interaction (NCI) for MD trajectories *homepage*: https://www.lct.jussieu.fr/pagesperso/contrera/nci-MD.html ======= ======================= -version toolchain +version toolchain ======= ======================= ``2.0`` ``iccifort/2019.5.281`` ======= ======================= @@ -1095,7 +1117,7 @@ This is the andi program for estimating the evolutionary distance between closel *homepage*: https://github.com/evolbioinf/andi/ ======== ============== -version toolchain +version toolchain ======== ============== ``0.13`` ``foss/2018b`` ======== ============== @@ -1111,7 +1133,7 @@ ANGEL: Robust Open Reading Frame prediction *homepage*: https://github.com/PacificBiosciences/ANGEL ======= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= ============== ``3.0`` ``-Python-3.7.2`` ``foss/2019a`` ======= ================= ============== @@ -1127,13 +1149,13 @@ Program for analysing NGS data. *homepage*: http://www.popgen.dk/angsd ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``0.910`` ``foss/2016a`` -``0.921`` ``foss/2018a`` -``0.925`` ``foss/2018b`` +``0.910`` ``foss/2016a`` +``0.921`` ``foss/2018a`` +``0.925`` ``foss/2018b`` ``0.933`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``0.935`` ``GCC/10.2.0`` +``0.935`` ``GCC/10.2.0`` ========= ====================================== @@ -1147,7 +1169,7 @@ This tool will calculate the bidirectional average nucleotide identity (gANI) an *homepage*: https://ani.jgi.doe.gov/html/home.php ======= ================== -version toolchain +version toolchain ======= ================== ``1.0`` ``GCCcore/10.3.0`` ======= ================== @@ -1163,7 +1185,7 @@ Annif is a multi-algorithm automated subject indexing tool for libraries, archiv *homepage*: https://github.com/NatLibFi/Annif ========== ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============================== ``0.40.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ========== ================= =============================== @@ -1179,10 +1201,10 @@ ANNOVAR is an efficient software tool to utilize update-to-date information to *homepage*: http://annovar.openbioinformatics.org/en/latest/ ============= ================ ================== -version versionsuffix toolchain +version versionsuffix toolchain ============= ================ ================== -``2016Feb01`` ``-Perl-5.22.1`` ``foss/2016a`` -``20191024`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``2016Feb01`` ``-Perl-5.22.1`` ``foss/2016a`` +``20191024`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` ``20200607`` ``-Perl-5.34.0`` ``GCCcore/11.2.0`` ============= ================ ================== @@ -1194,13 +1216,14 @@ version versionsuffix toolchain ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. -*homepage*: http://www.ansys.com +*homepage*: https://www.ansys.com -======== ========== -version toolchain -======== ========== -``15.0`` ``system`` -======== ========== +========== ========== +version toolchain +========== ========== +``15.0`` ``system`` +``2022R2`` ``system`` +========== ========== .. _list_software_ANSYS_CFD_698: @@ -1213,7 +1236,7 @@ ANSYS computational fluid dynamics (CFD) simulation software allows you to predi *homepage*: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics ======== ========== -version toolchain +version toolchain ======== ========== ``16.2`` ``system`` ``17.0`` ``system`` @@ -1230,7 +1253,7 @@ Apache Ant is a Java library and command-line tool whose mission is to drive pro *homepage*: http://ant.apache.org/ =========== =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain =========== =================== ========== ``1.8.4`` ``-Java-1.7.0_10`` ``system`` ``1.8.4`` ``-Java-1.7.0_21`` ``system`` @@ -1273,7 +1296,7 @@ antiSMASH allows the rapid genome-wide identification, annotation and analysis o *homepage*: https://github.com/antismash/antismash ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``5.1.2`` ``-Python-3.7.4`` ``foss/2019b`` ``5.2.0`` ``foss/2020b`` @@ -1291,14 +1314,14 @@ ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language to *homepage*: http://www.antlr2.org/ ========= ================== ==================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ==================================================================================================================== -``2.7.7`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b`` +``2.7.7`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b`` ``2.7.7`` ``-Java-11`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.7.7`` ``-Python-2.7.11`` ``foss/2016a`` -``2.7.7`` ``-Python-2.7.13`` ``intel/2017a`` -``2.7.7`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` -``2.7.7`` ``-Python-3.6.4`` ``intel/2018a`` +``2.7.7`` ``-Python-2.7.11`` ``foss/2016a`` +``2.7.7`` ``-Python-2.7.13`` ``intel/2017a`` +``2.7.7`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` +``2.7.7`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================== ==================================================================================================================== @@ -1312,13 +1335,13 @@ ANTs extracts information from complex datasets that include imaging. ANTs is us *homepage*: https://stnava.github.io/ANTs/ ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``2.2.0`` ``-Python-2.7.12`` ``foss/2016b`` +``2.2.0`` ``-Python-2.7.12`` ``foss/2016b`` ``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.3.1`` ``-Python-3.6.6`` ``foss/2018b`` -``2.3.2`` ``-Python-3.7.4`` ``foss/2019b`` -``2.3.5`` ``foss/2021a`` +``2.3.1`` ``-Python-3.6.6`` ``foss/2018b`` +``2.3.2`` ``-Python-3.7.4`` ``foss/2019b`` +``2.3.5`` ``foss/2021a`` ========= ================== =============================== @@ -1332,7 +1355,7 @@ An analysis and visualization platform for 'omics data. *homepage*: https://merenlab.org/software/anvio/ ======= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= =============== ``6.1`` ``-Python-3.7.4`` ``intel/2019b`` ======= ================= =============== @@ -1348,10 +1371,10 @@ Convert various sequence formats to FASTA *homepage*: https://github.com/tseemann/any2fasta ========= ================ ================================================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ================================================================================================ ``0.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.4.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``0.4.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` ========= ================ ================================================================================================ @@ -1365,12 +1388,13 @@ AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0 *homepage*: https://developer.amd.com/amd-aocc/ ========= ========================================================== -version toolchain +version toolchain ========= ========================================================== -``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.0.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.0.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``3.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``3.2.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``3.2.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.0.0`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========= ========================================================== @@ -1384,7 +1408,7 @@ AMD fork of LLVM, setup for OpenMP offloading to Accelerators *homepage*: https://github.com/ROCm-Developer-Tools/aomp ========== ===================================== -version toolchain +version toolchain ========== ===================================== ``13.0-2`` ``GCCcore/10.2.0``, ``gcccuda/2020a`` ========== ===================================== @@ -1400,7 +1424,7 @@ APBS is a software package for modeling biomolecular solvation through solutio *homepage*: http://www.poissonboltzmann.org/apbs ======= ======================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ======= ======================== ========== ``1.4`` ``-linux-static-x86_64`` ``system`` ======= ======================== ========== @@ -1416,7 +1440,7 @@ A PyTorch Extension: Tools for easy mixed precision and distributed training in *homepage*: https://github.com/nvidia/apex ============ ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ================== ``20200325`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``20210420`` ``fosscuda/2020b`` @@ -1432,12 +1456,12 @@ Apache Portable Runtime (APR) libraries. *homepage*: https://apr.apache.org/ -========= ================================================================================================ -version toolchain -========= ================================================================================================ -``1.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``iomkl/2018a`` -``1.7.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` -========= ================================================================================================ +========= ==================================================================================================================== +version toolchain +========= ==================================================================================================================== +``1.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``iomkl/2018a`` +``1.7.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +========= ==================================================================================================================== .. _list_software_APR-util_718: @@ -1449,11 +1473,11 @@ Apache Portable Runtime (APR) util libraries. *homepage*: http://apr.apache.org/ -========= ======================================================================================================================================================= -version toolchain -========= ======================================================================================================================================================= -``1.6.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``iomkl/2018a`` -========= ======================================================================================================================================================= +========= =========================================================================================================================================================================== +version toolchain +========= =========================================================================================================================================================================== +``1.6.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``iomkl/2018a`` +========= =========================================================================================================================================================================== .. _list_software_AptaSUITE_784: @@ -1466,7 +1490,7 @@ A full-featured bioinformatics software collection for the comprehensive analys *homepage*: https://drivenbyentropy.github.io/ ========= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========== ``0.9.4`` ``-Java-11`` ``system`` ========= ============= ========== @@ -1482,10 +1506,10 @@ a program to detect tRNA genes and tmRNA genes in nucleotide sequences *homepage*: http://www.ansikte.se/ARAGORN/ ========== ======================================= -version toolchain +version toolchain ========== ======================================= ``1.2.38`` ``foss/2016b``, ``iccifort/2019.5.281`` -``1.2.41`` ``foss/2021b`` +``1.2.41`` ``foss/2021b`` ========== ======================================= @@ -1499,12 +1523,12 @@ Arb is a C library for arbitrary-precision interval arithmetic. It has full sup *homepage*: https://arblib.org/ ========== ================================================================================ -version toolchain +version toolchain ========== ================================================================================ ``2.16.0`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` -``2.17.0`` ``GCC/8.3.0`` -``2.19.0`` ``GCC/10.3.0`` -``2.22.1`` ``GCC/11.2.0`` +``2.17.0`` ``GCC/8.3.0`` +``2.19.0`` ``GCC/10.3.0`` +``2.22.1`` ``GCC/11.2.0`` ========== ================================================================================ @@ -1518,7 +1542,7 @@ The Arcade Learning Environment (ALE) is a simple framework that allows research *homepage*: https://github.com/mgbellemare/Arcade-Learning-Environment ========= ============== -version toolchain +version toolchain ========= ============== ``0.7.3`` ``foss/2021b`` ========= ============== @@ -1534,7 +1558,7 @@ arcasHLA performs high resolution genotyping for HLA class I and class II genes *homepage*: https://github.com/RabadanLab/arcasHLA ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.2.0`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -1550,7 +1574,7 @@ Autoregressive Conditional Heteroskedasticity (ARCH) and other tools for financi *homepage*: https://pypi.org/project/arch ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``4.5.0`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== @@ -1566,7 +1590,7 @@ Provide an interface to ZIP archive files. *homepage*: https://metacpan.org/pod/Archive::Zip ======== ============================================================================== -version toolchain +version toolchain ======== ============================================================================== ``1.68`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ======== ============================================================================== @@ -1582,7 +1606,7 @@ ArchR is a full-featured R package for processing and analyzing single-cell ATAC *homepage*: https://www.archrproject.com ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.0.1`` ``-R-4.1.2`` ``foss/2021b`` ========= ============= ============== @@ -1598,12 +1622,13 @@ A library for detecting, labeling, and reasoning about microarchitectures *homepage*: https://github.com/archspec/archspec ========= ================= ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ====================================== -``0.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``0.1.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``0.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.1.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``0.1.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``0.1.3`` ``GCCcore/11.2.0`` +``0.1.3`` ``GCCcore/11.2.0`` +``0.1.4`` ``GCCcore/11.3.0`` ========= ================= ====================================== @@ -1617,7 +1642,7 @@ A parallel, multi-engine simulator for heterogeneous swarm robotics *homepage*: http://www.argos-sim.info ================ ============== ============== -version versionsuffix toolchain +version versionsuffix toolchain ================ ============== ============== ``3.0.0-beta53`` ``-Lua-5.2.4`` ``foss/2018b`` ``3.0.0-beta59`` ``GCC/11.2.0`` @@ -1634,7 +1659,7 @@ Argtable is an ANSI C library for parsing GNU style command line options with a *homepage*: http://argtable.sourceforge.net/ ======== ========================================================================================================================== -version toolchain +version toolchain ======== ========================================================================================================================== ``2.13`` ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` ======== ========================================================================================================================== @@ -1650,7 +1675,7 @@ aria2 is a lightweight multi-protocol & multi-source command-line download utili *homepage*: https://aria2.github.io ========== ================== -version toolchain +version toolchain ========== ================== ``1.35.0`` ``GCCcore/10.3.0`` ``1.36.0`` ``GCCcore/11.3.0`` @@ -1667,7 +1692,7 @@ Arlequin: An Integrated Software for Population Genetics Data Analysis *homepage*: http://cmpg.unibe.ch/software/arlequin35/Arlequin35.html =========== ============== -version toolchain +version toolchain =========== ============== ``3.5.2.2`` ``foss/2019b`` =========== ============== @@ -1683,19 +1708,19 @@ Armadillo is an open-source C++ linear algebra library (matrix maths) aiming tow *homepage*: https://arma.sourceforge.net/ =========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== =============================== -``7.600.2`` ``-Python-2.7.12`` ``foss/2016b`` -``7.800.0`` ``-Python-2.7.12`` ``intel/2016b`` -``7.950.1`` ``-Python-2.7.12`` ``intel/2016b`` +``7.600.2`` ``-Python-2.7.12`` ``foss/2016b`` +``7.800.0`` ``-Python-2.7.12`` ``intel/2016b`` +``7.950.1`` ``-Python-2.7.12`` ``intel/2016b`` ``8.300.1`` ``foss/2017b``, ``intel/2017b`` -``8.400.0`` ``foss/2018a`` -``9.600.5`` ``foss/2018b`` -``9.700.2`` ``foss/2019a`` -``9.880.1`` ``foss/2020a`` -``9.900.1`` ``foss/2019b``, ``foss/2020a`` -``10.5.3`` ``foss/2020b`` -``10.7.5`` ``foss/2021a`` +``8.400.0`` ``foss/2018a`` +``9.600.5`` ``foss/2018b`` +``9.700.2`` ``foss/2019a`` +``9.880.1`` ``foss/2020a`` +``9.900.1`` ``foss/2019b``, ``foss/2020a`` +``10.5.3`` ``foss/2020b`` +``10.7.5`` ``foss/2021a`` =========== ================== =============================== @@ -1709,7 +1734,7 @@ AROSICS is a python package to perform automatic subpixel co-registration of two *homepage*: https://github.com/GFZ/arosics ========= ============== -version toolchain +version toolchain ========= ============== ``1.7.6`` ``foss/2021a`` ========= ============== @@ -1725,7 +1750,7 @@ Arpackpp is a C++ interface to the ARPACK Fortran package, which implements the *homepage*: https://github.com/m-reuter/arpackpp ============== ============== -version toolchain +version toolchain ============== ============== ``2018.03.26`` ``foss/2017b`` ============== ============== @@ -1741,14 +1766,14 @@ ARPACK is a collection of Fortran77 subroutines designed to solve large scale ei *homepage*: https://github.com/opencollab/arpack-ng ========= ================================================================================ -version toolchain +version toolchain ========= ================================================================================ -``3.3.0`` ``foss/2016a``, ``intel/2016a`` -``3.4.0`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b``, ``intel/2017a`` +``3.3.0`` ``foss/2016a``, ``intel/2016a`` +``3.4.0`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b``, ``intel/2017a`` ``3.5.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b`` -``3.6.2`` ``intel/2018a`` +``3.6.2`` ``intel/2018a`` ``3.7.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` -``3.8.0`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` +``3.8.0`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a`` ========= ================================================================================ @@ -1762,7 +1787,7 @@ ArrayFire is a general-purpose library that simplifies the process of developin *homepage*: https://arrayfire.com/ ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``3.6.4`` ``foss/2018b`` ``3.6.4`` ``-CUDA-9.2.88`` ``foss/2018b`` @@ -1779,12 +1804,12 @@ Arriba is a command-line tool for the detection of gene fusions from RNA-Seq dat *homepage*: https://github.com/suhrig/arriba ========= ============================== -version toolchain +version toolchain ========= ============================== -``1.1.0`` ``foss/2018b`` +``1.1.0`` ``foss/2018b`` ``2.1.0`` ``GCC/10.2.0``, ``GCC/10.3.0`` -``2.2.1`` ``GCC/11.2.0`` -``2.3.0`` ``GCC/11.2.0`` +``2.2.1`` ``GCC/11.2.0`` +``2.3.0`` ``GCC/11.2.0`` ========= ============================== @@ -1798,17 +1823,17 @@ Apache Arrow (incl. PyArrow Python bindings), a cross-language development platf *homepage*: https://arrow.apache.org ========== ================== =================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =================================================== -``0.7.1`` ``-Python-3.6.3`` ``intel/2017b`` -``0.12.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``0.12.0`` ``-Python-3.6.6`` ``intel/2018b`` -``0.16.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.7.1`` ``-Python-3.6.3`` ``intel/2017b`` +``0.12.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.12.0`` ``-Python-3.6.6`` ``intel/2018b`` +``0.16.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``0.17.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``0.17.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``6.0.0`` ``foss/2021a``, ``foss/2021b`` -``6.0.1`` ``foss/2021a`` -``8.0.0`` ``foss/2022.05``, ``foss/2022a`` +``0.17.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``6.0.0`` ``foss/2021a``, ``foss/2021b`` +``6.0.1`` ``foss/2021a`` +``8.0.0`` ``foss/2022.05``, ``foss/2022a`` ========== ================== =================================================== @@ -1822,7 +1847,7 @@ R interface to the Apache Arrow C++ library *homepage*: https://cran.r-project.org/web/packages/arrow =========== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ============= ============== ``0.17.1`` ``-R-4.0.0`` ``foss/2020a`` ``6.0.0.2`` ``-R-4.1.0`` ``foss/2021a`` @@ -1842,7 +1867,7 @@ ART is a set of simulation tools to generate synthetic next-generation sequencin *homepage*: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ ============== ================================== -version toolchain +version toolchain ============== ================================== ``2016.06.05`` ``GCCcore/6.4.0``, ``intel/2016b`` ============== ================================== @@ -1858,7 +1883,7 @@ Initial implementation of an ARTIC bioinformatics platform for nanopore sequenc *homepage*: https://github.com/artic-network/artic-ncov2019 ============== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================= ============== ``2020.04.13`` ``-Python-3.6.6`` ``foss/2018b`` ``2021.06.24`` ``foss/2020b`` @@ -1875,7 +1900,7 @@ ARTS is a radiative transfer model for the millimeter and sub-millimeter spectr *homepage*: http://www.radiativetransfer.org/ ========== =============== -version toolchain +version toolchain ========== =============== ``2.2.64`` ``gompi/2019a`` ========== =============== @@ -1891,11 +1916,12 @@ Exploratory analysis of Bayesian models with Python *homepage*: https://github.com/arviz-devs/arviz ========== ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============================== ``0.7.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``0.11.1`` ``intel/2020b`` +``0.11.1`` ``intel/2020b`` ``0.11.4`` ``foss/2021b``, ``intel/2021b`` +``0.12.1`` ``foss/2022a``, ``intel/2022a`` ========== ================= =============================== @@ -1909,7 +1935,7 @@ ARWEN, tRNA detection in metazoan mitochondrial sequences *homepage*: http://mbio-serv2.mbioekol.lu.se/ARWEN ========= ================= -version toolchain +version toolchain ========= ================= ``1.2.3`` ``GCCcore/7.3.0`` ========= ================= @@ -1925,9 +1951,10 @@ ASAP focuses on fast and fluid image viewing with an easy-to-use interface for *homepage*: https://computationalpathologygroup.github.io/ASAP/ ======= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================ ============== ``2.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``2.1`` ``foss/2022a`` ======= ================ ============== @@ -1941,17 +1968,17 @@ ASAP is a calculator for doing large-scale classical molecular dynamics within t *homepage*: https://wiki.fysik.dtu.dk/asap/ =========== ================= ================================================ -version versionsuffix toolchain +version versionsuffix toolchain =========== ================= ================================================ -``3.10.7`` ``-Python-3.5.2`` ``foss/2016b`` -``3.10.7`` ``-Python-3.6.2`` ``foss/2017b`` -``3.10.8`` ``-Python-3.5.2`` ``foss/2016b`` -``3.10.8`` ``-Python-3.6.2`` ``foss/2017b`` -``3.10.8`` ``-Python-3.6.3`` ``foss/2017b`` +``3.10.7`` ``-Python-3.5.2`` ``foss/2016b`` +``3.10.7`` ``-Python-3.6.2`` ``foss/2017b`` +``3.10.8`` ``-Python-3.5.2`` ``foss/2016b`` +``3.10.8`` ``-Python-3.6.2`` ``foss/2017b`` +``3.10.8`` ``-Python-3.6.3`` ``foss/2017b`` ``3.10.10`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.11.10`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.12.2`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` -``3.12.7`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` +``3.11.10`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.12.2`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` +``3.12.7`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` =========== ================= ================================================ @@ -1965,34 +1992,34 @@ ASE is a python package providing an open source Atomic Simulation Environment *homepage*: https://wiki.fysik.dtu.dk/ase/ ============== ================== ==================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================== ==================================================================================== -``3.9.1.4567`` ``-Python-2.7.11`` ``intel/2016a`` -``3.10.0`` ``-Python-2.7.11`` ``intel/2016.02-GCC-4.9`` -``3.11.0`` ``-Python-2.7.12`` ``intel/2016b`` -``3.13.0`` ``-Python-2.7.12`` ``foss/2016b`` -``3.13.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.15.0`` ``-Python-2.7.12`` ``foss/2016b`` -``3.15.0`` ``-Python-2.7.14`` ``intel/2017b`` -``3.15.0`` ``-Python-3.5.2`` ``foss/2016b`` -``3.15.0`` ``-Python-3.6.2`` ``foss/2017b`` -``3.15.0`` ``-Python-3.6.3`` ``foss/2017b`` -``3.16.2`` ``-Python-3.6.4`` ``iomkl/2018.02``, ``iomkl/2018a`` -``3.16.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.17.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.17.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.18.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.18.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``3.19.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``3.20.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``3.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``3.20.1`` ``-Python-3.8.2`` ``intel/2020a`` -``3.21.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``3.21.1`` ``-Python-3.8.2`` ``foss/2020a`` +``3.9.1.4567`` ``-Python-2.7.11`` ``intel/2016a`` +``3.10.0`` ``-Python-2.7.11`` ``intel/2016.02-GCC-4.9`` +``3.11.0`` ``-Python-2.7.12`` ``intel/2016b`` +``3.13.0`` ``-Python-2.7.12`` ``foss/2016b`` +``3.13.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.15.0`` ``-Python-2.7.12`` ``foss/2016b`` +``3.15.0`` ``-Python-2.7.14`` ``intel/2017b`` +``3.15.0`` ``-Python-3.5.2`` ``foss/2016b`` +``3.15.0`` ``-Python-3.6.2`` ``foss/2017b`` +``3.15.0`` ``-Python-3.6.3`` ``foss/2017b`` +``3.16.2`` ``-Python-3.6.4`` ``iomkl/2018.02``, ``iomkl/2018a`` +``3.16.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``3.17.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``3.17.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.18.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.18.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.19.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``3.19.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``3.20.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``3.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.20.1`` ``-Python-3.8.2`` ``intel/2020a`` +``3.21.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``3.21.1`` ``-Python-3.8.2`` ``foss/2020a`` ``3.22.0`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021a`` -``3.22.1`` ``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` +``3.22.1`` ``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` ============== ================== ==================================================================================== @@ -2006,7 +2033,7 @@ Automatic Segmentation of Hippocampal Subfields (ASHS) *homepage*: https://sites.google.com/site/hipposubfields/home =================== ========== -version toolchain +version toolchain =================== ========== ``rev103_20140612`` ``system`` =================== ========== @@ -2022,7 +2049,7 @@ IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera too *homepage*: https://asperasoft.com ========= ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ========== ``3.7.2`` ``.354.010c3b8`` ``system`` ``3.9.0`` ``.1326.6985b21`` ``system`` @@ -2040,7 +2067,7 @@ Connect is an install-on-demand Web browser plug-in that facilitates high-speed *homepage*: http://downloads.asperasoft.com/connect2/ ========= ========== -version toolchain +version toolchain ========= ========== ``3.6.1`` ``system`` ``3.9.6`` ``system`` @@ -2057,7 +2084,7 @@ Open Asset Import Library (assimp) is a library to import and export various 3d *homepage*: https://github.com/assimp/assimp ========= ================= -version toolchain +version toolchain ========= ================= ``5.0.1`` ``GCCcore/8.3.0`` ========= ================= @@ -2073,7 +2100,7 @@ Assimulo is a simulation package for solving ordinary differential equations. *homepage*: https://jmodelica.org/assimulo/ ======= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== =============== ``2.9`` ``-Python-2.7.15`` ``intel/2018b`` ======= ================== =============== @@ -2089,7 +2116,7 @@ ASTRID-2 is a method for estimating species trees from gene trees. *homepage*: https://github.com/pranjalv123/ASTRID ========= =============== -version toolchain +version toolchain ========= =============== ``2.2.1`` ``gompi/2019a`` ========= =============== @@ -2100,20 +2127,21 @@ version toolchain *astropy* +++++++++ -The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages. +The Astropy Project is a community effort to develop a common core package for Astronomy in Python and foster an ecosystem of interoperable astronomy packages. The Astropy community is committed to supporting diversity and inclusion. *homepage*: https://www.astropy.org/ ========== ================== =============================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================================== -``2.0.12`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``2.0.14`` ``foss/2019a`` -``4.0.1`` ``-Python-3.7.4`` ``foss/2019b`` -``4.0.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``4.2.1`` ``intelcuda/2020b`` +``2.0.12`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``2.0.14`` ``foss/2019a`` +``4.0.1`` ``-Python-3.7.4`` ``foss/2019b`` +``4.0.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``4.2.1`` ``intelcuda/2020b`` ``4.3.1`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` -``5.0.4`` ``foss/2021a`` +``5.0.4`` ``foss/2021a`` +``5.1.1`` ``foss/2022a`` ========== ================== =============================================== @@ -2126,15 +2154,15 @@ AT-SPI 2 toolkit bridge *homepage*: https://wiki.gnome.org/Accessibility -========== ============================================================================== -version toolchain -========== ============================================================================== -``2.26.3`` ``fosscuda/2018b`` -``2.32.0`` ``GCCcore/8.2.0`` -``2.34.1`` ``GCCcore/8.3.0`` -``2.34.2`` ``GCCcore/9.3.0`` -``2.38.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -========== ============================================================================== +========== ================================================================================================== +version toolchain +========== ================================================================================================== +``2.26.3`` ``fosscuda/2018b`` +``2.32.0`` ``GCCcore/8.2.0`` +``2.34.1`` ``GCCcore/8.3.0`` +``2.34.2`` ``GCCcore/9.3.0`` +``2.38.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +========== ================================================================================================== .. _list_software_at-spi2-core_1110: @@ -2147,16 +2175,17 @@ Assistive Technology Service Provider Interface. *homepage*: https://wiki.gnome.org/Accessibility ========== ================== -version toolchain +version toolchain ========== ================== ``2.26.3`` ``fosscuda/2018b`` -``2.32.0`` ``GCCcore/8.2.0`` -``2.34.0`` ``GCCcore/8.3.0`` -``2.36.0`` ``GCCcore/9.3.0`` +``2.32.0`` ``GCCcore/8.2.0`` +``2.34.0`` ``GCCcore/8.3.0`` +``2.36.0`` ``GCCcore/9.3.0`` ``2.38.0`` ``GCCcore/10.2.0`` ``2.40.2`` ``GCCcore/10.3.0`` ``2.40.3`` ``GCCcore/11.2.0`` ``2.44.1`` ``GCCcore/11.3.0`` +``2.46.0`` ``GCCcore/12.2.0`` ========== ================== @@ -2170,19 +2199,19 @@ ATK provides the set of accessibility interfaces that are implemented by other *homepage*: https://developer.gnome.org/atk/ ========== ============================================================================= -version toolchain +version toolchain ========== ============================================================================= -``2.18.0`` ``intel/2016a`` -``2.20.0`` ``foss/2016a``, ``intel/2016a`` -``2.22.0`` ``foss/2016b``, ``intel/2016b`` -``2.26.0`` ``intel/2017a`` -``2.26.1`` ``foss/2018b``, ``intel/2017b`` -``2.27.1`` ``foss/2017b``, ``intel/2017b`` -``2.28.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a`` -``2.32.0`` ``GCCcore/8.2.0`` -``2.34.1`` ``GCCcore/8.3.0`` +``2.18.0`` ``intel/2016a`` +``2.20.0`` ``foss/2016a``, ``intel/2016a`` +``2.22.0`` ``foss/2016b``, ``intel/2016b`` +``2.26.0`` ``intel/2017a`` +``2.26.1`` ``foss/2018b``, ``intel/2017b`` +``2.27.1`` ``foss/2017b``, ``intel/2017b`` +``2.28.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a`` +``2.32.0`` ``GCCcore/8.2.0`` +``2.34.1`` ``GCCcore/8.3.0`` ``2.36.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``2.38.0`` ``GCCcore/11.3.0`` +``2.38.0`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========== ============================================================================= @@ -2196,7 +2225,7 @@ ATLAS (Automatically Tuned Linear Algebra Software) is the application of the A *homepage*: http://math-atlas.sourceforge.net ========== ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================== ``3.10.2`` ``-LAPACK-3.6.1`` ``GCC/5.4.0-2.26`` ========== ================= ================== @@ -2212,7 +2241,7 @@ atomate has implementations of FireWorks workflows for Materials Science. *homepage*: https://pythonhosted.org/atomate/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.4.4`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== @@ -2228,7 +2257,7 @@ AtomPAW is a Projector-Augmented Wave Dataset Generator that can be used both a *homepage*: http://users.wfu.edu/natalie/papers/pwpaw/man.html =========== =============== -version toolchain +version toolchain =========== =============== ``4.1.0.5`` ``intel/2018b`` ``4.1.0.6`` ``intel/2018b`` @@ -2245,12 +2274,12 @@ Tools to make using job arrays a lot more convenient. *homepage*: https://github.com/gjbex/atools ========= ================== ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ====================================== -``1.4.2`` ``-Python-2.7.12`` ``intel/2016b`` -``1.4.6`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +``1.4.2`` ``-Python-2.7.12`` ``intel/2016b`` +``1.4.6`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` ``1.4.8`` ``-Python-2.7.18`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.5.1`` ``GCCcore/11.2.0`` +``1.5.1`` ``GCCcore/11.2.0`` ========= ================== ====================================== @@ -2264,7 +2293,7 @@ Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. *homepage*: https://atropos.readthedocs.io ========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============== ``1.1.21`` ``-Python-3.6.6`` ``intel/2018b`` ========== ================= =============== @@ -2280,7 +2309,7 @@ ATSAS is a program suite for small-angle scattering data analysis from biologica *homepage*: http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html =========== =============== ========== -version versionsuffix toolchain +version versionsuffix toolchain =========== =============== ========== ``2.5.1-1`` ``.el6.x86_64`` ``system`` ``2.5.1-1`` ``.sl5.x86_64`` ``system`` @@ -2298,10 +2327,10 @@ Commands for Manipulating Filesystem Extended Attributes *homepage*: https://savannah.nongnu.org/projects/attr ========== ====================================== -version toolchain +version toolchain ========== ====================================== -``2.4.47`` ``GCCcore/8.2.0`` -``2.4.48`` ``GCCcore/9.3.0`` +``2.4.47`` ``GCCcore/8.2.0`` +``2.4.48`` ``GCCcore/9.3.0`` ``2.5.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ====================================== @@ -2316,12 +2345,28 @@ AttrDict is a Python library that provides mapping objects that allow their elem *homepage*: https://github.com/bcj/AttrDict ========= ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================= ``2.0.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========= ================= ================= +.. _list_software_attrdict3_914: + +*attrdict3* ++++++++++++ + +AttrDict is a Python library that provides mapping objects that allow their elements to be accessed both as keys and as attributes. + +*homepage*: https://github.com/pirofti/AttrDict3 + +========= ================== +version toolchain +========= ================== +``2.0.2`` ``GCCcore/11.2.0`` +========= ================== + + .. _list_software_augur_548: *augur* @@ -2332,7 +2377,7 @@ Pipeline components for real-time phylodynamic analysis *homepage*: https://github.com/nextstrain/augur ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``7.0.2`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================= =============== @@ -2348,15 +2393,15 @@ AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences *homepage*: https://bioinf.uni-greifswald.de/augustus/ ========= ================== ============================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============================================================== -``3.2.3`` ``-Python-2.7.13`` ``intel/2017a`` -``3.3`` ``foss/2018a`` -``3.3.2`` ``intel/2019a`` -``3.3.2`` ``-Python-2.7.13`` ``intel/2017a`` -``3.3.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``3.3.2`` ``-Python-2.7.15`` ``intel/2018b`` -``3.3.3`` ``foss/2019b``, ``intel/2019b`` +``3.2.3`` ``-Python-2.7.13`` ``intel/2017a`` +``3.3`` ``foss/2018a`` +``3.3.2`` ``intel/2019a`` +``3.3.2`` ``-Python-2.7.13`` ``intel/2017a`` +``3.3.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``3.3.2`` ``-Python-2.7.15`` ``intel/2018b`` +``3.3.3`` ``foss/2019b``, ``intel/2019b`` ``3.4.0`` ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` ========= ================== ============================================================== @@ -2371,7 +2416,7 @@ Austin is a Python frame stack sampler for CPython written in pure C. *homepage*: https://github.com/P403n1x87/austin ========= ============================== -version toolchain +version toolchain ========= ============================== ``3.2.0`` ``GCCcore/11.2.0``, ``system`` ========= ============================== @@ -2387,7 +2432,7 @@ AUTO is a publicly available software for continuation and bifurcation problems *homepage*: https://github.com/auto-07p ========= ============== -version toolchain +version toolchain ========= ============== ``0.9.3`` ``foss/2021a`` ========= ============== @@ -2403,11 +2448,11 @@ Autoconf is an extensible package of M4 macros that produce shell scripts to au *homepage*: https://www.gnu.org/software/autoconf/ ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= -version toolchain +version toolchain ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= -``2.68`` ``foss/2016b`` +``2.68`` ``foss/2016b`` ``2.69`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.71`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` +``2.71`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` ======== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= @@ -2421,10 +2466,10 @@ The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autocon *homepage*: https://www.gnu.org/software/autoconf-archive ============== ==================== -version toolchain +version toolchain ============== ==================== ``2019.01.06`` ``GCC/8.2.0-2.31.1`` -``2021.02.19`` ``GCCcore/10.2.0`` +``2021.02.19`` ``GCCcore/10.2.0`` ============== ==================== @@ -2438,9 +2483,9 @@ AutoDock is a suite of automated docking tools. It is designed to predict how s *homepage*: http://autodock.scripps.edu/ =========== ============== -version toolchain +version toolchain =========== ============== -``4.2.5.1`` ``GCC/5.2.0`` +``4.2.5.1`` ``GCC/5.2.0`` ``4.2.6`` ``GCC/10.3.0`` =========== ============== @@ -2455,7 +2500,7 @@ OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly *homepage*: https://github.com/ccsb-scripps/AutoDock-GPU ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``1.5.3`` ``-CUDA-11.3.1`` ``GCC/10.3.0`` ========= ================ ============== @@ -2471,9 +2516,9 @@ AutoDock Vina is an open-source program for doing molecular docking. *homepage*: https://vina.scripps.edu/ ========= ============== ============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============== ============================== -``1.1.2`` ``-linux_x86`` ``system`` +``1.1.2`` ``-linux_x86`` ``system`` ``1.2.3`` ``foss/2021a``, ``foss/2021b`` ========= ============== ============================== @@ -2488,7 +2533,7 @@ AutoGeneS automatically extracts informative genes and reveals the cellular hete *homepage*: https://github.com/theislab/AutoGeneS ========= ============== -version toolchain +version toolchain ========= ============== ``1.0.4`` ``foss/2020b`` ========= ============== @@ -2504,7 +2549,7 @@ AutoDock is a suite of automated docking tools. It is designed to predict how *homepage*: http://autodock.scripps.edu/ =========== ============= -version toolchain +version toolchain =========== ============= ``4.2.5.1`` ``GCC/5.2.0`` =========== ============= @@ -2520,18 +2565,18 @@ Automake: GNU Standards-compliant Makefile generator *homepage*: https://www.gnu.org/software/automake/automake.html ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain +version toolchain ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``1.11.3`` ``foss/2016b`` -``1.14`` ``GCC/4.8.2``, ``intel/2016a`` -``1.14.1`` ``GCC/4.8.2`` +``1.11.3`` ``foss/2016b`` +``1.14`` ``GCC/4.8.2``, ``intel/2016a`` +``1.14.1`` ``GCC/4.8.2`` ``1.15`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.15.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` -``1.16.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -``1.16.2`` ``GCCcore/10.2.0`` -``1.16.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` -``1.16.4`` ``GCCcore/11.2.0`` -``1.16.5`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` +``1.15.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +``1.16.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``1.16.2`` ``GCCcore/10.2.0`` +``1.16.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` +``1.16.4`` ``GCCcore/11.2.0`` +``1.16.5`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -2545,7 +2590,7 @@ Tool to find regions of homozygosity (ROHs) from sequencing data. *homepage*: https://github.com/mquinodo/AutoMap ======= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= ============== ``1.0`` ``-20200324`` ``foss/2019b`` ======= ============= ============== @@ -2561,7 +2606,7 @@ A tool that automatically formats Python code to conform to the PEP 8 style guid *homepage*: https://github.com/hhatto/autopep8 ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``1.4.4`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== @@ -2577,16 +2622,16 @@ This bundle collect the standard GNU build tools: Autoconf, Automake and libtoo *homepage*: https://autotools.io ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain +version toolchain ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``20150119`` ``GCC/4.9.2`` +``20150119`` ``GCC/4.9.2`` ``20150215`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``20170619`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` -``20180311`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -``20200321`` ``GCCcore/10.2.0`` -``20210128`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` -``20210726`` ``GCCcore/11.2.0`` -``20220317`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +``20170619`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` +``20180311`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``20200321`` ``GCCcore/10.2.0`` +``20210128`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` +``20210726`` ``GCCcore/11.2.0`` +``20220317`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -2600,7 +2645,7 @@ Avogadro is an advanced molecule editor and visualizer designed for cross-platfo *homepage*: https://two.avogadro.cc/index.html ========== ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ========== ``1.97.0`` ``-linux-x86_64`` ``system`` ========== ================= ========== @@ -2616,11 +2661,11 @@ Universal Command Line Environment for AWS *homepage*: https://pypi.python.org/pypi/awscli ============ ================== ================= -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ================= -``1.11.1`` ``-Python-2.7.12`` ``intel/2016b`` -``1.11.56`` ``-Python-2.7.12`` ``foss/2016b`` -``1.16.290`` ``-Python-3.6.6`` ``foss/2018b`` +``1.11.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.11.56`` ``-Python-2.7.12`` ``foss/2016b`` +``1.16.290`` ``-Python-3.6.6`` ``foss/2018b`` ``1.17.7`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``1.18.89`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``2.0.55`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` @@ -2633,7 +2678,7 @@ version versionsuffix toolchain --- -:ref:`list_software_BabelStream_1090` - :ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_Bambi_475` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_bamtofastq_1074` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_bcbio-gff_863` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BigDFT_496` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biom-format_1117` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_Blosc2_549` - :ref:`list_software_BLT_226` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_boost_histogram_1620` - :ref:`list_software_boto3_487` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_Brotli-python_1339` - :ref:`list_software_Brunsli_735` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_buildingspy_1194` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` +:ref:`list_software_BabelStream_1090` - :ref:`list_software_babl_401` - :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_BAli-Phy_694` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_Bambi_475` - :ref:`list_software_bamFilters_1033` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BAMSurgeon_947` - :ref:`list_software_bamtofastq_1074` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bashplotlib_1172` - :ref:`list_software_bat_311` - :ref:`list_software_BatMeth2_727` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_bcbio-gff_863` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl-convert_1119` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_Beagle_576` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_BEEF_274` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bgen_412` - :ref:`list_software_bgen-reader_1084` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_BiG-SCAPE_651` - :ref:`list_software_BigDFT_496` - :ref:`list_software_BinSanity_913` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-EUtilities_1352` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_Bio-SearchIO-hmmer_1659` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biogeme_728` - :ref:`list_software_biom-format_1117` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_BioPP_442` - :ref:`list_software_Biopython_956` - :ref:`list_software_BioServices_1118` - :ref:`list_software_BirdNET_616` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_Blosc2_549` - :ref:`list_software_BLT_226` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonito_619` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.MPI_795` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_boost_histogram_1620` - :ref:`list_software_boto3_487` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp_322` - :ref:`list_software_bpytop_670` - :ref:`list_software_Bracken_694` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_Brotli_620` - :ref:`list_software_Brotli-python_1339` - :ref:`list_software_Brunsli_735` - :ref:`list_software_bsddb3_562` - :ref:`list_software_BSMAPz_493` - :ref:`list_software_Bsoft_510` - :ref:`list_software_BSseeker2_838` - :ref:`list_software_BuDDy_440` - :ref:`list_software_BUFRLIB_518` - :ref:`list_software_buildenv_857` - :ref:`list_software_buildingspy_1194` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BUStools_795` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_byobu_545` - :ref:`list_software_bzip2_487` .. _list_software_BabelStream_1090: @@ -2646,7 +2691,7 @@ STREAM, for lots of devices written in many programming models *homepage*: https://uob-hpc.github.io/BabelStream ======= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= ============== ``3.4`` ``-omp`` ``GCC/11.2.0`` ======= ============= ============== @@ -2662,7 +2707,7 @@ babl is pixel encoding and color space conversion engine in C *homepage*: https://www.gegl.org/babl ========== ================== -version toolchain +version toolchain ========== ================== ``0.1.86`` ``GCCcore/10.3.0`` ========== ================== @@ -2677,13 +2722,13 @@ A fast algorithm for doing Bader's analysis on a charge density grid. *homepage*: http://theory.cm.utexas.edu/henkelman/code/bader/ -======== ======================= -version toolchain -======== ======================= -``1.02`` ``intel/2018a`` -``1.03`` ``intel/2018b`` -``1.04`` ``iccifort/2020.4.304`` -======== ======================= +======== ======================================= +version toolchain +======== ======================================= +``1.02`` ``intel/2018a`` +``1.03`` ``intel/2018b`` +``1.04`` ``GCC/11.2.0``, ``iccifort/2020.4.304`` +======== ======================================= .. _list_software_BAGEL_347: @@ -2696,7 +2741,7 @@ BAGEL (Brilliantly Advanced General Electronic-structure Library) is a parallel *homepage*: http://www.nubakery.org ========= =============== -version toolchain +version toolchain ========= =============== ``1.1.1`` ``intel/2016b`` ========= =============== @@ -2712,7 +2757,7 @@ BAli-Phy estimates multiple sequence alignments and evolutionary trees from DNA, *homepage*: http://www.bali-phy.org/ ========= ========== -version toolchain +version toolchain ========= ========== ``3.6.0`` ``system`` ========= ========== @@ -2728,7 +2773,7 @@ Count DNA sequence reads in BAM files *homepage*: https://github.com/genome/bam-readcount ========= ============================================= -version toolchain +version toolchain ========= ============================================= ``0.8.0`` ``GCC/11.2.0``, ``GCC/9.3.0``, ``foss/2018b`` ========= ============================================= @@ -2744,12 +2789,28 @@ Bambi is a high-level Bayesian model-building interface written in Python. It wo *homepage*: https://bambinos.github.io/bambi ========= =============================== -version toolchain +version toolchain ========= =============================== ``0.7.1`` ``foss/2021b``, ``intel/2021b`` ========= =============================== +.. _list_software_bamFilters_1033: + +*bamFilters* +++++++++++++ + +A utility tool to filter alignments from bam files, using identity percent, low complexity and read coverage. + +*homepage*: https://github.com/institut-de-genomique/bamFilters + +============== ============== +version toolchain +============== ============== +``2022-06-30`` ``GCC/11.3.0`` +============== ============== + + .. _list_software_BAMM_285: *BAMM* @@ -2760,7 +2821,7 @@ BAMM is oriented entirely towards detecting and quantifying heterogeneity in evo *homepage*: http://bamm-project.org/ ========= ============== -version toolchain +version toolchain ========= ============== ``2.5.0`` ``foss/2016b`` ========= ============== @@ -2776,7 +2837,7 @@ BamM is a c library, wrapped in python, that parses BAM files *homepage*: http://ecogenomics.github.io/BamM/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``1.7.3`` ``-Python-2.7.12`` ``foss/2016b`` ``1.7.3`` ``-Python-2.7.14`` ``foss/2018a`` @@ -2793,7 +2854,7 @@ Tools for adding mutations to existing .bam files, used for testing mutation cal *homepage*: https://github.com/adamewing/bamsurgeon ======= ================== ============= -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== ============= ``1.2`` ``-Python-2.7.16`` ``GCC/8.3.0`` ======= ================== ============= @@ -2809,7 +2870,7 @@ Convert 10x BAM files to the original FASTQs compatible with 10x pipelines. *homepage*: https://github.com/10XGenomics/bamtofastq ========= ================== -version toolchain +version toolchain ========= ================== ``1.4.0`` ``GCCcore/10.3.0`` ========= ================== @@ -2825,13 +2886,13 @@ BamTools provides both a programmer's API and an end-user's toolkit for handling *homepage*: https://github.com/pezmaster31/bamtools ========= ================================================================================================================================================================================================================================================ -version toolchain +version toolchain ========= ================================================================================================================================================================================================================================================ -``2.4.0`` ``foss/2016b`` -``2.4.1`` ``intel/2017a`` -``2.5.0`` ``foss/2016b``, ``intel/2017b`` +``2.4.0`` ``foss/2016b`` +``2.4.1`` ``intel/2017a`` +``2.5.0`` ``foss/2016b``, ``intel/2017b`` ``2.5.1`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018b`` -``2.5.2`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +``2.5.2`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` ========= ================================================================================================================================================================================================================================================ @@ -2845,7 +2906,7 @@ BamUtil is a repository that contains several programs that perform operations *homepage*: http://genome.sph.umich.edu/wiki/BamUtil ========== =============== -version toolchain +version toolchain ========== =============== ``1.0.13`` ``intel/2016b`` ``1.0.14`` ``intel/2018a`` @@ -2862,10 +2923,10 @@ Bandage is a program for visualising de novo assembly graphs *homepage*: http://rrwick.github.io/Bandage ========= ============= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ================== -``0.8.1`` ``_Centos`` ``system`` -``0.8.1`` ``_Ubuntu`` ``system`` +``0.8.1`` ``_Centos`` ``system`` +``0.8.1`` ``_Ubuntu`` ``system`` ``0.9.0`` ``GCCcore/11.2.0`` ========= ============= ================== @@ -2880,7 +2941,7 @@ Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal *homepage*: https://github.com/tseemann/barrnap ======= ====================================================================== -version toolchain +version toolchain ======= ====================================================================== ``0.9`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2020b``, ``gompi/2021b`` ======= ====================================================================== @@ -2891,18 +2952,19 @@ version toolchain *basemap* +++++++++ -The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python +The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python *homepage*: https://matplotlib.org/basemap/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.0.7`` ``-Python-2.7.13`` ``intel/2017a`` ``1.0.7`` ``-Python-3.6.3`` ``intel/2017b`` ``1.0.7`` ``-Python-3.6.4`` ``intel/2018a`` ``1.2.0`` ``-Python-3.6.6`` ``intel/2018b`` -``1.2.2`` ``-Python-3.8.2`` ``foss/2020a`` +``1.2.2`` ``-Python-3.8.2`` ``foss/2020a`` +``1.3.6`` ``foss/2022a`` ========= ================== =============== @@ -2916,7 +2978,7 @@ Bash is an sh-compatible command language interpreter that executes commands *homepage*: http://www.gnu.org/software/bash ======= ============= -version toolchain +version toolchain ======= ============= ``4.3`` ``GCC/4.9.2`` ======= ============= @@ -2932,7 +2994,7 @@ bashplotlib is a python package and command line tool for making basic plots in *homepage*: https://github.com/glamp/bashplotlib ========= ================== -version toolchain +version toolchain ========= ================== ``0.6.5`` ``GCCcore/10.3.0`` ========= ================== @@ -2948,7 +3010,7 @@ The BAT Python package supports the processing and analysis of Bro data with Pan *homepage*: https://pypi.python.org/pypi/bat ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.3.3`` ``-Python-3.6.3`` ``intel/2017b`` ========= ================= =============== @@ -2964,7 +3026,7 @@ An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sen *homepage*: https://github.com/GuoliangLi-HZAU/BatMeth2 ======= ============== -version toolchain +version toolchain ======= ============== ``2.1`` ``foss/2019b`` ======= ============== @@ -2980,7 +3042,7 @@ BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes *homepage*: http://www.rannala.org/?page_id=245 ========= ============== -version toolchain +version toolchain ========= ============== ``3.0.4`` ``foss/2016a`` ========= ============== @@ -2996,7 +3058,7 @@ BayeScan aims at identifying candidate loci under natural selection from genetic *homepage*: http://cmpg.unibe.ch/software/BayeScan/ ======= =============================================== -version toolchain +version toolchain ======= =============================================== ``2.1`` ``foss/2016a``, ``foss/2018a``, ``intel/2018a`` ======= =============================================== @@ -3012,7 +3074,7 @@ BayeScEnv is a Fst-based, genome-scan method that uses environmental variables t *homepage*: https://github.com/devillemereuil/bayescenv ======= ====================================================== -version toolchain +version toolchain ======= ====================================================== ``1.1`` ``GCC/8.3.0``, ``foss/2016a``, ``iccifort/2019.5.281`` ======= ====================================================== @@ -3028,7 +3090,7 @@ BayesTraits is a computer package for performing analyses of trait evolution a *homepage*: http://www.evolution.reading.ac.uk/BayesTraitsV1.html =============== ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain =============== ================= ========== ``1.0-linux32`` ``system`` ``2.0`` ``-Beta-Linux64`` ``system`` @@ -3045,29 +3107,29 @@ Bazel is a build tool that builds code quickly and reliably. It is used to build *homepage*: https://bazel.io/ ========== ============= ============================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ============================================================================= -``0.4.4`` ``system`` -``0.7.0`` ``GCCcore/6.4.0`` -``0.10.0`` ``GCCcore/6.4.0`` -``0.11.0`` ``GCCcore/6.4.0`` -``0.11.1`` ``GCCcore/6.4.0`` -``0.12.0`` ``GCCcore/6.4.0`` -``0.16.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``0.18.0`` ``GCCcore/7.3.0`` -``0.20.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``0.25.2`` ``GCCcore/8.2.0`` -``0.26.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.29.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.29.1`` ``-Java-1.8`` ``GCCcore/9.3.0`` -``1.1.0`` ``GCCcore/8.3.0`` -``2.0.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` -``3.4.1`` ``GCCcore/8.3.0`` -``3.6.0`` ``GCCcore/9.3.0`` -``3.7.1`` ``GCCcore/8.3.0`` +``0.4.4`` ``system`` +``0.7.0`` ``GCCcore/6.4.0`` +``0.10.0`` ``GCCcore/6.4.0`` +``0.11.0`` ``GCCcore/6.4.0`` +``0.11.1`` ``GCCcore/6.4.0`` +``0.12.0`` ``GCCcore/6.4.0`` +``0.16.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``0.18.0`` ``GCCcore/7.3.0`` +``0.20.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``0.25.2`` ``GCCcore/8.2.0`` +``0.26.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.29.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.29.1`` ``-Java-1.8`` ``GCCcore/9.3.0`` +``1.1.0`` ``GCCcore/8.3.0`` +``2.0.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +``3.4.1`` ``GCCcore/8.3.0`` +``3.6.0`` ``GCCcore/9.3.0`` +``3.7.1`` ``GCCcore/8.3.0`` ``3.7.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` -``4.2.2`` ``GCCcore/11.2.0`` -``5.1.1`` ``GCCcore/11.3.0`` +``4.2.2`` ``GCCcore/11.2.0`` +``5.1.1`` ``GCCcore/11.3.0`` ========== ============= ============================================================================= @@ -3081,7 +3143,7 @@ BBCP is an alternative to Gridftp when transferring large amounts of data, capa *homepage*: http://www.slac.stanford.edu/~abh/bbcp/ ================= ================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ================= ================== ========== ``12.01.30.00.0`` ``-amd64_linux26`` ``system`` ================= ================== ========== @@ -3097,7 +3159,7 @@ bbFTP is a file transfer software. It implements its own transfer protocol, wh *homepage*: https://software.in2p3.fr/bbftp/ ========= ============================================== -version toolchain +version toolchain ========= ============================================== ``3.2.1`` ``GCCcore/9.3.0``, ``intel/2016a``, ``system`` ========= ============================================== @@ -3113,18 +3175,19 @@ BBMap short read aligner, and other bioinformatic tools. *homepage*: https://sourceforge.net/projects/bbmap/ ========== =================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== =================== =============================== -``36.62`` ``-Java-1.8.0_112`` ``intel/2016b`` +``36.62`` ``-Java-1.8.0_112`` ``intel/2016b`` ``37.93`` ``foss/2018a``, ``intel/2018a`` -``38.26`` ``foss/2018b`` -``38.50b`` ``GCC/8.2.0-2.31.1`` -``38.76`` ``GCC/8.2.0-2.31.1`` -``38.79`` ``GCC/8.3.0`` -``38.87`` ``iccifort/2020.1.217`` -``38.90`` ``GCC/10.2.0``, ``GCC/9.3.0`` -``38.96`` ``GCC/10.3.0`` -``38.98`` ``GCC/11.2.0`` +``38.26`` ``foss/2018b`` +``38.50b`` ``GCC/8.2.0-2.31.1`` +``38.76`` ``GCC/8.2.0-2.31.1`` +``38.79`` ``GCC/8.3.0`` +``38.87`` ``iccifort/2020.1.217`` +``38.90`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``38.96`` ``GCC/10.3.0`` +``38.98`` ``GCC/11.2.0`` +``39.01`` ``GCC/11.3.0`` ========== =================== =============================== @@ -3138,7 +3201,7 @@ bc is an arbitrary precision numeric processing language. *homepage*: https://www.gnu.org/software/bc/ =========== ============= -version toolchain +version toolchain =========== ============= ``1.06.95`` ``GCC/4.8.2`` =========== ============= @@ -3154,7 +3217,7 @@ de Bruijn graph compaction in low memory *homepage*: https://github.com/GATB/bcalm ========= ============== -version toolchain +version toolchain ========= ============== ``2.2.0`` ``foss/2018a`` ========= ============== @@ -3170,7 +3233,7 @@ Read and write Generic Feature Format (GFF) with Biopython integration. *homepage*: https://github.com/chapmanb/bcbb/tree/master/gff ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.6.6`` ``-Python-3.8.2`` ``foss/2020a`` ``0.6.7`` ``foss/2021a`` @@ -3187,7 +3250,7 @@ The Byte Code Engineering Library (Apache Commons BCEL™) is intended to give *homepage*: https://commons.apache.org/proper/commons-bcel/ ========= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========== ``5.2`` ``-Java-1.8`` ``system`` ``6.5.0`` ``-Java-1.8`` ``system`` @@ -3204,18 +3267,18 @@ Samtools is a suite of programs for interacting with high-throughput sequencing *homepage*: http://www.htslib.org/ ========== ========================================================================================= -version toolchain +version toolchain ========== ========================================================================================= -``1.3`` ``foss/2016a``, ``intel/2016a`` -``1.3.1`` ``foss/2016b`` -``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` -``1.8`` ``GCC/6.4.0-2.28`` +``1.3`` ``foss/2016a``, ``intel/2016a`` +``1.3.1`` ``foss/2016b`` +``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` +``1.8`` ``GCC/6.4.0-2.28`` ``1.9`` ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` -``1.11`` ``GCC/10.2.0`` -``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` -``1.14`` ``GCC/11.2.0`` -``1.15.1`` ``GCC/11.3.0`` +``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` +``1.11`` ``GCC/10.2.0`` +``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` +``1.14`` ``GCC/11.2.0`` +``1.15.1`` ``GCC/11.3.0`` ========== ========================================================================================= @@ -3229,13 +3292,29 @@ Automatized phylogenetic tree building from bacterial core genomes. *homepage*: https://github.com/molbiodiv/bcgTree ========== ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================ =============== ``1.0.10`` ``-Perl-5.26.1`` ``intel/2018a`` ``1.1.0`` ``-Perl-5.28.0`` ``intel/2018b`` ========== ================ =============== +.. _list_software_bcl-convert_1119: + +*bcl-convert* ++++++++++++++ + +The Illumina BCL Convert v4.0 is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files. + +*homepage*: https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html + +=========== ============== ========== +version versionsuffix toolchain +=========== ============== ========== +``4.0.3-2`` ``el7.x86_64`` ``system`` +=========== ============== ========== + + .. _list_software_bcl2fastq2_948: *bcl2fastq2* @@ -3246,12 +3325,12 @@ bcl2fastq Conversion Software both demultiplexes data and converts BCL files gen *homepage*: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html ========== ================== ============================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ============================================================================================================= -``2.19.1`` ``-Python-2.7.12`` ``foss/2016b`` +``2.19.1`` ``-Python-2.7.12`` ``foss/2016b`` ``2.20.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``intel/2019a`` -``2.20.0`` ``-Python-2.7.12`` ``foss/2016b`` -``2.20.0`` ``-Python-2.7.14`` ``intel/2017b`` +``2.20.0`` ``-Python-2.7.12`` ``foss/2016b`` +``2.20.0`` ``-Python-2.7.14`` ``intel/2017b`` ========== ================== ============================================================================================================= @@ -3265,7 +3344,7 @@ bcolz provides columnar, chunked data containers that can be compressed either i *homepage*: https://bcolz.blosc.org/en/latest/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``1.1.1`` ``-Python-2.7.13`` ``foss/2017a`` ``1.2.1`` ``foss/2020b`` @@ -3283,7 +3362,7 @@ The bdbag utilities are a collection of software programs for working with BagIt *homepage*: https://github.com/fair-research/bdbag ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.4.1`` ``-Python-2.7.14`` ``intel/2018a`` ``1.4.1`` ``-Python-3.6.4`` ``intel/2018a`` @@ -3291,6 +3370,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_Beagle_576: + +*Beagle* +++++++++ + +Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. + +*homepage*: https://faculty.washington.edu/browning/beagle/beagle.html + +=================== ============= ========== +version versionsuffix toolchain +=================== ============= ========== +``5.4.22Jul22.46e`` ``-Java-11`` ``system`` +=================== ============= ========== + + .. _list_software_beagle-lib_964: *beagle-lib* @@ -3301,12 +3396,12 @@ beagle-lib is a high-performance library that can perform the core calculations *homepage*: https://github.com/beagle-dev/beagle-lib ========= ================ ================================================================================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ================================================================================================================================ -``2.1.2`` ``foss/2016a``, ``foss/2017a`` -``3.0.1`` ``foss/2018a``, ``intel/2018a`` -``3.0.2`` ``foss/2018b`` -``3.0.2`` ``-CUDA-9.2.88`` ``foss/2018b`` +``2.1.2`` ``foss/2016a``, ``foss/2017a`` +``3.0.1`` ``foss/2018a``, ``intel/2018a`` +``3.0.2`` ``foss/2018b`` +``3.0.2`` ``-CUDA-9.2.88`` ``foss/2018b`` ``3.1.2`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0``, ``gcccuda/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ========= ================ ================================================================================================================================ @@ -3321,19 +3416,19 @@ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequ *homepage*: http://beast2.org ========== ==================================== -version toolchain +version toolchain ========== ==================================== -``1.8.4`` ``system`` -``1.10.1`` ``intel/2018a`` +``1.8.4`` ``system`` +``1.10.1`` ``intel/2018a`` ``1.10.4`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1`` -``2.4.0`` ``foss/2016a`` -``2.4.7`` ``foss/2017a`` -``2.5.0`` ``foss/2018a`` -``2.5.1`` ``foss/2018b`` -``2.5.2`` ``GCC/8.2.0-2.31.1`` -``2.6.3`` ``gcccuda/2019b`` -``2.6.4`` ``GCC/10.2.0`` -``2.6.7`` ``GCC/10.3.0`` +``2.4.0`` ``foss/2016a`` +``2.4.7`` ``foss/2017a`` +``2.5.0`` ``foss/2018a`` +``2.5.1`` ``foss/2018b`` +``2.5.2`` ``GCC/8.2.0-2.31.1`` +``2.6.3`` ``gcccuda/2019b`` +``2.6.4`` ``GCC/10.2.0`` +``2.6.7`` ``GCC/10.3.0`` ========== ==================================== @@ -3347,15 +3442,15 @@ Beautiful Soup is a Python library designed for quick turnaround projects like s *homepage*: https://www.crummy.com/software/BeautifulSoup ========== ================= ========================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ========================================================== -``4.6.0`` ``-Python-3.6.3`` ``intel/2017b`` -``4.6.3`` ``-Python-3.6.4`` ``intel/2018a`` -``4.7.1`` ``-Python-3.6.6`` ``intel/2018b`` -``4.8.0`` ``GCCcore/8.2.0`` -``4.9.1`` ``GCCcore/8.3.0`` -``4.9.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``4.9.3`` ``GCCcore/10.2.0`` +``4.6.0`` ``-Python-3.6.3`` ``intel/2017b`` +``4.6.3`` ``-Python-3.6.4`` ``intel/2018a`` +``4.7.1`` ``-Python-3.6.6`` ``intel/2018b`` +``4.8.0`` ``GCCcore/8.2.0`` +``4.9.1`` ``GCCcore/8.3.0`` +``4.9.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``4.9.3`` ``GCCcore/10.2.0`` ``4.10.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ================= ========================================================== @@ -3370,15 +3465,16 @@ BEDOPS is an open-source command-line toolkit that performs highly efficient and *homepage*: http://bedops.readthedocs.io/en/latest/index.html ========== =============================== -version toolchain +version toolchain ========== =============================== -``2.4.1`` ``GCC/4.8.4`` -``2.4.2`` ``GCC/4.8.2`` -``2.4.20`` ``system`` -``2.4.26`` ``system`` -``2.4.30`` ``foss/2016b`` +``2.4.1`` ``GCC/4.8.4`` +``2.4.2`` ``GCC/4.8.2`` +``2.4.20`` ``system`` +``2.4.26`` ``system`` +``2.4.30`` ``foss/2016b`` ``2.4.32`` ``foss/2018a``, ``intel/2018a`` -``2.4.35`` ``foss/2018b`` +``2.4.35`` ``foss/2018b`` +``2.4.41`` ``foss/2021b`` ========== =============================== @@ -3392,13 +3488,13 @@ BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow *homepage*: https://bedtools.readthedocs.io/ ========== ======================================================================================= -version toolchain +version toolchain ========== ======================================================================================= -``2.25.0`` ``foss/2016a`` -``2.26.0`` ``GCCcore/6.4.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``2.27.1`` ``GCCcore/6.4.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` -``2.28.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2.29.2`` ``GCC/8.3.0``, ``GCC/9.3.0`` +``2.25.0`` ``foss/2016a`` +``2.26.0`` ``GCCcore/6.4.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +``2.27.1`` ``GCCcore/6.4.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` +``2.28.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.29.2`` ``GCC/8.3.0``, ``GCC/9.3.0`` ``2.30.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``iccifort/2020.4.304`` ========== ======================================================================================= @@ -3413,7 +3509,7 @@ BEEF is a library-based implementation of the Bayesian Error Estimation Function *homepage*: https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software ========= ================================================ -version toolchain +version toolchain ========= ================================================ ``0.1.1`` ``iccifort/2019.5.281``, ``iccifort/2020.4.304`` ========= ================================================ @@ -3429,9 +3525,9 @@ behave: Behavior-driven development (or BDD) is an agile software development te *homepage*: http://pythonhosted.org/behave ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== -``1.2.5`` ``-Python-2.7.12`` ``foss/2016b`` +``1.2.5`` ``-Python-2.7.12`` ``foss/2016b`` ``1.2.6`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================== =============== @@ -3446,14 +3542,14 @@ The BerkeleyGW Package is a set of computer codes that calculates the quasiparti *homepage*: https://www.berkeleygw.org ============= ================= ================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ============= ================= ================================================================ -``1.0.6`` ``intel/2016.02-GCC-4.9`` -``1.1-beta2`` ``intel/2016.02-GCC-4.9`` -``1.2.0`` ``intel/2017a``, ``intel/2018a`` +``1.0.6`` ``intel/2016.02-GCC-4.9`` +``1.1-beta2`` ``intel/2016.02-GCC-4.9`` +``1.2.0`` ``intel/2017a``, ``intel/2018a`` ``2.0.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` -``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``3.0.1`` ``foss/2020b``, ``foss/2021a`` +``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.0.1`` ``foss/2020b``, ``foss/2021a`` ============= ================= ================================================================ @@ -3467,7 +3563,7 @@ BFAST facilitates the fast and accurate mapping of short reads to reference sequ *homepage*: http://bfast.sourceforge.net/ ========== ============== -version toolchain +version toolchain ========== ============== ``0.7.0a`` ``foss/2016b`` ========== ============== @@ -3483,7 +3579,7 @@ BFC is a standalone high-performance tool for correcting sequencing errors from *homepage*: https://github.com/lh3/bfc ======= ============== -version toolchain +version toolchain ======= ============== ``1`` ``foss/2018a`` ======= ============== @@ -3499,10 +3595,10 @@ A BGEN file format reader. It fully supports the BGEN format specifications 1.2 *homepage*: https://github.com/limix/bgen ========= ================== -version toolchain +version toolchain ========= ================== -``3.0.2`` ``GCCcore/7.3.0`` -``3.0.3`` ``GCCcore/9.3.0`` +``3.0.2`` ``GCCcore/7.3.0`` +``3.0.3`` ``GCCcore/9.3.0`` ``4.1.3`` ``GCCcore/10.2.0`` ========= ================== @@ -3517,7 +3613,7 @@ A bgen file format reader. This python package is a wrapper around the bgen libr *homepage*: https://github.com/limix/bgen-reader-py ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== @@ -3533,7 +3629,7 @@ Bibtex parser in Python 2.7 and 3.x *homepage*: https://github.com/sciunto-org/python-bibtexparser ========= ================= -version toolchain +version toolchain ========= ================= ``1.1.0`` ``GCCcore/8.2.0`` ========= ================= @@ -3549,7 +3645,7 @@ BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynt *homepage*: https://bigscape-corason.secondarymetabolites.org/index.html ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``1.0.1`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================= =============== @@ -3565,7 +3661,7 @@ BigDFT: electronic structure calculation based on Daubechies wavelets. bigdft-su *homepage*: https://gitlab.com/l_sim/bigdft-suite ========= ============== -version toolchain +version toolchain ========= ============== ``1.9.1`` ``foss/2021b`` ========= ============== @@ -3581,7 +3677,7 @@ BinSanity contains a suite a scripts designed to cluster contigs generated from *homepage*: https://github.com/edgraham/BinSanity/wiki ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.3.5`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -3597,23 +3693,23 @@ binutils: GNU binary utilities *homepage*: https://directory.fsf.org/project/binutils/ ========== ======================================================================================================================================================================================== -version toolchain +version toolchain ========== ======================================================================================================================================================================================== ``2.25`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``system`` -``2.25.1`` ``system`` -``2.26`` ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``system`` -``2.27`` ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``system`` -``2.28`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``system`` -``2.29`` ``GCCcore/7.2.0``, ``GCCcore/system``, ``system`` -``2.30`` ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``system`` -``2.31.1`` ``GCCcore/7.4.0``, ``GCCcore/8.2.0``, ``system`` -``2.32`` ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` -``2.34`` ``GCCcore/10.1.0``, ``GCCcore/9.3.0``, ``system`` -``2.35`` ``GCCcore/10.2.0``, ``system`` -``2.36.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/8.4.0``, ``GCCcore/9.4.0``, ``system`` -``2.37`` ``GCCcore/11.2.0``, ``system`` -``2.38`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.5.0``, ``system`` -``2.39`` ``GCCcore/12.2.0``, ``system`` +``2.25.1`` ``system`` +``2.26`` ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``system`` +``2.27`` ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``system`` +``2.28`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``system`` +``2.29`` ``GCCcore/7.2.0``, ``GCCcore/system``, ``system`` +``2.30`` ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``system`` +``2.31.1`` ``GCCcore/7.4.0``, ``GCCcore/8.2.0``, ``system`` +``2.32`` ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` +``2.34`` ``GCCcore/10.1.0``, ``GCCcore/9.3.0``, ``system`` +``2.35`` ``GCCcore/10.2.0``, ``system`` +``2.36.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/8.4.0``, ``GCCcore/9.4.0``, ``system`` +``2.37`` ``GCCcore/11.2.0``, ``system`` +``2.38`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/9.5.0``, ``system`` +``2.39`` ``GCCcore/12.2.0``, ``system`` ========== ======================================================================================================================================================================================== @@ -3627,13 +3723,13 @@ Read files using HTSlib including BAM/CRAM, Tabix and BCF database files *homepage*: https://metacpan.org/release/Bio-DB-HTS ======== ================ ============================================== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================ ============================================== -``2.11`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``2.11`` ``-Perl-5.26.1`` ``intel/2018a`` -``2.11`` ``-Perl-5.28.0`` ``foss/2018b`` +``2.11`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``2.11`` ``-Perl-5.26.1`` ``intel/2018a`` +``2.11`` ``-Perl-5.28.0`` ``foss/2018b`` ``3.01`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` -``3.01`` ``-Perl-5.28.1`` ``GCC/8.2.0-2.31.1`` +``3.01`` ``-Perl-5.28.1`` ``GCC/8.2.0-2.31.1`` ======== ================ ============================================== @@ -3647,7 +3743,7 @@ BioPerl low-level API for retrieving and storing data from NCBI eUtils *homepage*: https://github.com/bioperl/bio-eutilities ======== ================= -version toolchain +version toolchain ======== ================= ``1.76`` ``GCCcore/8.3.0`` ======== ================= @@ -3663,7 +3759,7 @@ This is a Perl interface to the SAMtools sequence alignment interface. *homepage*: http://search.cpan.org/~lds/Bio-SamTools/ ======== ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================ =============== ``1.43`` ``-Perl-5.24.1`` ``intel/2017a`` ======== ================ =============== @@ -3679,7 +3775,7 @@ Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with *homepage*: https://metacpan.org/pod/Bio::SearchIO::hmmer3 ========= ============================== -version toolchain +version toolchain ========= ============================== ``1.7.3`` ``GCC/10.2.0``, ``GCC/10.3.0`` ========= ============================== @@ -3695,7 +3791,7 @@ Bioawk is an extension to Brian Kernighan's awk, adding the support of several *homepage*: https://github.com/lh3/bioawk ======= ============================================== -version toolchain +version toolchain ======= ============================================== ``1.0`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``foss/2018b`` ======= ============================================== @@ -3711,7 +3807,7 @@ Tools for processing BAM files *homepage*: https://github.com/gt1/biobambam2 ========== =============== -version toolchain +version toolchain ========== =============== ``2.0.87`` ``intel/2018a`` ========== =============== @@ -3727,9 +3823,10 @@ Biogeme is a open source Python package designed for the maximum likelihood esti *homepage*: https://pypi.python.org/pypi/biogeme ========== ============== -version toolchain +version toolchain ========== ============== ``3.1.2`` ``foss/2021a`` +``3.2.6`` ``foss/2022a`` ``3.2.8`` ``foss/2021a`` ``3.2.10`` ``foss/2022a`` ========== ============== @@ -3745,7 +3842,7 @@ The BIOM file format (canonically pronounced biome) is designed to be a general *homepage*: https://biom-format.org ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``2.1.10`` ``-Python-3.8.2`` ``foss/2020a`` ``2.1.12`` ``foss/2021b`` @@ -3762,7 +3859,7 @@ The BioMart Perl API allows you to go a step further with BioMart and integrat *homepage*: https://useast.ensembl.org/info/data/biomart/biomart_perl_api.html =============== ================ ================= -version versionsuffix toolchain +version versionsuffix toolchain =============== ================ ================= ``0.7_e6db561`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` =============== ================ ================= @@ -3778,19 +3875,19 @@ Bioperl is the product of a community effort to produce Perl code which is usefu *homepage*: https://bioperl.org/ =========== ================ ============================================================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================ ============================================================================== -``1.6.924`` ``-Perl-5.20.3`` ``intel/2016a`` -``1.6.924`` ``-Perl-5.22.1`` ``foss/2016a`` -``1.7.0`` ``-Perl-5.24.0`` ``foss/2016b`` -``1.7.1`` ``-Perl-5.24.0`` ``intel/2016b`` -``1.7.1`` ``-Perl-5.24.1`` ``intel/2017a`` -``1.7.2`` ``GCCcore/8.3.0`` -``1.7.2`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``1.7.2`` ``-Perl-5.26.1`` ``intel/2018a`` -``1.7.2`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` -``1.7.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -``1.7.7`` ``GCCcore/9.3.0`` +``1.6.924`` ``-Perl-5.20.3`` ``intel/2016a`` +``1.6.924`` ``-Perl-5.22.1`` ``foss/2016a`` +``1.7.0`` ``-Perl-5.24.0`` ``foss/2016b`` +``1.7.1`` ``-Perl-5.24.0`` ``intel/2016b`` +``1.7.1`` ``-Perl-5.24.1`` ``intel/2017a`` +``1.7.2`` ``GCCcore/8.3.0`` +``1.7.2`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``1.7.2`` ``-Perl-5.26.1`` ``intel/2018a`` +``1.7.2`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` +``1.7.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``1.7.7`` ``GCCcore/9.3.0`` ``1.7.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` =========== ================ ============================================================================== @@ -3805,7 +3902,7 @@ Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, *homepage*: https://github.com/BioPP/bpp-core ========= =================================== -version toolchain +version toolchain ========= =================================== ``2.4.1`` ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0`` ========= =================================== @@ -3821,27 +3918,27 @@ Biopython is a set of freely available tools for biological computation written *homepage*: https://www.biopython.org ======== ================== =============================================================== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================== =============================================================== -``1.65`` ``-Python-2.7.11`` ``foss/2016a`` -``1.68`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.68`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``1.70`` ``-Python-2.7.13`` ``foss/2017a`` -``1.70`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``1.70`` ``-Python-3.6.1`` ``intel/2017a`` -``1.70`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.71`` ``-Python-2.7.14`` ``intel/2018a`` -``1.71`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.72`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``1.72`` ``-Python-3.6.6`` ``foss/2018b`` -``1.73`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` -``1.73`` ``-Python-3.6.6`` ``foss/2018b`` -``1.74`` ``foss/2019a`` -``1.75`` ``-Python-2.7.16`` ``foss/2019b`` -``1.75`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``1.76`` ``-Python-2.7.18`` ``foss/2020b`` -``1.78`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``1.78`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.65`` ``-Python-2.7.11`` ``foss/2016a`` +``1.68`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``1.68`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``1.70`` ``-Python-2.7.13`` ``foss/2017a`` +``1.70`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``1.70`` ``-Python-3.6.1`` ``intel/2017a`` +``1.70`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``1.71`` ``-Python-2.7.14`` ``intel/2018a`` +``1.71`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.72`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``1.72`` ``-Python-3.6.6`` ``foss/2018b`` +``1.73`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` +``1.73`` ``-Python-3.6.6`` ``foss/2018b`` +``1.74`` ``foss/2019a`` +``1.75`` ``-Python-2.7.16`` ``foss/2019b`` +``1.75`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``1.76`` ``-Python-2.7.18`` ``foss/2020b`` +``1.78`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``1.78`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``1.79`` ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``intel/2021b`` ======== ================== =============================================================== @@ -3856,7 +3953,7 @@ Bioservices is a Python package that provides access to many Bioinformatices Web *homepage*: https://bioservices.readthedocs.io/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.7.9`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -3872,7 +3969,7 @@ BirdNET is a research platform that aims at recognizing birds by sound at scale. *homepage*: https://birdnet.cornell.edu/ ============ ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ================== ``20201214`` ``-Python-3.7.4`` ``fosscuda/2019b`` ============ ================= ================== @@ -3888,7 +3985,7 @@ Utilities to help analyze bisulfite-treated sequence data *homepage*: https://github.com/zwdzwd/biscuit ========= ============== -version toolchain +version toolchain ========= ============== ``0.1.4`` ``foss/2016a`` ========= ============== @@ -3904,11 +4001,11 @@ A tool to map bisulfite converted sequence reads and determine cytosine methylat *homepage*: https://www.bioinformatics.babraham.ac.uk/projects/bismark/ ========== =============================== -version toolchain +version toolchain ========== =============================== -``0.19.0`` ``intel/2017b`` +``0.19.0`` ``intel/2017b`` ``0.20.1`` ``foss/2018b``, ``intel/2018b`` -``0.23.1`` ``foss/2021b`` +``0.23.1`` ``foss/2021b`` ========== =============================== @@ -3922,21 +4019,21 @@ Bison is a general-purpose parser generator that converts an annotated context- *homepage*: https://www.gnu.org/software/bison ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain +version toolchain ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``2.7`` ``GCC/4.8.1``, ``GCC/4.8.4``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``system`` -``3.0.2`` ``GCC/4.8.2`` -``3.0.3`` ``GCC/4.9.2`` +``2.7`` ``GCC/4.8.1``, ``GCC/4.8.4``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``system`` +``3.0.2`` ``GCC/4.8.2`` +``3.0.3`` ``GCC/4.9.2`` ``3.0.4`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``GCCcore/system``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``3.0.5`` ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/system``, ``system`` -``3.2.2`` ``GCCcore/7.4.0`` -``3.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` -``3.5.2`` ``system`` -``3.5.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0``, ``system`` -``3.6.1`` ``GCCcore/10.1.0`` -``3.7.1`` ``GCCcore/10.2.0``, ``system`` -``3.7.6`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0``, ``system`` -``3.8.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0``, ``system`` +``3.0.5`` ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/system``, ``system`` +``3.2.2`` ``GCCcore/7.4.0`` +``3.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` +``3.5.2`` ``system`` +``3.5.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0``, ``system`` +``3.6.1`` ``GCCcore/10.1.0`` +``3.7.1`` ``GCCcore/10.2.0``, ``system`` +``3.7.6`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0``, ``system`` +``3.8.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0``, ``system`` ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -3950,12 +4047,12 @@ bitarray provides an object type which efficiently represents an array of boolea *homepage*: https://github.com/ilanschnell/bitarray ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.8.3`` ``-Python-2.7.15`` ``intel/2018b`` ``0.8.3`` ``-Python-3.6.6`` ``intel/2018b`` -``1.2.1`` ``-Python-3.7.4`` ``foss/2019b`` -``1.5.3`` ``-Python-2.7.16`` ``GCC/8.3.0`` +``1.2.1`` ``-Python-3.7.4`` ``foss/2019b`` +``1.5.3`` ``-Python-2.7.16`` ``GCC/8.3.0`` ========= ================== =============== @@ -3969,7 +4066,7 @@ The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoin *homepage*: http://www.netlib.org/blacs/ ======= =================== -version toolchain +version toolchain ======= =================== ``1.1`` ``gmvapich2/2016a`` ======= =================== @@ -3985,7 +4082,7 @@ The PacBio® long read aligner *homepage*: https://github.com/PacificBiosciences/blasr ============ =============== -version toolchain +version toolchain ============ =============== ``2.2`` ``intel/2016b`` ``5.3.3`` ``gompi/2019a`` @@ -4003,7 +4100,7 @@ Blasr_libcpp is a library used by blasr and other executables such as samtoh5, l *homepage*: https://github.com/PacificBiosciences/blasr_libcpp ============ =============== -version toolchain +version toolchain ============ =============== ``20170426`` ``intel/2017a`` ============ =============== @@ -4019,7 +4116,7 @@ Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing prima *homepage*: http://blast.ncbi.nlm.nih.gov/ ========== ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ========== ``2.2.26`` ``-Linux_x86_64`` ``system`` ``2.8.1`` ``-Linux_x86_64`` ``system`` @@ -4039,21 +4136,21 @@ Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing prim *homepage*: https://blast.ncbi.nlm.nih.gov/ ========== ================== =================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =================================================================================== -``2.2.31`` ``system`` -``2.3.0`` ``-Python-2.7.11`` ``foss/2016a`` -``2.6.0`` ``-Python-2.7.12`` ``foss/2016b`` -``2.6.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` -``2.6.0`` ``-Python-2.7.14`` ``intel/2017b`` -``2.7.1`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -``2.7.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.8.1`` ``foss/2018b`` +``2.2.31`` ``system`` +``2.3.0`` ``-Python-2.7.11`` ``foss/2016a`` +``2.6.0`` ``-Python-2.7.12`` ``foss/2016b`` +``2.6.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``2.6.0`` ``-Python-2.7.14`` ``intel/2017b`` +``2.7.1`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +``2.7.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.8.1`` ``foss/2018b`` ``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``gompi/2021b``, ``iimpi/2019a``, ``iimpi/2019b`` -``2.10.1`` ``gompi/2020a``, ``iimpi/2020a`` -``2.11.0`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a`` -``2.12.0`` ``gompi/2021b`` -``2.13.0`` ``gompi/2022a`` +``2.10.1`` ``gompi/2020a``, ``iimpi/2020a`` +``2.11.0`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a`` +``2.12.0`` ``gompi/2021b`` +``2.13.0`` ``gompi/2022a`` ========== ================== =================================================================================== @@ -4067,7 +4164,7 @@ BLAT on DNA is designed to quickly find sequences of 95% and greater similarity *homepage*: http://genome.ucsc.edu/FAQ/FAQblat.html ======= ==================================================================================================================== -version toolchain +version toolchain ======= ==================================================================================================================== ``3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a`` ======= ==================================================================================================================== @@ -4078,21 +4175,22 @@ version toolchain *Blender* +++++++++ -Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline, modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. +Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. -*homepage*: https://www.blender.org +*homepage*: https://www.blender.org/ ========= ============================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============================= =============================== -``2.77a`` ``-Python-3.5.2`` ``intel/2016b`` -``2.79`` ``-Python-3.6.1`` ``intel/2017a`` -``2.79b`` ``-Python-3.6.6`` ``intel/2018b`` -``2.79b`` ``-Python-3.6.6-CUDA-9.2.88`` ``foss/2018b`` +``2.77a`` ``-Python-3.5.2`` ``intel/2016b`` +``2.79`` ``-Python-3.6.1`` ``intel/2017a`` +``2.79b`` ``-Python-3.6.6`` ``intel/2018b`` +``2.79b`` ``-Python-3.6.6-CUDA-9.2.88`` ``foss/2018b`` ``2.81`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``3.0.0`` ``-linux-x64`` ``system`` -``3.1.2`` ``-linux-x64`` ``system`` -``3.2.2`` ``-linux-x64`` ``system`` +``3.0.0`` ``-linux-x64`` ``system`` +``3.1.2`` ``-linux-x64`` ``system`` +``3.2.2`` ``-linux-x64`` ``system`` +``3.3.1`` ``-linux-x86_64-CUDA-11.7.0`` ``system`` ========= ============================= =============================== @@ -4105,20 +4203,20 @@ AMD's fork of BLIS. BLIS is a portable software framework for instantiating high *homepage*: https://developer.amd.com/amd-cpu-libraries/blas-library/ -========= ============= ====================================================== -version versionsuffix toolchain -========= ============= ====================================================== -``0.3.2`` ``GCC/7.3.0-2.30`` -``0.6.0`` ``GCC/8.3.0-2.32`` -``0.8.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``0.8.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCCcore/10.3.0`` -``0.9.0`` ``GCC/11.3.0``, ``intel-compilers/2022.1.0`` -``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` -``2.2`` ``-amd`` ``GCCcore/9.3.0`` -``3.0`` ``-amd`` ``GCCcore/10.3.0`` +========= ============= ============================================================ +version versionsuffix toolchain +========= ============= ============================================================ +``0.3.2`` ``GCC/7.3.0-2.30`` +``0.6.0`` ``GCC/8.3.0-2.32`` +``0.8.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``0.8.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCCcore/10.3.0`` +``0.9.0`` ``GCC/11.3.0``, ``GCC/12.2.0``, ``intel-compilers/2022.1.0`` +``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` +``2.2`` ``-amd`` ``GCCcore/9.3.0`` +``3.0`` ``-amd`` ``GCCcore/10.3.0`` ``3.0.1`` ``-amd`` ``GCC/11.2.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``3.1`` ``-amd`` ``GCCcore/11.2.0`` -========= ============= ====================================================== +``3.1`` ``-amd`` ``GCCcore/11.2.0`` +========= ============= ============================================================ .. _list_software_Blitz++_603: @@ -4131,9 +4229,9 @@ Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in *homepage*: https://github.com/blitzpp/blitz ========= ========================================================= -version toolchain +version toolchain ========= ========================================================= -``0.10`` ``GCCcore/6.4.0``, ``foss/2016a`` +``0.10`` ``GCCcore/6.4.0``, ``foss/2016a`` ``1.0.2`` ``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ========= ========================================================= @@ -4148,7 +4246,7 @@ A modular command-line solution for visualisation, quality control and taxonomi *homepage*: https://blobtools.readme.io/docs ============ ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ============== ``20180528`` ``-Python-2.7.15`` ``foss/2018b`` ============ ================== ============== @@ -4164,16 +4262,17 @@ Blosc, an extremely fast, multi-threaded, meta-compressor library *homepage*: https://www.blosc.org/ ========== ================================================================== -version toolchain +version toolchain ========== ================================================================== -``1.11.1`` ``intel/2016b`` +``1.11.1`` ``intel/2016b`` ``1.12.1`` ``GCCcore/6.4.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2017a`` -``1.14.2`` ``GCCcore/6.4.0``, ``foss/2016a`` -``1.14.4`` ``GCCcore/7.3.0`` -``1.17.0`` ``GCCcore/8.2.0`` -``1.17.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.21.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``1.21.1`` ``GCCcore/11.2.0`` +``1.14.2`` ``GCCcore/6.4.0``, ``foss/2016a`` +``1.14.4`` ``GCCcore/7.3.0`` +``1.17.0`` ``GCCcore/8.2.0`` +``1.17.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.21.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.21.1`` ``GCCcore/11.2.0`` +``1.21.3`` ``GCCcore/11.3.0`` ========== ================================================================== @@ -4187,9 +4286,11 @@ Blosc, an extremely fast, multi-threaded, meta-compressor library *homepage*: https://www.blosc.org/ ========= ================== -version toolchain +version toolchain ========= ================== ``2.0.3`` ``GCCcore/10.2.0`` +``2.0.4`` ``GCCcore/10.3.0`` +``2.4.3`` ``GCCcore/11.3.0`` ========= ================== @@ -4203,7 +4304,7 @@ BLT is an extension to the Tk toolkit, adding new widgets, geometry managers, a *homepage*: http://blt.sourceforge.net/ ============ ================== -version toolchain +version toolchain ============ ================== ``20181223`` ``GCCcore/11.2.0`` ============ ================== @@ -4219,7 +4320,7 @@ Best Match Tagger for removing human reads from metagenomics datasets *homepage*: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/ ========= ================================================ -version toolchain +version toolchain ========= ================================================ ``3.101`` ``foss/2018b``, ``gompi/2019a``, ``gompi/2020b`` ========= ================================================ @@ -4235,7 +4336,7 @@ Bayesian nonparametric machine learning for python provides code for training p *homepage*: https://github.com/bnpy/bnpy ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``0.1.6`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== ============== @@ -4251,7 +4352,7 @@ BOINC is a program that lets you donate your idle computer time to science proje *homepage*: https://boinc.berkeley.edu ========== ============= ============= -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ============= ``7.2.42`` ``-client`` ``GCC/4.8.2`` ========== ============= ============= @@ -4267,18 +4368,19 @@ Statistical and novel interactive HTML plots for Python *homepage*: https://github.com/bokeh/bokeh =========== ================== ======================================================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ======================================================================== -``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` -``0.12.3`` ``-Python-3.5.2`` ``intel/2016b`` -``0.12.15`` ``-Python-3.6.4`` ``intel/2018a`` -``1.0.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.3.4`` ``-Python-3.7.2`` ``foss/2019a`` -``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``2.0.2`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` +``0.12.3`` ``-Python-3.5.2`` ``intel/2016b`` +``0.12.15`` ``-Python-3.6.4`` ``intel/2018a`` +``1.0.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.3.4`` ``-Python-3.7.2`` ``foss/2019a`` +``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2.0.2`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``2.2.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -``2.4.1`` ``foss/2021a`` -``2.4.2`` ``foss/2021b`` +``2.4.1`` ``foss/2021a`` +``2.4.2`` ``foss/2021b`` +``2.4.3`` ``foss/2022a`` =========== ================== ======================================================================== @@ -4292,7 +4394,7 @@ Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi *homepage*: http://www.icams.de/content/departments/cmat/boltztrap/ ========= =============== -version toolchain +version toolchain ========= =============== ``1.2.5`` ``intel/2016a`` ========= =============== @@ -4308,16 +4410,16 @@ Convolution Basecaller for Oxford Nanopore Reads *homepage*: https://github.com/nanoporetech/bonito ========= ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================== ``0.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``0.1.4`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``0.2.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``0.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``0.3.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``0.3.5`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``0.3.8`` ``fosscuda/2020b`` -``0.4.0`` ``fosscuda/2020b`` +``0.1.4`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``0.2.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``0.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``0.3.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``0.3.5`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``0.3.8`` ``fosscuda/2020b`` +``0.4.0`` ``fosscuda/2020b`` ========= ================= ================================== @@ -4331,7 +4433,7 @@ Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package f *homepage*: https://coin-or.github.io/Ipopt ========= =============== -version toolchain +version toolchain ========= =============== ``1.8.7`` ``intel/2019a`` ========= =============== @@ -4342,15 +4444,16 @@ version toolchain *Bonnie++* ++++++++++ -Bonnie++-1.97: Enhanced performance Test of Filesystem I/O +Enhanced performance Test of Filesystem I/O -*homepage*: http://www.coker.com.au/bonnie++/ +*homepage*: https://www.coker.com.au/bonnie++ -======== ============== -version toolchain -======== ============== -``1.97`` ``foss/2016a`` -======== ============== +========= ============== +version toolchain +========= ============== +``1.97`` ``foss/2016a`` +``2.00a`` ``GCC/10.3.0`` +========= ============== .. _list_software_Boost_519: @@ -4363,58 +4466,75 @@ Boost provides free peer-reviewed portable C++ source libraries. *homepage*: https://www.boost.org/ ========== ================== ==================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ==================================================================== -``1.54.0`` ``-Python-2.7.12`` ``foss/2016b`` -``1.55.0`` ``system`` -``1.55.0`` ``-Python-2.7.11`` ``foss/2016a`` -``1.57.0`` ``-Python-2.7.10`` ``gimkl/2.11.5`` -``1.58.0`` ``intel/2017a`` -``1.58.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``1.58.0`` ``-serial`` ``GCC/4.9.2`` -``1.59.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``1.60.0`` ``foss/2016a``, ``intel/2016a`` -``1.60.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``1.60.0`` ``-Python-3.5.1`` ``foss/2016a`` -``1.61.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``1.61.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``1.61.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.61.0`` ``-Python-3.5.1`` ``foss/2016a`` -``1.62.0`` ``-Python-2.7.12`` ``intel/2016b`` -``1.63.0`` ``foss/2017a`` -``1.63.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.63.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` -``1.63.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` -``1.63.0`` ``-Python-3.5.2`` ``foss/2016b`` -``1.64.0`` ``gompi/2019a``, ``gompic/2019a``, ``intel/2017a`` -``1.64.0`` ``-Python-2.7.13`` ``intel/2017a`` -``1.65.0`` ``-Python-2.7.13`` ``intel/2017a`` -``1.65.1`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``1.65.1`` ``-Python-2.7.13`` ``intel/2017a`` -``1.65.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``1.65.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.66.0`` ``foss/2018a``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018a`` -``1.66.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``1.66.0`` ``-Python-3.6.3`` ``intel/2018.01`` -``1.66.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.66.0`` ``-no_mpi`` ``GCCcore/6.4.0`` +``1.54.0`` ``-Python-2.7.12`` ``foss/2016b`` +``1.55.0`` ``system`` +``1.55.0`` ``-Python-2.7.11`` ``foss/2016a`` +``1.57.0`` ``-Python-2.7.10`` ``gimkl/2.11.5`` +``1.58.0`` ``intel/2017a`` +``1.58.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``1.58.0`` ``-serial`` ``GCC/4.9.2`` +``1.59.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``1.60.0`` ``foss/2016a``, ``intel/2016a`` +``1.60.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``1.60.0`` ``-Python-3.5.1`` ``foss/2016a`` +``1.61.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``1.61.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``1.61.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``1.61.0`` ``-Python-3.5.1`` ``foss/2016a`` +``1.62.0`` ``-Python-2.7.12`` ``intel/2016b`` +``1.63.0`` ``foss/2017a`` +``1.63.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``1.63.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``1.63.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` +``1.63.0`` ``-Python-3.5.2`` ``foss/2016b`` +``1.64.0`` ``gompi/2019a``, ``gompic/2019a``, ``intel/2017a`` +``1.64.0`` ``-Python-2.7.13`` ``intel/2017a`` +``1.65.0`` ``-Python-2.7.13`` ``intel/2017a`` +``1.65.1`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``1.65.1`` ``-Python-2.7.13`` ``intel/2017a`` +``1.65.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``1.65.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``1.66.0`` ``foss/2018a``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018a`` +``1.66.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``1.66.0`` ``-Python-3.6.3`` ``intel/2018.01`` +``1.66.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.66.0`` ``-no_mpi`` ``GCCcore/6.4.0`` ``1.67.0`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` -``1.67.0`` ``-Python-2.7.14`` ``foss/2018a`` -``1.68.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``1.68.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.69.0`` ``intel/2019.01`` +``1.67.0`` ``-Python-2.7.14`` ``foss/2018a`` +``1.68.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``1.68.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.69.0`` ``intel/2019.01`` ``1.70.0`` ``gompi/2019a``, ``gompic/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` ``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` -``1.72.0`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a`` -``1.72.0`` ``-no_mpi`` ``GCCcore/9.3.0`` -``1.74.0`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -``1.75.0`` ``GCC/11.2.0`` -``1.76.0`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` -``1.77.0`` ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` -``1.79.0`` ``GCC/11.2.0``, ``GCC/11.3.0`` +``1.72.0`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a`` +``1.72.0`` ``-no_mpi`` ``GCCcore/9.3.0`` +``1.74.0`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``1.75.0`` ``GCC/11.2.0`` +``1.76.0`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` +``1.77.0`` ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` +``1.79.0`` ``GCC/11.2.0``, ``GCC/11.3.0`` ========== ================== ==================================================================== +.. _list_software_Boost.MPI_795: + +*Boost.MPI* ++++++++++++ + +Boost provides free peer-reviewed portable C++ source libraries. + +*homepage*: https://www.boost.org/ + +========== =============== +version toolchain +========== =============== +``1.77.0`` ``gompi/2021b`` +``1.79.0`` ``gompi/2022a`` +========== =============== + + .. _list_software_Boost.Python_1207: *Boost.Python* @@ -4425,21 +4545,21 @@ Boost.Python is a C++ library which enables seamless interoperability between C+ *homepage*: https://boostorg.github.io/python ========== ================== ==================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ==================================================================== -``1.64.0`` ``gompi/2019a``, ``gompic/2019a`` -``1.65.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``1.66.0`` ``-Python-2.7.14`` ``intel/2018a`` -``1.66.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.67.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``1.67.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.64.0`` ``gompi/2019a``, ``gompic/2019a`` +``1.65.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``1.66.0`` ``-Python-2.7.14`` ``intel/2018a`` +``1.66.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.67.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``1.67.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.70.0`` ``gompi/2019a``, ``gompic/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` ``1.71.0`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` -``1.72.0`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a`` -``1.74.0`` ``GCC/10.2.0`` -``1.76.0`` ``GCC/10.3.0`` -``1.77.0`` ``GCC/11.2.0`` -``1.79.0`` ``GCC/11.3.0`` +``1.72.0`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a`` +``1.74.0`` ``GCC/10.2.0`` +``1.76.0`` ``GCC/10.3.0`` +``1.77.0`` ``GCC/11.2.0`` +``1.79.0`` ``GCC/11.3.0`` ========== ================== ==================================================================== @@ -4453,7 +4573,7 @@ Boost-histogram is a Python package providing Python bindings for Boost.Histogra *homepage*: https://boost-histogram.readthedocs.io ========= ============== -version toolchain +version toolchain ========= ============== ``1.2.1`` ``foss/2021a`` ========= ============== @@ -4469,9 +4589,10 @@ Boto3 is the Amazon Web Services (AWS) Software Development Kit (SDK) for Python *homepage*: https://github.com/boto/boto3 =========== ====================================== -version toolchain +version toolchain =========== ====================================== ``1.20.13`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.26.37`` ``GCCcore/11.3.0`` =========== ====================================== @@ -4485,10 +4606,10 @@ Fast NumPy array functions written in C *homepage*: https://kwgoodman.github.io/bottleneck-doc ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``1.2.1`` ``-Python-3.6.4`` ``intel/2018a`` -``1.3.2`` ``-Python-3.8.2`` ``foss/2020a`` +``1.3.2`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= =============== @@ -4502,14 +4623,14 @@ Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DN *homepage*: http://bowtie-bio.sourceforge.net/index.shtml =========== ===================================================================================================================================== -version toolchain +version toolchain =========== ===================================================================================================================================== -``1.1.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a`` -``1.2.1.1`` ``foss/2016b``, ``intel/2017b`` -``1.2.2`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` +``1.1.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a`` +``1.2.1.1`` ``foss/2016b``, ``intel/2017b`` +``1.2.2`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ``1.2.3`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` -``1.3.0`` ``GCC/10.2.0``, ``GCC/9.3.0`` -``1.3.1`` ``GCC/11.2.0`` +``1.3.0`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``1.3.1`` ``GCC/11.2.0`` =========== ===================================================================================================================================== @@ -4520,24 +4641,24 @@ version toolchain Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. -*homepage*: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml +*homepage*: https://bowtie-bio.sourceforge.net/bowtie2/index.shtml =========== ====================================================================================================== -version toolchain +version toolchain =========== ====================================================================================================== -``2.2.8`` ``foss/2016a`` -``2.2.9`` ``foss/2016a``, ``intel/2016b`` -``2.3.2`` ``foss/2016b``, ``foss/2017a``, ``intel/2017a`` -``2.3.3.1`` ``intel/2017b`` -``2.3.4`` ``intel/2017b`` -``2.3.4.1`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``2.3.4.2`` ``foss/2018b``, ``intel/2018b`` -``2.3.4.3`` ``foss/2017b`` +``2.2.8`` ``foss/2016a`` +``2.2.9`` ``foss/2016a``, ``intel/2016b`` +``2.3.2`` ``foss/2016b``, ``foss/2017a``, ``intel/2017a`` +``2.3.3.1`` ``intel/2017b`` +``2.3.4`` ``intel/2017b`` +``2.3.4.1`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``2.3.4.2`` ``foss/2018b``, ``intel/2018b`` +``2.3.4.3`` ``foss/2017b`` ``2.3.5.1`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` -``2.4.1`` ``GCC/9.3.0`` -``2.4.2`` ``GCC/10.2.0``, ``GCC/9.3.0`` -``2.4.4`` ``GCC/10.3.0``, ``GCC/11.2.0`` -``2.4.5`` ``GCC/11.3.0`` +``2.4.1`` ``GCC/9.3.0`` +``2.4.2`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``2.4.4`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``2.4.5`` ``GCC/11.3.0`` =========== ====================================================================================================== @@ -4551,7 +4672,7 @@ Bpipe - a tool for running and managing bioinformatics pipelines *homepage*: http://docs.bpipe.org/ =========== =============== -version toolchain +version toolchain =========== =============== ``0.9.9.2`` ``intel/2017a`` =========== =============== @@ -4567,9 +4688,9 @@ The aim of this project is to implement a versatile high-performance version of *homepage*: https://github.com/bpp/bpp ========= ============== -version toolchain +version toolchain ========= ============== -``4.3.8`` ``GCC/8.3.0`` +``4.3.8`` ``GCC/8.3.0`` ``4.4.0`` ``GCC/10.3.0`` ========= ============== @@ -4584,7 +4705,7 @@ Resource monitor that shows usage and stats for processor, memory, disks, networ *homepage*: https://github.com/aristocratos/bpytop/ ========== ================== -version toolchain +version toolchain ========== ================== ``1.0.60`` ``GCCcore/10.2.0`` ``1.0.67`` ``GCCcore/10.3.0`` @@ -4601,9 +4722,9 @@ Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate s *homepage*: https://ccb.jhu.edu/software/bracken/ ========= ================== -version toolchain +version toolchain ========= ================== -``2.6.0`` ``GCCcore/9.3.0`` +``2.6.0`` ``GCCcore/9.3.0`` ``2.6.2`` ``GCCcore/11.2.0`` ``2.7`` ``GCCcore/11.2.0`` ========= ================== @@ -4619,10 +4740,11 @@ BRAKER is a pipeline for fully automated prediction of protein coding genes with *homepage*: https://github.com/Gaius-Augustus/BRAKER ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``2.1.2`` ``intel/2019a`` ``2.1.5`` ``-Python-3.7.4`` ``intel/2019b`` +``2.1.6`` ``foss/2021b`` ========= ================= =============== @@ -4636,7 +4758,7 @@ BreakDancer is a Perl/C++ package that provides genome-wide detection of structu *homepage*: http://gmt.genome.wustl.edu/packages/breakdancer ========= =============== -version toolchain +version toolchain ========= =============== ``1.4.5`` ``intel/2017a`` ========= =============== @@ -4652,11 +4774,11 @@ breseq is a computational pipeline for the analysis of short-read re-sequencing *homepage*: https://barricklab.org/breseq ========== ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= =============== ``0.35.0`` ``-R-3.6.0`` ``intel/2019a`` -``0.35.4`` ``-R-4.0.0`` ``foss/2020a`` -``0.36.1`` ``foss/2021b`` +``0.35.4`` ``-R-4.0.0`` ``foss/2020a`` +``0.36.1`` ``foss/2021b`` ========== ============= =============== @@ -4669,11 +4791,11 @@ Brotli is a generic-purpose lossless compression algorithm that compresses data *homepage*: https://github.com/google/brotli -========= ================================================================================================= -version toolchain -========= ================================================================================================= -``1.0.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` -========= ================================================================================================= +========= ===================================================================================================================== +version toolchain +========= ===================================================================================================================== +``1.0.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/8.3.0`` +========= ===================================================================================================================== .. _list_software_Brotli-python_1339: @@ -4686,7 +4808,7 @@ Brotli is a generic-purpose lossless compression algorithm that compresses data *homepage*: https://github.com/google/brotli ========= ================== -version toolchain +version toolchain ========= ================== ``1.0.9`` ``GCCcore/10.3.0`` ========= ================== @@ -4701,11 +4823,11 @@ Brunsli is a lossless JPEG repacking library. *homepage*: https://github.com/google/brunsli/ -======= ================== -version toolchain -======= ================== -``0.1`` ``GCCcore/10.2.0`` -======= ================== +======= ====================================== +version toolchain +======= ====================================== +``0.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +======= ====================================== .. _list_software_bsddb3_562: @@ -4717,13 +4839,13 @@ bsddb3 is a nearly complete Python binding of the Oracle/Sleepycat C API for the *homepage*: https://pypi.org/project/bsddb3/ -========= ================== ================== -version versionsuffix toolchain -========= ================== ================== -``6.2.6`` ``GCCcore/8.2.0`` +========= ================== ====================================== +version versionsuffix toolchain +========= ================== ====================================== +``6.2.6`` ``GCCcore/8.2.0`` ``6.2.6`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``6.2.9`` ``GCCcore/10.2.0`` -========= ================== ================== +``6.2.9`` ``GCCcore/10.2.0``, ``GCCcore/11.3.0`` +========= ================== ====================================== .. _list_software_BSMAPz_493: @@ -4736,7 +4858,7 @@ Updated and optimized fork of BSMAP. BSMAPz is a short reads mapping program for *homepage*: https://github.com/zyndagj/BSMAPz ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.1.1`` ``-Python-2.7.16`` ``intel/2019b`` ========= ================== =============== @@ -4752,10 +4874,10 @@ Bsoft is a collection of programs and a platform for development of software fo *homepage*: https://lsbr.niams.nih.gov/bsoft/ ========= ============== -version toolchain +version toolchain ========= ============== ``2.0.2`` ``foss/2017b`` -``2.0.7`` ``GCC/9.3.0`` +``2.0.7`` ``GCC/9.3.0`` ========= ============== @@ -4769,7 +4891,7 @@ BS-Seeker2 is a seamless and versatile pipeline for accurately and fast mapping *homepage*: http://pellegrini-legacy.mcdb.ucla.edu/bs_seeker2 ========= ================== ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ====================================== ``2.1.8`` ``-Python-2.7.16`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ========= ================== ====================================== @@ -4785,7 +4907,7 @@ A Binary Decision Diagram library, with many highly efficient vectorized BDD ope *homepage*: http://buddy.sourceforge.net/ ======= ================== -version toolchain +version toolchain ======= ================== ``2.4`` ``GCCcore/10.2.0`` ======= ================== @@ -4801,7 +4923,7 @@ NCEP BUFRLIB software to encode or decode BUFR messages. It is not intended to b *homepage*: https://www.emc.ncep.noaa.gov/index.php?branch=BUFRLIB ============ ======================= -version toolchain +version toolchain ============ ======================= ``11.3.0.2`` ``iccifort/2020.1.217`` ============ ======================= @@ -4817,12 +4939,12 @@ This module sets a group of environment variables for compilers, linkers, maths *homepage*: None =========== ================ =================================================================================================================================================================================================================================================================================================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================ =================================================================================================================================================================================================================================================================================================================================================================================================================================== ``default`` ``FCC/4.5.0``, ``Fujitsu/21.05``, ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``intelcuda/2020b`` -``default`` ``-CUDA-11.3.1`` ``foss/2021a`` -``default`` ``-CUDA-11.4.1`` ``foss/2021b`` -``default`` ``-CUDA-11.7.0`` ``foss/2022a`` +``default`` ``-CUDA-11.3.1`` ``foss/2021a`` +``default`` ``-CUDA-11.4.1`` ``foss/2021b`` +``default`` ``-CUDA-11.7.0`` ``foss/2022a`` =========== ================ =================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -4836,7 +4958,7 @@ Python modules for automating Modelica simulations and for running unit test for *homepage*: https://simulationresearch.lbl.gov/modelica/buildingspy ========= ============== -version toolchain +version toolchain ========= ============== ``4.0.0`` ``foss/2022a`` ========= ============== @@ -4852,7 +4974,7 @@ Bullet professional 3D Game Multiphysics Library provides state of the art coll *homepage*: http://bulletphysics.org/ ========== =============================== -version toolchain +version toolchain ========== =============================== ``2.83.7`` ``foss/2016a``, ``intel/2016a`` ========== =============================== @@ -4868,17 +4990,17 @@ BUSCO: assessing genome assembly and annotation completeness with single-copy or *homepage*: https://busco.ezlab.org/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.22`` ``-Python-2.7.13`` ``intel/2017a`` ``2.0.1`` ``-Python-2.7.13`` ``intel/2017a`` ``3.0.2`` ``-Python-2.7.15`` ``intel/2018b`` -``4.0.5`` ``-Python-3.7.4`` ``foss/2019b`` -``4.0.6`` ``foss/2020b`` -``5.0.0`` ``foss/2020b`` -``5.1.2`` ``foss/2020b`` -``5.4.2`` ``foss/2021a`` -``5.4.3`` ``foss/2021b`` +``4.0.5`` ``-Python-3.7.4`` ``foss/2019b`` +``4.0.6`` ``foss/2020b`` +``5.0.0`` ``foss/2020b`` +``5.1.2`` ``foss/2020b`` +``5.4.2`` ``foss/2021a`` +``5.4.3`` ``foss/2021b`` ========= ================== =============== @@ -4892,7 +5014,7 @@ bustools is a program for manipulating BUS files for single cell RNA-Seq dataset *homepage*: https://github.com/BUStools/bustools ========== ================================= -version toolchain +version toolchain ========== ================================= ``0.40.0`` ``GCCcore/9.3.0``, ``foss/2018b`` ========== ================================= @@ -4907,15 +5029,15 @@ Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively sh *homepage*: http://bio-bwa.sourceforge.net/ -=========== ===================================================================================================================================================================================================================================================================================================== -version toolchain -=========== ===================================================================================================================================================================================================================================================================================================== -``0.7.12`` ``foss/2016b`` -``0.7.13`` ``foss/2016a``, ``intel/2016a`` -``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``0.7.16a`` ``foss/2016b``, ``intel/2017a`` -``0.7.17`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/11.2.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -=========== ===================================================================================================================================================================================================================================================================================================== +=========== ========================================================================================================================================================================================================================================================================================================================= +version toolchain +=========== ========================================================================================================================================================================================================================================================================================================================= +``0.7.12`` ``foss/2016b`` +``0.7.13`` ``foss/2016a``, ``intel/2016a`` +``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``0.7.16a`` ``foss/2016b``, ``intel/2017a`` +``0.7.17`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +=========== ========================================================================================================================================================================================================================================================================================================================= .. _list_software_bwa-meth_789: @@ -4928,7 +5050,7 @@ Fast and accurante alignment of BS-Seq reads. *homepage*: https://github.com/brentp/bwa-meth ========= ================================================================= -version toolchain +version toolchain ========= ================================================================= ``0.2.2`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` ========= ================================================================= @@ -4944,7 +5066,7 @@ Bwakit is a self-consistent installation-free package of scripts and precompiled *homepage*: https://github.com/lh3/bwa/tree/master/bwakit ========== ============== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============== ========== ``0.7.15`` ``_x64-linux`` ``system`` ========== ============== ========== @@ -4960,11 +5082,11 @@ The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl *homepage*: https://core.tcl-lang.org/bwidget/home ========== ======================================================== -version toolchain +version toolchain ========== ======================================================== -``1.9.13`` ``GCCcore/8.2.0`` +``1.9.13`` ``GCCcore/8.2.0`` ``1.9.14`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.9.15`` ``GCCcore/11.3.0`` +``1.9.15`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ======================================================== @@ -4978,7 +5100,7 @@ de Bruijn Workflow using Integral information of Short pair End reads *homepage*: https://github.com/Malfoy/BWISE ============ ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ============== ``20180820`` ``-Python-3.6.4`` ``foss/2018a`` ============ ================= ============== @@ -4994,17 +5116,17 @@ The bx-python project is a Python library and associated set of scripts to allow *homepage*: https://github.com/bxlab/bx-python ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== -``0.7.4`` ``-Python-2.7.12`` ``foss/2016b`` +``0.7.4`` ``-Python-2.7.12`` ``foss/2016b`` ``0.7.4`` ``-Python-2.7.13`` ``intel/2017a`` ``0.8.1`` ``-Python-2.7.14`` ``intel/2018a`` -``0.8.2`` ``-Python-3.6.6`` ``foss/2018b`` -``0.8.4`` ``foss/2019a`` -``0.8.8`` ``-Python-3.7.4`` ``foss/2019b`` -``0.8.9`` ``-Python-3.8.2`` ``foss/2020a`` -``0.8.11`` ``foss/2021a`` -``0.8.13`` ``foss/2021b`` +``0.8.2`` ``-Python-3.6.6`` ``foss/2018b`` +``0.8.4`` ``foss/2019a`` +``0.8.8`` ``-Python-3.7.4`` ``foss/2019b`` +``0.8.9`` ``-Python-3.8.2`` ``foss/2020a`` +``0.8.11`` ``foss/2021a`` +``0.8.13`` ``foss/2021b`` ========== ================== =============== @@ -5018,7 +5140,7 @@ A collection of data processing and image analysis tools for data in BXH or XCE *homepage*: http://www.nitrc.org/projects/bxh_xcede_tools/ ========== ========== -version toolchain +version toolchain ========== ========== ``1.11.1`` ``system`` ========== ========== @@ -5034,11 +5156,11 @@ Berkeley Yacc (byacc) is generally conceded to be the best yacc variant availab *homepage*: http://invisible-island.net/byacc/byacc.html ============ =============================== -version toolchain +version toolchain ============ =============================== -``20160324`` ``intel/2016a`` +``20160324`` ``intel/2016a`` ``20160606`` ``foss/2016b``, ``intel/2016b`` -``20170709`` ``GCCcore/6.4.0`` +``20170709`` ``GCCcore/6.4.0`` ============ =============================== @@ -5052,7 +5174,7 @@ Byobu is an elegant enhancement of the otherwise functional, plain, practical GN *homepage*: https://byobu.org ========= ============= -version toolchain +version toolchain ========= ============= ``5.133`` ``GCC/8.3.0`` ========= ============= @@ -5068,10 +5190,10 @@ bzip2 is a freely available, patent free, high-quality data compressor. It typi *homepage*: https://sourceware.org/bzip2 ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain +version toolchain ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.0.6`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -5081,7 +5203,7 @@ version toolchain --- -:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CASTEP_448` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_category_encoders_1808` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_CDBtools_762` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_CellTypist_1037` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMAverse_758` - :ref:`list_software_CmdStanR_764` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_colossalai_1066` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_Compress-Raw-Zlib_1633` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_CONN_302` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_Crumble_714` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CrystFEL_748` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDAcompat_929` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_CWIPI_380` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` +:ref:`list_software_c-ares_571` - :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_CaDiCaL_577` - :ref:`list_software_CAFE5_324` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calcam_577` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Calib_475` - :ref:`list_software_CAMPARI_509` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_captum_650` - :ref:`list_software_Cargo_492` - :ref:`list_software_Carma_484` - :ref:`list_software_carputils_983` - :ref:`list_software_Cartopy_738` - :ref:`list_software_CaSpER_510` - :ref:`list_software_CASTEP_448` - :ref:`list_software_CastXML_636` - :ref:`list_software_CAT-BAT_476` - :ref:`list_software_Catch2_533` - :ref:`list_software_category_encoders_1808` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causallift_1064` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CAVIAR_438` - :ref:`list_software_Cbc_264` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCfits_572` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_cctools_759` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_CDAT_284` - :ref:`list_software_cdbfasta_824` - :ref:`list_software_CDBtools_762` - :ref:`list_software_cddlib_610` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdo-bindings_1201` - :ref:`list_software_cdsapi_628` - :ref:`list_software_cell2location_1323` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_CellRanger-ARC_1250` - :ref:`list_software_CellRanger-ATAC_1317` - :ref:`list_software_CellRank_780` - :ref:`list_software_CellTypist_1037` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_Cereal_588` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFDEMcoupling_1216` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_Cgl_278` - :ref:`list_software_CGmapTools_985` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_CHARMM_440` - :ref:`list_software_charmm_632` - :ref:`list_software_CHASE_356` - :ref:`list_software_Check_478` - :ref:`list_software_check_510` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_Chemaxon-Marvin_1485` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_CHERAB_421` - :ref:`list_software_chewBBACA_752` - :ref:`list_software_chi2comb_775` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_cicero_629` - :ref:`list_software_CIF2Cell_644` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_CIRI-long_772` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-AOMP_831` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLEASE_429` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CliMetLab_845` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_CloudCompare_1214` - :ref:`list_software_Clp_287` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CMAverse_758` - :ref:`list_software_CmdStanR_764` - :ref:`list_software_cmocean_726` - :ref:`list_software_CMSeq_441` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_Co-phylog_882` - :ref:`list_software_COBRApy_592` - :ref:`list_software_CoCoALib_700` - :ref:`list_software_CodAn_453` - :ref:`list_software_code-server_1119` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Cogent_608` - :ref:`list_software_Coin_393` - :ref:`list_software_CoinUtils_922` - :ref:`list_software_colossalai_1066` - :ref:`list_software_Commet_613` - :ref:`list_software_CompareM_788` - :ref:`list_software_Compress-Raw-Zlib_1633` - :ref:`list_software_COMSOL_461` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_CONN_302` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_CoSymLib_770` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CPPE_296` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cppy_444` - :ref:`list_software_cpu_features_1286` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CREST_385` - :ref:`list_software_CRF++_305` - :ref:`list_software_CRISPR-DAV_731` - :ref:`list_software_CRISPResso2_959` - :ref:`list_software_cromwell_869` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_Crumble_714` - :ref:`list_software_cryoCARE_728` - :ref:`list_software_cryoDRGN_744` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CrystFEL_748` - :ref:`list_software_CSB_216` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_CSBLAST_524` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_CTPL_307` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_CUDA-Samples_1055` - :ref:`list_software_CUDAcompat_929` - :ref:`list_software_CUDAcore_710` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_CuPy_385` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_cuTENSOR_691` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_CWIPI_380` - :ref:`list_software_cwltool_772` - :ref:`list_software_cxxopts_793` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_Cytoscape_939` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_c-ares_571: @@ -5094,9 +5216,9 @@ c-ares is a C library for asynchronous DNS requests (including name resolves) *homepage*: https://c-ares.org/ ========== ====================================== -version toolchain +version toolchain ========== ====================================== -``1.17.2`` ``GCCcore/10.3.0`` +``1.17.2`` ``GCCcore/10.3.0`` ``1.18.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ====================================== @@ -5111,7 +5233,7 @@ Convert3D Medical Image Processing Tool *homepage*: https://sourceforge.net/projects/c3d/ ========= ========== -version toolchain +version toolchain ========= ========== ``1.0.0`` ``system`` ========= ========== @@ -5127,7 +5249,7 @@ cadaver is a command-line WebDAV client for Unix. *homepage*: http://www.webdav.org/cadaver/ ========== =============== -version toolchain +version toolchain ========== =============== ``0.23.3`` ``intel/2017a`` ========== =============== @@ -5143,7 +5265,7 @@ CaDiCaL is a simplified satisfiability solver. The original goal of the developm *homepage*: https://github.com/arminbiere/cadical ========= ============= -version toolchain +version toolchain ========= ============= ``1.3.0`` ``GCC/9.3.0`` ========= ============= @@ -5159,7 +5281,7 @@ Software for Computational Analysis of gene Family Evolution The purpose of CAF *homepage*: https://github.com/hahnlab/CAFE5 ========= ============== -version toolchain +version toolchain ========= ============== ``5.0.0`` ``GCC/10.2.0`` ========= ============== @@ -5175,12 +5297,12 @@ Caffe is a deep learning framework made with expression, speed, and modularity *homepage*: https://github.com/BVLC/caffe ======= ============================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============================== =============== ``1.0`` ``-CUDA-9.1.85-Python-2.7.14`` ``intel/2017b`` ``1.0`` ``-Python-2.7.13`` ``intel/2017a`` ``1.0`` ``-Python-2.7.14`` ``intel/2017b`` -``rc3`` ``-CUDA-7.5.18-Python-2.7.11`` ``foss/2016a`` +``rc3`` ``-CUDA-7.5.18-Python-2.7.11`` ``foss/2016a`` ======= ============================== =============== @@ -5194,15 +5316,15 @@ Cairo is a 2D graphics library with support for multiple output devices. Curren *homepage*: https://cairographics.org =========== ================ =================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================ =================================================================================================================== -``1.14.6`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``1.14.6`` ``-GLib-2.48.0`` ``foss/2016a``, ``intel/2016a`` -``1.14.8`` ``intel/2017a`` -``1.14.10`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017b`` -``1.14.12`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.14.6`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``1.14.6`` ``-GLib-2.48.0`` ``foss/2016a``, ``intel/2016a`` +``1.14.8`` ``intel/2017a`` +``1.14.10`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017b`` +``1.14.12`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.16.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.17.4`` ``GCCcore/11.3.0`` +``1.17.4`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` =========== ================ =================================================================================================================== @@ -5216,7 +5338,7 @@ The Cairomm package provides a C++ interface to Cairo. *homepage*: http://cairographics.org ========== ==================================== -version toolchain +version toolchain ========== ==================================== ``1.12.2`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ========== ==================================== @@ -5232,7 +5354,7 @@ Calcam is a Python package providing tools for spatial calibration of cameras, *homepage*: https://euratom-software.github.io/calcam ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``2.1.0`` ``-Python-2.7.14`` ``intel/2018a`` ``2.1.0`` ``-Python-3.6.4`` ``intel/2018a`` @@ -5249,7 +5371,7 @@ Calendrical module is for calendrical calculations. *homepage*: https://www.funaba.org/code#calendrical ========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============== ``2.0.1`` ``-Python-3.6.3`` ``intel/2017b`` ``2.0.2a`` ``-Python-3.6.4`` ``intel/2018a`` @@ -5267,7 +5389,7 @@ Calib clusters paired-end reads using their barcodes and sequences. Calib is sui *homepage*: https://github.com/vpc-ccg/calib ========= ============= -version toolchain +version toolchain ========= ============= ``0.3.4`` ``GCC/9.3.0`` ========= ============= @@ -5283,7 +5405,7 @@ CAMPARI is a joint package for performing and analyzing molecular simulations, i *homepage*: http://campari.sourceforge.net/V4/index.html ======= =============== -version toolchain +version toolchain ======= =============== ``4.0`` ``intel/2020b`` ======= =============== @@ -5299,13 +5421,13 @@ Chemical kinetics, thermodynamics, and transport tool suite *homepage*: https://github.com/Cantera/cantera ========= ================== ================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================================================ -``2.2.1`` ``-Python-2.7.12`` ``intel/2016b`` -``2.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.3.0`` ``-Python-2.7.13`` ``intel/2017a`` +``2.2.1`` ``-Python-2.7.12`` ``intel/2016b`` +``2.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``2.3.0`` ``-Python-2.7.13`` ``intel/2017a`` ``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``2.4.0`` ``-Python-2.7.14`` ``intel/2018a`` +``2.4.0`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== ================================================ @@ -5319,18 +5441,18 @@ Canu is a fork of the Celera Assembler designed for high-noise single-molecule s *homepage*: https://canu.readthedocs.io ========= ================ ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ====================================== -``1.4`` ``foss/2016b`` -``1.7`` ``intel/2018a`` -``1.8`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``1.8`` ``-Perl-5.28.0`` ``foss/2018b`` -``1.8`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -``1.9`` ``-Java-11`` ``GCCcore/8.3.0`` -``2.1.1`` ``GCCcore/10.2.0`` -``2.1.1`` ``-Java-11`` ``GCCcore/9.3.0`` +``1.4`` ``foss/2016b`` +``1.7`` ``intel/2018a`` +``1.8`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``1.8`` ``-Perl-5.28.0`` ``foss/2018b`` +``1.8`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``1.9`` ``-Java-11`` ``GCCcore/8.3.0`` +``2.1.1`` ``GCCcore/10.2.0`` +``2.1.1`` ``-Java-11`` ``GCCcore/9.3.0`` ``2.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``2.2`` ``-Java-11`` ``GCCcore/10.3.0`` +``2.2`` ``-Java-11`` ``GCCcore/10.3.0`` ========= ================ ====================================== @@ -5344,7 +5466,7 @@ Copy number variant (CNV) calling from DNA sequencing data *homepage*: https://github.com/Illumina/canvas =============== ========== -version toolchain +version toolchain =============== ========== ``1.39.0.1598`` ``system`` =============== ========== @@ -5360,7 +5482,7 @@ CAP3 assembly program *homepage*: http://seq.cs.iastate.edu/ ========================= ========== -version toolchain +version toolchain ========================= ========== ``20071221-intel-x86`` ``system`` ``20071221-intel-x86_64`` ``system`` @@ -5378,16 +5500,33 @@ Cap’n Proto is an insanely fast data interchange format and capability-based R *homepage*: https://capnproto.org ========== ========================================================== -version toolchain +version toolchain ========== ========================================================== -``0.6.1`` ``GCCcore/6.4.0`` -``0.7.0`` ``GCCcore/7.3.0`` -``0.8.0`` ``GCCcore/9.3.0`` +``0.6.1`` ``GCCcore/6.4.0`` +``0.7.0`` ``GCCcore/7.3.0`` +``0.8.0`` ``GCCcore/9.3.0`` ``0.9.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``0.10.2`` ``GCCcore/11.3.0`` +``0.10.2`` ``GCCcore/11.3.0`` ========== ========================================================== +.. _list_software_captum_650: + +*captum* +++++++++ + +Captum is a model interpretability and understanding library for PyTorch. Captum means comprehension in Latin and contains general purpose implementations of integrated gradients, saliency maps, smoothgrad, vargrad and others for PyTorch models. It has quick integration for models built with domain-specific libraries such as torchvision, torchtext, and others. + +*homepage*: https://captum.ai/ + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``0.5.0`` ``foss/2022a`` +``0.5.0`` ``-CUDA-11.7.0`` ``foss/2022a`` +========= ================ ============== + + .. _list_software_Cargo_492: *Cargo* @@ -5398,7 +5537,7 @@ The Rust package manager *homepage*: https://crates.io/ ========== ============== -version toolchain +version toolchain ========== ============== ``0.13.0`` ``foss/2016b`` ========== ============== @@ -5414,7 +5553,7 @@ Carma - A molecular dynamics analysis program *homepage*: http://utopia.duth.gr/~glykos/Carma.html ======== ============== -version toolchain +version toolchain ======== ============== ``2.01`` ``foss/2019b`` ======== ============== @@ -5430,7 +5569,7 @@ carputils is a Python framework for generating and running openCARP examples. *homepage*: https://git.opencarp.org/openCARP/carputils ============ ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ============== ``20200915`` ``-Python-3.8.2`` ``foss/2020a`` ``20210513`` ``foss/2020b`` @@ -5447,13 +5586,13 @@ Cartopy is a Python package designed to make drawing maps for data analysis and *homepage*: https://scitools.org.uk/cartopy/docs/latest/ ================ ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ================ ================= =============================== -``0.18.0`` ``-Python-3.7.4`` ``foss/2019b`` -``0.18.0`` ``-Python-3.8.2`` ``foss/2020a`` +``0.18.0`` ``-Python-3.7.4`` ``foss/2019b`` +``0.18.0`` ``-Python-3.8.2`` ``foss/2020a`` ``0.19.0.post1`` ``foss/2020b``, ``intel/2020b`` -``0.20.0`` ``foss/2021a`` -``0.20.3`` ``foss/2021b`` +``0.20.0`` ``foss/2021a`` +``0.20.3`` ``foss/2021b``, ``foss/2022a`` ================ ================= =============================== @@ -5467,7 +5606,7 @@ CaSpER is a signal processing approach for identification, visualization, and in *homepage*: https://github.com/akdess/CaSpER ======= ============== -version toolchain +version toolchain ======= ============== ``2.0`` ``foss/2019b`` ======= ============== @@ -5483,7 +5622,7 @@ CASTEP is an electronic structure materials modelling code based on density func *homepage*: http://www.castep.org ========== ====================================================================================== -version toolchain +version toolchain ========== ====================================================================================== ``21.1.1`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``foss/2019b``, ``intel/2019b``, ``iomkl/2019b`` ========== ====================================================================================== @@ -5499,14 +5638,30 @@ CastXML is a C-family abstract syntax tree XML output tool. *homepage*: https://github.com/CastXML/CastXML ============ ================= -version toolchain +version toolchain ============ ================= ``0.4.3`` ``GCCcore/8.3.0`` -``20160617`` ``foss/2016a`` -``20180806`` ``foss/2018a`` +``20160617`` ``foss/2016a`` +``20180806`` ``foss/2018a`` ============ ================= +.. _list_software_CAT-BAT_476: + +*CAT-BAT* ++++++++++ + +Tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs). + +*homepage*: https://github.com/dutilh/CAT + +========= ============== +version toolchain +========= ============== +``5.2.3`` ``GCC/10.3.0`` +========= ============== + + .. _list_software_Catch2_533: *Catch2* @@ -5517,7 +5672,7 @@ A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD *homepage*: https://github.com/catchorg/Catch2 ========== ========== -version toolchain +version toolchain ========== ========== ``2.9.1`` ``system`` ``2.11.0`` ``system`` @@ -5535,7 +5690,7 @@ A set of scikit-learn-style transformers for encoding categorical variables into *homepage*: https://github.com/scikit-learn-contrib/category_encoders ========= ============== -version toolchain +version toolchain ========= ============== ``2.4.1`` ``foss/2021b`` ========= ============== @@ -5551,7 +5706,7 @@ Catalyst Micro-kinetic Analysis Package for automated creation of micro-kinetic *homepage*: https://catmap.readthedocs.io/ ============ ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============== ``20170927`` ``-Python-2.7.14`` ``intel/2017b`` ============ ================== =============== @@ -5567,7 +5722,7 @@ CausalLift: Python package for Uplift Modeling in real-world business; applicabl *homepage*: https://github.com/Minyus/causallift ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.0.6`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -5583,7 +5738,7 @@ Causal ML: A Python Package for Uplift Modeling and Causal Inference with ML *homepage*: https://github.com/uber/causalml ================== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ================= ============== ``0.3.0-20180610`` ``-Python-3.7.2`` ``foss/2019a`` ``0.8.0-20200909`` ``-Python-3.8.2`` ``foss/2020a`` @@ -5600,7 +5755,7 @@ SNV expectation maximisation based mutation calling algorithm aimed at detecti *homepage*: http://cancerit.github.io/CaVEMan/ ========== ============== -version toolchain +version toolchain ========== ============== ``1.13.2`` ``foss/2018a`` ========== ============== @@ -5616,7 +5771,7 @@ CAusal Variants Identication in Associated Regions. A statistical framework tha *homepage*: https://github.com/fhormoz/caviar ================ ============== -version toolchain +version toolchain ================ ============== ``2.2-20190419`` ``foss/2019b`` ================ ============== @@ -5632,9 +5787,9 @@ Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming *homepage*: https://github.com/coin-or/Cbc ========== ============================== -version toolchain +version toolchain ========== ============================== -``2.10.3`` ``foss/2018b`` +``2.10.3`` ``foss/2018b`` ``2.10.5`` ``foss/2020b``, ``foss/2021a`` ========== ============================== @@ -5649,7 +5804,7 @@ C interface to the BLAS *homepage*: https://www.netlib.org/blas/ ============ ================================================ -version toolchain +version toolchain ============ ================================================ ``20110120`` ``foss/2016b``, ``intel/2019b``, ``intel/2020a`` ============ ================================================ @@ -5665,16 +5820,16 @@ Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by cach *homepage*: https://ccache.dev/ ========== ============= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ================== -``3.2.5`` ``system`` -``3.3.1`` ``system`` -``3.3.3`` ``system`` -``3.3.4`` ``-f90`` ``system`` -``3.7.11`` ``system`` -``4.2.1`` ``system`` +``3.2.5`` ``system`` +``3.3.1`` ``system`` +``3.3.3`` ``system`` +``3.3.4`` ``-f90`` ``system`` +``3.7.11`` ``system`` +``4.2.1`` ``system`` ``4.6.1`` ``GCCcore/11.2.0`` -``4.6.3`` ``system`` +``4.6.3`` ``system`` ========== ============= ================== @@ -5688,7 +5843,7 @@ CCfits is an object oriented interface to the cfitsio library. It is designed to *homepage*: https://heasarc.gsfc.nasa.gov/fitsio/CCfits/ ======= ================= -version toolchain +version toolchain ======= ================= ``2.5`` ``GCCcore/9.3.0`` ======= ================= @@ -5704,10 +5859,10 @@ Clozure CL (often called CCL for short) is a free Common Lisp implementation wi *homepage*: https://ccl.clozure.com/ ========== ================== -version toolchain +version toolchain ========== ================== -``1.11.5`` ``system`` -``1.12`` ``GCCcore/9.3.0`` +``1.11.5`` ``system`` +``1.12`` ``GCCcore/9.3.0`` ``1.12.1`` ``GCCcore/10.3.0`` ========== ================== @@ -5722,11 +5877,11 @@ cclib is a Python library that provides parsers for computational chemistry log *homepage*: https://cclib.github.io/ ========= ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============================== -``1.5`` ``-Python-3.5.2`` ``foss/2016b`` +``1.5`` ``-Python-3.5.2`` ``foss/2016b`` ``1.6.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.7.2`` ``foss/2021b`` +``1.7.2`` ``foss/2021b`` ========= ================= =============================== @@ -5740,7 +5895,7 @@ The Cooperating Computing Tools (CCTools) help you to design and deploy scalabl *homepage*: https://ccl.cse.nd.edu/ ========== ================= -version toolchain +version toolchain ========== ================= ``7.0.22`` ``GCCcore/8.3.0`` ========== ================= @@ -5756,11 +5911,11 @@ CD-HIT is a very widely used program for clustering and comparing protein or nu *homepage*: https://github.com/weizhongli/cdhit ========= ============== ===================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============== ===================================================================================================================== -``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` -``4.6.6`` ``foss/2016b`` -``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` +``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` +``4.6.6`` ``foss/2016b`` +``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` ``4.8.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018b``, ``iccifort/2019.5.281`` ========= ============== ===================================================================================================================== @@ -5775,7 +5930,7 @@ CDAT is a powerful and complete front-end to a rich set of visual-data explorat *homepage*: https://github.com/CDAT/cdat ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``8.2.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -5791,7 +5946,7 @@ Fasta file indexing and retrival tool *homepage*: https://sourceforge.net/projects/cdbfasta ======== ================================================================================ -version toolchain +version toolchain ======== ================================================================================ ``0.99`` ``GCC/8.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281`` ======== ================================================================================ @@ -5807,7 +5962,7 @@ CDB (Constant DataBase) indexing and retrieval tools for FASTA files *homepage*: http://compbio.dfci.harvard.edu/tgi ======== ============== -version toolchain +version toolchain ======== ============== ``0.99`` ``GCC/10.2.0`` ======== ============== @@ -5823,7 +5978,7 @@ An efficient implementation of the Double Description Method *homepage*: https://github.com/cddlib/cddlib ========= ================= -version toolchain +version toolchain ========= ================= ``0.94i`` ``GCCcore/8.2.0`` ``0.94j`` ``GCCcore/8.3.0`` @@ -5840,11 +5995,11 @@ cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for anal *homepage*: https://github.com/Magdoll/cDNA_Cupcake ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``5.8`` ``-Python-2.7.14`` ``intel/2018a`` -``24.2.0`` ``-Python-3.8.2`` ``foss/2020a`` -``26.0.0`` ``foss/2021a`` +``24.2.0`` ``-Python-3.8.2`` ``foss/2020a`` +``26.0.0`` ``foss/2021a`` ========== ================== =============== @@ -5858,19 +6013,37 @@ CDO is a collection of command line Operators to manipulate and analyse Climate *homepage*: https://code.zmaw.de/projects/cdo ========== ================================================================== -version toolchain +version toolchain ========== ================================================================== -``1.7.2`` ``intel/2016b`` -``1.8.1`` ``intel/2017a`` -``1.9.1`` ``intel/2017b`` -``1.9.2`` ``intel/2017b`` -``1.9.5`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``1.9.8`` ``intel/2019b`` +``1.7.2`` ``intel/2016b`` +``1.8.1`` ``intel/2017a`` +``1.9.1`` ``intel/2017b`` +``1.9.2`` ``intel/2017b`` +``1.9.5`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +``1.9.8`` ``intel/2019b`` ``1.9.10`` ``gompi/2019b``, ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2021b`` -``2.0.5`` ``gompi/2021b`` +``2.0.5`` ``gompi/2021b`` +``2.0.6`` ``gompi/2022a`` +``2.1.1`` ``gompi/2021a`` ========== ================================================================== +.. _list_software_cdo-bindings_1201: + +*cdo-bindings* +++++++++++++++ + +Python interface to CDO. + +*homepage*: https://github.com/Try2Code/cdo-bindings + +========= ============== +version toolchain +========= ============== +``1.5.7`` ``foss/2021b`` +========= ============== + + .. _list_software_cdsapi_628: *cdsapi* @@ -5880,13 +6053,14 @@ Climate Data Store API *homepage*: https://pypi.org/project/cdsapi -========= ================= ================= -version versionsuffix toolchain -========= ================= ================= -``0.1.4`` ``foss/2019a`` -``0.1.4`` ``-Python-3.6.6`` ``foss/2018b`` +========= ================= ================== +version versionsuffix toolchain +========= ================= ================== +``0.1.4`` ``foss/2019a`` +``0.1.4`` ``-Python-3.6.6`` ``foss/2018b`` ``0.3.0`` ``GCCcore/9.3.0`` -========= ================= ================= +``0.5.1`` ``GCCcore/11.3.0`` +========= ================= ================== .. _list_software_cell2location_1323: @@ -5899,7 +6073,7 @@ Comprehensive mapping of tissue cell architecture via integrated single cell an *homepage*: https://github.com/BayraktarLab/cell2location/ ============== ================== -version toolchain +version toolchain ============== ================== ``0.05-alpha`` ``fosscuda/2020b`` ============== ================== @@ -5915,7 +6089,7 @@ A Comprehensive Toolbox for Gene Expression Deconvolution *homepage*: http://web.cbio.uct.ac.za/~renaud/CRAN/web/CellMix ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.6.2`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== @@ -5931,7 +6105,7 @@ Cell Ranger is a set of analysis pipelines that process Chromium single-cell RN *homepage*: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger ========= ========== -version toolchain +version toolchain ========= ========== ``3.0.0`` ``system`` ``3.0.2`` ``system`` @@ -5957,7 +6131,7 @@ Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cel *homepage*: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc ========= ========== -version toolchain +version toolchain ========= ========== ``1.0.1`` ``system`` ``2.0.0`` ``system`` @@ -5975,7 +6149,7 @@ Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Ce *homepage*: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac ========= ========== -version toolchain +version toolchain ========= ========== ``1.2.0`` ``system`` ``2.0.0`` ``system`` @@ -5993,7 +6167,7 @@ CellRank is a toolkit to uncover cellular dynamics based on Markov state modeli *homepage*: https://cellrank.readthedocs.io/en/stable/ ========= ============== -version toolchain +version toolchain ========= ============== ``1.4.0`` ``foss/2021a`` ========= ============== @@ -6009,7 +6183,7 @@ A tool for semi-automatic cell type annotation *homepage*: https://www.celltypist.org/ ========= ============== -version toolchain +version toolchain ========= ============== ``1.0.0`` ``foss/2021b`` ========= ============== @@ -6024,13 +6198,13 @@ Classifier for metagenomic sequences *homepage*: https://ccb.jhu.edu/software/centrifuge -============== =============================== -version toolchain -============== =============================== -``1.0.3`` ``foss/2018b`` -``1.0.4`` ``gompi/2020b`` +============== ================================ +version toolchain +============== ================================ +``1.0.3`` ``foss/2018b`` +``1.0.4`` ``gompi/2020b``, ``gompi/2021a`` ``1.0.4-beta`` ``foss/2018b``, ``gompi/2020a`` -============== =============================== +============== ================================ .. _list_software_Cereal_588: @@ -6043,7 +6217,7 @@ cereal is a header-only C++11 serialization library. cereal takes arbitrary data *homepage*: https://uscilab.github.io/cereal/ ========= ========== -version toolchain +version toolchain ========= ========== ``1.3.0`` ``system`` ========= ========== @@ -6059,7 +6233,7 @@ CESM is a fully-coupled, community, global climate model that provides state-of- *homepage*: https://www.cesm.ucar.edu/models/cesm2/ ======= ================================================================ -version toolchain +version toolchain ======= ================================================================ ``2`` ``foss/2018b``, ``foss/2021b``, ``intel/2018b``, ``iomkl/2018b`` ======= ================================================================ @@ -6075,7 +6249,7 @@ CFDEMcoupling is an open source CFD-DEM engine. It provides the possibility to c *homepage*: https://www.cfdem.com/cfdemrcoupling-open-source-cfd-dem-framework ========= ============== -version toolchain +version toolchain ========= ============== ``3.8.0`` ``foss/2018a`` ========= ============== @@ -6090,17 +6264,17 @@ CFITSIO is a library of C and Fortran subroutines for reading and writing data f *homepage*: https://heasarc.gsfc.nasa.gov/fitsio/ -======== ===================================================== -version toolchain -======== ===================================================== -``3.38`` ``foss/2016a``, ``intel/2016a`` +======== ========================================================== +version toolchain +======== ========================================================== +``3.38`` ``foss/2016a``, ``intel/2016a`` ``3.41`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``intel/2016b`` -``3.42`` ``GCCcore/6.4.0``, ``intel/2017b`` -``3.45`` ``GCCcore/7.3.0``, ``intel/2018b`` -``3.47`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.48`` ``GCCcore/9.3.0`` -``3.49`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` -======== ===================================================== +``3.42`` ``GCCcore/6.4.0``, ``intel/2017b`` +``3.45`` ``GCCcore/7.3.0``, ``intel/2018b`` +``3.47`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.48`` ``GCCcore/9.3.0`` +``3.49`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +======== ========================================================== .. _list_software_cftime_632: @@ -6113,11 +6287,11 @@ Time-handling functionality from netcdf4-python *homepage*: https://github.com/Unidata/cftime =========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== =============================== -``1.0.0`` ``-Python-3.6.4`` ``intel/2018a`` -``1.0.0b1`` ``-Python-3.6.2`` ``foss/2017b`` -``1.0.1`` ``-Python-2.7.15`` ``intel/2018b`` +``1.0.0`` ``-Python-3.6.4`` ``intel/2018a`` +``1.0.0b1`` ``-Python-3.6.2`` ``foss/2017b`` +``1.0.1`` ``-Python-2.7.15`` ``intel/2018b`` ``1.0.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` =========== ================== =============================== @@ -6131,27 +6305,27 @@ The goal of the CGAL Open Source Project is to provide easy access to efficient *homepage*: https://www.cgal.org/ -========== ================== ================================================= -version versionsuffix toolchain -========== ================== ================================================= -``4.8`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``4.8.1`` ``foss/2016b``, ``intel/2016b`` -``4.8.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``4.9`` ``-Python-2.7.12`` ``intel/2016b`` -``4.9`` ``-Python-2.7.13`` ``intel/2017a`` -``4.11`` ``-Python-2.7.13`` ``intel/2017a`` -``4.11`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``4.11`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``4.11.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``4.11.1`` ``-Python-2.7.15`` ``foss/2018b`` -``4.11.1`` ``-Python-3.6.4`` ``foss/2018a`` -``4.11.1`` ``-Python-3.6.6`` ``foss/2018b`` -``4.14`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``4.14.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``4.14.3`` ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a`` -``4.14.3`` ``-Python-3.8.2`` ``gompi/2020a``, ``iimpi/2020a`` -``5.2`` ``gompi/2020b`` -========== ================== ================================================= +========== ================== ================================================================== +version versionsuffix toolchain +========== ================== ================================================================== +``4.8`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``4.8.1`` ``foss/2016b``, ``intel/2016b`` +``4.8.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``4.9`` ``-Python-2.7.12`` ``intel/2016b`` +``4.9`` ``-Python-2.7.13`` ``intel/2017a`` +``4.11`` ``-Python-2.7.13`` ``intel/2017a`` +``4.11`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``4.11`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``4.11.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``4.11.1`` ``-Python-2.7.15`` ``foss/2018b`` +``4.11.1`` ``-Python-3.6.4`` ``foss/2018a`` +``4.11.1`` ``-Python-3.6.6`` ``foss/2018b`` +``4.14`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``4.14.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``4.14.3`` ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``iimpi/2021a`` +``4.14.3`` ``-Python-3.8.2`` ``gompi/2020a``, ``iimpi/2020a`` +``5.2`` ``gompi/2020b`` +========== ================== ================================================================== .. _list_software_cget_419: @@ -6164,7 +6338,7 @@ Cmake package retrieval. This can be used to download and install cmake packages *homepage*: https://cget.readthedocs.io/en/latest/index.html ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.1.6`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================= ============== @@ -6180,9 +6354,9 @@ The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that *homepage*: https://github.com/coin-or/Cgl ========== ============================== -version toolchain +version toolchain ========== ============================== -``0.60.2`` ``foss/2018b`` +``0.60.2`` ``foss/2018b`` ``0.60.3`` ``foss/2020b``, ``foss/2021a`` ========== ============================== @@ -6197,7 +6371,7 @@ Command-line Toolset for Bisulfite Sequencing Data Analysis *homepage*: https://cgmaptools.github.io/ ========= =============== -version toolchain +version toolchain ========= =============== ``0.1.2`` ``intel/2019b`` ========= =============== @@ -6213,9 +6387,9 @@ The CGNS system is designed to facilitate the exchange of data between sites and *homepage*: https://cgns.github.io/ ========= =================== -version toolchain +version toolchain ========= =================== -``3.3.1`` ``foss/2016b`` +``3.3.1`` ``foss/2016b`` ``4.1.0`` ``intelcuda/2019b`` ========= =================== @@ -6230,12 +6404,13 @@ CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-los *homepage*: https://github.com/team-charls/charls ========= ==================================== -version toolchain +version toolchain ========= ==================================== ``2.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.1.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2.2.0`` ``GCCcore/10.2.0`` -``2.3.4`` ``GCCcore/10.3.0`` +``2.2.0`` ``GCCcore/10.2.0`` +``2.3.4`` ``GCCcore/10.3.0`` +``2.4.1`` ``GCCcore/11.3.0`` ========= ==================================== @@ -6249,7 +6424,7 @@ CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely *homepage*: http://www.charmm.org ======== =============================== -version toolchain +version toolchain ======== =============================== ``37b2`` ``foss/2016a``, ``intel/2016a`` ======== =============================== @@ -6265,7 +6440,7 @@ CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely *homepage*: http://www.charmm.org ======== =============================== -version toolchain +version toolchain ======== =============================== ``43b2`` ``foss/2017b``, ``intel/2017b`` ======== =============================== @@ -6281,7 +6456,7 @@ Case-control HAplotype Sharing analyses. Haplotype sharing analyses for genome *homepage*: http://people.duke.edu/~asallen/Software.html ============ ========== -version toolchain +version toolchain ============ ========== ``20130626`` ``system`` ============ ========== @@ -6297,7 +6472,7 @@ Check is a unit testing framework for C. It features a simple interface for defi *homepage*: https://libcheck.github.io/check/ ========== ============================================================================= -version toolchain +version toolchain ========== ============================================================================= ``0.15.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ========== ============================================================================= @@ -6313,7 +6488,7 @@ Check is a unit testing framework for C. It features a simple interface for def *homepage*: https://libcheck.github.io/check/ ========== ================= -version toolchain +version toolchain ========== ================= ``0.12.0`` ``GCCcore/6.4.0`` ========== ================= @@ -6329,16 +6504,16 @@ CheckM provides a set of tools for assessing the quality of genomes recovered fr *homepage*: https://github.com/Ecogenomics/CheckM ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== ``1.0.13`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``1.0.13`` ``-Python-2.7.15`` ``foss/2018b`` +``1.0.13`` ``-Python-2.7.15`` ``foss/2018b`` ``1.0.13`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.0.18`` ``-Python-2.7.15`` ``foss/2019a`` -``1.0.18`` ``-Python-2.7.18`` ``foss/2020b`` +``1.0.18`` ``-Python-2.7.15`` ``foss/2019a`` +``1.0.18`` ``-Python-2.7.18`` ``foss/2020b`` ``1.1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.1.3`` ``foss/2021a``, ``foss/2021b`` -``1.1.3`` ``-Python-3.8.2`` ``intel/2020a`` +``1.1.3`` ``foss/2021a``, ``foss/2021b`` +``1.1.3`` ``-Python-3.8.2`` ``intel/2020a`` ========== ================== =============================== @@ -6352,12 +6527,28 @@ Cheetah is an open source template engine and code generation tool. *homepage*: https://cheetahtemplate.org ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``2.4.4`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============== +.. _list_software_Chemaxon-Marvin_1485: + +*Chemaxon-Marvin* ++++++++++++++++++ + +Marvin suite is a chemically intelligent desktop toolkit built to help you draw, edit, publish, render, import and export your chemical structures and as well as allowing you to convert between various chemical and graphical file formats. It is free for individual, academic and non-commercial use. + +*homepage*: https://chemaxon.com/products/marvin + +========= ========== +version toolchain +========= ========== +``21.14`` ``system`` +========= ========== + + .. _list_software_CheMPS2_562: *CheMPS2* @@ -6368,16 +6559,17 @@ CheMPS2 is a scientific library which contains a spin-adapted implementation of *homepage*: https://github.com/SebWouters/CheMPS2 =========== ================================================================================= -version toolchain +version toolchain =========== ================================================================================= -``1.6`` ``intel/2016a`` -``1.7-rc2`` ``intel/2016a`` -``1.7.1`` ``intel/2016a`` -``1.7.2`` ``intel/2016a`` -``1.8`` ``intel/2016b`` -``1.8.8`` ``intel/2018b`` +``1.6`` ``intel/2016a`` +``1.7-rc2`` ``intel/2016a`` +``1.7.1`` ``intel/2016a`` +``1.7.2`` ``intel/2016a`` +``1.8`` ``intel/2016b`` +``1.8.8`` ``intel/2018b`` ``1.8.9`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b`` -``1.8.11`` ``foss/2021b`` +``1.8.11`` ``foss/2021b`` +``1.8.12`` ``foss/2022a`` =========== ================================================================================= @@ -6391,9 +6583,9 @@ CHERAB is a python library for forward modelling diagnostics based on spectrosc *homepage*: https://cherab.github.io/documentation/index.html ========= ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============================== -``1.2.0`` ``-Python-3.6.6`` ``intel/2018b`` +``1.2.0`` ``-Python-3.6.6`` ``intel/2018b`` ``1.3.0`` ``foss/2020b``, ``intel/2020b`` ========= ================= =============================== @@ -6408,7 +6600,7 @@ chewBBACA stands for "BSR-Based Allele Calling Algorithm". chewBBACA is a compre *homepage*: https://github.com/B-UMMI/chewBBACA ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``2.5.5`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================= =============== @@ -6424,7 +6616,7 @@ Cumulative density function of linear combinations of independent chi-square ran *homepage*: https://github.com/limix/chi2comb ========= ================= -version toolchain +version toolchain ========= ================= ``0.0.3`` ``GCCcore/7.3.0`` ========= ================= @@ -6440,7 +6632,7 @@ UCSF Chimera is a highly extensible program for interactive visualization and *homepage*: https://www.cgl.ucsf.edu/chimera/ ======== ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================= ========== ``1.10`` ``-linux_x86_64`` ``system`` ``1.16`` ``-linux_x86_64`` ``system`` @@ -6457,7 +6649,7 @@ ChimPipe is a computational method for the detection of novel transcription-indu *homepage*: https://chimpipe.readthedocs.org/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``0.9.5`` ``foss/2018b`` ``0.9.5`` ``-Python-2.7.12`` ``foss/2016b`` @@ -6474,7 +6666,7 @@ Chromaprint is the core component of the AcoustID project. It's a client-side li *homepage*: https://acoustid.org/chromaprint ========= ================= -version toolchain +version toolchain ========= ================= ``1.4.3`` ``GCCcore/8.2.0`` ========= ================= @@ -6490,7 +6682,7 @@ Cicero is an R package that provides tools for analyzing single-cell chromatin a *homepage*: https://cole-trapnell-lab.github.io/cicero-release ============ ===================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ===================== ============== ``1.3.4.11`` ``-R-4.0.3-Monocle3`` ``foss/2020b`` ============ ===================== ============== @@ -6506,7 +6698,7 @@ CIF2Cell is a tool to generate the geometrical setup for various electronic stru *homepage*: https://sourceforge.net/projects/cif2cell ========== ================== ================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================= ``1.2.10`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` ========== ================== ================= @@ -6522,7 +6714,7 @@ CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. *homepage*: https://circexplorer2.readthedocs.io/ ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``1.1.10`` ``-Python-2.7.14`` ``intel/2017b`` ========== ================== =============== @@ -6538,11 +6730,11 @@ CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. *homepage*: http://circexplorer2.readthedocs.io/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``2.3.2`` ``-Python-2.7.14`` ``intel/2017b`` ``2.3.3`` ``-Python-2.7.14`` ``intel/2018a`` -``2.3.8`` ``-Python-2.7.18`` ``foss/2020b`` +``2.3.8`` ``-Python-2.7.18`` ``foss/2020b`` ========= ================== =============== @@ -6555,14 +6747,14 @@ Circos is a software package for visualizing data and information. It visualize *homepage*: http://www.circos.ca/ -========== ================ ================= -version versionsuffix toolchain -========== ================ ================= -``0.69-5`` ``-Perl-5.24.0`` ``foss/2016b`` +========== ================ ===================================== +version versionsuffix toolchain +========== ================ ===================================== +``0.69-5`` ``-Perl-5.24.0`` ``foss/2016b`` ``0.69-6`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` ``0.69-6`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -``0.69-9`` ``GCCcore/9.3.0`` -========== ================ ================= +``0.69-9`` ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +========== ================ ===================================== .. _list_software_CIRI_295: @@ -6575,7 +6767,7 @@ CircRNA Identifier. A de novo circular RNA identification tool *homepage*: https://sourceforge.net/projects/ciri/ ========= ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =============== ``2.0.6`` ``-Perl-5.26.0`` ``intel/2017b`` ========= ================ =============== @@ -6591,7 +6783,7 @@ Circular RNA Identification for Long-Reads Nanopore Sequencing Data *homepage*: https://github.com/bioinfo-biols/CIRI-long/ ========= ============== -version toolchain +version toolchain ========= ============== ``1.0.2`` ``foss/2020b`` ========= ============== @@ -6607,7 +6799,7 @@ cisTEM is user-friendly software to process cryo-EM images of macromolecular com *homepage*: https://cistem.org/ ============== ============== -version toolchain +version toolchain ============== ============== ``1.0.0-beta`` ``foss/2018a`` ============== ============== @@ -6623,7 +6815,7 @@ A python package that allows to count antibody TAGS from a CITE-seq and/or cell *homepage*: https://github.com/Hoohm/CITE-seq-Count ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` ``1.4.3`` ``-Python-3.7.4`` ``foss/2019b`` @@ -6640,37 +6832,37 @@ C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard lib *homepage*: https://clang.llvm.org/ ========== ================== ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ====================================== -``3.3`` ``GCC/4.8.1`` -``3.4`` ``GCC/4.8.2`` -``3.4.1`` ``GCC/4.8.2`` -``3.4.2`` ``GCC/4.8.2`` -``3.6.0`` ``GCC/4.9.2`` -``3.6.1`` ``GCC/4.9.2`` -``3.7.0`` ``GNU/4.9.3-2.25`` -``3.7.1`` ``GCC/4.9.3-2.25``, ``foss/2016a`` -``3.8.0`` ``GCC/4.9.3-2.25`` -``3.8.1`` ``GCC/5.4.0-2.26``, ``foss/2016b`` -``5.0.0`` ``GCC/6.4.0-2.28`` -``5.0.1`` ``GCC/6.4.0-2.28`` +``3.3`` ``GCC/4.8.1`` +``3.4`` ``GCC/4.8.2`` +``3.4.1`` ``GCC/4.8.2`` +``3.4.2`` ``GCC/4.8.2`` +``3.6.0`` ``GCC/4.9.2`` +``3.6.1`` ``GCC/4.9.2`` +``3.7.0`` ``GNU/4.9.3-2.25`` +``3.7.1`` ``GCC/4.9.3-2.25``, ``foss/2016a`` +``3.8.0`` ``GCC/4.9.3-2.25`` +``3.8.1`` ``GCC/5.4.0-2.26``, ``foss/2016b`` +``5.0.0`` ``GCC/6.4.0-2.28`` +``5.0.1`` ``GCC/6.4.0-2.28`` ``6.0.1`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30`` -``7.0.0`` ``GCC/6.4.0-2.28`` -``7.0.1`` ``GCC/7.3.0-2.30`` -``8.0.0`` ``GCCcore/8.2.0`` -``8.0.0`` ``-CUDA-10.1.105`` ``GCCcore/8.2.0`` -``8.0.1`` ``-CUDA-10.1.105`` ``GCC/8.2.0-2.31.1`` -``8.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` -``9.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``9.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` -``10.0.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``10.0.1`` ``GCCcore/9.3.0`` -``11.0.0`` ``GCCcore/9.3.0`` -``11.0.1`` ``GCCcore/10.2.0``, ``gcccuda/2020b`` +``7.0.0`` ``GCC/6.4.0-2.28`` +``7.0.1`` ``GCC/7.3.0-2.30`` +``8.0.0`` ``GCCcore/8.2.0`` +``8.0.0`` ``-CUDA-10.1.105`` ``GCCcore/8.2.0`` +``8.0.1`` ``-CUDA-10.1.105`` ``GCC/8.2.0-2.31.1`` +``8.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` +``9.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``9.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` +``10.0.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``10.0.1`` ``GCCcore/9.3.0`` +``11.0.0`` ``GCCcore/9.3.0`` +``11.0.1`` ``GCCcore/10.2.0``, ``gcccuda/2020b`` ``12.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``12.0.1`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` +``12.0.1`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` ``13.0.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``13.0.1`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` +``13.0.1`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` ========== ================== ====================================== @@ -6684,7 +6876,7 @@ AOMP is an open source Clang/LLVM based compiler with added support for the Open *homepage*: https://github.com/RadeonOpenCompute/llvm-project ========= ================== -version toolchain +version toolchain ========= ================== ``4.5.0`` ``GCCcore/11.2.0`` ========= ================== @@ -6700,10 +6892,10 @@ Python bindings for libclang *homepage*: https://clang.llvm.org ========== ================== ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ====================================== -``8.0.0`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` -``10.0.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``8.0.0`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``10.0.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``13.0.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ================== ====================================== @@ -6718,7 +6910,7 @@ C version of LAPACK *homepage*: http://www.netlib.org/clapack ========= =========================================================================== -version toolchain +version toolchain ========= =========================================================================== ``3.2.1`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a`` ========= =========================================================================== @@ -6734,7 +6926,7 @@ CLuster Expansion in Atomic Simulation Environment (CLEASE) is a package that au *homepage*: https://gitlab.com/computationalmaterials/clease ========== =============== -version toolchain +version toolchain ========== =============== ``0.10.6`` ``intel/2021a`` ========== =============== @@ -6750,21 +6942,37 @@ The CLHEP project is intended to be a set of HEP-specific foundation and utilit *homepage*: https://proj-clhep.web.cern.ch/proj-clhep/ =========== ================================================================ -version toolchain +version toolchain =========== ================================================================ -``2.1.1.0`` ``intel/2016a`` -``2.1.3.1`` ``intel/2016a`` -``2.2.0.8`` ``intel/2016a`` -``2.3.1.1`` ``intel/2016a`` -``2.3.4.3`` ``foss/2017b``, ``intel/2017b`` -``2.4.0.0`` ``intel/2017b`` +``2.1.1.0`` ``intel/2016a`` +``2.1.3.1`` ``intel/2016a`` +``2.2.0.8`` ``intel/2016a`` +``2.3.1.1`` ``intel/2016a`` +``2.3.4.3`` ``foss/2017b``, ``intel/2017b`` +``2.4.0.0`` ``intel/2017b`` ``2.4.1.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018b`` -``2.4.1.3`` ``foss/2019b``, ``foss/2020a`` -``2.4.4.0`` ``GCC/10.2.0``, ``GCC/11.2.0`` -``2.4.5.1`` ``GCC/11.2.0`` +``2.4.1.3`` ``foss/2019b``, ``foss/2020a`` +``2.4.4.0`` ``GCC/10.2.0``, ``GCC/11.2.0`` +``2.4.5.1`` ``GCC/11.2.0`` =========== ================================================================ +.. _list_software_CliMetLab_845: + +*CliMetLab* ++++++++++++ + +CliMetLab is a Python package aiming at simplifying access to climate and meteorological datasets, allowing users to focus on science instead of technical issues such as data access and data formats. It is mostly intended to be used in Jupyter notebooks, and be interoperable with all popular data analytic packages, such as Numpy, Pandas, Xarray, SciPy, Matplotlib, etc. as well as machine learning frameworks, such as Tensorflow, Keras or PyTorch. + +*homepage*: https://climetlab.readthedocs.io/ + +========== ============== +version toolchain +========== ============== +``0.12.6`` ``foss/2022a`` +========== ============== + + .. _list_software_CLISP_379: *CLISP* @@ -6775,7 +6983,7 @@ Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functio *homepage*: https://clisp.sourceforge.io/ ======== ==================================== -version toolchain +version toolchain ======== ==================================== ``2.49`` ``GCCcore/6.4.0``, ``GCCcore/9.3.0`` ======== ==================================== @@ -6791,7 +6999,7 @@ Efficient Inference of Recombination in Whole Bacterial Genomes *homepage*: https://github.com/xavierdidelot/ClonalFrameML ======== ============== -version toolchain +version toolchain ======== ============== ``1.11`` ``foss/2016b`` ======== ============== @@ -6807,12 +7015,28 @@ CLooG is a free software and library to generate code for scanning Z-polyhedra. *homepage*: http://www.bastoul.net/cloog/index.php ========== ============= -version toolchain +version toolchain ========== ============= ``0.18.1`` ``GCC/4.8.2`` ========== ============= +.. _list_software_CloudCompare_1214: + +*CloudCompare* +++++++++++++++ + +3D point cloud and mesh processing software + +*homepage*: https://www.cloudcompare.org/ + +========== ============== +version toolchain +========== ============== +``2.12.4`` ``foss/2021b`` +========== ============== + + .. _list_software_Clp_287: *Clp* @@ -6823,11 +7047,11 @@ Clp (Coin-or linear programming) is an open-source linear programming solver. It *homepage*: https://github.com/coin-or/Clp ========== ============================== -version toolchain +version toolchain ========== ============================== -``1.17.3`` ``foss/2018b`` +``1.17.3`` ``foss/2018b`` ``1.17.6`` ``foss/2020b``, ``foss/2021a`` -``1.17.7`` ``foss/2021b`` +``1.17.7`` ``foss/2021b`` ========== ============================== @@ -6841,9 +7065,9 @@ Clustal Omega is a multiple sequence alignment program for proteins. It produce *homepage*: http://www.clustal.org/omega/ ========= ============================================================================================================= -version toolchain +version toolchain ========= ============================================================================================================= -``1.2.0`` ``foss/2016b`` +``1.2.0`` ``foss/2016b`` ``1.2.4`` ``GCC/10.3.0``, ``GCC/8.3.0``, ``foss/2018b``, ``intel-compilers/2021.2.0``, ``intel/2018a``, ``intel/2018b`` ========= ============================================================================================================= @@ -6858,7 +7082,7 @@ ClustalW2 is a general purpose multiple sequence alignment program for DNA or pr *homepage*: https://www.ebi.ac.uk/Tools/msa/clustalw2/ ======= =========================================================================================================================================================================== -version toolchain +version toolchain ======= =========================================================================================================================================================================== ``2.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``foss/2016b``, ``foss/2018b``, ``foss/2021a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b``, ``intel/2020a`` ======= =========================================================================================================================================================================== @@ -6874,7 +7098,7 @@ Cluster-Buster: Finding dense clusters of motifs in DNA sequences *homepage*: https://github.com/weng-lab/cluster-buster/ ============ =============== -version toolchain +version toolchain ============ =============== ``20160106`` ``intel/2016a`` ============ =============== @@ -6890,7 +7114,7 @@ ClusterShell is an event-driven open source Python library, designed to run loca *homepage*: https://cea-hpc.github.io/clustershell/ ========= ========== -version toolchain +version toolchain ========= ========== ``1.7.3`` ``system`` ========= ========== @@ -6906,47 +7130,48 @@ CMake, the cross-platform, open-source build system. CMake is a family of tools *homepage*: https://www.cmake.org ========== ================================================================================================================================================= -version toolchain +version toolchain ========== ================================================================================================================================================= -``2.8.11`` ``GCC/4.8.1`` -``2.8.12`` ``GCC/4.8.1``, ``GCC/4.8.2`` -``3.0.0`` ``GCC/4.8.3`` -``3.1.0`` ``GCC/4.9.2`` -``3.1.3`` ``GCC/4.9.2``, ``system`` -``3.2.1`` ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` -``3.3.1`` ``system`` -``3.3.2`` ``GNU/4.9.3-2.25``, ``gimkl/2.11.5`` +``2.8.11`` ``GCC/4.8.1`` +``2.8.12`` ``GCC/4.8.1``, ``GCC/4.8.2`` +``3.0.0`` ``GCC/4.8.3`` +``3.1.0`` ``GCC/4.9.2`` +``3.1.3`` ``GCC/4.9.2``, ``system`` +``3.2.1`` ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` +``3.3.1`` ``system`` +``3.3.2`` ``GNU/4.9.3-2.25``, ``gimkl/2.11.5`` ``3.4.1`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``foss/2016a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``3.4.3`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a`` -``3.5.1`` ``intel/2016a`` -``3.5.2`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``system`` -``3.6.1`` ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``foss/2016b``, ``intel/2016b``, ``system`` -``3.6.2`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` -``3.7.1`` ``GCCcore/5.4.0``, ``GCCcore/6.2.0``, ``foss/2016b``, ``intel/2016b`` -``3.7.2`` ``GCCcore/6.3.0``, ``foss/2016b``, ``intel/2016b`` -``3.8.0`` ``GCCcore/6.3.0`` -``3.8.1`` ``GCCcore/6.3.0`` -``3.8.2`` ``GCCcore/6.3.0`` -``3.9.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``system`` -``3.9.4`` ``GCCcore/6.4.0`` -``3.9.5`` ``GCCcore/6.4.0`` -``3.9.6`` ``system`` -``3.10.0`` ``GCCcore/6.4.0`` -``3.10.1`` ``GCCcore/6.4.0`` -``3.10.2`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` -``3.10.3`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` -``3.11.1`` ``GCCcore/6.4.0`` -``3.11.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``3.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``system`` -``3.13.3`` ``GCCcore/8.2.0`` -``3.15.1`` ``system`` -``3.15.3`` ``GCCcore/8.3.0`` -``3.16.4`` ``GCCcore/9.3.0`` -``3.18.4`` ``GCCcore/10.2.0``, ``system`` -``3.20.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``3.21.1`` ``GCCcore/11.2.0`` -``3.22.1`` ``GCCcore/11.2.0`` -``3.23.1`` ``GCCcore/11.3.0`` +``3.4.3`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a`` +``3.5.1`` ``intel/2016a`` +``3.5.2`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``system`` +``3.6.1`` ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``foss/2016b``, ``intel/2016b``, ``system`` +``3.6.2`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` +``3.7.1`` ``GCCcore/5.4.0``, ``GCCcore/6.2.0``, ``foss/2016b``, ``intel/2016b`` +``3.7.2`` ``GCCcore/6.3.0``, ``foss/2016b``, ``intel/2016b`` +``3.8.0`` ``GCCcore/6.3.0`` +``3.8.1`` ``GCCcore/6.3.0`` +``3.8.2`` ``GCCcore/6.3.0`` +``3.9.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``system`` +``3.9.4`` ``GCCcore/6.4.0`` +``3.9.5`` ``GCCcore/6.4.0`` +``3.9.6`` ``system`` +``3.10.0`` ``GCCcore/6.4.0`` +``3.10.1`` ``GCCcore/6.4.0`` +``3.10.2`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` +``3.10.3`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` +``3.11.1`` ``GCCcore/6.4.0`` +``3.11.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``3.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``system`` +``3.13.3`` ``GCCcore/8.2.0`` +``3.15.1`` ``system`` +``3.15.3`` ``GCCcore/8.3.0`` +``3.16.4`` ``GCCcore/9.3.0`` +``3.18.4`` ``GCCcore/10.2.0``, ``system`` +``3.20.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``3.21.1`` ``GCCcore/11.2.0`` +``3.22.1`` ``GCCcore/11.2.0`` +``3.23.1`` ``GCCcore/11.3.0`` +``3.24.3`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========== ================================================================================================================================================= @@ -6960,7 +7185,7 @@ The R package CMAverse provides a suite of functions for reproducible causal med *homepage*: https://bs1125.github.io/CMAverse/ ============ ============== -version toolchain +version toolchain ============ ============== ``20220112`` ``foss/2021b`` ============ ============== @@ -6976,12 +7201,28 @@ CmdStanR is a lightweight interface to Stan for R users *homepage*: https://mc-stan.org/cmdstanr ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``0.5.0`` ``-R-4.1.2`` ``foss/2021b`` ========= ============= ============== +.. _list_software_cmocean_726: + +*cmocean* ++++++++++ + +This package contains colormaps for commonly-used oceanographic variables. Most of the colormaps started from matplotlib colormaps, but have now been adjusted using the viscm tool to be perceptually uniform. + +*homepage*: https://github.com/matplotlib/cmocean + +======= ============== +version toolchain +======= ============== +``2.0`` ``foss/2022a`` +======= ============== + + .. _list_software_CMSeq_441: *CMSeq* @@ -6992,7 +7233,7 @@ CMSeq is a set of commands to provide an interface to .bam files for coverage an *homepage*: https://github.com/SegataLab/cmseq/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.0.3`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -7008,7 +7249,7 @@ Integer Linear Program for the Copy-Number Tree Problem *homepage*: https://compbio.cs.brown.edu/projects/cnt-ilp/ ============ ==================== -version toolchain +version toolchain ============ ==================== ``20171031`` ``GCC/8.2.0-2.31.1`` ============ ==================== @@ -7024,12 +7265,12 @@ A command-line toolkit and Python library for detecting copy number variants an *homepage*: https://github.com/etal/cnvkit ========= ========================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ========================= =============== ``0.9.2`` ``-Python-2.7.14`` ``intel/2017b`` ``0.9.3`` ``-Python-3.6.4`` ``intel/2018a`` -``0.9.6`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` -``0.9.8`` ``-R-4.0.3`` ``foss/2020b`` +``0.9.6`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` +``0.9.8`` ``-R-4.0.3`` ``foss/2020b`` ========= ========================= =============== @@ -7043,7 +7284,7 @@ a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads *homepage*: https://github.com/abyzovlab/CNVnator ========= ============== -version toolchain +version toolchain ========= ============== ``0.3.3`` ``foss/2016b`` ========= ============== @@ -7059,12 +7300,28 @@ Co-phylog: an assembly-free phylogenomic approach for closely related organisms *homepage*: https://github.com/yhg926/co-phylog ============ ================== -version toolchain +version toolchain ============ ================== ``20201012`` ``GCC/7.3.0-2.30`` ============ ================== +.. _list_software_COBRApy_592: + +*COBRApy* ++++++++++ + +COBRApy is a package for constraint-based modeling of metabolic networks. + +*homepage*: https://opencobra.github.io/cobrapy/ + +========== ============== +version toolchain +========== ============== +``0.26.0`` ``foss/2021a`` +========== ============== + + .. _list_software_CoCoALib_700: *CoCoALib* @@ -7075,13 +7332,29 @@ CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebr *homepage*: http://cocoa.dima.unige.it/cocoalib =========== ==================== -version toolchain +version toolchain =========== ==================== ``0.99601`` ``GCC/8.2.0-2.31.1`` -``0.99700`` ``GCC/8.3.0`` +``0.99700`` ``GCC/8.3.0`` =========== ==================== +.. _list_software_CodAn_453: + +*CodAn* ++++++++ + +CodAn (Coding sequence Annotator) is a computational tool designed to characterize the CDS and UTR regions on transcripts from any Eukaryote species. + +*homepage*: https://github.com/pedronachtigall/CodAn + +======= ============== +version toolchain +======= ============== +``1.2`` ``foss/2021b`` +======= ============== + + .. _list_software_code-server_1119: *code-server* @@ -7092,7 +7365,7 @@ Run VS Code on any machine anywhere and access it in the browser. *homepage*: https://github.com/cdr/code-server ========= ========== -version toolchain +version toolchain ========= ========== ``3.7.3`` ``system`` ========= ========== @@ -7108,7 +7381,7 @@ Full-spectrum copy number variation detection by high-throughput DNA sequencing *homepage*: https://github.com/yuchaojiang/CODEX2 ============ ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= =============== ``20180227`` ``-R-3.4.3`` ``intel/2017b`` ============ ============= =============== @@ -7124,7 +7397,7 @@ Cogent is a tool for reconstructing the coding genome using high-quality full-le *homepage*: https://github.com/Magdoll/Cogent ========= ============== -version toolchain +version toolchain ========= ============== ``8.0.0`` ``foss/2021a`` ========= ============== @@ -7140,7 +7413,7 @@ Coin is an OpenGL-based, 3D graphics library that has its roots in the Open Inve *homepage*: https://coin3d.github.io ========= ============================== -version toolchain +version toolchain ========= ============================== ``4.0.0`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========= ============================== @@ -7156,11 +7429,11 @@ CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functi *homepage*: https://github.com/coin-or/CoinUtils ========== ================================== -version toolchain +version toolchain ========== ================================== -``2.11.3`` ``GCCcore/7.3.0``, ``foss/2018b`` +``2.11.3`` ``GCCcore/7.3.0``, ``foss/2018b`` ``2.11.4`` ``GCC/10.3.0``, ``GCCcore/10.2.0`` -``2.11.6`` ``GCC/11.2.0`` +``2.11.6`` ``GCC/11.2.0`` ========== ================================== @@ -7174,7 +7447,7 @@ Colossal-AI: A Unified Deep Learning System for Big Model Era *homepage*: https://colossalai.org/ ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``0.1.8`` ``-CUDA-11.3.1`` ``foss/2021a`` ========= ================ ============== @@ -7190,7 +7463,7 @@ COMMET ("COmpare Multiple METagenomes") provides a global similarity overview be *homepage*: https://colibread.inria.fr/software/commet/ ============ ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ============== ``20150415`` ``-Python-2.7.11`` ``foss/2016a`` ============ ================== ============== @@ -7206,7 +7479,7 @@ A toolbox for comparative genomics. *homepage*: https://github.com/dparks1134/CompareM ========== ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ============== ``0.0.23`` ``-Python-2.7.15`` ``foss/2018b`` ``0.1.2`` ``foss/2021b`` @@ -7223,7 +7496,7 @@ Low-Level Interface to zlib or zlib-ng compression library *homepage*: https://metacpan.org/pod/Compress::Raw::Zlib ========= ================== -version toolchain +version toolchain ========= ================== ``2.202`` ``GCCcore/11.3.0`` ========= ================== @@ -7239,7 +7512,7 @@ COMSOL Multiphysics is a general-purpose software platform, based on advanced nu *homepage*: https://www.comsol.com ============= ========== -version toolchain +version toolchain ============= ========== ``5.4.0.225`` ``system`` ============= ========== @@ -7255,7 +7528,7 @@ Con3F is a Python package to read, manipulate and convert force field files *homepage*: https://github.ugent.be/CMM/con3f ================ ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ================ ================= =============== ``1.0-20190329`` ``-Python-3.7.2`` ``intel/2019a`` ================ ================= =============== @@ -7271,7 +7544,7 @@ Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsu *homepage*: https://concoct.readthedocs.io ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``1.0.0`` ``-Python-2.7.14`` ``foss/2017b`` ``1.0.0`` ``-Python-2.7.15`` ``foss/2018b`` @@ -7291,12 +7564,12 @@ configparser is a Python library that brings the updated configparser from Pytho *homepage*: https://docs.python.org/3/library/configparser.html ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``3.5.0`` ``-Python-2.7.11`` ``foss/2016a`` +``3.5.0`` ``-Python-2.7.11`` ``foss/2016a`` ``3.5.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.5.0`` ``-Python-3.5.2`` ``intel/2016b`` -``3.5.0`` ``-Python-3.6.3`` ``intel/2017b`` +``3.5.0`` ``-Python-3.5.2`` ``intel/2016b`` +``3.5.0`` ``-Python-3.6.3`` ``intel/2017b`` ========= ================== =============================== @@ -7310,10 +7583,10 @@ HTTP proxy for node.js including a REST API for updating the routing table. Dev *homepage*: https://github.com/jupyterhub/configurable-http-proxy ========= ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================== -``1.3.0`` ``-nodejs-4.4.7`` ``foss/2016a`` -``3.1.1`` ``-nodejs-8.9.4`` ``foss/2017a`` +``1.3.0`` ``-nodejs-4.4.7`` ``foss/2016a`` +``3.1.1`` ``-nodejs-8.9.4`` ``foss/2017a`` ``4.2.1`` ``GCCcore/10.2.0`` ``4.4.0`` ``GCCcore/10.3.0`` ========= ================= ================== @@ -7329,7 +7602,7 @@ CONN is an open-source Matlab/SPM-based cross-platform software for the computa *homepage*: https://web.conn-toolbox.org/home ======= ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= ========== ``21a`` ``-MATLAB-2021a`` ``system`` ======= ================= ========== @@ -7345,12 +7618,12 @@ Connectome Workbench is an open source, freely available visualization and disc *homepage*: https://www.humanconnectome.org/software/connectome-workbench ========= =============== ================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =============== ================================================== -``1.2.2`` ``system`` +``1.2.2`` ``system`` ``1.3.2`` ``GCCcore/8.2.0``, ``foss/2017b``, ``intel/2017b`` -``1.4.2`` ``-rh_linux64`` ``system`` -``1.5.0`` ``GCCcore/10.3.0`` +``1.4.2`` ``-rh_linux64`` ``system`` +``1.5.0`` ``GCCcore/10.3.0`` ========= =============== ================================================== @@ -7364,10 +7637,10 @@ Copy number and genotype annotation from whole genome and whole exome sequencin *homepage*: https://github.com/BoevaLab/FREEC ======== ======================================== -version toolchain +version toolchain ======== ======================================== ``11.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1`` -``11.6`` ``GCC/10.2.0`` +``11.6`` ``GCC/10.2.0`` ======== ======================================== @@ -7381,9 +7654,9 @@ Schrodinger-developed 2D Coordinate Generation *homepage*: https://github.com/schrodinger/coordgenlibs ========= ================================================================== -version toolchain +version toolchain ========= ================================================================== -``1.3.2`` ``gompi/2019a``, ``iimpi/2019a`` +``1.3.2`` ``gompi/2019a``, ``iimpi/2019a`` ``3.0.1`` ``gompi/2019b``, ``gompi/2021a``, ``gompi/2022a``, ``iimpi/2020a`` ========= ================================================================== @@ -7398,7 +7671,7 @@ Coot is for macromolecular model building, model completion and validation, par *homepage*: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot ========= =========================================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= =========================================== ========== ``0.8.1`` ``-binary-Linux-x86_64-rhel-6-python-gtk2`` ``system`` ========= =========================================== ========== @@ -7414,7 +7687,7 @@ Tool to check available cores and OMP threads *homepage*: https://github.com/gjbex/core-counter ========= ========== -version toolchain +version toolchain ========= ========== ``1.1.1`` ``system`` ========= ========== @@ -7430,13 +7703,13 @@ The GNU Core Utilities are the basic file, shell and text manipulation utilities *homepage*: https://www.gnu.org/software/coreutils/ ======== ==================================== -version toolchain +version toolchain ======== ==================================== -``8.23`` ``GCC/4.9.2`` -``8.27`` ``GCCcore/5.4.0`` -``8.29`` ``GCCcore/6.4.0`` +``8.23`` ``GCC/4.9.2`` +``8.27`` ``GCCcore/5.4.0`` +``8.29`` ``GCCcore/6.4.0`` ``8.32`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``9.0`` ``GCCcore/11.2.0`` +``9.0`` ``GCCcore/11.2.0`` ======== ==================================== @@ -7450,13 +7723,29 @@ Make some beautiful corner plots. *homepage*: https://corner.readthedocs.io/en/latest/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.0.1`` ``-Python-2.7.15`` ``foss/2019a`` ``2.0.1`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================== ============== +.. _list_software_CoSymLib_770: + +*CoSymLib* +++++++++++ + +Cosymlib is a python library for computing continuous symmetry & shape measures (CSMs & CShMs). Although its main aim is to provide simple and ready-to-use tools for the analysis of the symmetry & shape of molecules, many of the procedures contained in cosymlib can be easily applied to any finite geometrical object defined by a set of vertices or a by mass distribution function. + +*homepage*: https://cosymlib.readthedocs.io + +========== ============== +version toolchain +========== ============== +``0.10.9`` ``foss/2022a`` +========== ============== + + .. _list_software_coverage_844: *coverage* @@ -7467,9 +7756,9 @@ Coverage.py is a tool for measuring code coverage of Python programs. It monito *homepage*: https://coverage.readthedocs.io ========= ================== ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ====================================== -``4.5.1`` ``-Python-2.7.14`` ``intel/2017b`` +``4.5.1`` ``-Python-2.7.14`` ``intel/2017b`` ``5.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ================== ====================================== @@ -7484,7 +7773,7 @@ Configurable talking characters in ASCII art *homepage*: https://github.com/tnalpgge/rank-amateur-cowsay ======== ========== -version toolchain +version toolchain ======== ========== ``3.04`` ``system`` ======== ========== @@ -7500,18 +7789,18 @@ CP2K is a freely available (GPL) program, written in Fortran 95, to perform atom *homepage*: https://www.cp2k.org/ ======= ============= ================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= ================================================================================================= -``3.0`` ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` -``3.0`` ``-psmp`` ``intel/2016b`` -``4.1`` ``intel/2016b`` -``4.1`` ``-psmp`` ``foss/2016b`` +``3.0`` ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` +``3.0`` ``-psmp`` ``intel/2016b`` +``4.1`` ``intel/2016b`` +``4.1`` ``-psmp`` ``foss/2016b`` ``5.1`` ``foss/2018a``, ``foss/2020a``, ``foss/2020b``, ``intel/2017b``, ``intel/2018a``, ``intel/2020a`` -``6.1`` ``foss/2019a``, ``intel/2018a``, ``intel/2020a`` -``7.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` -``7.1`` ``-psmp`` ``foss/2020b`` -``8.1`` ``foss/2020b`` -``8.2`` ``foss/2021a``, ``intel/2021a`` +``6.1`` ``foss/2019a``, ``intel/2018a``, ``intel/2020a`` +``7.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` +``7.1`` ``-psmp`` ``foss/2020b`` +``8.1`` ``foss/2020b`` +``8.2`` ``foss/2021a``, ``intel/2021a`` ======= ============= ================================================================================================= @@ -7525,7 +7814,7 @@ CPB is a novel two-step Pearson correlation based biclustering approach to mine *homepage*: http://tda.gatech.edu/software/cpb/index.html ============= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============= ================== ============== ``11-4-2011`` ``-Python-2.7.13`` ``foss/2017a`` ============= ================== ============== @@ -7541,13 +7830,29 @@ IBM ILOG CPLEX Optimizer's mathematical programming technology enables analytic *homepage*: https://www.ibm.com/analytics/cplex-optimizer ========= ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================= ``12.9`` ``GCCcore/8.2.0`` ``12.10`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========= ================= ================= +.. _list_software_CPPE_296: + +*CPPE* +++++++ + +CPPE is an open-source, light-weight C++ and Python library for Polarizable Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE for ground-state self-consistent field (SCF) calculations and post-SCF methods. A convenient Python interface is also available. + +*homepage*: https://github.com/maxscheurer/cppe + +========= ============== +version toolchain +========= ============== +``0.3.1`` ``GCC/11.3.0`` +========= ============== + + .. _list_software_CppUnit_707: *CppUnit* @@ -7558,9 +7863,9 @@ CppUnit is the C++ port of the famous JUnit framework for unit testing. *homepage*: https://freedesktop.org/wiki/Software/cppunit/ ========== ============================================================================ -version toolchain +version toolchain ========== ============================================================================ -``1.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a`` +``1.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a`` ``1.15.1`` ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ============================================================================ @@ -7575,10 +7880,10 @@ A small C++ header library which makes it easier to write Python extension modul *homepage*: https://github.com/nucleic/cppy ========= ====================================== -version toolchain +version toolchain ========= ====================================== ``1.1.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.2.1`` ``GCCcore/11.3.0`` +``1.2.1`` ``GCCcore/11.3.0`` ========= ====================================== @@ -7592,7 +7897,7 @@ A cross-platform C library to retrieve CPU features (such as available instructi *homepage*: https://github.com/google/cpu_features ========= ================== -version toolchain +version toolchain ========= ================== ``0.6.0`` ``GCCcore/10.2.0`` ========= ================== @@ -7608,7 +7913,7 @@ Cram is a functional testing framework for command line applications. *homepage*: https://bitheap.org/cram ======= ================= -version toolchain +version toolchain ======= ================= ``0.7`` ``GCCcore/8.2.0`` ======= ================= @@ -7624,7 +7929,7 @@ CRAMTools is a set of Java tools and APIs for efficient compression of sequence *homepage*: https://github.com/enasequence/cramtools/ ======= ================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== ========== ``2.0`` ``-Java-1.7.0_80`` ``system`` ``3.0`` ``-Java-1.7.0_80`` ``system`` @@ -7641,7 +7946,7 @@ Toolchain using Cray compiler wrapper, using PrgEnv-cray (PE release: June 2019) *homepage*: https://pubs.cray.com/discover ========= ========== -version toolchain +version toolchain ========= ========== ``19.06`` ``system`` ========= ========== @@ -7657,7 +7962,7 @@ Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June *homepage*: https://pubs.cray.com/discover ========= ========== -version toolchain +version toolchain ========= ========== ``19.06`` ``system`` ========= ========== @@ -7673,7 +7978,7 @@ Toolchain using Cray compiler wrapper, using PrgEnv-intel (PE release: June 2019 *homepage*: https://pubs.cray.com/discover ========= ========== -version toolchain +version toolchain ========= ========== ``19.06`` ``system`` ========= ========== @@ -7689,7 +7994,7 @@ Toolchain using Cray compiler wrapper, PrgEnv-pgi compiler (PE release: June 201 *homepage*: https://pubs.cray.com/discover ========= ========== -version toolchain +version toolchain ========= ========== ``19.06`` ``system`` ========= ========== @@ -7705,10 +8010,10 @@ Conditional Reciprocal Best BLAST - high confidence ortholog assignment. CRB-BL *homepage*: https://github.com/cboursnell/crb-blast ========= =============== ================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========= =============== ================================================= ``0.6.9`` ``gompi/2021a``, ``gompi/2021b``, ``intel/2017a`` -``0.6.9`` ``-Ruby-2.6.1`` ``foss/2018b`` +``0.6.9`` ``-Ruby-2.6.1`` ``foss/2018b`` ========= =============== ================================================= @@ -7722,7 +8027,7 @@ CREST is an utility/driver program for the xtb program. Originally it was design *homepage*: https://xtb-docs.readthedocs.io/en/latest/crest.html ======== =============== -version toolchain +version toolchain ======== =============== ``2.11`` ``intel/2021a`` ======== =============== @@ -7738,7 +8043,7 @@ CRF++ is a simple, customizable, and open source implementation of Conditional *homepage*: https://taku910.github.io/crfpp/ ======== ========================================================= -version toolchain +version toolchain ======== ========================================================= ``0.58`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ======== ========================================================= @@ -7754,7 +8059,7 @@ CRISPR-DAV is a pipeline to analyze amplicon-based NGS data of CRISPR clones in *homepage*: https://github.com/pinetree1/crispr-dav/ ========= ============== -version toolchain +version toolchain ========= ============== ``2.3.4`` ``foss/2020b`` ========= ============== @@ -7770,7 +8075,7 @@ CRISPResso2 is a software pipeline designed to enable rapid and intuitive interp *homepage*: https://github.com/pinellolab/CRISPResso2/ ========== ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ============== ``2.0.44`` ``-Python-2.7.16`` ``foss/2019b`` ``2.1.2`` ``-Python-2.7.18`` ``foss/2020b`` @@ -7788,7 +8093,7 @@ Cromwell is a Workflow Management System geared towards scientific workflows. *homepage*: http://cromwell.readthedocs.io/ ======= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= ========== ``56`` ``-Java-11`` ``system`` ======= ============= ========== @@ -7804,7 +8109,7 @@ CrossMap is a program for genome coordinates conversion between different assem *homepage*: http://crossmap.sourceforge.net ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.3.9`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= ============== @@ -7820,7 +8125,7 @@ CrossTalkZ is a statistical method and software to assess the significance of cr *homepage*: http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/ ======= ============== -version toolchain +version toolchain ======= ============== ``1.4`` ``foss/2016a`` ======= ============== @@ -7836,7 +8141,7 @@ CRPropa is a publicly available code to study the propagation of ultra high ener *homepage*: https://crpropa.desy.de ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``3.1.5`` ``-Python-3.7.2`` ``foss/2019a`` ``3.1.6`` ``-Python-3.8.2`` ``foss/2020a`` @@ -7853,12 +8158,28 @@ Exploration of controlled loss of quality values for compressing CRAM files *homepage*: https://github.com/jkbonfield/crumble ========= ============== -version toolchain +version toolchain ========= ============== ``0.8.3`` ``GCC/11.2.0`` ========= ============== +.. _list_software_cryoCARE_728: + +*cryoCARE* +++++++++++ + +This package is a memory efficient implementation of cryoCARE. This setup trains a denoising U-Net for tomographic reconstruction according to the Noise2Noise training paradigm. Therefore the user has to provide two tomograms of the same sample. The simplest way to achieve this is with direct- detector movie-frames. You can use Warp to generate two reconstructed tomograms based on the even/odd frames. Alternatively, the movie-frames can be split in two halves (e.g. with MotionCor2 -SplitSum 1 or with IMOD alignframes -debug 10000) from which two identical, up to random noise, tomograms can be reconstructed. These two (even and odd) tomograms can be used as input to this cryoCARE implementation. + +*homepage*: https://github.com/juglab/cryoCARE_pip + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``0.2.1`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== + + .. _list_software_cryoDRGN_744: *cryoDRGN* @@ -7869,11 +8190,11 @@ cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous rec *homepage*: https://cb.csail.mit.edu/cb/cryodrgn/ ============== ================ ================== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================ ================== ``0.3.2`` ``fosscuda/2020b`` -``0.3.5`` ``-CUDA-11.3.1`` ``foss/2021a`` -``1.0.0-beta`` ``-CUDA-11.3.1`` ``foss/2021a`` +``0.3.5`` ``-CUDA-11.3.1`` ``foss/2021a`` +``1.0.0-beta`` ``-CUDA-11.3.1`` ``foss/2021a`` ============== ================ ================== @@ -7887,7 +8208,7 @@ CryptoMiniSat is an advanced SAT solver *homepage*: https://github.com/msoos/cryptominisat ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``5.0.1`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== @@ -7903,7 +8224,7 @@ CrystFEL is a suite of programs for processing diffraction data acquired "serial *homepage*: http://www.desy.de/~twhite/crystfel/ ========= =============================== -version toolchain +version toolchain ========= =============================== ``0.8.0`` ``foss/2019a``, ``intel/2019a`` ========= =============================== @@ -7919,7 +8240,7 @@ Computational Structural Biology Toolbox CSB is a python library and application *homepage*: https://github.com/csb-toolbox ========= ============== -version toolchain +version toolchain ========= ============== ``1.2.5`` ``foss/2020b`` ========= ============== @@ -7935,7 +8256,7 @@ CSBDeep is a toolbox for Content-aware Image Restoration (CARE). *homepage*: https://csbdeep.bioimagecomputing.com/ ========= ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================== ``0.4.1`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ========= ================= ================================== @@ -7951,7 +8272,7 @@ Context-specific extension of BLAST that significantly improves sensitivity and *homepage*: https://github.com/soedinglab/csblast/ ========= ================= -version toolchain +version toolchain ========= ================= ``2.2.3`` ``GCCcore/8.3.0`` ========= ================= @@ -7967,7 +8288,7 @@ Cscope is a developer's tool for browsing source code. *homepage*: http://cscope.sourceforge.net/ ======== ========== -version toolchain +version toolchain ======== ========== ``15.9`` ``system`` ======== ========== @@ -7983,7 +8304,7 @@ csvkit is a suite of command-line tools for converting to and working with CSV, *homepage*: https://github.com/wireservice/csvkit ========= ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================= ``1.0.4`` ``GCCcore/8.2.0`` ``1.0.5`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` @@ -8000,7 +8321,7 @@ Ctags generates an index (or tag) file of language objects found in source files *homepage*: http://ctags.sourceforge.net/ ======= ========== -version toolchain +version toolchain ======= ========== ``5.8`` ``system`` ======= ========== @@ -8015,13 +8336,29 @@ Program for finding CTFs of electron micrographs. *homepage*: https://grigoriefflab.umassmed.edu/ctffind4 -========== ================ ====================================================================== -version versionsuffix toolchain -========== ================ ====================================================================== -``4.1.13`` ``foss/2019a``, ``fosscuda/2019a``, ``fosscuda/2019b`` -``4.1.14`` ``foss/2019b``, ``foss/2021b``, ``fosscuda/2019b``, ``fosscuda/2020b`` -``4.1.14`` ``-CUDA-11.3.1`` ``foss/2021a`` -========== ================ ====================================================================== +========== ================ ====================================================================================== +version versionsuffix toolchain +========== ================ ====================================================================================== +``4.1.13`` ``foss/2019a``, ``fosscuda/2019a``, ``fosscuda/2019b`` +``4.1.14`` ``foss/2019b``, ``foss/2021b``, ``foss/2022a``, ``fosscuda/2019b``, ``fosscuda/2020b`` +``4.1.14`` ``-CUDA-11.3.1`` ``foss/2021a`` +========== ================ ====================================================================================== + + +.. _list_software_CTPL_307: + +*CTPL* +++++++ + +Modern and efficient C++ Thread Pool Library + +*homepage*: https://github.com/vit-vit/CTPL.git + +========= ============== +version toolchain +========= ============== +``0.0.2`` ``GCC/11.3.0`` +========= ============== .. _list_software_Cube_383: @@ -8034,7 +8371,7 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is *homepage*: http://www.scalasca.org/software/cube-4.x/download.html ========= ============== -version toolchain +version toolchain ========= ============== ``4.3.4`` ``foss/2016a`` ========= ============== @@ -8050,10 +8387,11 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is *homepage*: https://www.scalasca.org/software/cube-4.x/download.html ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``4.4.4`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +``4.4.4`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` ``4.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``4.8`` ``GCCcore/11.3.0`` ========= ====================================== @@ -8067,10 +8405,11 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is *homepage*: https://www.scalasca.org/software/cube-4.x/download.html ========= ======================================================= -version toolchain +version toolchain ========= ======================================================= ``4.4.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``4.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``4.8`` ``GCCcore/11.3.0`` ========= ======================================================= @@ -8084,10 +8423,11 @@ Cube, which is used as performance report explorer for Scalasca and Score-P, is *homepage*: https://www.scalasca.org/software/cube-4.x/download.html ========= =========================================================================== -version toolchain +version toolchain ========= =========================================================================== ``4.4.3`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``4.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``4.8`` ``GCCcore/11.3.0`` ========= =========================================================================== @@ -8101,37 +8441,55 @@ CUDA (formerly Compute Unified Device Architecture) is a parallel computing pla *homepage*: https://developer.nvidia.com/cuda-toolkit ================= ========================================================================== -version toolchain +version toolchain ================= ========================================================================== -``5.5.22`` ``GCC/4.8.2``, ``system`` -``6.0.37`` ``system`` -``6.5.14`` ``system`` -``7.0.28`` ``system`` -``7.5.18`` ``GCC/4.9.4-2.25``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``system`` -``8.0.44`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``system`` -``8.0.61`` ``system`` -``8.0.61_375.26`` ``GCC/5.4.0-2.26`` -``9.0.176`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``system`` -``9.1.85`` ``GCC/6.4.0-2.28``, ``system`` -``9.2.88`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30``, ``system`` -``9.2.148.1`` ``system`` -``10.0.130`` ``system`` +``5.5.22`` ``GCC/4.8.2``, ``system`` +``6.0.37`` ``system`` +``6.5.14`` ``system`` +``7.0.28`` ``system`` +``7.5.18`` ``GCC/4.9.4-2.25``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``system`` +``8.0.44`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``system`` +``8.0.61`` ``system`` +``8.0.61_375.26`` ``GCC/5.4.0-2.26`` +``9.0.176`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``system`` +``9.1.85`` ``GCC/6.4.0-2.28``, ``system`` +``9.2.88`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30``, ``system`` +``9.2.148.1`` ``system`` +``10.0.130`` ``system`` ``10.1.105`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``system`` -``10.1.168`` ``system`` -``10.1.243`` ``GCC/8.3.0``, ``iccifort/2019.5.281``, ``system`` -``10.2.89`` ``GCC/8.3.0`` -``11.0.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` -``11.1.1`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -``11.3.1`` ``system`` -``11.4.1`` ``system`` -``11.4.2`` ``system`` -``11.5.0`` ``system`` -``11.5.1`` ``system`` -``11.6.0`` ``system`` -``11.7.0`` ``system`` +``10.1.168`` ``system`` +``10.1.243`` ``GCC/8.3.0``, ``iccifort/2019.5.281``, ``system`` +``10.2.89`` ``GCC/8.3.0`` +``11.0.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` +``11.1.1`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``11.3.1`` ``system`` +``11.4.1`` ``system`` +``11.4.2`` ``system`` +``11.5.0`` ``system`` +``11.5.1`` ``system`` +``11.6.0`` ``system`` +``11.7.0`` ``system`` +``11.8.0`` ``system`` +``12.0.0`` ``system`` ================= ========================================================================== +.. _list_software_CUDA-Samples_1055: + +*CUDA-Samples* +++++++++++++++ + +Samples for CUDA Developers which demonstrates features in CUDA Toolkit + +*homepage*: https://github.com/NVIDIA/cuda-samples + +======== ================ ============== +version versionsuffix toolchain +======== ================ ============== +``11.3`` ``-CUDA-11.3.1`` ``GCC/10.3.0`` +======== ================ ============== + + .. _list_software_CUDAcompat_929: *CUDAcompat* @@ -8142,7 +8500,7 @@ Using the CUDA Forward Compatibility package, system administrators can run app *homepage*: https://docs.nvidia.com/deploy/cuda-compatibility/index.html ======== ============== ========== -version versionsuffix toolchain +version versionsuffix toolchain ======== ============== ========== ``11`` ``system`` ``11.6`` ``system`` @@ -8162,7 +8520,7 @@ CUDA (formerly Compute Unified Device Architecture) is a parallel computing pla *homepage*: https://developer.nvidia.com/cuda-toolkit ========== ========== -version toolchain +version toolchain ========== ========== ``11.0.2`` ``system`` ``11.1.1`` ``system`` @@ -8183,40 +8541,42 @@ The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library *homepage*: https://developer.nvidia.com/cudnn -============ ================== =========================================================== -version versionsuffix toolchain -============ ================== =========================================================== -``4.0`` ``system`` -``5.0`` ``-CUDA-7.5.18`` ``system`` -``5.0-rc`` ``system`` -``5.1`` ``-CUDA-8.0.44`` ``system`` -``6.0`` ``-CUDA-8.0.61`` ``system`` -``6.0.21`` ``-CUDA-7.5.18`` ``system`` -``6.0.21`` ``-CUDA-8.0.44`` ``system`` -``7.0.2`` ``-CUDA-9.0.176`` ``system`` -``7.0.5`` ``-CUDA-8.0.44`` ``system`` -``7.0.5`` ``-CUDA-9.0.176`` ``system`` -``7.0.5`` ``-CUDA-9.1.85`` ``system`` -``7.0.5.15`` ``fosscuda/2017b``, ``fosscuda/2018a``, ``intelcuda/2017b`` -``7.1.4.18`` ``fosscuda/2018b`` -``7.4.2.24`` ``gcccuda/2019a`` -``7.4.2.24`` ``-CUDA-10.0.130`` ``system`` -``7.5.0.56`` ``-CUDA-10.0.130`` ``system`` -``7.6.2.24`` ``-CUDA-10.1.243`` ``system`` -``7.6.4.38`` ``gcccuda/2019a``, ``gcccuda/2019b`` -``7.6.4.38`` ``-CUDA-10.0.130`` ``system`` -``8.0.4.30`` ``-CUDA-11.0.2`` ``system`` -``8.0.4.30`` ``-CUDA-11.1.1`` ``system`` -``8.0.5.39`` ``-CUDA-11.1.1`` ``system`` -``8.1.0.77`` ``-CUDA-11.2.1`` ``system`` -``8.1.1.33`` ``-CUDA-11.2.1`` ``system`` -``8.2.1.32`` ``-CUDA-11.3.1`` ``system`` -``8.2.2.26`` ``-CUDA-11.4.0`` ``system`` -``8.2.2.26`` ``-CUDA-11.4.1`` ``system`` -``8.4.0.27`` ``-CUDA-11.6.0`` ``system`` -``8.4.1.50`` ``-CUDA-11.6.0`` ``system`` -``8.4.1.50`` ``-CUDA-11.7.0`` ``system`` -============ ================== =========================================================== +============= ================== =========================================================== +version versionsuffix toolchain +============= ================== =========================================================== +``4.0`` ``system`` +``5.0`` ``-CUDA-7.5.18`` ``system`` +``5.0-rc`` ``system`` +``5.1`` ``-CUDA-8.0.44`` ``system`` +``6.0`` ``-CUDA-8.0.61`` ``system`` +``6.0.21`` ``-CUDA-7.5.18`` ``system`` +``6.0.21`` ``-CUDA-8.0.44`` ``system`` +``7.0.2`` ``-CUDA-9.0.176`` ``system`` +``7.0.5`` ``-CUDA-8.0.44`` ``system`` +``7.0.5`` ``-CUDA-9.0.176`` ``system`` +``7.0.5`` ``-CUDA-9.1.85`` ``system`` +``7.0.5.15`` ``fosscuda/2017b``, ``fosscuda/2018a``, ``intelcuda/2017b`` +``7.1.4.18`` ``fosscuda/2018b`` +``7.4.2.24`` ``gcccuda/2019a`` +``7.4.2.24`` ``-CUDA-10.0.130`` ``system`` +``7.5.0.56`` ``-CUDA-10.0.130`` ``system`` +``7.6.2.24`` ``-CUDA-10.1.243`` ``system`` +``7.6.4.38`` ``gcccuda/2019a``, ``gcccuda/2019b`` +``7.6.4.38`` ``-CUDA-10.0.130`` ``system`` +``8.0.4.30`` ``-CUDA-11.0.2`` ``system`` +``8.0.4.30`` ``-CUDA-11.1.1`` ``system`` +``8.0.5.39`` ``-CUDA-11.1.1`` ``system`` +``8.1.0.77`` ``-CUDA-11.2.1`` ``system`` +``8.1.1.33`` ``-CUDA-11.2.1`` ``system`` +``8.2.1.32`` ``-CUDA-11.3.1`` ``system`` +``8.2.2.26`` ``-CUDA-11.4.0`` ``system`` +``8.2.2.26`` ``-CUDA-11.4.1`` ``system`` +``8.4.0.27`` ``-CUDA-11.6.0`` ``system`` +``8.4.1.50`` ``-CUDA-11.6.0`` ``system`` +``8.4.1.50`` ``-CUDA-11.7.0`` ``system`` +``8.6.0.163`` ``-CUDA-11.8.0`` ``system`` +``8.7.0.84`` ``-CUDA-11.8.0`` ``system`` +============= ================== =========================================================== .. _list_software_Cufflinks_933: @@ -8229,10 +8589,10 @@ Transcript assembly, differential expression, and differential regulation for RN *homepage*: http://cole-trapnell-lab.github.io/cufflinks/ ============ ================================================================================================= -version toolchain +version toolchain ============ ================================================================================================= ``2.2.1`` ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``gompi/2019b``, ``intel/2017b``, ``intel/2018a`` -``20190706`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``gompi/2019a`` +``20190706`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``gompi/2019a`` ============ ================================================================================================= @@ -8245,11 +8605,11 @@ Automated testing framework for C. *homepage*: https://sourceforge.net/projects/cunit/ -========= ===================================== -version toolchain -========= ===================================== -``2.1-3`` ``GCCcore/11.2.0``, ``GCCcore/6.4.0`` -========= ===================================== +========= ========================================================= +version toolchain +========= ========================================================= +``2.1-3`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0`` +========= ========================================================= .. _list_software_CuPy_385: @@ -8262,7 +8622,7 @@ CuPy is an open-source array library accelerated with NVIDIA CUDA. *homepage*: https://cupy.dev ========= ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================== ``8.2.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``8.5.0`` ``fosscuda/2020b`` @@ -8279,31 +8639,32 @@ libcurl is a free and easy-to-use client-side URL transfer library, supporting *homepage*: https://curl.haxx.se ========== =================================================================================== -version toolchain +version toolchain ========== =================================================================================== -``7.33.0`` ``GCC/4.8.2`` -``7.34.0`` ``GCC/4.8.2`` -``7.40.0`` ``GCC/4.9.2`` -``7.46.0`` ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``7.47.0`` ``foss/2016a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a`` +``7.33.0`` ``GCC/4.8.2`` +``7.34.0`` ``GCC/4.8.2`` +``7.40.0`` ``GCC/4.9.2`` +``7.46.0`` ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` +``7.47.0`` ``foss/2016a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a`` ``7.49.1`` ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``7.52.1`` ``gimkl/2017a``, ``intel/2016b`` -``7.53.1`` ``GCCcore/6.3.0`` -``7.54.0`` ``GCCcore/6.3.0`` -``7.55.1`` ``GCCcore/6.4.0`` -``7.56.0`` ``GCCcore/6.4.0`` -``7.56.1`` ``GCCcore/6.4.0`` -``7.58.0`` ``GCCcore/6.4.0`` -``7.59.0`` ``GCCcore/6.4.0`` -``7.60.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``7.63.0`` ``GCCcore/8.2.0`` -``7.66.0`` ``GCCcore/8.3.0`` -``7.69.1`` ``GCCcore/9.3.0`` -``7.72.0`` ``GCCcore/10.2.0`` -``7.76.0`` ``GCCcore/10.3.0`` -``7.78.0`` ``GCCcore/11.2.0`` -``7.83.0`` ``GCCcore/11.3.0`` -``7.84.0`` ``GCCcore/12.1.0`` +``7.52.1`` ``gimkl/2017a``, ``intel/2016b`` +``7.53.1`` ``GCCcore/6.3.0`` +``7.54.0`` ``GCCcore/6.3.0`` +``7.55.1`` ``GCCcore/6.4.0`` +``7.56.0`` ``GCCcore/6.4.0`` +``7.56.1`` ``GCCcore/6.4.0`` +``7.58.0`` ``GCCcore/6.4.0`` +``7.59.0`` ``GCCcore/6.4.0`` +``7.60.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``7.63.0`` ``GCCcore/8.2.0`` +``7.66.0`` ``GCCcore/8.3.0`` +``7.69.1`` ``GCCcore/9.3.0`` +``7.72.0`` ``GCCcore/10.2.0`` +``7.76.0`` ``GCCcore/10.3.0`` +``7.78.0`` ``GCCcore/11.2.0`` +``7.83.0`` ``GCCcore/11.3.0`` +``7.84.0`` ``GCCcore/12.1.0`` +``7.86.0`` ``GCCcore/12.2.0`` ========== =================================================================================== @@ -8317,7 +8678,7 @@ A simple JIT job management framework in Python. *homepage*: https://pypi.python.org/pypi/custodian ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.1.0`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== @@ -8333,26 +8694,27 @@ Cutadapt finds and removes adapter sequences, primers, poly-A tails and other t *homepage*: https://opensource.scilifelab.se/projects/cutadapt/ ========= ================== ================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================================================ -``1.9.1`` ``-Python-2.7.11`` ``foss/2016a`` -``1.9.1`` ``-Python-2.7.12`` ``foss/2016b`` -``1.14`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` -``1.15`` ``-Python-3.5.2`` ``foss/2016b`` +``1.9.1`` ``-Python-2.7.11`` ``foss/2016a`` +``1.9.1`` ``-Python-2.7.12`` ``foss/2016b`` +``1.14`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``1.15`` ``-Python-3.5.2`` ``foss/2016b`` ``1.16`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``1.16`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.16`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.18`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``1.18`` ``-Python-2.7.15`` ``foss/2018b`` -``1.18`` ``-Python-2.7.18`` ``GCC/10.2.0`` -``1.18`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``2.1`` ``-Python-3.6.6`` ``foss/2018b`` -``2.7`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``2.8`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``2.10`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``2.10`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``3.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``3.5`` ``GCCcore/11.2.0`` +``1.16`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``1.16`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.18`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.18`` ``-Python-2.7.15`` ``foss/2018b`` +``1.18`` ``-Python-2.7.18`` ``GCC/10.2.0`` +``1.18`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``2.1`` ``-Python-3.6.6`` ``foss/2018b`` +``2.7`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.8`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.10`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.10`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``3.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``3.5`` ``GCCcore/11.2.0`` +``4.2`` ``GCCcore/11.3.0`` ========= ================== ================================================ @@ -8366,11 +8728,12 @@ The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providin *homepage*: https://developer.nvidia.com/cutensor =========== ================ ================= -version versionsuffix toolchain +version versionsuffix toolchain =========== ================ ================= ``1.2.2.5`` ``gcccuda/2019b`` -``1.2.2.5`` ``-CUDA-11.1.1`` ``system`` -``1.6.0.3`` ``-CUDA-11.3.1`` ``system`` +``1.2.2.5`` ``-CUDA-11.1.1`` ``system`` +``1.6.0.3`` ``-CUDA-11.3.1`` ``system`` +``1.6.1.5`` ``-CUDA-11.7.0`` ``system`` =========== ================ ================= @@ -8384,7 +8747,7 @@ CVS is a version control system, an important component of Source Configuration *homepage*: https://savannah.nongnu.org/projects/cvs =========== ======================================================================= -version toolchain +version toolchain =========== ======================================================================= ``1.11.23`` ``GCC/4.8.2``, ``GCCcore/11.2.0``, ``GCCcore/4.9.3``, ``GCCcore/6.4.0`` =========== ======================================================================= @@ -8400,13 +8763,13 @@ CVXOPT is a free software package for convex optimization based on the Python pr *homepage*: https://cvxopt.org ========= ================== ============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============================== -``1.1.9`` ``-Python-2.7.13`` ``intel/2017a`` -``1.2.1`` ``-Python-3.6.4`` ``intel/2018a`` -``1.2.3`` ``foss/2019a`` -``1.2.3`` ``-Python-3.6.6`` ``intel/2018b`` -``1.2.4`` ``-Python-3.7.4`` ``intel/2019b`` +``1.1.9`` ``-Python-2.7.13`` ``intel/2017a`` +``1.2.1`` ``-Python-3.6.4`` ``intel/2018a`` +``1.2.3`` ``foss/2019a`` +``1.2.3`` ``-Python-3.6.6`` ``intel/2018b`` +``1.2.4`` ``-Python-3.7.4`` ``intel/2019b`` ``1.2.6`` ``foss/2020b``, ``foss/2021a`` ========= ================== ============================== @@ -8421,7 +8784,7 @@ CVXPY is a Python-embedded modeling language for convex optimization problems. *homepage*: https://www.cvxpy.org/ ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``1.0.24`` ``foss/2019a`` ``1.0.28`` ``-Python-3.7.4`` ``foss/2019b`` @@ -8438,12 +8801,28 @@ CWIPI (Coupling With Interpolation Parallel Interface) library helps in chaining *homepage*: https://w3.onera.fr/cwipi/ ========== =============== -version toolchain +version toolchain ========== =============== ``0.12.0`` ``gompi/2021a`` ========== =============== +.. _list_software_cwltool_772: + +*cwltool* ++++++++++ + +Common workflow language (CWL) reference implementation. + +*homepage*: https://github.com/common-workflow-language/cwltool + +====================== ============== +version toolchain +====================== ============== +``3.1.20221018083734`` ``foss/2021a`` +====================== ============== + + .. _list_software_cxxopts_793: *cxxopts* @@ -8454,7 +8833,7 @@ cxxopts is a lightweight C++ command line option parser *homepage*: https://github.com/jarro2783/cxxopts ========= ========== -version toolchain +version toolchain ========= ========== ``3.0.0`` ``system`` ========= ========== @@ -8470,7 +8849,7 @@ The cysignals package provides mechanisms to handle interrupts (and other signa *homepage*: https://pypi.org/project/cysignals/ ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== ``1.10.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.10.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` @@ -8487,17 +8866,17 @@ Cython is an optimising static compiler for both the Python programming language *homepage*: https://cython.org/ =========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== =============================== -``0.23.4`` ``-Python-2.7.10`` ``gimkl/2.11.5`` -``0.24.1`` ``-Python-2.7.11`` ``foss/2016a`` -``0.25.2`` ``-Python-2.7.12`` ``foss/2016b`` -``0.25.2`` ``-Python-3.6.4`` ``intel/2018a`` -``0.27.3`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``0.23.4`` ``-Python-2.7.10`` ``gimkl/2.11.5`` +``0.24.1`` ``-Python-2.7.11`` ``foss/2016a`` +``0.25.2`` ``-Python-2.7.12`` ``foss/2016b`` +``0.25.2`` ``-Python-3.6.4`` ``intel/2018a`` +``0.27.3`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``0.29.10`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``0.29.10`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``0.29.22`` ``GCCcore/10.2.0`` -``3.0a5`` ``GCCcore/10.2.0`` +``0.29.22`` ``GCCcore/10.2.0`` +``3.0a5`` ``GCCcore/10.2.0`` =========== ================== =============================== @@ -8511,13 +8890,29 @@ Cython implementation of the toolz package, which provides high performance util *homepage*: https://github.com/pytoolz/cytoolz ========== ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================= -``0.10.1`` ``-Python-3.6.6`` ``foss/2018b`` +``0.10.1`` ``-Python-3.6.6`` ``foss/2018b`` ``0.10.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================= ================= +.. _list_software_Cytoscape_939: + +*Cytoscape* ++++++++++++ + +Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web. + +*homepage*: https://cytoscape.org/ + +========= ============= ========== +version versionsuffix toolchain +========= ============= ========== +``3.9.1`` ``-Java-11`` ``system`` +========= ============= ========== + + .. _list_software_cytosim_776: *cytosim* @@ -8528,7 +8923,7 @@ Cytosim is a cytoskeleton simulation engine written in C++ working on Mac OS, G *homepage*: https://github.com/nedelec/cytosim ============ ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= =============== ``20190117`` ``-mkl`` ``gomkl/2019a`` ============ ============= =============== @@ -8544,9 +8939,9 @@ cython + htslib == fast VCF and BCF processing *homepage*: https://github.com/brentp/cyvcf2 =========== ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================= =============================== -``0.10.10`` ``-Python-3.6.6`` ``foss/2018b`` +``0.10.10`` ``-Python-3.6.6`` ``foss/2018b`` ``0.11.5`` ``foss/2019a``, ``intel/2019a`` =========== ================= =============================== @@ -8557,7 +8952,7 @@ version versionsuffix toolchain --- -:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dakota_596` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_deepmedic_928` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_Detectron2_986` - :ref:`list_software_detonate_852` - :ref:`list_software_Devito_619` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dlib_411` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dRep_395` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_DualSPHysics_1180` - :ref:`list_software_DUBStepR_713` - :ref:`list_software_dune-core_898` - :ref:`list_software_dune-fem_785` - :ref:`list_software_dxpy_453` - :ref:`list_software_DyMat_479` +:ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_Dakota_596` - :ref:`list_software_Dalton_610` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_dd_200` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_decona_618` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepLabCut_953` - :ref:`list_software_deepmedic_928` - :ref:`list_software_DeepMod2_720` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_Detectron2_986` - :ref:`list_software_detonate_852` - :ref:`list_software_Devito_619` - :ref:`list_software_DFA_203` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFT-D4_387` - :ref:`list_software_DFTB+_331` - :ref:`list_software_dftd3-lib_825` - :ref:`list_software_DGL_215` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_Dice_373` - :ref:`list_software_dicom2nifti_1112` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dijitso_758` - :ref:`list_software_dill_421` - :ref:`list_software_DIRAC_355` - :ref:`list_software_distributed_1187` - :ref:`list_software_DistributedStream_1775` - :ref:`list_software_DL_POLY_4_710` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_dlb_306` - :ref:`list_software_dlib_411` - :ref:`list_software_dm-reverb_900` - :ref:`list_software_dm-tree_686` - :ref:`list_software_DMCfun_541` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_DosageConvertor_1557` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_dotNET-SDK_829` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_DoubletFinder_1319` - :ref:`list_software_Doxygen_734` - :ref:`list_software_DRAGMAP_508` - :ref:`list_software_Drake_487` - :ref:`list_software_dRep_395` - :ref:`list_software_DROP_309` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_dSFMT_414` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dtcwt_550` - :ref:`list_software_DualSPHysics_1180` - :ref:`list_software_DUBStepR_713` - :ref:`list_software_dune-core_898` - :ref:`list_software_dune-fem_785` - :ref:`list_software_dxpy_453` - :ref:`list_software_DyMat_479` .. _list_software_dadi_402: @@ -8570,7 +8965,7 @@ version versionsuffix toolchain *homepage*: https://bitbucket.org/gutenkunstlab/dadi ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.7.0`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== @@ -8586,7 +8981,7 @@ A port of the web-based software 'DAGitty', available at , f *homepage*: https://cran.r-project.org/web/packages/dagitty/ ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``0.2-2`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== @@ -8602,7 +8997,7 @@ The Dakota project delivers both state-of-the-art research and robust, usable s *homepage*: https://dakota.sandia.gov/ ========== ============== -version toolchain +version toolchain ========== ============== ``6.16.0`` ``foss/2021b`` ========== ============== @@ -8618,10 +9013,10 @@ The Dalton code is a powerful tool for a wide range of molecular properties at *homepage*: https://daltonprogram.org/ ========== ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= =============== ``2016`` ``-i8`` ``intel/2017b`` -``2020.0`` ``foss/2021a`` +``2020.0`` ``foss/2021a`` ========== ============= =============== @@ -8635,7 +9030,7 @@ X protocol and ancillary headers for xinerama *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== -version toolchain +version toolchain ========= =============================== ``1.2.1`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -8651,7 +9046,7 @@ dammit is a simple de novo transcriptome annotator. It was born out of the obse *homepage*: http://www.camillescott.org/dammit/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.3.2`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== @@ -8667,7 +9062,7 @@ A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing *homepage*: https://sites.google.com/site/danposdoc ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.2.2`` ``-Python-2.7.12`` ``foss/2016b`` ========= ================== ============== @@ -8683,10 +9078,11 @@ DAS Tool is an automated method that integrates the results of a flexible number *homepage*: https://github.com/cmks/DAS_Tool ========= ========================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ========================== ============== ``1.1.1`` ``-R-3.5.1-Python-2.7.15`` ``foss/2018b`` ``1.1.1`` ``-R-4.1.2`` ``foss/2021b`` +``1.1.3`` ``-R-4.1.0`` ``foss/2021a`` ========= ========================== ============== @@ -8699,31 +9095,32 @@ Dask natively scales Python. Dask provides advanced parallelism for analytics, e *homepage*: https://dask.org/ -============ ================== ======================================================================== -version versionsuffix toolchain -============ ================== ======================================================================== -``0.8.2`` ``-Python-2.7.11`` ``intel/2016a`` -``0.8.2`` ``-Python-3.5.1`` ``intel/2016a`` -``0.11.0`` ``-Python-2.7.11`` ``foss/2016a`` -``0.11.0`` ``-Python-2.7.12`` ``intel/2016b`` -``0.11.0`` ``-Python-3.5.2`` ``intel/2016b`` -``0.12.0`` ``-Python-2.7.12`` ``intel/2016b`` -``0.12.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``0.16.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``0.16.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``0.17.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` -``0.17.0`` ``-Python-3.6.1`` ``intel/2017a`` -``0.17.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``0.19.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``1.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.1.4`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``2.3.0`` ``-Python-3.7.2`` ``foss/2019a`` -``2.8.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``2.18.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``2021.2.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -``2021.9.1`` ``foss/2021a`` -``2022.1.0`` ``foss/2021b`` -============ ================== ======================================================================== +============= ================== ======================================================================== +version versionsuffix toolchain +============= ================== ======================================================================== +``0.8.2`` ``-Python-2.7.11`` ``intel/2016a`` +``0.8.2`` ``-Python-3.5.1`` ``intel/2016a`` +``0.11.0`` ``-Python-2.7.11`` ``foss/2016a`` +``0.11.0`` ``-Python-2.7.12`` ``intel/2016b`` +``0.11.0`` ``-Python-3.5.2`` ``intel/2016b`` +``0.12.0`` ``-Python-2.7.12`` ``intel/2016b`` +``0.12.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``0.16.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``0.16.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``0.17.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``0.17.0`` ``-Python-3.6.1`` ``intel/2017a`` +``0.17.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.19.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``1.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.1.4`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``2.3.0`` ``-Python-3.7.2`` ``foss/2019a`` +``2.8.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2.18.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``2021.2.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +``2021.9.1`` ``foss/2021a`` +``2022.1.0`` ``foss/2021b`` +``2022.10.0`` ``foss/2022a`` +============= ================== ======================================================================== .. _list_software_datamash_835: @@ -8736,9 +9133,9 @@ GNU datamash performs basic numeric, textual and statistical operations on input *homepage*: https://www.gnu.org/software/datamash/ ======= ======================================================== -version toolchain +version toolchain ======= ======================================================== -``1.3`` ``foss/2018a`` +``1.3`` ``foss/2018a`` ``1.5`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ======= ======================================================== @@ -8753,9 +9150,9 @@ The davix project aims to make file management over HTTP-based protocols simple. *homepage*: https://dmc.web.cern.ch/projects/davix/home ========= ================= -version toolchain +version toolchain ========= ================= -``0.6.6`` ``intel/2017a`` +``0.6.6`` ``intel/2017a`` ``0.7.5`` ``GCCcore/8.3.0`` ========= ================= @@ -8770,13 +9167,13 @@ Berkeley DB enables the development of custom data management solutions, withou *homepage*: http://www.oracle.com/technetwork/products/berkeleydb =========== =========================================================================================================================================================================== -version toolchain +version toolchain =========== =========================================================================================================================================================================== -``4.8.30`` ``intel/2016a`` -``6.2.23`` ``foss/2016a`` -``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` -``18.1.25`` ``GCCcore/7.3.0`` -``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.8.30`` ``intel/2016a`` +``6.2.23`` ``foss/2016a`` +``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` +``18.1.25`` ``GCCcore/7.3.0`` +``18.1.32`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``18.1.40`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` =========== =========================================================================================================================================================================== @@ -8791,11 +9188,11 @@ Perl5 access to Berkeley DB version 1.x. *homepage*: https://perldoc.perl.org/DB_File.html ========= ================ ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ================== -``1.835`` ``GCCcore/9.3.0`` -``1.835`` ``-Perl-5.20.3`` ``intel/2016a`` -``1.835`` ``-Perl-5.22.1`` ``foss/2016a`` +``1.835`` ``GCCcore/9.3.0`` +``1.835`` ``-Perl-5.20.3`` ``intel/2016a`` +``1.835`` ``-Perl-5.22.1`` ``foss/2016a`` ``1.855`` ``GCCcore/10.2.0`` ``1.856`` ``GCCcore/10.3.0`` ``1.857`` ``GCCcore/11.2.0`` @@ -8813,16 +9210,16 @@ Perl binding for MySQL *homepage*: https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm ========= ================ ============================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============================================== -``4.032`` ``-Perl-5.22.2`` ``intel/2016a`` -``4.033`` ``-Perl-5.24.0`` ``intel/2016b`` -``4.042`` ``-Perl-5.24.1`` ``intel/2017a`` -``4.046`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``4.046`` ``-Perl-5.26.1`` ``intel/2018a`` -``4.048`` ``-Perl-5.28.0`` ``foss/2018b`` +``4.032`` ``-Perl-5.22.2`` ``intel/2016a`` +``4.033`` ``-Perl-5.24.0`` ``intel/2016b`` +``4.042`` ``-Perl-5.24.1`` ``intel/2017a`` +``4.046`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``4.046`` ``-Perl-5.26.1`` ``intel/2018a`` +``4.048`` ``-Perl-5.28.0`` ``foss/2018b`` ``4.050`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` -``4.050`` ``-Perl-5.28.1`` ``foss/2019a`` +``4.050`` ``-Perl-5.28.1`` ``foss/2019a`` ========= ================ ============================================== @@ -8836,9 +9233,9 @@ DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Th *homepage*: https://github.com/yechengxi/DBG2OLC ============ ========================================================== -version toolchain +version toolchain ============ ========================================================== -``20170208`` ``intel/2016b``, ``intel/2017a`` +``20170208`` ``intel/2016b``, ``intel/2017a`` ``20180221`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ============ ========================================================== @@ -8853,18 +9250,19 @@ D-Bus is a message bus system, a simple way for applications to talk to one ano *homepage*: https://dbus.freedesktop.org/ =========== ========================================================== -version toolchain +version toolchain =========== ========================================================== -``1.10.8`` ``foss/2016a``, ``intel/2016a`` -``1.10.12`` ``intel/2016b`` -``1.10.20`` ``GCCcore/6.4.0`` -``1.11.20`` ``intel/2017a`` -``1.13.0`` ``intel/2017b`` -``1.13.6`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.13.8`` ``GCCcore/8.2.0`` -``1.13.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.10.8`` ``foss/2016a``, ``intel/2016a`` +``1.10.12`` ``intel/2016b`` +``1.10.20`` ``GCCcore/6.4.0`` +``1.11.20`` ``intel/2017a`` +``1.13.0`` ``intel/2017b`` +``1.13.6`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.13.8`` ``GCCcore/8.2.0`` +``1.13.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.13.18`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.14.0`` ``GCCcore/11.3.0`` +``1.14.0`` ``GCCcore/11.3.0`` +``1.15.2`` ``GCCcore/12.2.0`` =========== ========================================================== @@ -8878,12 +9276,12 @@ D-Bus is a message bus system, a simple way for applications to talk to one anot *homepage*: https://dbus.freedesktop.org/doc/dbus-glib ========= ======================================================================== -version toolchain +version toolchain ========= ======================================================================== -``0.106`` ``foss/2016a``, ``intel/2016a`` -``0.108`` ``intel/2016b``, ``intel/2017a`` +``0.106`` ``foss/2016a``, ``intel/2016a`` +``0.108`` ``intel/2016b``, ``intel/2017a`` ``0.110`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b`` -``0.112`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``0.112`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ======================================================================== @@ -8897,13 +9295,14 @@ dcm2niix is designed to convert neuroimaging data from the DICOM format to the N *homepage*: https://github.com/rordenlab/dcm2niix ================ ==================================== -version toolchain +version toolchain ================ ==================================== ``1.0.20180622`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.0.20190902`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.0.20200331`` ``GCCcore/8.3.0`` -``1.0.20201102`` ``GCCcore/8.3.0`` -``1.0.20211006`` ``GCCcore/10.3.0`` +``1.0.20200331`` ``GCCcore/8.3.0`` +``1.0.20201102`` ``GCCcore/8.3.0`` +``1.0.20211006`` ``GCCcore/10.3.0`` +``1.0.20220720`` ``GCCcore/11.3.0`` ================ ==================================== @@ -8917,11 +9316,12 @@ DCMTK is a collection of libraries and applications implementing large parts the *homepage*: https://dicom.offis.de/dcmtk ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``3.6.3`` ``GCCcore/7.3.0`` -``3.6.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.6.3`` ``GCCcore/7.3.0`` +``3.6.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.6.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``3.6.7`` ``GCCcore/11.3.0`` ========= ====================================== @@ -8935,7 +9335,7 @@ dd is a package for working with binary decision diagrams that includes both a p *homepage*: https://github.com/tulip-control/dd ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.5.6`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -8951,10 +9351,10 @@ deal.II is a C++ program library targeted at the computational solution of part *homepage*: https://www.dealii.org ========= =============================== -version toolchain +version toolchain ========= =============================== ``9.1.1`` ``foss/2019a``, ``intel/2019a`` -``9.3.3`` ``foss/2021a`` +``9.3.3`` ``foss/2021a`` ========= =============================== @@ -8968,7 +9368,7 @@ DEAP is a novel evolutionary computation framework for rapid prototyping and tes *homepage*: http://deap.readthedocs.org/en/master/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.9.2`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== @@ -8984,7 +9384,7 @@ fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanop *homepage*: https://github.com/Saskia-Oosterbroek/decona ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.1.2`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -9000,7 +9400,7 @@ decomposition (deconfounding) of OMICS datasets in heterogeneous tissues *homepage*: http://web.cbio.uct.ac.za/~renaud/CRAN/ ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.0.1`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== @@ -9016,7 +9416,7 @@ Deconvolution of transcriptome through Immune Component Analysis (DeconICA) is a *homepage*: https://urszulaczerwinska.github.io/DeconICA ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``0.1.0`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== @@ -9032,16 +9432,33 @@ DeepDiff: Deep Difference of dictionaries, iterables and almost any other object *homepage*: https://zepworks.com/deepdiff/current/ ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``3.3.0`` ``-Python-2.7.15`` ``intel/2018b`` +``3.3.0`` ``-Python-2.7.15`` ``intel/2018b`` ``3.3.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``4.0.6`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``5.0.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``5.7.0`` ``GCCcore/11.2.0`` +``4.0.6`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``5.0.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``5.7.0`` ``GCCcore/11.2.0`` +``5.8.1`` ``GCCcore/11.3.0`` ========= ================== =============================== +.. _list_software_DeepLabCut_953: + +*DeepLabCut* +++++++++++++ + +Markerless tracking of user-defined features with deep learning + +*homepage*: http://www.mousemotorlab.org/deeplabcut + +=========== ================ ============== +version versionsuffix toolchain +=========== ================ ============== +``2.2.0.6`` ``-CUDA-11.3.1`` ``foss/2021a`` +=========== ================ ============== + + .. _list_software_deepmedic_928: *deepmedic* @@ -9052,13 +9469,29 @@ Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Med *homepage*: https://biomedia.doc.ic.ac.uk/software/deepmedic/ ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``0.8.2`` ``foss/2021a`` ``0.8.2`` ``-CUDA-11.3.1`` ``foss/2021a`` ========= ================ ============== +.. _list_software_DeepMod2_720: + +*DeepMod2* +++++++++++ + +DeepMod2 is a computational tool for detecting DNA methylation and modifications from Oxford Nanopore reads. + +*homepage*: https://github.com/WGLab/DeepMod2 + +========= ============== +version toolchain +========= ============== +``0.0.1`` ``foss/2021a`` +========= ============== + + .. _list_software_DeepSurv_814: *DeepSurv* @@ -9069,7 +9502,7 @@ DeepSurv is a deep learning approach to survival analysis. *homepage*: https://github.com/jaredleekatzman/DeepSurv ================== ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ================== ================= ================== ``2.0.0-20180922`` ``-Python-3.6.6`` ``fosscuda/2018b`` ================== ================= ================== @@ -9085,14 +9518,14 @@ deepTools is a suite of python tools particularly developed for the efficient an *homepage*: https://deeptools.readthedocs.io/ ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``2.5.4`` ``-Python-3.6.3`` ``intel/2017b`` -``3.3.1`` ``-Python-3.6.6`` ``foss/2018b`` +``3.3.1`` ``-Python-3.6.6`` ``foss/2018b`` ``3.3.1`` ``-Python-3.7.4`` ``intel/2019b`` -``3.3.1`` ``-Python-3.8.2`` ``foss/2020a`` -``3.5.0`` ``foss/2021a`` -``3.5.1`` ``foss/2021b`` +``3.3.1`` ``-Python-3.8.2`` ``foss/2020a`` +``3.5.0`` ``foss/2021a`` +``3.5.1`` ``foss/2021b`` ========= ================= =============== @@ -9106,11 +9539,11 @@ Delly is an integrated structural variant (SV) prediction method that can discov *homepage*: https://github.com/dellytools/delly/ ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== -``0.7.8`` ``-linux_x86_64`` ``system`` +``0.7.8`` ``-linux_x86_64`` ``system`` ``0.8.7`` ``gompi/2020b`` -``1.1.5`` ``GCC/11.3.0`` +``1.1.5`` ``GCC/11.3.0`` ========= ================= =============== @@ -9124,7 +9557,7 @@ Cell type-specific deconvolution of heterogeneous tumor samples with two or thre *homepage*: https://bioinformatics.mdanderson.org/main/DeMixT ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``0.2.1`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== @@ -9139,14 +9572,14 @@ A Python library for phylogenetics and phylogenetic computing: reading, writing *homepage*: https://dendropy.org/ -========= ================== ======================================================================== -version versionsuffix toolchain -========= ================== ======================================================================== +========= ================== ============================================================================== +version versionsuffix toolchain +========= ================== ============================================================================== ``4.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2019a`` -``4.4.0`` ``-Python-2.7.15`` ``intel/2018b`` -``4.5.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``4.5.2`` ``-Python-2.7.18`` ``GCCcore/10.2.0`` -========= ================== ======================================================================== +``4.4.0`` ``-Python-2.7.15`` ``intel/2018b`` +``4.5.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.5.2`` ``-Python-2.7.18`` ``GCCcore/10.2.0`` +========= ================== ============================================================================== .. _list_software_destiny_768: @@ -9159,7 +9592,7 @@ R packages to create and plot diffusion maps. *homepage*: https://bioconductor.org/packages/destiny ========= ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= =============== ``2.5.6`` ``-R-3.4.0`` ``intel/2017a`` ========= ============= =============== @@ -9175,7 +9608,7 @@ Detectron2 is Facebook AI Research's next generation library that provides state *homepage*: https://github.com/facebookresearch/detectron2 ======= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================ ============== ``0.6`` ``foss/2021a`` ``0.6`` ``-CUDA-11.3.1`` ``foss/2021a`` @@ -9192,7 +9625,7 @@ DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evalu *homepage*: http://deweylab.biostat.wisc.edu/detonate/ ======== =============== -version toolchain +version toolchain ======== =============== ``1.11`` ``intel/2017b`` ======== =============== @@ -9208,7 +9641,7 @@ Devito is a domain-specific Language (DSL) and code generation framework for pe *homepage*: https://www.devitoproject.org ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``4.6.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -9224,9 +9657,9 @@ Python library for modeling DFAs, Moore Machines, and Transition Systems. *homepage*: https://github.com/mvcisback/dfa ========= ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================== -``0.3.4`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``0.3.4`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``2.1.2`` ``GCCcore/10.2.0`` ========= ================= ================== @@ -9241,7 +9674,7 @@ DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock *homepage*: http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english ========= ===================================================================================== -version toolchain +version toolchain ========= ===================================================================================== ``3.2.0`` ``GCC/8.3.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel/2019a`` ========= ===================================================================================== @@ -9257,7 +9690,7 @@ Generally Applicable Atomic-Charge Dependent London Dispersion Correction. *homepage*: https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4 ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``3.2.0`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================= =============== @@ -9273,12 +9706,12 @@ DFTB+ is a fast and efficient versatile quantum mechanical simulation package. I *homepage*: https://www.dftb-plus.info ========= ====================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ====================== =============== ``1.3.1`` ``intel/2017a`` ``17.1`` ``-Python-2.7.14`` ``intel/2017b`` -``19.1`` ``-Python-2.7.16`` ``foss/2019b`` -``19.1`` ``-Python-2.7.16-mpi`` ``foss/2019b`` +``19.1`` ``-Python-2.7.16`` ``foss/2019b`` +``19.1`` ``-Python-2.7.16-mpi`` ``foss/2019b`` ``21.1`` ``intel/2021a`` ========= ====================== =============== @@ -9293,7 +9726,7 @@ This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers *homepage*: https://github.com/dftbplus/dftd3-lib ======= =========================================== -version toolchain +version toolchain ======= =========================================== ``0.9`` ``GCC/8.3.0``, ``intel-compilers/2021.2.0`` ======= =========================================== @@ -9309,7 +9742,7 @@ DGL is an easy-to-use, high performance and scalable Python package for deep lea *homepage*: https://www.dgl.ai ========= =============================== ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =============================== ================== ``0.6.1`` ``-Python-3.7.4-PyTorch-1.8.1`` ``fosscuda/2019b`` ========= =============================== ================== @@ -9325,7 +9758,7 @@ DIAL (De novo Identification of Alleles) is a collection of programs to automat *homepage*: http://www.bx.psu.edu/miller_lab/ ============== ============== -version toolchain +version toolchain ============== ============== ``2011.06.06`` ``foss/2016a`` ============== ============== @@ -9341,20 +9774,36 @@ Accelerated BLAST compatible local sequence aligner *homepage*: https://github.com/bbuchfink/diamond ========== ================================================================ -version toolchain +version toolchain ========== ================================================================ ``0.9.22`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -``0.9.24`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``0.9.30`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``0.9.36`` ``GCC/9.3.0`` -``2.0.4`` ``GCC/9.3.0`` -``2.0.6`` ``GCC/7.3.0-2.30`` -``2.0.7`` ``GCC/10.2.0`` -``2.0.11`` ``GCC/10.3.0`` -``2.0.13`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``0.9.24`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``0.9.30`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``0.9.36`` ``GCC/9.3.0`` +``2.0.4`` ``GCC/9.3.0`` +``2.0.6`` ``GCC/7.3.0-2.30`` +``2.0.7`` ``GCC/10.2.0`` +``2.0.11`` ``GCC/10.3.0`` +``2.0.13`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========== ================================================================ +.. _list_software_Dice_373: + +*Dice* +++++++ + +Dice contains code for performing SHCI, VMC, GFMC, DMC, FCIQMC, stochastic MRCI and SC-NEVPT2, and AFQMC calculations with a focus on ab initio systems. + +*homepage*: https://github.com/sanshar/Dice + +============ ============== +version toolchain +============ ============== +``20221025`` ``foss/2022a`` +============ ============== + + .. _list_software_dicom2nifti_1112: *dicom2nifti* @@ -9365,7 +9814,7 @@ Python library for converting dicom files to nifti *homepage*: https://github.com/icometrix/dicom2nifti ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``2.2.12`` ``-Python-3.8.2`` ``foss/2020a`` ``2.3.0`` ``foss/2020b`` @@ -9382,7 +9831,7 @@ DicomBrowser is an application for inspecting and modifying DICOM metadata in ma *homepage*: http://nrg.wustl.edu/software/dicom-browser/ =========== ================== ========== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ========== ``1.7.0b5`` ``-Java-1.7.0_80`` ``system`` =========== ================== ========== @@ -9398,7 +9847,7 @@ Diffutils: GNU diff utilities - find the differences between files *homepage*: http://www.gnu.org/software/diffutils/diffutils.html ======= ============= -version toolchain +version toolchain ======= ============= ``3.3`` ``GCC/4.8.2`` ======= ============= @@ -9414,7 +9863,7 @@ dijitso is a Python module for distributed just-in-time shared library building. *homepage*: https://bitbucket.org/fenics-project/dijitso ============ ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ============== ``2019.1.0`` ``-Python-3.7.4`` ``foss/2019b`` ============ ================= ============== @@ -9430,10 +9879,10 @@ dill extends python's pickle module for serializing and de-serializing python ob *homepage*: https://pypi.org/project/dill/ ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``0.3.0`` ``GCCcore/8.2.0`` -``0.3.3`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +``0.3.0`` ``GCCcore/8.2.0`` +``0.3.3`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` ``0.3.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ====================================== @@ -9448,10 +9897,10 @@ DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electr *homepage*: http://www.diracprogram.org ======== ============================ =============================== -version versionsuffix toolchain +version versionsuffix toolchain ======== ============================ =============================== -``19.0`` ``-Python-2.7.18-int64`` ``intel/2020a`` -``19.0`` ``-Python-2.7.18-mpi-int64`` ``intel/2020a`` +``19.0`` ``-Python-2.7.18-int64`` ``intel/2020a`` +``19.0`` ``-Python-2.7.18-mpi-int64`` ``intel/2020a`` ``22.0`` ``foss/2021a``, ``intel/2021a`` ======== ============================ =============================== @@ -9466,7 +9915,7 @@ Dask.distributed is a lightweight library for distributed computing in Python. *homepage*: https://distributed.readthedocs.io/ ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``1.14.3`` ``-Python-2.7.12`` ``intel/2016b`` ``1.14.3`` ``-Python-3.5.2`` ``intel/2016b`` @@ -9484,7 +9933,7 @@ A MPI distributed stream benchmark, useful to identifying nodes with poor memory *homepage*: https://github.com/adrianjhpc/DistributedStream ======= =============== -version toolchain +version toolchain ======= =============== ``1.0`` ``gompi/2021a`` ======= =============== @@ -9500,7 +9949,7 @@ DL_POLY is a general purpose classical molecular dynamics (MD) simulation softwa *homepage*: https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx ========= =============================== -version toolchain +version toolchain ========= =============================== ``5.0.0`` ``foss/2020b``, ``intel/2020b`` ========= =============================== @@ -9516,14 +9965,30 @@ DL_POLY Classic is a freely available molecular dynamics program developed from *homepage*: http://ccpforge.cse.rl.ac.uk/gf/project/dl_poly_classic/ ======== ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================= =============================== -``1.9`` ``intel/2016b`` -``1.9`` ``-PLUMED-2.2.3`` ``intel/2016b`` +``1.9`` ``intel/2016b`` +``1.9`` ``-PLUMED-2.2.3`` ``intel/2016b`` ``1.10`` ``foss/2019b``, ``intel/2019b`` ======== ================= =============================== +.. _list_software_dlb_306: + +*dlb* ++++++ + +DLB is a dynamic library designed to speed up HPC hybrid applications (i.e., two levels of parallelism) by improving the load balance of the outer level of parallelism (e.g., MPI) by dynamically redistributing the computational resources at the inner level of parallelism (e.g., OpenMP). at run time. + +*homepage*: https://pm.bsc.es/dlb/ + +======= ================================ +version toolchain +======= ================================ +``3.2`` ``gompi/2022a``, ``iimpi/2022a`` +======= ================================ + + .. _list_software_dlib_411: *dlib* @@ -9534,7 +9999,7 @@ Dlib is a modern C++ toolkit containing machine learning algorithms and tools fo *homepage*: https://github.com/davisking/dlib ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``19.22`` ``foss/2021a`` ``19.22`` ``-CUDA-11.3.1`` ``foss/2021a`` @@ -9551,9 +10016,10 @@ Reverb is an efficient and easy-to-use data storage and transport system designe *homepage*: https://github.com/deepmind/reverb ========= ============== -version toolchain +version toolchain ========= ============== ``0.2.0`` ``foss/2020b`` +``0.7.0`` ``foss/2021b`` ========= ============== @@ -9567,10 +10033,10 @@ dm-tree provides tree, a library for working with nested data structures. In a w *homepage*: https://github.com/deepmind/tree ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``0.1.1`` ``GCCcore/8.3.0`` -``0.1.5`` ``GCCcore/10.2.0`` +``0.1.1`` ``GCCcore/8.3.0`` +``0.1.5`` ``GCCcore/10.2.0`` ``0.1.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ====================================== @@ -9585,7 +10051,7 @@ Diffusion Model of Conflict (DMC) in Reaction Time Tasks *homepage*: https://cran.r-project.org/web/packages/DMCfun ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.3.0`` ``-R-3.6.2`` ``foss/2019b`` ========= ============= ============== @@ -9601,13 +10067,13 @@ DMTCP is a tool to transparently checkpoint the state of multiple simultaneous a *homepage*: http://dmtcp.sourceforge.net/index.html ========= ================================================= -version toolchain +version toolchain ========= ================================================= -``2.4.5`` ``system`` -``2.5.0`` ``foss/2016a`` -``2.5.1`` ``system`` +``2.4.5`` ``system`` +``2.5.0`` ``foss/2016a`` +``2.5.1`` ``system`` ``2.5.2`` ``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2018b`` -``2.6.0`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +``2.6.0`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` ========= ================================================= @@ -9621,7 +10087,7 @@ DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Prob *homepage*: https://bitbucket.org/fenics-project/dolfin ================== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ================= ============== ``2018.1.0.post1`` ``-Python-3.6.4`` ``foss/2018a`` ``2019.1.0.post0`` ``-Python-3.7.4`` ``foss/2019b`` @@ -9638,11 +10104,11 @@ Delft object-oriented radar interferometric software *homepage*: http://doris.tudelft.nl/ ============= =============================== -version toolchain +version toolchain ============= =============================== -``4.02`` ``intel/2017a`` +``4.02`` ``intel/2017a`` ``4.04beta4`` ``foss/2018a``, ``intel/2017a`` -``4.06beta2`` ``intel/2017a`` +``4.06beta2`` ``intel/2017a`` ============= =============================== @@ -9656,7 +10122,7 @@ DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minim *homepage*: http://genome.sph.umich.edu/wiki/DosageConvertor ========= ============== -version toolchain +version toolchain ========= ============== ``1.0.4`` ``GCC/10.2.0`` ========= ============== @@ -9672,9 +10138,9 @@ version toolchain *homepage*: https://www.microsoft.com/net/ ========== ================== -version toolchain +version toolchain ========== ================== -``2.0.7`` ``GCCcore/6.4.0`` +``2.0.7`` ``GCCcore/6.4.0`` ``5.0.17`` ``GCCcore/10.3.0`` ``6.0.1`` ``GCCcore/11.2.0`` ========== ================== @@ -9690,7 +10156,7 @@ version toolchain *homepage*: https://www.microsoft.com/net/ =========== ============== ========== -version versionsuffix toolchain +version versionsuffix toolchain =========== ============== ========== ``3.1.300`` ``-linux-x64`` ``system`` ``6.0.101`` ``-linux-x64`` ``system`` @@ -9707,12 +10173,13 @@ Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles *homepage*: https://github.com/google/double-conversion ========= ============================================================================= -version toolchain +version toolchain ========= ============================================================================= -``3.0.3`` ``foss/2018a`` -``3.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.0.3`` ``foss/2018a`` +``3.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``3.2.0`` ``GCCcore/11.3.0`` +``3.2.0`` ``GCCcore/11.3.0`` +``3.2.1`` ``GCCcore/12.2.0`` ========= ============================================================================= @@ -9726,7 +10193,7 @@ R package for detecting doublets in single-cell RNA sequencing data *homepage*: https://github.com/chris-mcginnis-ucsf/DoubletFinder ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``2.0.3`` ``-R-4.0.0`` ``foss/2020a`` ========= ============= ============== @@ -9742,22 +10209,39 @@ Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (C *homepage*: https://www.doxygen.org =========== ======================================================================================================================================================= -version toolchain +version toolchain =========== ======================================================================================================================================================= -``1.8.9.1`` ``GCC/4.9.2`` -``1.8.10`` ``GNU/4.9.3-2.25``, ``intel/2016.02-GCC-4.9`` +``1.8.9.1`` ``GCC/4.9.2`` +``1.8.10`` ``GNU/4.9.3-2.25``, ``intel/2016.02-GCC-4.9`` ``1.8.11`` ``GCC/4.9.2``, ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``1.8.13`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``gimkl/2017a`` -``1.8.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``1.8.15`` ``GCCcore/8.2.0`` -``1.8.16`` ``GCCcore/8.3.0`` -``1.8.17`` ``GCCcore/9.3.0`` -``1.8.20`` ``GCCcore/10.2.0`` -``1.9.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.9.4`` ``GCCcore/11.3.0`` +``1.8.13`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``gimkl/2017a`` +``1.8.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``1.8.15`` ``GCCcore/8.2.0`` +``1.8.16`` ``GCCcore/8.3.0`` +``1.8.17`` ``GCCcore/9.3.0`` +``1.8.20`` ``GCCcore/10.2.0`` +``1.9.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.9.4`` ``GCCcore/11.3.0`` +``1.9.5`` ``GCCcore/12.2.0`` =========== ======================================================================================================================================================= +.. _list_software_DRAGMAP_508: + +*DRAGMAP* ++++++++++ + +Dragmap is the Dragen mapper/aligner Open Source Software. + +*homepage*: https://github.com/Illumina/DRAGMAP + +========= ============== +version toolchain +========= ============== +``1.3.0`` ``foss/2021b`` +========= ============== + + .. _list_software_Drake_487: *Drake* @@ -9768,7 +10252,7 @@ Drake is a simple-to-use, extensible, text-based data workflow tool that organiz *homepage*: https://github.com/Factual/drake ========= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========== ``1.0.3`` ``-Java-1.8`` ``system`` ========= ============= ========== @@ -9784,7 +10268,7 @@ dRep is a python program which performs rapid pair-wise comparison of genome set *homepage*: https://drep.readthedocs.io/en/latest/ ========= ============== -version toolchain +version toolchain ========= ============== ``3.0.0`` ``foss/2021a`` ========= ============== @@ -9800,7 +10284,7 @@ Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare d *homepage*: https://gagneurlab-drop.readthedocs.io ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.0.3`` ``-R-4.0.3`` ``foss/2020b`` ``1.1.0`` ``-R-4.0.3`` ``foss/2020b`` @@ -9818,7 +10302,7 @@ Pipeline for initial analysis of droplet-based single-cell RNA-seq data *homepage*: https://github.com/hms-dbmi/dropEst ========= ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= =============== ``0.7.1`` ``-R-3.4.3`` ``intel/2017b`` ========= ============= =============== @@ -9834,7 +10318,7 @@ Digital Sorting Algorithm *homepage*: https://github.com/zhandong/DSA ======= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= ============== ``1.0`` ``-R-3.5.1`` ``foss/2018b`` ======= ============= ============== @@ -9850,7 +10334,7 @@ Double precision SIMD-oriented Fast Mersenne Twister. *homepage*: https://github.com/MersenneTwister-Lab/dSFMT ========= ================== -version toolchain +version toolchain ========= ================== ``2.2.5`` ``GCCcore/10.2.0`` ========= ================== @@ -9866,7 +10350,7 @@ DNA Sequence Reads Compression is an application designed for compression of dat *homepage*: http://sun.aei.polsl.pl/dsrc ========= ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ========== ``2.0rc`` ``-linux-64-bit`` ``system`` ========= ================= ========== @@ -9882,9 +10366,9 @@ Fast calculation of the ABBA-BABA statistics across many populations/species *homepage*: https://github.com/millanek/Dsuite ============ ============================================ -version toolchain +version toolchain ============ ============================================ -``20190713`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``20190713`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``20210718`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` ============ ============================================ @@ -9899,10 +10383,10 @@ The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined co *homepage*: https://github.com/LLNL/dtcmp ========= ================================================================== -version toolchain +version toolchain ========= ================================================================== ``1.1.0`` ``gompi/2019a``, ``gompi/2020a``, ``iimpi/2019a``, ``iimpi/2020a`` -``1.1.2`` ``gompi/2020b`` +``1.1.2`` ``gompi/2020b`` ========= ================================================================== @@ -9916,9 +10400,9 @@ Dual-Tree Complex Wavelet Transform library for Python *homepage*: https://github.com/rjw57/dtcwt ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== -``0.12.0`` ``-Python-2.7.15`` ``foss/2018b`` +``0.12.0`` ``-Python-2.7.15`` ``foss/2018b`` ``0.12.0`` ``-Python-3.7.4`` ``intel/2019b`` ========== ================== =============== @@ -9933,7 +10417,7 @@ DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysic *homepage*: https://dual.sphysics.org/ =========== ===================== ============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ===================== ============== ``5.0.175`` ``GCC/11.2.0`` ``5.0.175`` ``-CUDA-%(cudaver)s`` ``GCC/11.2.0`` @@ -9950,7 +10434,7 @@ DUBStepR (Determining the Underlying Basis using Step-wise Regression) is a feat *homepage*: https://github.com/prabhakarlab/DUBStepR ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.2.0`` ``-R-4.1.2`` ``foss/2021b`` ========= ============= ============== @@ -9966,7 +10450,7 @@ The Dune core modules build the stable basis of Dune. They follow a consistent *homepage*: https://www.dune-project.org/groups/core/ =============== ============== -version toolchain +version toolchain =============== ============== ``2.8.0.post1`` ``foss/2020b`` =============== ============== @@ -9982,7 +10466,7 @@ DUNE-FEM is a discretization module based on DUNE containing all the building bl *homepage*: https://www.dune-project.org/modules/dune-fem/ =========== ============== -version toolchain +version toolchain =========== ============== ``2.8.0.6`` ``foss/2020b`` =========== ============== @@ -9998,7 +10482,7 @@ DNAnexus Platform API bindings for Python *homepage*: http://autodoc.dnanexus.com/ =========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== =============== ``0.266.1`` ``-Python-2.7.14`` ``intel/2018a`` =========== ================== =============== @@ -10014,7 +10498,7 @@ Read and process result files from Dymola and OpenModelica with Python. *homepage*: https://www.j-raedler.de/projects/DyMat ======= =============== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= =============== ============== ``0.7`` ``-2020-12-12`` ``foss/2021b`` ======= =============== ============== @@ -10026,7 +10510,7 @@ version versionsuffix toolchain --- -:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_eht-imaging_1098` - :ref:`list_software_Eigen_488` - :ref:`list_software_EigenExa_774` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_einops_654` - :ref:`list_software_elastix_762` - :ref:`list_software_elbencho_832` - :ref:`list_software_ELFIO_367` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_elprep_648` - :ref:`list_software_ELSI_301` - :ref:`list_software_ELSI-RCI_568` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_Embree_592` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_enchant-2_832` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_epiScanpy_940` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESL-Bundle_875` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExaML_439` - :ref:`list_software_Excel-Writer-XLSX_1559` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_expecttest_1097` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` +:ref:`list_software_E-ANTIC_481` - :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecBuild_696` - :ref:`list_software_ecCodes_694` - :ref:`list_software_eccodes-python_1445` - :ref:`list_software_ED2_187` - :ref:`list_software_edlib_512` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_EGTtools_785` - :ref:`list_software_eht-imaging_1098` - :ref:`list_software_Eigen_488` - :ref:`list_software_EigenExa_774` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_einops_654` - :ref:`list_software_elastix_762` - :ref:`list_software_elbencho_832` - :ref:`list_software_ELFIO_367` - :ref:`list_software_elfutils_872` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_elprep_648` - :ref:`list_software_ELSI_301` - :ref:`list_software_ELSI-RCI_568` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_Embree_592` - :ref:`list_software_emcee_511` - :ref:`list_software_EMU_231` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_enchant-2_832` - :ref:`list_software_EnsEMBLCoreAPI_1193` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_epiScanpy_940` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESL-Bundle_875` - :ref:`list_software_ESM-2_324` - :ref:`list_software_ESMF_299` - :ref:`list_software_ESMPy_430` - :ref:`list_software_ESMValTool_934` - :ref:`list_software_eSpeak-NG_795` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_ExaML_439` - :ref:`list_software_Excel-Writer-XLSX_1559` - :ref:`list_software_ExifTool_810` - :ref:`list_software_exiv2_494` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_expecttest_1097` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_E-ANTIC_481: @@ -10039,10 +10523,10 @@ E-ANTIC is a C/C++ library to deal with real embedded number fields built on top *homepage*: https://github.com/videlec/e-antic ========= ==================== -version toolchain +version toolchain ========= ==================== ``0.1.2`` ``GCC/8.2.0-2.31.1`` -``0.1.5`` ``GCC/8.3.0`` +``0.1.5`` ``GCC/8.3.0`` ========= ==================== @@ -10056,7 +10540,7 @@ Command-line tools for processing biological sequencing data. Barcode demultiple *homepage*: http://expressionanalysis.github.io/ea-utils/ ============ =============================================== -version toolchain +version toolchain ============ =============================================== ``1.04.807`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ============ =============================================== @@ -10072,7 +10556,7 @@ Python and JavaScript bindings for calling the Earth Engine API *homepage*: https://github.com/google/earthengine-api =========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== =============== ``0.1.143`` ``-Python-2.7.14`` ``intel/2018a`` =========== ================== =============== @@ -10088,7 +10572,7 @@ EasyBuild is a software build and installation framework written in Python that *homepage*: https://easybuilders.github.io/easybuild ========== ========== -version toolchain +version toolchain ========== ========== ``1.0.0`` ``system`` ``1.0.1`` ``system`` @@ -10182,6 +10666,7 @@ version toolchain ``4.5.5`` ``system`` ``4.6.0`` ``system`` ``4.6.1`` ``system`` +``4.6.2`` ``system`` ========== ========== @@ -10195,12 +10680,28 @@ EasyQC is an R-package that provides advanced functionality to (1) perform file *homepage*: http://www.uni-regensburg.de/medizin/epidemiologie-praeventivmedizin/genetische-epidemiologie/software/ ======= ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= =============== ``9.2`` ``-R-3.3.1`` ``intel/2016b`` ======= ============= =============== +.. _list_software_ecBuild_696: + +*ecBuild* ++++++++++ + +A CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems + +*homepage*: https://ecbuild.readthedocs.io/ + +========= ========== +version toolchain +========= ========== +``3.7.0`` ``system`` +========= ========== + + .. _list_software_ecCodes_694: *ecCodes* @@ -10211,19 +10712,20 @@ ecCodes is a package developed by ECMWF which provides an application programmin *homepage*: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home ========== ================== ================================ -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================================ -``2.7.3`` ``intel/2018a`` -``2.7.3`` ``-Python-2.7.14`` ``intel/2017b`` -``2.8.2`` ``intel/2018a`` +``2.7.3`` ``intel/2018a`` +``2.7.3`` ``-Python-2.7.14`` ``intel/2017b`` +``2.8.2`` ``intel/2018a`` ``2.9.2`` ``intel/2018b``, ``iomkl/2018b`` -``2.12.5`` ``gompi/2019a`` +``2.12.5`` ``gompi/2019a`` ``2.15.0`` ``gompi/2019b``, ``iimpi/2019b`` -``2.17.0`` ``foss/2018b``, ``gompi/2019b`` -``2.18.0`` ``gompi/2020a`` -``2.20.0`` ``gompi/2020b`` -``2.22.1`` ``gompi/2021a`` +``2.17.0`` ``foss/2018b``, ``gompi/2019b`` +``2.18.0`` ``gompi/2020a`` +``2.20.0`` ``gompi/2020b`` +``2.22.1`` ``gompi/2021a`` ``2.24.2`` ``gompi/2021b``, ``iimpi/2021b`` +``2.27.0`` ``gompi/2022a`` ========== ================== ================================ @@ -10237,7 +10739,7 @@ Python 3 interface to decode and encode GRIB and BUFR files via the ECMWF ecCode *homepage*: https://github.com/ecmwf/eccodes-python ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.0.0`` ``-Python-3.7.4`` ``foss/2019b`` ``1.0.0`` ``-Python-3.8.2`` ``foss/2020a`` @@ -10255,7 +10757,7 @@ The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial bios *homepage*: https://github.com/EDmodel/ED2 ============ ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= =============== ``20170201`` ``intel/2017a`` ``20170201`` ``-serial`` ``intel/2017a`` @@ -10272,11 +10774,11 @@ Lightweight, super fast library for sequence alignment using edit (Levenshtein) *homepage*: https://martinsos.github.io/edlib =============== ================= ============================================== -version versionsuffix toolchain +version versionsuffix toolchain =============== ================= ============================================== -``1.3.8.post1`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``1.3.8.post1`` ``-Python-3.8.2`` ``GCC/9.3.0`` -``1.3.8.post2`` ``-Python-3.8.2`` ``iccifort/2020.1.217`` +``1.3.8.post1`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``1.3.8.post1`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``1.3.8.post2`` ``-Python-3.8.2`` ``iccifort/2020.1.217`` ``1.3.9`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0`` =============== ================= ============================================== @@ -10291,7 +10793,7 @@ EggLib is a C++/Python library and program package for evolutionary genetics and *homepage*: http://egglib.sourceforge.net/ ========== =============== -version toolchain +version toolchain ========== =============== ``2.1.10`` ``intel/2016a`` ========== =============== @@ -10307,14 +10809,31 @@ EggNOG-mapper is a tool for fast functional annotation of novel sequences. It us *homepage*: https://github.com/eggnogdb/eggnog-mapper ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.0.3`` ``-Python-2.7.14`` ``intel/2018a`` -``2.1.4`` ``foss/2020b`` -``2.1.7`` ``foss/2021b`` +``2.1.4`` ``foss/2020b`` +``2.1.7`` ``foss/2021b`` ========= ================== =============== +.. _list_software_EGTtools_785: + +*EGTtools* +++++++++++ + +EGTtools provides a centralized repository with analytical and numerical methods to study/model game theoretical problems under the Evolutionary Game Theory (EGT) framework. + +*homepage*: https://github.com/Socrats/EGTTools + +=============== ============== +version toolchain +=============== ============== +``0.1.10.dev2`` ``foss/2021b`` +``0.1.11`` ``foss/2022a`` +=============== ============== + + .. _list_software_eht-imaging_1098: *eht-imaging* @@ -10325,7 +10844,7 @@ Python modules for simulating and manipulating VLBI data and producing images wi *homepage*: https://github.com/achael/eht-imaging ========= ============== -version toolchain +version toolchain ========= ============== ``1.2.2`` ``foss/2021a`` ========= ============== @@ -10341,21 +10860,21 @@ Eigen is a C++ template library for linear algebra: matrices, vectors, numerical *homepage*: https://eigen.tuxfamily.org ========== ========================================================== -version toolchain +version toolchain ========== ========================================================== -``3.2.3`` ``foss/2016a``, ``foss/2016b`` -``3.2.5`` ``system`` -``3.2.6`` ``system`` -``3.2.7`` ``foss/2016a``, ``intel/2016a`` -``3.2.8`` ``foss/2016a``, ``intel/2016a``, ``system`` -``3.2.9`` ``foss/2016b``, ``intel/2016b`` -``3.2.10`` ``intel/2016b`` -``3.3.2`` ``foss/2016b``, ``intel/2016b`` -``3.3.3`` ``GCCcore/6.3.0``, ``intel/2016b`` -``3.3.4`` ``system`` -``3.3.5`` ``system`` -``3.3.7`` ``GCCcore/9.3.0``, ``system`` -``3.3.8`` ``GCCcore/10.2.0`` +``3.2.3`` ``foss/2016a``, ``foss/2016b`` +``3.2.5`` ``system`` +``3.2.6`` ``system`` +``3.2.7`` ``foss/2016a``, ``intel/2016a`` +``3.2.8`` ``foss/2016a``, ``intel/2016a``, ``system`` +``3.2.9`` ``foss/2016b``, ``intel/2016b`` +``3.2.10`` ``intel/2016b`` +``3.3.2`` ``foss/2016b``, ``intel/2016b`` +``3.3.3`` ``GCCcore/6.3.0``, ``intel/2016b`` +``3.3.4`` ``system`` +``3.3.5`` ``system`` +``3.3.7`` ``GCCcore/9.3.0``, ``system`` +``3.3.8`` ``GCCcore/10.2.0`` ``3.3.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ``3.4.0`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ========================================================== @@ -10371,7 +10890,7 @@ EigenExa, a part of KMATHLIB, is a high performance eigen-solver. *homepage*: https://www.r-ccs.riken.jp/labs/lpnctrt/projects/eigenexa/ ======== =============== -version toolchain +version toolchain ======== =============== ``2.11`` ``intel/2020b`` ======== =============== @@ -10387,11 +10906,11 @@ The EIGENSOFT package combines functionality from our population genetics method *homepage*: http://www.hsph.harvard.edu/alkes-price/software/ ========= =============================================================================== -version toolchain +version toolchain ========= =============================================================================== -``6.0.1`` ``foss/2016a`` -``6.1.1`` ``foss/2016a`` -``6.1.4`` ``foss/2016b`` +``6.0.1`` ``foss/2016a`` +``6.1.1`` ``foss/2016a`` +``6.1.4`` ``foss/2016b`` ``7.2.1`` ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2021a``, ``intel/2019a`` ========= =============================================================================== @@ -10405,12 +10924,12 @@ Flexible and powerful tensor operations for readable and reliable code. Supports *homepage*: https://einops.rocks/ -========= ================== -version toolchain -========= ================== +========= ====================================== +version toolchain +========= ====================================== ``0.3.2`` ``GCCcore/10.2.0`` -``0.4.1`` ``GCCcore/10.3.0`` -========= ================== +``0.4.1`` ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +========= ====================================== .. _list_software_elastix_762: @@ -10423,7 +10942,7 @@ elastix: a toolbox for rigid and nonrigid registration of images. *homepage*: http://elastix.isi.uu.nl/ ========= ============== -version toolchain +version toolchain ========= ============== ``4.9.0`` ``foss/2018a`` ========= ============== @@ -10439,7 +10958,7 @@ A distributed storage benchmark for files, objects & blocks with support for GPU *homepage*: https://github.com/breuner/elbencho ========= ============== -version toolchain +version toolchain ========= ============== ``2.0-3`` ``GCC/10.3.0`` ========= ============== @@ -10455,7 +10974,7 @@ ELFIO is a header-only C++ library intended for reading and generating files in *homepage*: http://elfio.sourceforge.net ======= ========== -version toolchain +version toolchain ======= ========== ``3.9`` ``system`` ======= ========== @@ -10471,12 +10990,12 @@ The elfutils project provides libraries and tools for ELF files and DWARF data. *homepage*: https://elfutils.org/ ========= ============================================================================ -version toolchain +version toolchain ========= ============================================================================ -``0.182`` ``GCCcore/9.3.0`` -``0.183`` ``GCCcore/10.2.0`` +``0.182`` ``GCCcore/9.3.0`` +``0.183`` ``GCCcore/10.2.0`` ``0.185`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.187`` ``GCCcore/11.3.0`` +``0.187`` ``GCCcore/11.3.0`` ========= ============================================================================ @@ -10490,14 +11009,14 @@ An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code wi *homepage*: http://elk.sourceforge.net/ ========== =============== -version toolchain +version toolchain ========== =============== ``4.0.15`` ``intel/2016b`` ``4.3.6`` ``intel/2017a`` ``6.3.2`` ``intel/2019b`` -``7.0.12`` ``foss/2020b`` -``7.2.42`` ``foss/2021a`` -``8.5.2`` ``foss/2022a`` +``7.0.12`` ``foss/2020b`` +``7.2.42`` ``foss/2021a`` +``8.5.2`` ``foss/2022a`` ========== =============== @@ -10511,20 +11030,20 @@ Eigenvalue SoLvers for Petaflop-Applications. *homepage*: https://elpa.rzg.mpg.de =================== ================================================================================= -version toolchain +version toolchain =================== ================================================================================= -``2015.02.002`` ``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` -``2016.05.004`` ``intel/2016b``, ``intel/2017a`` -``2016.11.001.pre`` ``foss/2018b``, ``intel/2018b`` -``2017.11.001`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` -``2018.05.001`` ``foss/2018b``, ``intel/2018b`` -``2018.11.001`` ``intel/2019a`` +``2015.02.002`` ``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` +``2016.05.004`` ``intel/2016b``, ``intel/2017a`` +``2016.11.001.pre`` ``foss/2018b``, ``intel/2018b`` +``2017.11.001`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` +``2018.05.001`` ``foss/2018b``, ``intel/2018b`` +``2018.11.001`` ``intel/2019a`` ``2019.11.001`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a``, ``iomkl/2019b`` -``2020.05.001`` ``intel/2020a`` -``2020.11.001`` ``foss/2020b``, ``intel/2020b`` -``2021.05.001`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a``, ``intel/2021b`` -``2021.05.002`` ``intel/2020b`` -``2021.11.001`` ``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` +``2020.05.001`` ``intel/2020a`` +``2020.11.001`` ``foss/2020b``, ``intel/2020b`` +``2021.05.001`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a``, ``intel/2021b`` +``2021.05.002`` ``intel/2020b`` +``2021.11.001`` ``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` =================== ================================================================================= @@ -10538,7 +11057,7 @@ ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or *homepage*: http://ccb.jhu.edu/software/ELPH/index.shtml ========= ============== -version toolchain +version toolchain ========= ============== ``1.0.1`` ``foss/2018b`` ========= ============== @@ -10554,7 +11073,7 @@ elPrep is a high-performance tool for analyzing .sam/.bam files (up to and inclu *homepage*: https://github.com/ExaScience/elprep ========= ========== -version toolchain +version toolchain ========= ========== ``5.1.1`` ``system`` ========= ========== @@ -10570,10 +11089,10 @@ ELSI provides and enhances scalable, open-source software library solutions for *homepage*: https://wordpress.elsi-interchange.org/ ========= ============= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= =============================== -``2.5.0`` ``intel/2019b`` -``2.5.0`` ``-PEXSI`` ``intel/2019b`` +``2.5.0`` ``intel/2019b`` +``2.5.0`` ``-PEXSI`` ``intel/2019b`` ``2.6.4`` ``-PEXSI`` ``foss/2020b``, ``intel/2020b`` ``2.7.1`` ``-PEXSI`` ``foss/2021a``, ``intel/2021a`` ========= ============= =============================== @@ -10589,7 +11108,7 @@ ELSI-RCI provides and enhances open-source software packages which iteratively s *homepage*: https://wordpress.elsi-interchange.org/ ========= =========================================================================================================================== -version toolchain +version toolchain ========= =========================================================================================================================== ``0.1.0`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``foss/2020b``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0``, ``intel/2020b`` ========= =========================================================================================================================== @@ -10605,18 +11124,18 @@ GNU Emacs is an extensible, customizable text editor--and more. At its core is *homepage*: https://www.gnu.org/software/emacs/ ======== ============= ======================================================= -version versionsuffix toolchain +version versionsuffix toolchain ======== ============= ======================================================= -``24.3`` ``GCC/4.8.3`` -``24.3`` ``-bare`` ``GCC/4.8.3`` -``24.4`` ``GCC/4.9.2`` -``24.5`` ``GCC/4.9.3-2.25`` -``25.1`` ``foss/2016a`` +``24.3`` ``GCC/4.8.3`` +``24.3`` ``-bare`` ``GCC/4.8.3`` +``24.4`` ``GCC/4.9.2`` +``24.5`` ``GCC/4.9.3-2.25`` +``25.1`` ``foss/2016a`` ``25.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``26.3`` ``GCCcore/8.3.0`` -``27.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``27.2`` ``GCCcore/11.2.0`` -``28.1`` ``GCCcore/10.2.0`` +``26.3`` ``GCCcore/8.3.0`` +``27.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``27.2`` ``GCCcore/11.2.0`` +``28.1`` ``GCCcore/10.2.0`` ======== ============= ======================================================= @@ -10630,11 +11149,11 @@ EMAN2 is a broadly based greyscale scientific image processing suite with a pri *homepage*: https://blake.bcm.edu/emanwiki/EMAN2 ========= =============================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =============================== ================================== -``2.3`` ``system`` +``2.3`` ``system`` ``2.3`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a`` -``2.21a`` ``-Python-2.7.14-Boost-1.63.0`` ``foss/2018a`` +``2.21a`` ``-Python-2.7.14-Boost-1.63.0`` ``foss/2018a`` ========= =============================== ================================== @@ -10648,12 +11167,12 @@ EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a fre *homepage*: http://emboss.sourceforge.net/ ========= ================= ================================================================================================================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================================================================================================================================================ ``6.6.0`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018b``, ``foss/2021a``, ``foss/2021b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` -``6.6.0`` ``-Java-11`` ``GCC/8.3.0`` -``6.6.0`` ``-Java-13`` ``GCC/10.2.0`` -``6.6.0`` ``-X11-20170314`` ``intel/2017a`` +``6.6.0`` ``-Java-11`` ``GCC/8.3.0`` +``6.6.0`` ``-Java-13`` ``GCC/10.2.0`` +``6.6.0`` ``-X11-20170314`` ``intel/2017a`` ========= ================= ================================================================================================================================================================ @@ -10667,10 +11186,10 @@ Intel® Embree is a collection of high-performance ray tracing kernels, develope *homepage*: https://embree.github.io/ ========== ====================================== -version toolchain +version toolchain ========== ====================================== ``3.4.0`` ``iccifort/2018.1.163-GCC-6.4.0-2.28`` -``3.13.4`` ``system`` +``3.13.4`` ``system`` ========== ====================================== @@ -10684,9 +11203,9 @@ Emcee is an extensible, pure-Python implementation of Goodman & Weare's Affine *homepage*: https://dfm.io/emcee ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``2.2.1`` ``foss/2019a`` +``2.2.1`` ``foss/2019a`` ``2.2.1`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.2.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ========= ================== =============================== @@ -10702,7 +11221,7 @@ EMU infers population structure in the presence of missingness and works for bot *homepage*: http://www.popgen.dk/software/index.php/EMU ======== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================= ============== ``0.66`` ``-Python-3.7.4`` ``foss/2019b`` ======== ================= ============== @@ -10718,9 +11237,9 @@ enaBrowserTools is a set of scripts that interface with the ENA web services to *homepage*: https://github.com/enasequence/enaBrowserTools/ ========= ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================== -``1.5.4`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``1.5.4`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``1.6`` ``GCCcore/10.3.0`` ========= ================= ================== @@ -10735,7 +11254,7 @@ Enchant is a library (and command-line program) that wraps a number of different *homepage*: https://abiword.github.io/enchant/ ========= =============== -version toolchain +version toolchain ========= =============== ``1.6.1`` ``intel/2017a`` ========= =============== @@ -10750,11 +11269,11 @@ Enchant aims to provide a simple but comprehensive abstraction for dealing with *homepage*: https://github.com/AbiWord/enchant -========= ================== -version toolchain -========= ================== -``2.3.3`` ``GCCcore/11.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``2.3.3`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ====================================== .. _list_software_EnsEMBLCoreAPI_1193: @@ -10767,7 +11286,7 @@ The Ensembl Core Perl API and SQL schema *homepage*: https://www.ensembl.org/info/docs/api/index.html ================== ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ================ ============== ``96.0-r20190601`` ``-Perl-5.28.1`` ``foss/2019a`` ================== ================ ============== @@ -10783,12 +11302,12 @@ Entry points are a way for Python packages to advertise objects with some common *homepage*: https://github.com/takluyver/entrypoints ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``0.2.2`` ``-Python-2.7.11`` ``foss/2016a`` +``0.2.2`` ``-Python-2.7.11`` ``foss/2016a`` ``0.2.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``0.2.2`` ``-Python-3.5.1`` ``foss/2016a`` -``0.2.2`` ``-Python-3.5.2`` ``intel/2016b`` +``0.2.2`` ``-Python-3.5.1`` ``foss/2016a`` +``0.2.2`` ``-Python-3.5.2`` ``intel/2016b`` ========= ================== =============================== @@ -10802,7 +11321,7 @@ The Enthought Python Distribution provides scientists with a comprehensive set o *homepage*: http://www.enthought.com/products/edudownload.php ============= ========== -version toolchain +version toolchain ============= ========== ``7.3-2-rh5`` ``system`` ============= ========== @@ -10818,7 +11337,7 @@ Package implementing EPIC method to estimate the proportion of immune, stromal, *homepage*: https://gfellerlab.shinyapps.io/EPIC_1-1 ======= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= ============== ``1.1`` ``-R-3.5.1`` ``foss/2018b`` ======= ============= ============== @@ -10834,7 +11353,7 @@ EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and si *homepage*: https://github.com/colomemaria/episcanpy ========= ============== -version toolchain +version toolchain ========= ============== ``0.3.1`` ``foss/2021a`` ========= ============== @@ -10850,7 +11369,7 @@ EricScript is a computational framework for the discovery of gene fusions in pai *homepage*: https://sites.google.com/site/bioericscript/home ========= ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= =============== ``0.5.5`` ``-R-3.4.0`` ``intel/2017a`` ========= ============= =============== @@ -10866,12 +11385,29 @@ The ESL Bundle is a collection of libraries and utilities broadly used in elect *homepage*: https://esl.cecam.org ========= =============================== -version toolchain +version toolchain ========= =============================== ``0.6.1`` ``foss/2020b``, ``intel/2020b`` ========= =============================== +.. _list_software_ESM-2_324: + +*ESM-2* ++++++++ + +ESM-2 outperforms all tested single-sequence protein language models across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate accurate structure predictions end to end directly from the sequence of a protein. + +*homepage*: https://github.com/facebookresearch/esm + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``2.0.0`` ``foss/2021a`` +``2.0.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== + + .. _list_software_ESMF_299: *ESMF* @@ -10882,18 +11418,18 @@ The Earth System Modeling Framework (ESMF) is a suite of software tools for deve *homepage*: https://www.earthsystemcog.org/projects/esmf/ ============ ================ ================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ============ ================ ================================================================================= -``6.3.0rp1`` ``intel/2017a`` -``6.3.0rp1`` ``-HDF5-1.8.18`` ``intel/2017a`` -``7.0.0`` ``foss/2016a`` -``7.0.2`` ``intel/2017b`` +``6.3.0rp1`` ``intel/2017a`` +``6.3.0rp1`` ``-HDF5-1.8.18`` ``intel/2017a`` +``7.0.0`` ``foss/2016a`` +``7.0.2`` ``intel/2017b`` ``7.1.0r`` ``foss/2018b``, ``foss/2019a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``8.0.0`` ``foss/2019b``, ``intel/2019b`` -``8.0.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` -``8.1.1`` ``foss/2021a``, ``intel/2021a`` -``8.2.0`` ``foss/2021b``, ``intel/2021b`` -``8.3.0`` ``foss/2022a`` +``8.0.0`` ``foss/2019b``, ``intel/2019b`` +``8.0.1`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` +``8.1.1`` ``foss/2021a``, ``intel/2021a`` +``8.2.0`` ``foss/2021b``, ``intel/2021b`` +``8.3.0`` ``foss/2022a``, ``intel/2022a`` ============ ================ ================================================================================= @@ -10907,11 +11443,11 @@ Earth System Modeling Framework (ESMF) Python Interface *homepage*: https://earthsystemmodeling.org/esmpy ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``8.0.0`` ``-Python-3.7.4`` ``intel/2019b`` ``8.0.1`` ``intel/2020b`` -``8.0.1`` ``-Python-3.8.2`` ``foss/2020a`` +``8.0.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= =============== @@ -10925,7 +11461,7 @@ The Earth System Model eValuation Tool (ESMValTool) is a community diagnostics *homepage*: https://www.esmvaltool.org/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.1.0`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== @@ -10941,7 +11477,7 @@ The eSpeak NG is a compact open source software text-to-speech synthesizer for L *homepage*: https://github.com/espeak-ng/espeak-ng ======== =============== -version toolchain +version toolchain ======== =============== ``1.50`` ``gompi/2020a`` ======== =============== @@ -10957,7 +11493,7 @@ Open-source library and tools for audio and music analysis, description and synt *homepage*: https://essentia.upf.edu ============= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============= ================== ============== ``2.1_beta5`` ``-Python-2.7.15`` ``foss/2019a`` ============= ================== ============== @@ -10972,14 +11508,14 @@ A Python framework for the analysis and visualization of trees *homepage*: http://etetoolkit.org -============ ================== ============================== -version versionsuffix toolchain -============ ================== ============================== -``3.0.0b36`` ``-Python-2.7.12`` ``intel/2016b`` -``3.1.1`` ``-Python-3.6.6`` ``foss/2018b`` -``3.1.2`` ``foss/2020b``, ``foss/2021b`` -``3.1.2`` ``-Python-3.8.2`` ``foss/2020a`` -============ ================== ============================== +============ ================== ============================================== +version versionsuffix toolchain +============ ================== ============================================== +``3.0.0b36`` ``-Python-2.7.12`` ``intel/2016b`` +``3.1.1`` ``-Python-3.6.6`` ``foss/2018b`` +``3.1.2`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` +``3.1.2`` ``-Python-3.8.2`` ``foss/2020a`` +============ ================== ============================================== .. _list_software_ETSF_IO_553: @@ -10992,7 +11528,7 @@ A library of F90 routines to read/write the ETSF file format has been written. *homepage*: http://www.etsf.eu/resources/software/libraries_and_tools ========= ================================================================================================= -version toolchain +version toolchain ========= ================================================================================================= ``1.0.4`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ========= ================================================================================================= @@ -11008,11 +11544,11 @@ eudev is a fork of systemd-udev with the goal of obtaining better compatibility *homepage*: https://wiki.gentoo.org/wiki/Project:Eudev ========= ================================================= -version toolchain +version toolchain ========= ================================================= ``3.1.5`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``3.2`` ``GCCcore/4.9.3`` -``3.2.2`` ``GCCcore/6.4.0`` +``3.2`` ``GCCcore/4.9.3`` +``3.2.2`` ``GCCcore/6.4.0`` ========= ================================================= @@ -11026,7 +11562,7 @@ EvidentialGene is a genome informatics project for "Evidence Directed Gene Cons *homepage*: http://arthropods.eugenes.org/EvidentialGene/ ============== ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================ =============== ``2018.01.01`` ``-Perl-5.24.1`` ``intel/2017a`` ``2022.01.14`` ``gompi/2021b`` @@ -11043,7 +11579,7 @@ evmix: Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corre *homepage*: https://cran.r-project.org/web/packages/evmix ======= ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= =============== ``2.6`` ``-R-3.3.1`` ``intel/2016b`` ======= ============= =============== @@ -11059,7 +11595,7 @@ ExaBayes is a software package for Bayesian tree inference. It is particularly *homepage*: https://cme.h-its.org/exelixis/web/software/exabayes/ ======= ============== -version toolchain +version toolchain ======= ============== ``1.5`` ``foss/2016b`` ======= ============== @@ -11075,7 +11611,7 @@ Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI *homepage*: https://github.com/stamatak/ExaML/ ========== =============== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== =============== =============== ``3.0.22`` ``-hybrid-avx`` ``gompi/2021a`` ========== =============== =============== @@ -11091,7 +11627,7 @@ The Excel::Writer::XLSX module can be used to create an Excel file in the 2007+ *homepage*: https://metacpan.org/pod/Excel::Writer::XLSX ======== ============== -version toolchain +version toolchain ======== ============== ``1.09`` ``foss/2020b`` ======== ============== @@ -11107,7 +11643,7 @@ Perl module (Image::ExifTool) and program (exiftool) to read EXIF information f *homepage*: https://owl.phy.queensu.ca/~phil/exiftool/ ========= ================= -version toolchain +version toolchain ========= ================= ``12.00`` ``GCCcore/9.3.0`` ========= ================= @@ -11123,9 +11659,10 @@ Exiv2 is a Cross-platform C++ library and a command line utility to manage image *homepage*: https://exiv2.org ========== ================== -version toolchain +version toolchain ========== ================== ``0.27.4`` ``GCCcore/10.3.0`` +``0.27.5`` ``GCCcore/11.2.0`` ========== ================== @@ -11139,7 +11676,7 @@ Exonerate is a generic tool for pairwise sequence comparison. It allows you to *homepage*: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate ========= ============================================================================================================================================================================================================================================= -version toolchain +version toolchain ========= ============================================================================================================================================================================================================================================= ``2.4.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a`` ========= ============================================================================================================================================================================================================================================= @@ -11155,19 +11692,19 @@ Expat is an XML parser library written in C. It is a stream-oriented parser in w *homepage*: https://libexpat.github.io ========= ========================================================================================================================= -version toolchain +version toolchain ========= ========================================================================================================================= -``2.1.0`` ``GCC/4.9.2``, ``foss/2016a``, ``intel/2016a`` -``2.1.1`` ``foss/2016a``, ``intel/2016a`` +``2.1.0`` ``GCC/4.9.2``, ``foss/2016a``, ``intel/2016a`` +``2.1.1`` ``foss/2016a``, ``intel/2016a`` ``2.2.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` -``2.2.4`` ``GCCcore/6.4.0`` -``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.2.6`` ``GCCcore/8.2.0`` -``2.2.7`` ``GCCcore/8.3.0`` -``2.2.9`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``2.4.1`` ``GCCcore/11.2.0`` -``2.4.8`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0`` -``2.4.9`` ``GCCcore/12.2.0`` +``2.2.4`` ``GCCcore/6.4.0`` +``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.2.6`` ``GCCcore/8.2.0`` +``2.2.7`` ``GCCcore/8.3.0`` +``2.2.9`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``2.4.1`` ``GCCcore/11.2.0`` +``2.4.8`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0`` +``2.4.9`` ``GCCcore/12.2.0`` ========= ========================================================================================================================= @@ -11181,7 +11718,7 @@ Expect is a tool for automating interactive applications such as telnet, ftp, *homepage*: https://core.tcl.tk/expect/index ========== ==================================== -version toolchain +version toolchain ========== ==================================== ``5.45.4`` ``GCCcore/7.3.0``, ``GCCcore/9.3.0`` ========== ==================================== @@ -11197,7 +11734,7 @@ This library implements expect tests (also known as "golden" tests). Expect test *homepage*: https://github.com/ezyang/expecttest ========= ============================================================================== -version toolchain +version toolchain ========= ============================================================================== ``0.1.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ============================================================================== @@ -11213,7 +11750,7 @@ Streaming quantification for high-throughput sequencing *homepage*: https://pachterlab.github.io/eXpress ========= =============== -version toolchain +version toolchain ========= =============== ``1.5.1`` ``intel/2017b`` ========= =============== @@ -11229,9 +11766,9 @@ Extrae is the core instrumentation package developed by the Performance Tools gr *homepage*: https://www.bsc.es/computer-sciences/performance-tools ========= =============== -version toolchain +version toolchain ========= =============== -``3.4.1`` ``foss/2017a`` +``3.4.1`` ``foss/2017a`` ``3.7.1`` ``intel/2019a`` ``3.8.0`` ``gompi/2020b`` ``3.8.3`` ``gompi/2021a`` @@ -11244,7 +11781,7 @@ version toolchain --- -:ref:`list_software_f90cache_707` - :ref:`list_software_f90wrap_649` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_Fastaq_608` - :ref:`list_software_FastFold_787` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastparquet_1200` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_FFTW.MPI_587` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_fio_318` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMPy_348` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoBiS_435` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FOX-Toolkit_1024` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeBarcodes_1189` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FSON_310` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` +:ref:`list_software_f90cache_707` - :ref:`list_software_f90wrap_649` - :ref:`list_software_Faber_480` - :ref:`list_software_FabIO_417` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_fastahack_934` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_Fastaq_608` - :ref:`list_software_FastFold_787` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastparquet_1200` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-pair_1016` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_fastqsplitter_1430` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FastViromeExplorer_1873` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FBPIC_356` - :ref:`list_software_FCC_204` - :ref:`list_software_FCM_214` - :ref:`list_software_fdict_522` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_FEniCS_504` - :ref:`list_software_fermi-lite_1006` - :ref:`list_software_Ferret_616` - :ref:`list_software_festival_862` - :ref:`list_software_fetchMG_670` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffmpi_530` - :ref:`list_software_ffnet_531` - :ref:`list_software_fftlib_631` - :ref:`list_software_FFTW_311` - :ref:`list_software_FFTW.MPI_587` - :ref:`list_software_fgbio_519` - :ref:`list_software_FGSL_300` - :ref:`list_software_FHI-aims_686` - :ref:`list_software_FIAT_292` - :ref:`list_software_FIGARO_440` - :ref:`list_software_FigureGen_892` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_filevercmp_1069` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_fio_318` - :ref:`list_software_Fiona_493` - :ref:`list_software_Firefox_723` - :ref:`list_software_FIRESTARTER_843` - :ref:`list_software_FireWorks_924` - :ref:`list_software_FIt-SNE_534` - :ref:`list_software_FIX_231` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLAC_278` - :ref:`list_software_FLAIR_366` - :ref:`list_software_flair-NLP_805` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_flatbuffers_1172` - :ref:`list_software_flatbuffers-python_1891` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_Flexbar_708` - :ref:`list_software_FlexiBLAS_794` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_Flink_500` - :ref:`list_software_FLINT_381` - :ref:`list_software_flook_539` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMM3D_343` - :ref:`list_software_FMPy_348` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_FMS_230` - :ref:`list_software_fmt_327` - :ref:`list_software_FoBiS_435` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_FORD_299` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FOX-Toolkit_1024` - :ref:`list_software_FPM_227` - :ref:`list_software_fpocket_748` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeBarcodes_1189` - :ref:`list_software_freebayes_950` - :ref:`list_software_FreeFEM_602` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSASA_682` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_FreeTDS_621` - :ref:`list_software_freetype_868` - :ref:`list_software_freetype-py_1146` - :ref:`list_software_FreeXL_550` - :ref:`list_software_freud-analysis_1447` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FRUIT_394` - :ref:`list_software_FRUIT_processor_1481` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_fsom_437` - :ref:`list_software_FSON_310` - :ref:`list_software_FTGL_301` - :ref:`list_software_Fujitsu_746` - :ref:`list_software_fullrmc_757` - :ref:`list_software_fumi_tools_1089` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_FuSeq_484` - :ref:`list_software_FusionCatcher_1326` - :ref:`list_software_futhark_757` - :ref:`list_software_futile_649` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: @@ -11257,7 +11794,7 @@ f90cache is a compiler cache. It acts as a caching pre-processor to Fortran comp *homepage*: http://people.irisa.fr/Edouard.Canot/f90cache/ ======== ========== -version toolchain +version toolchain ======== ========== ``0.96`` ``system`` ======== ========== @@ -11273,7 +11810,7 @@ f90wrap is a tool to automatically generate Python extension modules which inter *homepage*: https://github.com/jameskermode/f90wrap ========= ============== -version toolchain +version toolchain ========= ============== ``0.2.8`` ``foss/2021a`` ========= ============== @@ -11289,7 +11826,7 @@ Faber started as a clone of Boost.Build, to experiment with a new Python fronte *homepage*: https://stefanseefeld.github.io/faber ======= ================= -version toolchain +version toolchain ======= ================= ``0.3`` ``GCCcore/8.3.0`` ======= ================= @@ -11305,7 +11842,7 @@ FabIO is an I/O library for images produced by 2D X-ray detectors and written in *homepage*: http://www.silx.org ========== ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================== ``0.10.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``0.11.0`` ``foss/2020b``, ``fosscuda/2020b`` @@ -11322,7 +11859,7 @@ Faceswap is a tool that utilizes deep learning to recognize and swap faces in pi *homepage*: https://github.com/deepfakes/faceswap ============ ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ============== ``20180212`` ``-Python-3.6.3`` ``foss/2017b`` ============ ================= ============== @@ -11338,7 +11875,7 @@ Falcon: a set of tools for fast aligning long reads for consensus and assembly *homepage*: https://github.com/PacificBiosciences/FALCON ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.8.8`` ``intel/2017b`` ``1.8.8`` ``-Python-2.7.16`` ``intel/2019b`` @@ -11355,7 +11892,7 @@ Fast Artificial Neural Network Library is a free open source neural network libr *homepage*: http://leenissen.dk ========= ================================== -version toolchain +version toolchain ========= ================================== ``2.2.0`` ``GCCcore/6.4.0``, ``intel/2018a`` ========= ================================== @@ -11371,7 +11908,7 @@ A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing *homepage*: http://simpsonlab.github.io/2017/02/27/packing_fast5/ ========= ========== -version toolchain +version toolchain ========= ========== ``0.6.5`` ``system`` ========= ========== @@ -11387,7 +11924,7 @@ The FASTA programs find regions of local or global (new) similarity between pro *homepage*: http://fasta.bioch.virginia.edu =========== ============== -version toolchain +version toolchain =========== ============== ``36.3.5e`` ``foss/2016b`` =========== ============== @@ -11403,7 +11940,7 @@ Utilities for indexing and sequence extraction from FASTA files. *homepage*: https://github.com/ekg/fastahack ========= ============================================================================= -version toolchain +version toolchain ========= ============================================================================= ``1.0.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ========= ============================================================================= @@ -11419,7 +11956,7 @@ FastA index (.fai) handler compatible with samtools faidx *homepage*: https://github.com/lpryszcz/FastaIndex =========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== =============== ``0.11rc7`` ``-Python-2.7.14`` ``intel/2017b`` =========== ================== =============== @@ -11435,12 +11972,12 @@ FastANI is developed for fast alignment-free computation of whole-genome Averag *homepage*: https://github.com/ParBLiSS/FastANI ======== ===================================================================================================== -version toolchain +version toolchain ======== ===================================================================================================== -``1.1`` ``foss/2018b``, ``intel/2018b`` -``1.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``1.3`` ``iccifort/2019.5.281`` -``1.31`` ``iccifort/2020.1.217`` +``1.1`` ``foss/2018b``, ``intel/2018b`` +``1.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``1.3`` ``iccifort/2019.5.281`` +``1.31`` ``iccifort/2020.1.217`` ``1.33`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.4.0`` ======== ===================================================================================================== @@ -11455,7 +11992,7 @@ Python3 scripts to manipulate FASTA and FASTQ files. *homepage*: https://github.com/sanger-pathogens/Fastaq ========== ============== -version toolchain +version toolchain ========== ============== ``3.17.0`` ``GCC/10.3.0`` ========== ============== @@ -11471,7 +12008,7 @@ Optimizing Protein Structure Prediction Model Training and Inference on GPU Clus *homepage*: https://github.com/hpcaitech/FastFold ============ ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================ ============== ``20220729`` ``-CUDA-11.3.1`` ``foss/2021a`` ============ ================ ============== @@ -11487,9 +12024,9 @@ FastME: a comprehensive, accurate and fast distance-based phylogeny inference pr *homepage*: http://www.atgc-montpellier.fr/fastme/ =========== ======================================================================================== -version toolchain +version toolchain =========== ======================================================================================== -``2.1.5`` ``foss/2016a`` +``2.1.5`` ``foss/2016a`` ``2.1.6.1`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``iccifort/2019.5.281``, ``intel/2018a``, ``intel/2018b`` =========== ======================================================================================== @@ -11504,11 +12041,11 @@ A tool designed to provide fast all-in-one preprocessing for FastQ files. This *homepage*: https://github.com/OpenGene/fastp ========== ============================================================ -version toolchain +version toolchain ========== ============================================================ -``0.19.7`` ``foss/2018b`` +``0.19.7`` ``foss/2018b`` ``0.20.0`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``0.23.2`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +``0.23.2`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` ========== ============================================================ @@ -11522,7 +12059,7 @@ fastparquet is a python implementation of the parquet format, aiming to integrat *homepage*: https://fastparquet.readthedocs.io/ ========= ============== -version toolchain +version toolchain ========= ============== ``0.7.2`` ``foss/2021a`` ``0.8.0`` ``foss/2021b`` @@ -11539,7 +12076,7 @@ fastPHASE: software for haplotype reconstruction, and estimating missing genoty *homepage*: http://stephenslab.uchicago.edu/software.html#fastphase ========= ========== -version toolchain +version toolchain ========= ========== ``1.4.8`` ``system`` ========= ========== @@ -11555,7 +12092,7 @@ Match up paired end fastq files quickly and efficiently. *homepage*: https://github.com/linsalrob/fastq-pair ======= ================= -version toolchain +version toolchain ======= ================= ``1.0`` ``GCCcore/8.2.0`` ======= ================= @@ -11571,7 +12108,7 @@ This package provides a number of small and efficient programs to perform commo *homepage*: https://homes.cs.washington.edu/~dcjones/fastq-tools/ ========= ============================== -version toolchain +version toolchain ========= ============================== ``0.8`` ``foss/2016b``, ``foss/2018b`` ``0.8.3`` ``GCC/10.3.0``, ``GCC/11.2.0`` @@ -11588,12 +12125,12 @@ FastQ Screen allows you to screen a library of sequences in FastQ format agains *homepage*: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/ ========== ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================ =============== -``0.11.3`` ``-Perl-5.24.0`` ``foss/2016b`` -``0.11.4`` ``-Perl-5.24.0`` ``foss/2016b`` +``0.11.3`` ``-Perl-5.24.0`` ``foss/2016b`` +``0.11.4`` ``-Perl-5.24.0`` ``foss/2016b`` ``0.12.0`` ``-Perl-5.26.1`` ``intel/2018a`` -``0.13.0`` ``-Perl-5.28.0`` ``foss/2018b`` +``0.13.0`` ``-Perl-5.28.0`` ``foss/2018b`` ========== ================ =============== @@ -11607,7 +12144,7 @@ FastQC is a quality control application for high throughput sequence data. It re *homepage*: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ========== =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== =================== ========== ``0.10.1`` ``-Java-1.7.0_80`` ``system`` ``0.11.2`` ``-Java-1.7.0_60`` ``system`` @@ -11635,7 +12172,7 @@ Splits fastq files evenly. *homepage*: https://github.com/LUMC/fastqsplitter ========= ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================= ``1.2.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========= ================= ================= @@ -11651,7 +12188,7 @@ FastQTL is a QTL mapper *homepage*: http://fastqtl.sourceforge.net/ ========= ============================== -version toolchain +version toolchain ========= ============================== ``2.184`` ``GCC/11.2.0``, ``foss/2018b`` ========= ============================== @@ -11667,7 +12204,7 @@ fastqz is a compressor for FASTQ files. FASTQ is the output of DNA sequencing ma *homepage*: http://mattmahoney.net/dc/fastqz/ ======= ============= -version toolchain +version toolchain ======= ============= ``1.5`` ``GCC/4.8.2`` ======= ============= @@ -11683,7 +12220,7 @@ Fast Robinson Foulds Supertrees *homepage*: https://github.com/pranjalv123/FastRFS ================ =============== -version toolchain +version toolchain ================ =============== ``1.0-20190613`` ``gompi/2019a`` ================ =============== @@ -11699,7 +12236,7 @@ fastStructure is a fast algorithm for inferring population structure from large *homepage*: https://rajanil.github.io/fastStructure/ ======= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== ============== ``1.0`` ``-Python-2.7.11`` ``foss/2016a`` ``1.0`` ``-Python-2.7.12`` ``foss/2016b`` @@ -11717,12 +12254,12 @@ FastTree infers approximately-maximum-likelihood phylogenetic trees from alignme *homepage*: http://www.microbesonline.org/fasttree/ -========== =================================================================================================================== -version toolchain -========== =================================================================================================================== -``2.1.10`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``2.1.11`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== =================================================================================================================== +========== ======================================================================================================================================= +version toolchain +========== ======================================================================================================================================= +``2.1.10`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +``2.1.11`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ======================================================================================================================================= .. _list_software_FastViromeExplorer_1873: @@ -11735,7 +12272,7 @@ Identify the viruses/phages and their abundance in the viral metagenomics data. *homepage*: https://code.vt.edu/saima5/FastViromeExplorer ============ ============== -version toolchain +version toolchain ============ ============== ``20180422`` ``foss/2019b`` ============ ============== @@ -11751,7 +12288,7 @@ The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/ *homepage*: http://hannonlab.cshl.edu/fastx_toolkit/ ========== ================================================================================================================= -version toolchain +version toolchain ========== ================================================================================================================= ``0.0.14`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2018a`` ========== ================================================================================================================= @@ -11767,7 +12304,7 @@ FATSLiM stands for “Fast Analysis Toolbox for Simulations of Lipid Membranes *homepage*: https://github.com/FATSLiM/fatslim ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.2.1`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================= ============== @@ -11783,7 +12320,7 @@ Exact methods for simulating fractional Brownian motion and fractional Gaussian *homepage*: https://pypi.org/project/fbm ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.2.0`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== @@ -11799,7 +12336,7 @@ FBPIC (Fourier-Bessel Particle-In-Cell) is a Particle-In-Cell (PIC) code for rel *homepage*: https://fbpic.github.io/ ========== ================== -version toolchain +version toolchain ========== ================== ``0.20.3`` ``fosscuda/2020b`` ========== ================== @@ -11815,7 +12352,7 @@ Fujitsu Compiler based compiler toolchain. *homepage*: (none) ========= ========== -version toolchain +version toolchain ========= ========== ``4.5.0`` ``system`` ========= ========== @@ -11831,7 +12368,7 @@ FCM is a set of tools for managing and building source code. *homepage*: http://www.metoffice.gov.uk/research/collaboration/fcm ========= ========== -version toolchain +version toolchain ========= ========== ``2.3.1`` ``system`` ========= ========== @@ -11846,11 +12383,11 @@ A variable and dictionary in pure fortran for retaining any data-type and a fast *homepage*: https://github.com/zerothi/fdict -========= ======================================= -version toolchain -========= ======================================= -``0.8.0`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -========= ======================================= +========= =================================================================================================================================== +version toolchain +========= =================================================================================================================================== +``0.8.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` +========= =================================================================================================================================== .. _list_software_FDS_221: @@ -11863,18 +12400,18 @@ Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-spee *homepage*: https://pages.nist.gov/fds-smv ========= ============= ================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ================================ -``6.0.1`` ``-no-OFED`` ``system`` -``6.5.2`` ``intel/2016b`` -``6.5.3`` ``intel/2017a`` +``6.0.1`` ``-no-OFED`` ``system`` +``6.5.2`` ``intel/2016b`` +``6.5.3`` ``intel/2017a`` ``6.6.0`` ``intel/2017b``, ``intel/2018a`` -``6.7.0`` ``intel/2018a`` -``6.7.4`` ``intel/2020a`` -``6.7.5`` ``intel/2020a`` -``6.7.6`` ``intel/2020b`` -``6.7.7`` ``intel/2021b`` -``6.7.9`` ``intel/2022a`` +``6.7.0`` ``intel/2018a`` +``6.7.4`` ``intel/2020a`` +``6.7.5`` ``intel/2020a`` +``6.7.6`` ``intel/2020b`` +``6.7.7`` ``intel/2021b`` +``6.7.9`` ``intel/2022a`` ========= ============= ================================ @@ -11888,7 +12425,7 @@ Forensic DNA Sequencing Tools Tools for characterisation and filtering of PCR st *homepage*: https://git.lumc.nl/jerryhoogenboom/fdstools ============ ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ============== ``20160322`` ``-Python-2.7.11`` ``foss/2016a`` ============ ================== ============== @@ -11904,7 +12441,7 @@ High performance FDTD-method Maxwell solver for the design, analysis and optimiz *homepage*: http://www.lumerical.com/tcad-products/fdtd/ ============= ========== -version toolchain +version toolchain ============= ========== ``8.6.2`` ``system`` ``8.11.337`` ``system`` @@ -11923,7 +12460,7 @@ feh is an X11 image viewer aimed mostly at console users. Unlike most other view *homepage*: https://feh.finalrewind.org/ ======== ================= -version toolchain +version toolchain ======== ================= ``2.26`` ``GCCcore/6.4.0`` ======== ================= @@ -11939,7 +12476,7 @@ FEniCS is a computing platform for solving partial differential equations (PDEs) *homepage*: https://fenicsproject.org/ ============ ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ============== ``2019.1.0`` ``-Python-3.7.4`` ``foss/2019b`` ============ ================= ============== @@ -11954,11 +12491,11 @@ Standalone C library for assembling Illumina short reads in small regions. *homepage*: https://github.com/lh3/fermi-lite -============ ========================================================= -version toolchain -============ ========================================================= -``20190320`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -============ ========================================================= +============ ============================================================================= +version toolchain +============ ============================================================================= +``20190320`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +============ ============================================================================= .. _list_software_Ferret_616: @@ -11971,10 +12508,10 @@ Ferret is an interactive computer visualization and analysis environment designe *homepage*: https://ferret.pmel.noaa.gov/Ferret/ ========= =============== -version toolchain +version toolchain ========= =============== ``7.3`` ``intel/2017b`` -``7.5.0`` ``foss/2019b`` +``7.5.0`` ``foss/2019b`` ========= =============== @@ -11988,7 +12525,7 @@ University of Edinburgh's Festival Speech Synthesis Systems is a free software m *homepage*: ['http://festvox.org/festival/'] ========= ================= -version toolchain +version toolchain ========= ================= ``2.5.0`` ``GCCcore/9.3.0`` ========= ================= @@ -12004,7 +12541,7 @@ The program “fetchMG” was written to extract the 40 MGs from genomes and met *homepage*: http://vm-lux.embl.de/~mende/fetchMG/about.html ======= ==================================== -version toolchain +version toolchain ======= ==================================== ``1.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ======= ==================================== @@ -12020,7 +12557,7 @@ The FEniCS Form Compiler (FFC) is a compiler for finite element variational form *homepage*: https://bitbucket.org/fenics-project/ffc ================== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ================= ============== ``2018.1.0`` ``-Python-3.6.4`` ``foss/2018a`` ``2019.1.0.post0`` ``-Python-3.7.4`` ``foss/2019b`` @@ -12037,7 +12574,7 @@ Finite Field Linear Algebra Subroutines / Package *homepage*: https://linbox-team.github.io/fflas-ffpack/ ========= ============== -version toolchain +version toolchain ========= ============== ``2.2.0`` ``foss/2016a`` ========= ============== @@ -12053,30 +12590,30 @@ A complete, cross-platform solution to record, convert and stream audio and vide *homepage*: https://www.ffmpeg.org/ =========== =================================================== -version toolchain +version toolchain =========== =================================================== -``0.10.16`` ``gimkl/2.11.5``, ``intel/2016a`` -``2.8.6`` ``intel/2016a`` -``2.8.7`` ``foss/2016a``, ``intel/2016a`` -``3.0.2`` ``foss/2016a``, ``intel/2016a`` -``3.1.3`` ``foss/2016b``, ``intel/2016b`` -``3.2.4`` ``gimkl/2017a`` -``3.3.1`` ``foss/2016b`` -``3.3.4`` ``intel/2017a`` -``3.4`` ``GCCcore/6.4.0`` -``3.4.1`` ``foss/2017b``, ``intel/2017b`` -``3.4.2`` ``foss/2018a``, ``intel/2018a`` -``3.4.5`` ``foss/2018b`` -``4.0`` ``foss/2018a``, ``intel/2018a`` -``4.0.1`` ``intel/2018a`` +``0.10.16`` ``gimkl/2.11.5``, ``intel/2016a`` +``2.8.6`` ``intel/2016a`` +``2.8.7`` ``foss/2016a``, ``intel/2016a`` +``3.0.2`` ``foss/2016a``, ``intel/2016a`` +``3.1.3`` ``foss/2016b``, ``intel/2016b`` +``3.2.4`` ``gimkl/2017a`` +``3.3.1`` ``foss/2016b`` +``3.3.4`` ``intel/2017a`` +``3.4`` ``GCCcore/6.4.0`` +``3.4.1`` ``foss/2017b``, ``intel/2017b`` +``3.4.2`` ``foss/2018a``, ``intel/2018a`` +``3.4.5`` ``foss/2018b`` +``4.0`` ``foss/2018a``, ``intel/2018a`` +``4.0.1`` ``intel/2018a`` ``4.1`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``4.1.3`` ``GCCcore/8.2.0`` -``4.2.1`` ``GCCcore/8.3.0`` -``4.2.2`` ``GCCcore/9.3.0`` -``4.3.1`` ``GCCcore/10.2.0`` -``4.3.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``4.4.2`` ``GCCcore/11.3.0`` -``5.0.1`` ``GCCcore/11.3.0`` +``4.1.3`` ``GCCcore/8.2.0`` +``4.2.1`` ``GCCcore/8.3.0`` +``4.2.2`` ``GCCcore/9.3.0`` +``4.3.1`` ``GCCcore/10.2.0`` +``4.3.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``4.4.2`` ``GCCcore/11.3.0`` +``5.0.1`` ``GCCcore/11.3.0`` =========== =================================================== @@ -12090,7 +12627,7 @@ Fujitsu Compiler based compiler toolchain, including Fujitsu MPI for MPI support *homepage*: (none) ========= ========== -version toolchain +version toolchain ========= ========== ``4.5.0`` ``system`` ========= ========== @@ -12106,7 +12643,7 @@ Feed-forward neural network solution for python *homepage*: http://ffnet.sourceforge.net/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.8.3`` ``-Python-2.7.11`` ``intel/2016a`` ========= ================== =============== @@ -12122,7 +12659,7 @@ A library that intercepts FFTW calls and adds features on top of it. In particu *homepage*: https://github.com/flwende/fftlib ============ =============== -version toolchain +version toolchain ============ =============== ``20170628`` ``gompi/2020b`` ============ =============== @@ -12138,20 +12675,20 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: https://www.fftw.org ========== ============= ======================================================================================================================================================================================================================================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ======================================================================================================================================================================================================================================================================================================================= -``1.0.0`` ``-fujitsu`` ``FCC/4.5.0`` -``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` -``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` -``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` -``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` -``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` -``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` +``1.0.0`` ``-fujitsu`` ``FCC/4.5.0`` +``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` +``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` +``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` +``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` +``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` +``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` ``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a``, ``intel/2020b``, ``iomkl/2018b`` -``3.3.8`` ``-amd`` ``gompi/2020a`` -``3.3.8`` ``-serial`` ``GCC/9.3.0`` -``3.3.9`` ``gompi/2021a``, ``intel/2021a`` -``3.3.10`` ``GCC/11.3.0``, ``gompi/2021b``, ``iimpi/2021b``, ``iimpi/2022a`` +``3.3.8`` ``-amd`` ``gompi/2020a`` +``3.3.8`` ``-serial`` ``GCC/9.3.0`` +``3.3.9`` ``gompi/2021a``, ``intel/2021a`` +``3.3.10`` ``GCC/11.3.0``, ``GCC/12.2.0``, ``NVHPC/22.7-CUDA-11.7.0``, ``gompi/2021b``, ``iimpi/2021b``, ``iimpi/2022a`` ========== ============= ======================================================================================================================================================================================================================================================================================================================= @@ -12164,11 +12701,11 @@ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT *homepage*: https://www.fftw.org -========== ================================== -version toolchain -========== ================================== -``3.3.10`` ``gompi/2022.05``, ``gompi/2022a`` -========== ================================== +========== ========================================================================================== +version toolchain +========== ========================================================================================== +``3.3.10`` ``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``nvompi/2022.07`` +========== ========================================================================================== .. _list_software_fgbio_519: @@ -12181,7 +12718,7 @@ A set of tools to analyze genomic data with a focus on Next Generation Sequencin *homepage*: https://fulcrumgenomics.github.io/fgbio ========= ========== -version toolchain +version toolchain ========= ========== ``1.3.0`` ``system`` ========= ========== @@ -12197,7 +12734,7 @@ FGSL: A Fortran interface to the GNU Scientific Library *homepage*: https://www.lrz.de/services/software/mathematik/gsl/fortran/ ========= =============== -version toolchain +version toolchain ========= =============== ``1.1.0`` ``intel/2016b`` ========= =============== @@ -12213,7 +12750,7 @@ FHI-aims is an efficient, accurate all-electron, full-potential electronic struc *homepage*: https://aimsclub.fhi-berlin.mpg.de/ ============ =============== -version toolchain +version toolchain ============ =============== ``200112_2`` ``intel/2019b`` ============ =============== @@ -12229,11 +12766,11 @@ The FInite element Automatic Tabulator (FIAT) supports generation of arbitrary o *homepage*: https://bitbucket.org/fenics-project/fiat ============ ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============================== ``1.6.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``2018.1.0`` ``-Python-3.6.4`` ``foss/2018a`` -``2019.1.0`` ``-Python-3.7.4`` ``foss/2019b`` +``2018.1.0`` ``-Python-3.6.4`` ``foss/2018a`` +``2019.1.0`` ``-Python-3.7.4`` ``foss/2019b`` ============ ================== =============================== @@ -12247,7 +12784,7 @@ FIGARO: An efficient and objective tool for optimizing microbiome rRNA gene trim *homepage*: https://github.com/Zymo-Research/figaro ========= =============== -version toolchain +version toolchain ========= =============== ``1.1.2`` ``intel/2020b`` ========= =============== @@ -12263,7 +12800,7 @@ FigureGen is a Fortran program that creates images for ADCIRC files. It reads me *homepage*: https://ccht.ccee.ncsu.edu/category/software/figuregen/ =============== ============== -version toolchain +version toolchain =============== ============== ``51-20190516`` ``foss/2019a`` =============== ============== @@ -12278,13 +12815,15 @@ Fiji is an image processing package—a 'batteries-included' distribution of Im *homepage*: https://fiji.sc/ -================= ========== -version toolchain -================= ========== -``20170530`` ``system`` -``20191119-2057`` ``system`` -``20201104-1356`` ``system`` -================= ========== +================= ============= ========== +version versionsuffix toolchain +================= ============= ========== +``2.9.0`` ``-Java-1.8`` ``system`` +``2.9.0`` ``-Java-8`` ``system`` +``20170530`` ``system`` +``20191119-2057`` ``system`` +``20201104-1356`` ``system`` +================= ============= ========== .. _list_software_file_416: @@ -12297,19 +12836,19 @@ The file command is 'a file type guesser', that is, a command-line tool that te *homepage*: https://www.darwinsys.com/file/ ======== ==================================== -version toolchain +version toolchain ======== ==================================== -``5.17`` ``GCC/4.8.2`` -``5.25`` ``intel/2016a`` -``5.28`` ``foss/2016b`` -``5.30`` ``intel/2017a`` -``5.33`` ``GCCcore/6.4.0`` -``5.35`` ``GCCcore/7.3.0`` +``5.17`` ``GCC/4.8.2`` +``5.25`` ``intel/2016a`` +``5.28`` ``foss/2016b`` +``5.30`` ``intel/2017a`` +``5.33`` ``GCCcore/6.4.0`` +``5.35`` ``GCCcore/7.3.0`` ``5.38`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``5.39`` ``GCCcore/10.2.0`` -``5.40`` ``GCCcore/10.3.0`` -``5.41`` ``GCCcore/11.2.0`` -``5.43`` ``GCCcore/11.3.0`` +``5.39`` ``GCCcore/10.2.0`` +``5.40`` ``GCCcore/10.3.0`` +``5.41`` ``GCCcore/11.2.0`` +``5.43`` ``GCCcore/11.3.0`` ======== ==================================== @@ -12323,9 +12862,9 @@ filevercmp function as in sort --version-sort. *homepage*: https://github.com/ekg/filevercmp ============ ========================================================== -version toolchain +version toolchain ============ ========================================================== -``20141119`` ``GCCcore/9.3.0`` +``20141119`` ``GCCcore/9.3.0`` ``20191210`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ============ ========================================================== @@ -12340,9 +12879,10 @@ Filtlong is a tool for filtering long reads by quality. It can take a set of lo *homepage*: https://github.com/rrwick/Filtlong ========= ============================== -version toolchain +version toolchain ========= ============================== ``0.2.0`` ``GCC/10.2.0``, ``foss/2016b`` +``0.2.1`` ``GCC/10.3.0`` ========= ============================== @@ -12356,7 +12896,7 @@ circRNA detection from RNA-seq reads *homepage*: https://github.com/marvin-jens/find_circ ================ ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ================ ================== =============== ``1.2-20170228`` ``-Python-2.7.14`` ``intel/2017b`` ================ ================== =============== @@ -12372,7 +12912,7 @@ Find haplotypes and impute genotypes using multiple chip sets and sequence data *homepage*: http://aipl.arsusda.gov/software/findhap/ ======= ========== -version toolchain +version toolchain ======= ========== ``4`` ``system`` ======= ========== @@ -12388,7 +12928,7 @@ findutils: The GNU find, locate, updatedb, and xargs utilities *homepage*: http://www.gnu.org/software/findutils/findutils.html ========= ============= -version toolchain +version toolchain ========= ============= ``4.4.2`` ``GCC/4.8.2`` ========= ============= @@ -12404,7 +12944,7 @@ A package for population structure inference from RAD-seq data *homepage*: http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html ============ =============== -version toolchain +version toolchain ============ =============== ``20180709`` ``intel/2018a`` ============ =============== @@ -12420,7 +12960,7 @@ fineSTRUCTURE is a fast and powerful algorithm for identifying population struct *homepage*: https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure_info.html ========= =============== -version toolchain +version toolchain ========= =============== ``2.1.3`` ``intel/2017b`` ========= =============== @@ -12436,7 +12976,7 @@ Flexible I/O tester *homepage*: https://github.com/axboe/fio ======== ================== -version toolchain +version toolchain ======== ================== ``3.30`` ``GCCcore/10.3.0`` ``3.32`` ``GCCcore/11.3.0`` @@ -12453,13 +12993,13 @@ Fiona is designed to be simple and dependable. It focuses on reading and writing *homepage*: https://github.com/Toblerity/Fiona ================ ================= =================================================== -version versionsuffix toolchain +version versionsuffix toolchain ================ ================= =================================================== ``1.8.13`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``1.8.13.post1`` ``-Python-3.7.2`` ``foss/2019a`` -``1.8.16`` ``-Python-3.8.2`` ``foss/2020a`` -``1.8.20`` ``foss/2020b``, ``foss/2021a``, ``intel/2020b`` -``1.8.21`` ``foss/2021b`` +``1.8.13.post1`` ``-Python-3.7.2`` ``foss/2019a`` +``1.8.16`` ``-Python-3.8.2`` ``foss/2020a`` +``1.8.20`` ``foss/2020b``, ``foss/2021a``, ``intel/2020b`` +``1.8.21`` ``foss/2021b``, ``foss/2022a`` ================ ================= =================================================== @@ -12473,7 +13013,7 @@ Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It i *homepage*: https://www.mozilla.org/en-US/firefox/new/ ========== ========== -version toolchain +version toolchain ========== ========== ``44.0.2`` ``system`` ========== ========== @@ -12489,7 +13029,7 @@ FIRESTARTER: A Processor Stress Test Utility. FIRESTARTER maximizes the energy c *homepage*: https://github.com/tud-zih-energy/FIRESTARTER/ ======= ==================================== -version toolchain +version toolchain ======= ==================================== ``2.0`` ``gcccuda/2020a``, ``gcccuda/2020b`` ======= ==================================== @@ -12505,7 +13045,7 @@ FireWorks helps run calculation workflows, with a centralized workflow server c *homepage*: https://pypi.python.org/pypi/FireWorks ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.4.2`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== @@ -12521,7 +13061,7 @@ t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualiz *homepage*: https://github.com/KlugerLab/FIt-SNE ========= =============== -version toolchain +version toolchain ========= =============== ``1.1.0`` ``gompi/2018b`` ========= =============== @@ -12537,7 +13077,7 @@ FIX attempts to auto-classify ICA components into "good" vs "bad" components, so *homepage*: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX =========== ======================== ============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ======================== ============== ``1.06.12`` ``-Octave-Python-3.7.2`` ``foss/2019a`` =========== ======================== ============== @@ -12553,7 +13093,7 @@ X.org FixesProto protocol headers. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ======= ================================================= -version toolchain +version toolchain ======= ================================================= ``5.0`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ======= ================================================= @@ -12569,10 +13109,10 @@ FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but l *homepage*: https://xiph.org/flac/ ========= ========================================================== -version toolchain +version toolchain ========= ========================================================== ``1.3.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.3.4`` ``GCCcore/11.3.0`` +``1.3.4`` ``GCCcore/11.3.0`` ========= ========================================================== @@ -12586,13 +13126,30 @@ FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, iso *homepage*: https://github.com/BrooksLabUCSC/flair ================== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ================= ============== ``1.5`` ``-Python-3.7.4`` ``foss/2019b`` ``1.5.1-20200630`` ``-Python-3.7.4`` ``foss/2019b`` ================== ================= ============== +.. _list_software_flair-NLP_805: + +*flair-NLP* ++++++++++++ + +A very simple framework for state-of-the-art NLP + +*homepage*: https://github.com/flairNLP/flair + +========== ================ ============== +version versionsuffix toolchain +========== ================ ============== +``0.11.3`` ``foss/2021a`` +``0.11.3`` ``-CUDA-11.3.1`` ``foss/2021a`` +========== ================ ============== + + .. _list_software_FLANN_367: *FLANN* @@ -12600,13 +13157,15 @@ version versionsuffix toolchain FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces. -*homepage*: http://www.cs.ubc.ca/research/flann/ +*homepage*: https://github.com/mariusmuja/flann/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.8.4`` ``-Python-2.7.11`` ``intel/2016a`` ``1.8.4`` ``-Python-2.7.14`` ``intel/2017b`` +``1.8.4`` ``-Python-3.8.2`` ``foss/2020a`` +``1.9.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== =============== @@ -12620,10 +13179,10 @@ FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate softwa *homepage*: https://ccb.jhu.edu/software/FLASH/ ========== ============================================================= -version toolchain +version toolchain ========== ============================================================= ``1.2.11`` ``GCC/8.3.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b`` -``2.2.00`` ``GCC/11.2.0``, ``foss/2018b``, ``foss/2020b`` +``2.2.00`` ``GCC/11.2.0``, ``foss/2018b``, ``foss/2020b`` ========== ============================================================= @@ -12637,12 +13196,12 @@ Flask is a lightweight WSGI web application framework. It is designed to make ge *homepage*: https://www.palletsprojects.com/p/flask/ ========= ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================== -``1.0.2`` ``-Python-3.6.6`` ``foss/2018b`` +``1.0.2`` ``-Python-3.6.6`` ``foss/2018b`` ``1.1.2`` ``GCCcore/10.2.0`` -``1.1.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``1.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``1.1.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``1.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``1.1.4`` ``GCCcore/10.3.0`` ``2.0.2`` ``GCCcore/11.2.0`` ``2.2.2`` ``GCCcore/11.3.0`` @@ -12659,9 +13218,9 @@ FlatBuffers: Memory Efficient Serialization Library *homepage*: https://github.com/google/flatbuffers/ ========== ========================================================== -version toolchain +version toolchain ========== ========================================================== -``1.12.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.12.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``2.0.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ========================================================== @@ -12676,10 +13235,10 @@ Python Flatbuffers runtime library. *homepage*: https://github.com/google/flatbuffers/ ======== ================= ========================================================== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================= ========================================================== -``1.12`` ``GCCcore/10.2.0`` -``1.12`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``1.12`` ``GCCcore/10.2.0`` +``1.12`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``2.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ======== ================= ========================================================== @@ -12694,7 +13253,7 @@ FLEUR is a feature-full, freely available FLAPW (full potential linearized augme *homepage*: http://www.flapw.de/ ========= =============== -version toolchain +version toolchain ========= =============== ``0.26e`` ``intel/2016a`` ========= =============== @@ -12710,14 +13269,14 @@ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, some *homepage*: http://flex.sourceforge.net/ ========== ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain +version toolchain ========== ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``2.5.35`` ``system`` -``2.5.38`` ``GCC/4.8.2`` -``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` -``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.6.2`` ``intel/2016b`` -``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` +``2.5.35`` ``system`` +``2.5.38`` ``GCC/4.8.2`` +``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` +``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` +``2.6.2`` ``intel/2016b`` +``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` ``2.6.4`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``GCCcore/system``, ``system`` ========== ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -12732,7 +13291,7 @@ The program Flexbar preprocesses high-throughput sequencing data efficiently *homepage*: https://github.com/seqan/flexbar ========= ============== -version toolchain +version toolchain ========= ============== ``3.5.0`` ``foss/2018b`` ========= ============== @@ -12747,13 +13306,14 @@ FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK *homepage*: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release -========= ============================== -version toolchain -========= ============================== +========= ========================================== +version toolchain +========= ========================================== ``3.0.4`` ``GCC/10.3.0``, ``GCC/11.2.0`` -``3.1.3`` ``GCC/11.2.0`` -``3.2.0`` ``GCC/11.3.0`` -========= ============================== +``3.1.3`` ``GCC/11.2.0`` +``3.2.0`` ``GCC/11.3.0``, ``NVHPC/22.7-CUDA-11.7.0`` +``3.2.1`` ``GCC/12.2.0`` +========= ========================================== .. _list_software_FlexiDot_799: @@ -12766,7 +13326,7 @@ Highly customizable, ambiguity-aware dotplots for visual sequence analyses *homepage*: https://github.com/molbio-dresden/flexidot ======== ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================== ============== ``1.06`` ``-Python-2.7.15`` ``foss/2018b`` ======== ================== ============== @@ -12782,7 +13342,7 @@ Apache Flink is a framework and distributed processing engine for stateful compu *homepage*: https://flink.apache.org/ ========== =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== =================== ========== ``1.11.2`` ``-bin-scala_2.11`` ``system`` ========== =================== ========== @@ -12798,11 +13358,11 @@ FLINT (Fast Library for Number Theory) is a C library in support of computations *homepage*: https://www.flintlib.org/ ========= =============================================================================================== -version toolchain +version toolchain ========= =============================================================================================== ``2.5.2`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` -``2.7.1`` ``GCC/10.3.0`` -``2.8.4`` ``GCC/11.2.0`` +``2.7.1`` ``GCC/10.3.0`` +``2.8.4`` ``GCC/11.2.0`` ========= =============================================================================================== @@ -12815,11 +13375,11 @@ The fortran-Lua-hook library. *homepage*: https://github.com/ElectronicStructureLibrary/flook -========= ======================================= -version toolchain -========= ======================================= -``0.8.1`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -========= ======================================= +========= =================================================================================================================================== +version toolchain +========= =================================================================================================================================== +``0.8.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` +========= =================================================================================================================================== .. _list_software_FLTK_305: @@ -12832,14 +13392,14 @@ FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows *homepage*: https://www.fltk.org ========= =================================================================================================================================================================================================== -version toolchain +version toolchain ========= =================================================================================================================================================================================================== -``1.3.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``1.3.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.3.4`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b`` -``1.3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``1.3.6`` ``GCCcore/10.3.0`` -``1.3.7`` ``GCCcore/11.2.0`` -``1.3.8`` ``GCCcore/11.3.0`` +``1.3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.3.6`` ``GCCcore/10.3.0`` +``1.3.7`` ``GCCcore/11.2.0`` +``1.3.8`` ``GCCcore/11.3.0`` ========= =================================================================================================================================================================================================== @@ -12853,7 +13413,7 @@ ANSYS FLUENT software contains the broad physical modeling capabilities needed t *homepage*: https://www.ansys.com/products/fluids/ansys-fluent ========== ========== -version toolchain +version toolchain ========== ========== ``14.5`` ``system`` ``15.0.7`` ``system`` @@ -12877,16 +13437,16 @@ Flye is a de novo assembler for long and noisy reads, such as those produced by *homepage*: https://github.com/fenderglass/Flye ========= ================== ============================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============================================ -``2.4`` ``-Python-2.7.15`` ``intel/2018b`` -``2.6`` ``-Python-3.7.2`` ``foss/2019a`` -``2.6`` ``-Python-3.7.4`` ``intel/2019b`` -``2.8.1`` ``-Python-3.8.2`` ``intel/2020a`` -``2.8.2`` ``-Python-3.8.2`` ``foss/2020a`` -``2.8.3`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``2.4`` ``-Python-2.7.15`` ``intel/2018b`` +``2.6`` ``-Python-3.7.2`` ``foss/2019a`` +``2.6`` ``-Python-3.7.4`` ``intel/2019b`` +``2.8.1`` ``-Python-3.8.2`` ``intel/2020a`` +``2.8.2`` ``-Python-3.8.2`` ``foss/2020a`` +``2.8.3`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` ``2.9`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` -``2.9.1`` ``GCC/11.2.0`` +``2.9.1`` ``GCC/11.2.0`` ========= ================== ============================================ @@ -12900,7 +13460,7 @@ FMI library is intended as a foundation for applications interfacing FMUs (Func *homepage*: https://jmodelica.org/ ========= =============== -version toolchain +version toolchain ========= =============== ``2.0.3`` ``intel/2018b`` ========= =============== @@ -12916,7 +13476,7 @@ Flatiron Institute Fast Multipole Libraries: a set of libraries to compute N-bod *homepage*: https://fmm3d.readthedocs.io ============ ============== -version toolchain +version toolchain ============ ============== ``20211018`` ``foss/2020b`` ============ ============== @@ -12932,7 +13492,7 @@ FMPy is a free Python library to simulate Functional Mock-up Units (FMUs). *homepage*: https://github.com/CATIA-Systems/FMPy ========= ============== -version toolchain +version toolchain ========= ============== ``0.3.2`` ``foss/2021a`` ========= ============== @@ -12948,13 +13508,29 @@ FMRIprep is a functional magnetic resonance imaging (fMRI) data preprocessing pi *homepage*: https://fmriprep.readthedocs.io ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.1.8`` ``-Python-3.6.6`` ``foss/2018b`` ``1.4.1`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== +.. _list_software_FMS_230: + +*FMS* ++++++ + +The Flexible Modeling System (FMS) is a software framework for supporting the efficient development, construction, execution, and scientific interpretation of atmospheric, oceanic, and climate system models. + +*homepage*: https://github.com/NOAA-GFDL/FMS + +=========== ================================ +version toolchain +=========== ================================ +``2022.02`` ``gompi/2022a``, ``iimpi/2022a`` +=========== ================================ + + .. _list_software_fmt_327: *fmt* @@ -12965,15 +13541,15 @@ fmt (formerly cppformat) is an open-source formatting library. *homepage*: http://fmtlib.net/ ========= ==================================== -version toolchain +version toolchain ========= ==================================== -``3.0.1`` ``foss/2016b``, ``intel/2016b`` -``3.0.2`` ``GCCcore/6.4.0``, ``intel/2017a`` +``3.0.1`` ``foss/2016b``, ``intel/2016b`` +``3.0.2`` ``GCCcore/6.4.0``, ``intel/2017a`` ``5.3.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``6.2.1`` ``GCCcore/9.3.0`` -``7.0.3`` ``GCCcore/9.3.0`` -``7.1.1`` ``GCCcore/11.2.0`` -``9.1.0`` ``GCCcore/11.3.0`` +``6.2.1`` ``GCCcore/9.3.0`` +``7.0.3`` ``GCCcore/9.3.0`` +``7.1.1`` ``GCCcore/11.2.0`` +``9.1.0`` ``GCCcore/11.3.0`` ========= ==================================== @@ -12987,7 +13563,7 @@ A Fortran Building System for automatic building modern Fortran projects *homepage*: https://github.com/szaghi/FoBiS ========= ================== -version toolchain +version toolchain ========= ================== ``3.0.5`` ``GCCcore/10.3.0`` ========= ================== @@ -13003,7 +13579,7 @@ FoldX is used to provide a fast and quantitative estimation of the importance of *homepage*: http://foldx.crg.es/ =============== ========== -version toolchain +version toolchain =============== ========== ``2.5.2`` ``system`` ``3.0-beta5.1`` ``system`` @@ -13022,20 +13598,21 @@ Fontconfig is a library designed to provide system-wide font configuration, cus *homepage*: https://www.freedesktop.org/wiki/Software/fontconfig/ =========== ================== ====================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ====================================================================================== -``2.11.94`` ``foss/2016a``, ``intel/2016a`` -``2.11.95`` ``foss/2016a``, ``intel/2016a`` +``2.11.94`` ``foss/2016a``, ``intel/2016a`` +``2.11.95`` ``foss/2016a``, ``intel/2016a`` ``2.12.1`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` -``2.12.1`` ``-libpng-1.6.29`` ``GCCcore/6.3.0`` -``2.12.4`` ``GCCcore/6.4.0`` -``2.12.6`` ``GCCcore/6.4.0`` -``2.13.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.13.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2.13.92`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``2.13.93`` ``GCCcore/10.3.0`` -``2.13.94`` ``GCCcore/11.2.0`` -``2.14.0`` ``GCCcore/11.3.0`` +``2.12.1`` ``-libpng-1.6.29`` ``GCCcore/6.3.0`` +``2.12.4`` ``GCCcore/6.4.0`` +``2.12.6`` ``GCCcore/6.4.0`` +``2.13.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.13.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.13.92`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.13.93`` ``GCCcore/10.3.0`` +``2.13.94`` ``GCCcore/11.2.0`` +``2.14.0`` ``GCCcore/11.3.0`` +``2.14.1`` ``GCCcore/12.2.0`` =========== ================== ====================================================================================== @@ -13049,7 +13626,7 @@ X11 font extension wire protocol *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= -version toolchain +version toolchain ========= ================================================= ``2.1.3`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= @@ -13065,7 +13642,7 @@ FORD is an automatic documentation generator for modern Fortran programs *homepage*: https://github.com/Fortran-FOSS-Programmers/ford/wiki ========== ================== -version toolchain +version toolchain ========== ================== ``6.1.1`` ``GCCcore/10.2.0`` ``6.1.6`` ``GCCcore/10.3.0`` @@ -13083,7 +13660,7 @@ GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for M *homepage*: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain =========== ========== -version toolchain +version toolchain =========== ========== ``2016.04`` ``system`` ``2016.06`` ``system`` @@ -13103,7 +13680,9 @@ version toolchain ``2021a`` ``system`` ``2021b`` ``system`` ``2022.05`` ``system`` +``2022.10`` ``system`` ``2022a`` ``system`` +``2022b`` ``system`` =========== ========== @@ -13117,7 +13696,7 @@ GCC based compiler toolchain __with CUDA support__, and including OpenMPI for M *homepage*: (none) ========= ========== -version toolchain +version toolchain ========= ========== ``2017b`` ``system`` ``2018a`` ``system`` @@ -13139,7 +13718,7 @@ FoX is an XML library written in Fortran 95. It allows software developers to re *homepage*: http://homepages.see.leeds.ac.uk/~earawa/FoX/ ========= =============================================================== -version toolchain +version toolchain ========= =============================================================== ``4.1.2`` ``GCC/11.2.0``, ``GCC/9.3.0``, ``intel/2017b``, ``intel/2018a`` ========= =============================================================== @@ -13155,7 +13734,7 @@ FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and e *homepage*: https://www.fox-toolkit.org/ ========== ===================================== -version toolchain +version toolchain ========== ===================================== ``1.6.57`` ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ========== ===================================== @@ -13171,7 +13750,7 @@ Effing package management! Build packages for multiple platforms (deb, rpm, etc) *homepage*: https://github.com/jordansissel/fpm ========= =============== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= =============== ========== ``1.3.3`` ``-Ruby-2.1.6`` ``system`` ========= =============== ========== @@ -13187,7 +13766,7 @@ The fpocket suite of programs is a very fast open source protein pocket detectio *homepage*: https://github.com/Discngine/fpocket =========== =============== -version toolchain +version toolchain =========== =============== ``3.1.4.2`` ``gompi/2020a`` =========== =============== @@ -13203,7 +13782,7 @@ fqtrim is a versatile stand-alone utility that can be used to trim adapters, pol *homepage*: http://ccb.jhu.edu/software/fqtrim/ ========= =============== -version toolchain +version toolchain ========= =============== ``0.9.4`` ``intel/2016b`` ``0.9.5`` ``intel/2017a`` @@ -13220,7 +13799,7 @@ Fqzcomp is a basic fastq compressor, designed primarily for high performance. D *homepage*: http://sourceforge.net/projects/fqzcomp/ ======= ============= -version toolchain +version toolchain ======= ============= ``4.6`` ``GCC/4.8.2`` ======= ============= @@ -13235,11 +13814,11 @@ FragGeneScan is an application for finding (fragmented) genes in short reads. *homepage*: http://omics.informatics.indiana.edu/FragGeneScan/ -======== ========================================================================= -version toolchain -======== ========================================================================= -``1.31`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``foss/2018b`` -======== ========================================================================= +======== ============================================================================================= +version toolchain +======== ============================================================================================= +``1.31`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``foss/2018b`` +======== ============================================================================================= .. _list_software_FRANz_417: @@ -13252,7 +13831,7 @@ A fast and flexible parentage inference program for natural populations. *homepage*: https://www.bioinf.uni-leipzig.de/Software/FRANz ========= ============== -version toolchain +version toolchain ========= ============== ``2.0.0`` ``foss/2018a`` ========= ============== @@ -13268,7 +13847,7 @@ A package for the generation and decoding of FREE divergence error-correcting DN *homepage*: https://github.com/hawkjo/freebarcodes ========== ============== -version toolchain +version toolchain ========== ============== ``3.0.a5`` ``foss/2021b`` ========== ============== @@ -13284,10 +13863,11 @@ Bayesian haplotype-based genetic polymorphism discovery and genotyping. *homepage*: https://github.com/freebayes/freebayes ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.3.5`` ``GCC/10.2.0`` -``1.3.5`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``1.3.5`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``1.3.6`` ``-R-4.1.0`` ``foss/2021a`` ``1.3.6`` ``-R-4.1.2`` ``foss/2021b`` ========= ================= ============== @@ -13302,7 +13882,7 @@ FreeFEM offers a fast interpolation algorithm and a language for the manipulatio *homepage*: https://freefem.org ======= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= ============== ``4.5`` ``-Python-3.7.4`` ``foss/2019b`` ======= ================= ============== @@ -13318,9 +13898,9 @@ FreeFem++ is a partial differential equation solver. It has its own language. fr *homepage*: http://www.freefem.org/ ========== ==================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ==================== =============== -``3.58`` ``-downloaded-deps`` ``foss/2017b`` +``3.58`` ``-downloaded-deps`` ``foss/2017b`` ``3.60`` ``-downloaded-deps`` ``intel/2018a`` ``3.61-1`` ``-downloaded-deps`` ``intel/2018a`` ========== ==================== =============== @@ -13336,12 +13916,12 @@ freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit ( *homepage*: http://freeglut.sourceforge.net/ ========= ================ ====================================================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ====================================================================================================================================================================================== ``3.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``3.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` -``3.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``3.2.2`` ``GCCcore/11.3.0`` +``3.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` +``3.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``3.2.2`` ``GCCcore/11.3.0`` ========= ================ ====================================================================================================================================================================================== @@ -13354,11 +13934,11 @@ FreeImage is an Open Source library project for developers who would like to sup *homepage*: http://freeimage.sourceforge.net -========== =================================================================================================================== -version toolchain -========== =================================================================================================================== -``3.18.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========== =================================================================================================================== +========== ======================================================================================================================================= +version toolchain +========== ======================================================================================================================================= +``3.18.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========== ======================================================================================================================================= .. _list_software_FreeSASA_682: @@ -13371,7 +13951,7 @@ FreeSASA is a command line tool, C-library and Python module for calculating sol *homepage*: https://freesasa.github.io ========= ============= -version toolchain +version toolchain ========= ============= ``2.0.3`` ``GCC/8.3.0`` ========= ============= @@ -13387,7 +13967,7 @@ FreeSurfer is a set of tools for analysis and visualization of structural and f *homepage*: https://surfer.nmr.mgh.harvard.edu/ ========= =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= =================== ========== ``5.3.0`` ``-centos4_x86_64`` ``system`` ``5.3.0`` ``-centos6_x86_64`` ``system`` @@ -13399,6 +13979,7 @@ version versionsuffix toolchain ``7.2.0`` ``-centos7_x86_64`` ``system`` ``7.2.0`` ``-centos8_x86_64`` ``system`` ``7.2.0`` ``-ubuntu18_amd64`` ``system`` +``7.3.2`` ``-centos7_x86_64`` ``system`` ``7.3.2`` ``-centos8_x86_64`` ``system`` ========= =================== ========== @@ -13413,7 +13994,7 @@ FreeTDS is a set of libraries for Unix and Linux that allows your programs to n *homepage*: https://www.freetds.org/ ========= ================== -version toolchain +version toolchain ========= ================== ``1.3.3`` ``GCCcore/10.3.0`` ========= ================== @@ -13429,23 +14010,23 @@ FreeType 2 is a software font engine that is designed to be small, efficient, h *homepage*: https://freetype.org ========== ================== ====================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ====================================================================== -``2.6.2`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``2.6.3`` ``foss/2016a``, ``intel/2016a`` -``2.6.5`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` -``2.7`` ``foss/2016b``, ``intel/2016b`` +``2.6.2`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``2.6.3`` ``foss/2016a``, ``intel/2016a`` +``2.6.5`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` +``2.7`` ``foss/2016b``, ``intel/2016b`` ``2.7.1`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``gimkl/2017a``, ``intel/2016b`` -``2.7.1`` ``-libpng-1.6.29`` ``GCCcore/6.3.0`` -``2.8`` ``GCCcore/6.4.0`` -``2.8.1`` ``GCCcore/6.4.0`` -``2.9`` ``GCCcore/6.4.0`` -``2.9.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``2.10.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.10.3`` ``GCCcore/10.2.0`` -``2.10.4`` ``GCCcore/10.3.0`` -``2.11.0`` ``GCCcore/11.2.0`` -``2.12.1`` ``GCCcore/11.3.0`` +``2.7.1`` ``-libpng-1.6.29`` ``GCCcore/6.3.0`` +``2.8`` ``GCCcore/6.4.0`` +``2.8.1`` ``GCCcore/6.4.0`` +``2.9`` ``GCCcore/6.4.0`` +``2.9.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``2.10.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.10.3`` ``GCCcore/10.2.0`` +``2.10.4`` ``GCCcore/10.3.0`` +``2.11.0`` ``GCCcore/11.2.0`` +``2.12.1`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========== ================== ====================================================================== @@ -13459,7 +14040,7 @@ Python binding for the freetype library *homepage*: https://github.com/rougier/freetype-py ========= ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================= ``2.2.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========= ================= ================= @@ -13470,16 +14051,17 @@ version versionsuffix toolchain *FreeXL* ++++++++ -FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. +FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. *homepage*: https://www.gaia-gis.it/fossil/freexl/index ========= ======================================================= -version toolchain +version toolchain ========= ======================================================= -``1.0.2`` ``foss/2016b``, ``intel/2016b`` -``1.0.3`` ``GCCcore/6.4.0`` +``1.0.2`` ``foss/2016b``, ``intel/2016b`` +``1.0.3`` ``GCCcore/6.4.0`` ``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.0.6`` ``GCCcore/11.2.0`` ========= ======================================================= @@ -13493,7 +14075,7 @@ The freud Python library provides a simple, flexible, powerful set of tools for *homepage*: https://github.com/glotzerlab/freud ========= ============== -version toolchain +version toolchain ========= ============== ``2.6.2`` ``foss/2020b`` ========= ============== @@ -13509,14 +14091,14 @@ The Free Implementation of the Unicode Bidirectional Algorithm. *homepage*: https://github.com/fribidi/fribidi ========== ========================================================== -version toolchain +version toolchain ========== ========================================================== -``1.0.1`` ``foss/2018a``, ``intel/2018a`` -``1.0.2`` ``GCCcore/6.4.0`` -``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``1.0.9`` ``GCCcore/9.3.0`` +``1.0.1`` ``foss/2018a``, ``intel/2018a`` +``1.0.2`` ``GCCcore/6.4.0`` +``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.0.9`` ``GCCcore/9.3.0`` ``1.0.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.0.12`` ``GCCcore/11.3.0`` +``1.0.12`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========== ========================================================== @@ -13530,7 +14112,7 @@ FORTRAN Unit Test Framework (FRUIT) *homepage*: https://fortranxunit.sourceforge.io ========= =============== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =============== =============================== ``3.4.3`` ``-Ruby-2.5.1`` ``foss/2018a``, ``intel/2018a`` ========= =============== =============================== @@ -13546,7 +14128,7 @@ FORTRAN Unit Test Framework (FRUIT) *homepage*: https://fortranxunit.sourceforge.io ========= =============== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =============== =============================== ``3.4.3`` ``-Ruby-2.5.1`` ``foss/2018a``, ``intel/2018a`` ========= =============== =============================== @@ -13562,22 +14144,22 @@ FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain ima *homepage*: https://www.fmrib.ox.ac.uk/fsl/ =========== ============================== ================================================ -version versionsuffix toolchain +version versionsuffix toolchain =========== ============================== ================================================ -``5.0.9`` ``intel/2016a`` -``5.0.9`` ``-Mesa-11.2.1`` ``intel/2016a`` -``5.0.9`` ``-centos6_64`` ``system`` +``5.0.9`` ``intel/2016a`` +``5.0.9`` ``-Mesa-11.2.1`` ``intel/2016a`` +``5.0.9`` ``-centos6_64`` ``system`` ``5.0.10`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``5.0.11`` ``foss/2018b`` -``5.0.11`` ``-Python-3.6.6`` ``foss/2018b`` -``6.0.1`` ``-Python-2.7.15`` ``foss/2019a`` -``6.0.1`` ``-Python-3.7.2`` ``foss/2019a`` -``6.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` -``6.0.2`` ``-Python-2.7.15-CUDA-9.2.88`` ``foss/2018b`` -``6.0.2`` ``-Python-3.7.2`` ``foss/2019a`` -``6.0.3`` ``-Python-3.7.4`` ``foss/2019b`` -``6.0.4`` ``-Python-3.7.4`` ``foss/2019b`` -``6.0.5.1`` ``foss/2021a`` +``5.0.11`` ``foss/2018b`` +``5.0.11`` ``-Python-3.6.6`` ``foss/2018b`` +``6.0.1`` ``-Python-2.7.15`` ``foss/2019a`` +``6.0.1`` ``-Python-3.7.2`` ``foss/2019a`` +``6.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` +``6.0.2`` ``-Python-2.7.15-CUDA-9.2.88`` ``foss/2018b`` +``6.0.2`` ``-Python-3.7.2`` ``foss/2019a`` +``6.0.3`` ``-Python-3.7.4`` ``foss/2019b`` +``6.0.4`` ``-Python-3.7.4`` ``foss/2019b`` +``6.0.5.1`` ``foss/2021a`` =========== ============================== ================================================ @@ -13591,7 +14173,7 @@ FSLeyes is the FSL image viewer. *homepage*: https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``0.15.0`` ``-Python-2.7.13`` ``intel/2017a`` ========== ================== =============== @@ -13607,7 +14189,7 @@ A tiny C library for managing SOM (Self-Organizing Maps) neural networks. *homepage*: https://github.com/ekg/fsom ============ ============================================================================= -version toolchain +version toolchain ============ ============================================================================= ``20141119`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ============ ============================================================================= @@ -13623,7 +14205,7 @@ Fortran 95 JSON Parser *homepage*: https://github.com/josephalevin/fson ========= ============== -version toolchain +version toolchain ========= ============== ``1.0.5`` ``GCC/10.2.0`` ========= ============== @@ -13639,10 +14221,10 @@ FTGL is a free open source library to enable developers to use arbitrary fonts i *homepage*: https://github.com/frankheckenbach/ftgl ============= ========================================================================================================== -version toolchain +version toolchain ============= ========================================================================================================== ``2.1.3-rc5`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2018b``, ``intel/2017b`` -``2.4.0`` ``GCCcore/11.3.0`` +``2.4.0`` ``GCCcore/11.3.0`` ============= ========================================================================================================== @@ -13656,7 +14238,7 @@ Toolchain using Fujitsu compilers and libraries. *homepage*: (none) ========= ========== -version toolchain +version toolchain ========= ========== ``21.05`` ``system`` ========= ========== @@ -13672,7 +14254,7 @@ Reverse Monte Carlo (RMC) is probably best known for its applications in conden *homepage*: https://bachiraoun.github.io/fullrmc ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``3.2.0`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============== @@ -13688,10 +14270,10 @@ This tool is intended to deduplicate UMIs from single-end and paired-end sequen *homepage*: https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools ========== ================= ============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============================== ``0.18.2`` ``GCC/10.3.0``, ``GCC/11.2.0`` -``0.18.2`` ``-Python-3.6.6`` ``foss/2018b`` +``0.18.2`` ``-Python-3.6.6`` ``foss/2018b`` ========== ================= ============================== @@ -13705,7 +14287,7 @@ FUNWAVE–TVD is the TVD version of the fully nonlinear Boussinesq wave model (F *homepage*: https://fengyanshi.github.io ================ ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ================ ============= =============== ``3.1-20170525`` ``intel/2017a`` ``3.1-20170525`` ``-no-storm`` ``intel/2017a`` @@ -13722,10 +14304,10 @@ The reference implementation of the Linux FUSE (Filesystem in Userspace) interfa *homepage*: https://github.com/libfuse/libfuse ========= =============== -version toolchain +version toolchain ========= =============== ``3.2.6`` ``intel/2018a`` -``3.4.1`` ``foss/2018a`` +``3.4.1`` ``foss/2018a`` ========= =============== @@ -13739,7 +14321,7 @@ FuSeq is a novel method to discover fusion genes from paired-end RNA sequencing *homepage*: https://github.com/nghiavtr/FuSeq ========= =============== -version toolchain +version toolchain ========= =============== ``1.1.2`` ``gompi/2019b`` ========= =============== @@ -13755,7 +14337,7 @@ FusionCatcher searches for novel/known somatic fusion genes, translocations, and *homepage*: https://github.com/ndaniel/fusioncatcher ======== ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================== ============== ``1.20`` ``-Python-2.7.16`` ``foss/2019b`` ``1.30`` ``-Python-2.7.16`` ``foss/2019b`` @@ -13772,7 +14354,7 @@ Futhark is a small programming language designed to be compiled to efficient par *homepage*: https://futhark-lang.org/ ========== ========== -version toolchain +version toolchain ========== ========== ``0.19.5`` ``system`` ========== ========== @@ -13788,7 +14370,7 @@ The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Ex *homepage*: https://launchpad.net/futile ========= ================================================================================================= -version toolchain +version toolchain ========= ================================================================================================= ``1.8.3`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` ========= ================================================================================================= @@ -13804,12 +14386,12 @@ python-future is the missing compatibility layer between Python 2 and Python 3. *homepage*: https://python-future.org/ ========== ================== ================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================================================ ``0.16.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``0.16.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``0.16.0`` ``-Python-3.6.3`` ``intel/2017b`` -``0.16.0`` ``-Python-3.6.6`` ``foss/2018b`` +``0.16.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.16.0`` ``-Python-3.6.3`` ``intel/2017b`` +``0.16.0`` ``-Python-3.6.6`` ``foss/2018b`` ========== ================== ================================================ @@ -13823,7 +14405,7 @@ Extract sequences from a fastx (fasta or fastq) file given a subsequence. *homepage*: https://github.com/ctSkennerton/fxtract ======= ================= -version toolchain +version toolchain ======= ================= ``2.3`` ``GCCcore/8.2.0`` ======= ================= @@ -13835,7 +14417,7 @@ version toolchain --- -:ref:`list_software_G-PhoCS_561` - :ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_gcloud_638` - :ref:`list_software_GConf_461` - :ref:`list_software_GCTA_287` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_genozip_764` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_gfbf_405` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_Gibbs2_537` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GLM-AED_471` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPy_272` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap_784` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gRPC_332` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-bad_1393` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_gsutil_664` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GTK4_282` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` +:ref:`list_software_G-PhoCS_561` - :ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_gappa_521` - :ref:`list_software_GARLI_367` - :ref:`list_software_garnett_757` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gaussian_827` - :ref:`list_software_gawk_426` - :ref:`list_software_Gblocks_709` - :ref:`list_software_GBprocesS_872` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_gcloud_638` - :ref:`list_software_GConf_461` - :ref:`list_software_GCTA_287` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdbm_410` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_GDRCopy_632` - :ref:`list_software_Geant4_547` - :ref:`list_software_Geant4-data_1002` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEGL_287` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gemmi_527` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_gengetopt_973` - :ref:`list_software_Genome_Profiler_1533` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenomeTools_1132` - :ref:`list_software_GenomeWorks_1137` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_genozip_764` - :ref:`list_software_gensim_643` - :ref:`list_software_geocube_730` - :ref:`list_software_geopandas_946` - :ref:`list_software_geopy_548` - :ref:`list_software_georges_748` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_GetOrganelle_1209` - :ref:`list_software_gettext_773` - :ref:`list_software_gexiv2_597` - :ref:`list_software_gfbf_405` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_gh_207` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_Gibbs2_537` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_GIMP_301` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-extras_1032` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLFW_304` - :ref:`list_software_GLib_350` - :ref:`list_software_glib-networking_1555` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GLM-AED_471` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_Glucose_722` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_goalign_737` - :ref:`list_software_GOATOOLS_616` - :ref:`list_software_gobff_516` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_goblf_522` - :ref:`list_software_Godon_503` - :ref:`list_software_gofasta_741` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_gotree_646` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_GPy_272` - :ref:`list_software_GPyOpt_579` - :ref:`list_software_GPyTorch_784` - :ref:`list_software_Grace_482` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_graphite2_902` - :ref:`list_software_GraPhlAn_749` - :ref:`list_software_GraphMap_784` - :ref:`list_software_GraphMap2_834` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASP_381` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_gretl_542` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_groff_532` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_Groovy_646` - :ref:`list_software_gRPC_332` - :ref:`list_software_GSEA_288` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_gsport_671` - :ref:`list_software_GST-plugins-bad_1393` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_gsutil_664` - :ref:`list_software_gsw_337` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_GTK+_273` - :ref:`list_software_GTK2_280` - :ref:`list_software_GTK3_281` - :ref:`list_software_GTK4_282` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_gubbins_746` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_G-PhoCS_561: @@ -13848,7 +14430,7 @@ G-PhoCS is a software package for inferring ancestral population sizes, populati *homepage*: http://compgen.cshl.edu/GPhoCS/ ========= ======================================== -version toolchain +version toolchain ========= ======================================== ``1.2.3`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ========= ======================================== @@ -13861,13 +14443,14 @@ version toolchain Library contains GRIB2 encoder/decoder ('C' version). -*homepage*: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ +*homepage*: https://github.com/NOAA-EMC/NCEPLIBS-g2c ========= ======================================================================================================================== -version toolchain +version toolchain ========= ======================================================================================================================== ``1.6.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``1.6.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.6.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.7.0`` ``GCCcore/11.3.0`` ========= ======================================================================================================================== @@ -13881,11 +14464,11 @@ Library contains GRIB2 encoder/decoder and search/indexing routines. *homepage*: https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ ========= ===================================================================== -version toolchain +version toolchain ========= ===================================================================== -``1.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +``1.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.1.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2018b`` -``3.2.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``3.2.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ===================================================================== @@ -13899,7 +14482,7 @@ g2log, efficient asynchronous logger using C++11 *homepage*: https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11 ======= ================================= -version toolchain +version toolchain ======= ================================= ``1.0`` ``GCCcore/8.3.0``, ``foss/2016b`` ======= ================================= @@ -13915,7 +14498,7 @@ Gaia is a C++ library with python bindings which implements similarity measures *homepage*: https://github.com/MTG/gaia ========= ================== ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================= ``2.4.5`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ========= ================== ================= @@ -13931,13 +14514,13 @@ The General Atomic and Molecular Electronic Structure System (GAMESS) is a gene *homepage*: http://www.msg.chem.iastate.edu/gamess/index.html =============== ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain =============== ============= =============== ``20141205-R1`` ``intel/2016a`` ``20170420-R1`` ``intel/2016b`` ``20170420-R1`` ``-sockets`` ``intel/2016b`` -``20180214-R1`` ``foss/2016b`` -``20180214-R1`` ``-sockets`` ``foss/2016b`` +``20180214-R1`` ``foss/2016b`` +``20180214-R1`` ``-sockets`` ``foss/2016b`` =============== ============= =============== @@ -13951,10 +14534,10 @@ GAP is a system for computational discrete algebra, with particular emphasis on *homepage*: https://www.gap-system.org ========== =============== -version toolchain +version toolchain ========== =============== ``4.9.3`` ``intel/2018b`` -``4.11.0`` ``foss/2019a`` +``4.11.0`` ``foss/2019a`` ========== =============== @@ -13968,7 +14551,7 @@ GapCloser is designed to close the gaps emerging during the scaffolding process *homepage*: https://sourceforge.net/projects/soapdenovo2/files/GapCloser/ =========== =============================== -version toolchain +version toolchain =========== =============================== ``1.12-r6`` ``foss/2018a``, ``intel/2017b`` =========== =============================== @@ -13984,7 +14567,7 @@ GapFiller is a seed-and-extend local assembler to fill the gap within paired rea *homepage*: https://sourceforge.net/projects/gapfiller ========= =============== -version toolchain +version toolchain ========= =============== ``2.1.1`` ``intel/2017a`` ========= =============== @@ -14000,7 +14583,7 @@ gappa is a collection of commands for working with phylogenetic data. Its main f *homepage*: https://github.com/lczech/gappa ========= ============== -version toolchain +version toolchain ========= ============== ``0.7.1`` ``GCC/10.3.0`` ========= ============== @@ -14016,7 +14599,7 @@ GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for infer *homepage*: https://code.google.com/archive/p/garli/ ======== =============== -version toolchain +version toolchain ======== =============== ``2.01`` ``gompi/2019a`` ======== =============== @@ -14032,7 +14615,7 @@ Garnett is a software package that faciliates automated cell type classification *homepage*: https://cole-trapnell-lab.github.io/garnett ========== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ============== ``0.1.20`` ``-R-4.0.3`` ``foss/2020b`` ========== ============= ============== @@ -14048,7 +14631,7 @@ The Genomic Association Tester (GAT) is a tool for computing the significance of *homepage*: https://gat.readthedocs.io/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``1.2.2`` ``-Python-2.7.11`` ``foss/2016a`` ========= ================== ============== @@ -14064,19 +14647,19 @@ GATE is an advanced opensource software developed by the international OpenGATE *homepage*: http://www.opengatecollaboration.org/ =========== =============================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain =========== =============================== =============================== -``6.2`` ``-Python-2.7.11`` ``intel/2016a`` -``7.1`` ``-Python-2.7.11`` ``intel/2016a`` -``7.2`` ``-Python-2.7.11`` ``intel/2016a`` +``6.2`` ``-Python-2.7.11`` ``intel/2016a`` +``7.1`` ``-Python-2.7.11`` ``intel/2016a`` +``7.2`` ``-Python-2.7.11`` ``intel/2016a`` ``8.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``8.0`` ``-Python-2.7.14-Geant4-10.04`` ``intel/2017b`` -``8.1.p01`` ``-Python-2.7.15`` ``foss/2018b`` +``8.0`` ``-Python-2.7.14-Geant4-10.04`` ``intel/2017b`` +``8.1.p01`` ``-Python-2.7.15`` ``foss/2018b`` ``8.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``8.2`` ``-Python-2.7.15`` ``foss/2018b`` -``9.0`` ``-Python-3.7.4`` ``foss/2019b`` -``9.1`` ``foss/2021b`` -``9.2`` ``foss/2021b`` +``8.2`` ``-Python-2.7.15`` ``foss/2018b`` +``9.0`` ``-Python-3.7.4`` ``foss/2019b`` +``9.1`` ``foss/2021b`` +``9.2`` ``foss/2021b`` =========== =============================== =============================== @@ -14090,46 +14673,47 @@ The Genome Analysis Toolkit or GATK is a software package developed at the Broad *homepage*: https://www.broadinstitute.org/gatk/ ============ =================== ================== -version versionsuffix toolchain +version versionsuffix toolchain ============ =================== ================== -``1.0.5083`` ``system`` -``2.5-2`` ``-Java-1.7.0_10`` ``system`` -``2.6-5`` ``-Java-1.7.0_10`` ``system`` -``2.7-4`` ``system`` -``2.7-4`` ``-Java-1.7.0_10`` ``system`` -``2.8-1`` ``-Java-1.7.0_10`` ``system`` -``3.0-0`` ``-Java-1.7.0_10`` ``system`` -``3.3-0`` ``-Java-1.7.0_21`` ``system`` -``3.3-0`` ``-Java-1.7.0_80`` ``system`` -``3.3-0`` ``-Java-1.8.0_66`` ``system`` -``3.5`` ``-Java-1.8.0_66`` ``system`` -``3.5`` ``-Java-1.8.0_74`` ``system`` -``3.6`` ``-Java-1.8.0_92`` ``system`` -``3.7`` ``-Java-1.8.0_112`` ``system`` -``3.8-0`` ``-Java-1.8.0_144`` ``system`` -``4.0.1.2`` ``-Java-1.8`` ``system`` -``4.0.4.0`` ``-Python-2.7.14`` ``intel/2018a`` -``4.0.4.0`` ``-Python-3.6.4`` ``intel/2018a`` -``4.0.5.1`` ``-Python-3.6.4`` ``foss/2018a`` -``4.0.7.0`` ``-Python-2.7.14`` ``intel/2018a`` -``4.0.7.0`` ``-Python-3.6.4`` ``intel/2018a`` -``4.0.8.1`` ``-Python-2.7.15`` ``foss/2018b`` -``4.0.8.1`` ``-Python-3.6.6`` ``foss/2018b`` -``4.0.10.0`` ``-Python-3.6.6`` ``foss/2018b`` -``4.0.12.0`` ``-Python-3.6.6`` ``foss/2018b`` -``4.1.0.0`` ``-Python-3.6.6`` ``foss/2018b`` -``4.1.2.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` -``4.1.3.0`` ``-Java-1.8`` ``GCCcore/8.3.0`` -``4.1.4.1`` ``-Java-1.8`` ``GCCcore/8.3.0`` -``4.1.4.1`` ``-Java-11`` ``GCCcore/8.3.0`` -``4.1.5.0`` ``-Java-1.8`` ``GCCcore/9.3.0`` -``4.1.5.0`` ``-Java-11`` ``GCCcore/9.3.0`` -``4.1.8.1`` ``-Java-1.8`` ``GCCcore/9.3.0`` +``1.0.5083`` ``system`` +``2.5-2`` ``-Java-1.7.0_10`` ``system`` +``2.6-5`` ``-Java-1.7.0_10`` ``system`` +``2.7-4`` ``system`` +``2.7-4`` ``-Java-1.7.0_10`` ``system`` +``2.8-1`` ``-Java-1.7.0_10`` ``system`` +``3.0-0`` ``-Java-1.7.0_10`` ``system`` +``3.3-0`` ``-Java-1.7.0_21`` ``system`` +``3.3-0`` ``-Java-1.7.0_80`` ``system`` +``3.3-0`` ``-Java-1.8.0_66`` ``system`` +``3.5`` ``-Java-1.8.0_66`` ``system`` +``3.5`` ``-Java-1.8.0_74`` ``system`` +``3.6`` ``-Java-1.8.0_92`` ``system`` +``3.7`` ``-Java-1.8.0_112`` ``system`` +``3.8-0`` ``-Java-1.8.0_144`` ``system`` +``4.0.1.2`` ``-Java-1.8`` ``system`` +``4.0.4.0`` ``-Python-2.7.14`` ``intel/2018a`` +``4.0.4.0`` ``-Python-3.6.4`` ``intel/2018a`` +``4.0.5.1`` ``-Python-3.6.4`` ``foss/2018a`` +``4.0.7.0`` ``-Python-2.7.14`` ``intel/2018a`` +``4.0.7.0`` ``-Python-3.6.4`` ``intel/2018a`` +``4.0.8.1`` ``-Python-2.7.15`` ``foss/2018b`` +``4.0.8.1`` ``-Python-3.6.6`` ``foss/2018b`` +``4.0.10.0`` ``-Python-3.6.6`` ``foss/2018b`` +``4.0.12.0`` ``-Python-3.6.6`` ``foss/2018b`` +``4.1.0.0`` ``-Python-3.6.6`` ``foss/2018b`` +``4.1.2.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` +``4.1.3.0`` ``-Java-1.8`` ``GCCcore/8.3.0`` +``4.1.4.1`` ``-Java-1.8`` ``GCCcore/8.3.0`` +``4.1.4.1`` ``-Java-11`` ``GCCcore/8.3.0`` +``4.1.5.0`` ``-Java-1.8`` ``GCCcore/9.3.0`` +``4.1.5.0`` ``-Java-11`` ``GCCcore/9.3.0`` +``4.1.8.1`` ``-Java-1.8`` ``GCCcore/9.3.0`` ``4.2.0.0`` ``-Java-1.8`` ``GCCcore/10.2.0`` ``4.2.0.0`` ``-Java-11`` ``GCCcore/10.2.0`` ``4.2.3.0`` ``-Java-11`` ``GCCcore/11.2.0`` ``4.2.5.0`` ``-Java-11`` ``GCCcore/11.2.0`` ``4.2.6.1`` ``-Java-11`` ``GCCcore/11.2.0`` +``4.3.0.0`` ``-Java-11`` ``GCCcore/11.3.0`` ============ =================== ================== @@ -14143,7 +14727,7 @@ Gaussian provides state-of-the-art capabilities for electronic structure modelin *homepage*: https://www.gaussian.com/ =========== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain =========== ============= ========== ``09.e.01`` ``-AVX`` ``system`` ``16.A.03`` ``-AVX2`` ``system`` @@ -14160,9 +14744,9 @@ The awk utility interprets a special-purpose programming language that makes it *homepage*: https://www.gnu.org/software/gawk ========= ============================================== -version toolchain +version toolchain ========= ============================================== -``5.1.0`` ``GCC/10.2.0`` +``5.1.0`` ``GCC/10.2.0`` ``5.1.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` ========= ============================================== @@ -14177,7 +14761,7 @@ Selection of conserved blocks from multiple alignments for their use in phylogen *homepage*: http://molevol.cmima.csic.es/castresana/Gblocks.html ========= ========== -version toolchain +version toolchain ========= ========== ``0.91b`` ``system`` ========= ========== @@ -14193,7 +14777,7 @@ GBprocesS allows for the extraction of genomic inserts from NGS data for GBS exp *homepage*: https://gbprocess.readthedocs.io/ ======= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= =============== ``2.3`` ``-Python-3.8.2`` ``intel/2020a`` ======= ================= =============== @@ -14209,7 +14793,7 @@ Inference of Ploidy from (Genotyping-by-Sequencing) GBS Data *homepage*: https://cran.r-project.org/web/packages/gbs2ploidy ======= ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= =============== ``1.0`` ``-R-3.4.3`` ``intel/2017b`` ======= ============= =============== @@ -14225,16 +14809,16 @@ The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage *homepage*: https://hboehm.info/gc/ ========== ==================================== -version toolchain +version toolchain ========== ==================================== -``7.4.4`` ``GCC/4.9.3-2.25``, ``foss/2016a`` -``7.6.0`` ``GCCcore/6.4.0`` -``7.6.4`` ``GCCcore/7.3.0`` -``7.6.10`` ``GCCcore/8.2.0`` +``7.4.4`` ``GCC/4.9.3-2.25``, ``foss/2016a`` +``7.6.0`` ``GCCcore/6.4.0`` +``7.6.4`` ``GCCcore/7.3.0`` +``7.6.10`` ``GCCcore/8.2.0`` ``7.6.12`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``8.0.4`` ``GCCcore/10.3.0`` -``8.2.0`` ``GCCcore/11.2.0`` -``8.2.2`` ``GCCcore/11.3.0`` +``8.0.4`` ``GCCcore/10.3.0`` +``8.2.0`` ``GCCcore/11.2.0`` +``8.2.2`` ``GCCcore/11.3.0`` ========== ==================================== @@ -14248,7 +14832,7 @@ GC3Pie is a Python package for running large job campaigns on diverse batch-orie *homepage*: https://gc3pie.readthedocs.org ========= ========== -version toolchain +version toolchain ========= ========== ``2.4.2`` ``system`` ``2.5.0`` ``system`` @@ -14266,7 +14850,7 @@ The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran *homepage*: http://gcc.gnu.org/ ========== =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== =================== ========== ``4.8.1`` ``system`` ``4.8.1`` ``-CLooG`` ``system`` @@ -14344,7 +14928,7 @@ The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran *homepage*: http://gcc.gnu.org/ ========== ========== -version toolchain +version toolchain ========== ========== ``4.9.2`` ``system`` ``4.9.3`` ``system`` @@ -14392,7 +14976,7 @@ GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit. *homepage*: (none) =========== ========== -version toolchain +version toolchain =========== ========== ``2016.08`` ``system`` ``2017b`` ``system`` @@ -14415,7 +14999,7 @@ Libraries and tools for interacting with Google Cloud products and services. *homepage*: https://cloud.google.com/sdk =========== ========== -version toolchain +version toolchain =========== ========== ``382.0.0`` ``system`` =========== ========== @@ -14431,7 +15015,7 @@ GConf is a system for storing application preferences. It is intended for user *homepage*: https://projects.gnome.org/gconf/ ========= ================================================================================================================================================================================ -version toolchain +version toolchain ========= ================================================================================================================================================================================ ``3.2.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ========= ================================================================================================================================================================================ @@ -14447,7 +15031,7 @@ GCTA (Genome-wide Complex Trait Analysis) is a software package, which was init *homepage*: https://yanglab.westlake.edu.cn/software/gcta/ ============== ============================== -version toolchain +version toolchain ============== ============================== ``1.94.0beta`` ``foss/2021b``, ``gfbf/2022a`` ============== ============================== @@ -14463,7 +15047,7 @@ Gctf: real-time CTF determination and correction, Kai Zhang, 2016 *homepage*: https://www.mrc-lmb.cam.ac.uk/kzhang/ ======== ========== -version toolchain +version toolchain ======== ========== ``1.06`` ``system`` ======== ========== @@ -14479,13 +15063,14 @@ GD.pm - Interface to Gd Graphics Library *homepage*: https://github.com/lstein/Perl-GD ======== ================ ================== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================ ================== -``2.66`` ``-Perl-5.24.0`` ``foss/2016b`` -``2.68`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``2.69`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -``2.71`` ``GCCcore/9.3.0`` +``2.66`` ``-Perl-5.24.0`` ``foss/2016b`` +``2.68`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``2.69`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``2.71`` ``GCCcore/9.3.0`` ``2.73`` ``GCCcore/10.3.0`` +``2.75`` ``GCCcore/11.3.0`` ======== ================ ================== @@ -14499,34 +15084,34 @@ GDAL is a translator library for raster geospatial data formats that is released *homepage*: https://www.gdal.org ========= ============================== ================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ============================== ================================================================ -``2.0.2`` ``foss/2016a``, ``intel/2016a`` -``2.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``2.1.1`` ``foss/2016a`` -``2.1.1`` ``-Python-2.7.12`` ``intel/2016b`` -``2.1.2`` ``-Python-2.7.12`` ``intel/2016b`` -``2.1.3`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.1.3`` ``-Python-2.7.13`` ``intel/2017a`` -``2.1.3`` ``-Python-3.6.1`` ``intel/2017a`` -``2.2.0`` ``-Python-2.7.13-HDF5-1.8.18`` ``intel/2017a`` -``2.2.0`` ``-Python-2.7.13-HDF5-HDF`` ``intel/2017a`` -``2.2.0`` ``-Python-3.6.1`` ``intel/2017a`` -``2.2.2`` ``-Python-2.7.14`` ``intel/2017b`` -``2.2.2`` ``-Python-2.7.14-HDF5-1.8.19`` ``intel/2017b`` +``2.0.2`` ``foss/2016a``, ``intel/2016a`` +``2.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` +``2.1.1`` ``foss/2016a`` +``2.1.1`` ``-Python-2.7.12`` ``intel/2016b`` +``2.1.2`` ``-Python-2.7.12`` ``intel/2016b`` +``2.1.3`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``2.1.3`` ``-Python-2.7.13`` ``intel/2017a`` +``2.1.3`` ``-Python-3.6.1`` ``intel/2017a`` +``2.2.0`` ``-Python-2.7.13-HDF5-1.8.18`` ``intel/2017a`` +``2.2.0`` ``-Python-2.7.13-HDF5-HDF`` ``intel/2017a`` +``2.2.0`` ``-Python-3.6.1`` ``intel/2017a`` +``2.2.2`` ``-Python-2.7.14`` ``intel/2017b`` +``2.2.2`` ``-Python-2.7.14-HDF5-1.8.19`` ``intel/2017b`` ``2.2.3`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``2.2.3`` ``-Python-2.7.15`` ``foss/2018b`` -``2.2.3`` ``-Python-3.6.3`` ``foss/2017b`` -``2.2.3`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` -``2.2.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.0.0`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` -``3.0.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.0.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``3.0.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``3.2.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``3.3.0`` ``foss/2021a`` -``3.3.2`` ``foss/2021b`` -``3.5.0`` ``foss/2022a`` +``2.2.3`` ``-Python-2.7.15`` ``foss/2018b`` +``2.2.3`` ``-Python-3.6.3`` ``foss/2017b`` +``2.2.3`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` +``2.2.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.0.0`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` +``3.0.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.0.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``3.0.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``3.2.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``3.3.0`` ``foss/2021a`` +``3.3.2`` ``foss/2021b`` +``3.5.0`` ``foss/2022a`` ========= ============================== ================================================================ @@ -14540,24 +15125,24 @@ The GNU Project Debugger *homepage*: https://www.gnu.org/software/gdb/gdb.html ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== -``7.8.2`` ``GCC/4.9.2`` -``7.9`` ``GCC/4.9.2`` +``7.8.2`` ``GCC/4.9.2`` +``7.9`` ``GCC/4.9.2`` ``7.10.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``7.11`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``7.11.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``8.0.1`` ``-Python-2.7.14`` ``foss/2017b`` -``8.0.1`` ``-Python-3.6.3`` ``foss/2017b`` -``8.1`` ``-Python-2.7.14`` ``foss/2018a`` -``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` -``8.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``9.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``10.1`` ``GCCcore/10.2.0`` -``10.2`` ``GCCcore/10.3.0`` -``10.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``11.1`` ``GCCcore/11.2.0`` -``12.1`` ``GCCcore/11.3.0`` +``8.0.1`` ``-Python-2.7.14`` ``foss/2017b`` +``8.0.1`` ``-Python-3.6.3`` ``foss/2017b`` +``8.1`` ``-Python-2.7.14`` ``foss/2018a`` +``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` +``8.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``9.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``10.1`` ``GCCcore/10.2.0`` +``10.2`` ``GCCcore/10.3.0`` +``10.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``11.1`` ``GCCcore/11.2.0`` +``12.1`` ``GCCcore/11.3.0`` ========== ================== =============================== @@ -14571,7 +15156,7 @@ Browser-based frontend to gdb (gnu debugger). Add breakpoints, view the stack, v *homepage*: https://gdbgui.com ============ ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ================= ``0.13.1.2`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ============ ================= ================= @@ -14587,9 +15172,9 @@ GNU dbm (or GDBM, for short) is a library of database functions that use extensi *homepage*: https://www.gnu.org.ua/software/gdbm/gdbm.html ========== ================== -version toolchain +version toolchain ========== ================== -``1.18.1`` ``foss/2020a`` +``1.18.1`` ``foss/2020a`` ``1.21`` ``GCCcore/10.2.0`` ========== ================== @@ -14604,12 +15189,12 @@ The gdc-client provides several convenience functions over the GDC API which pr *homepage*: https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``1.0.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.0.1`` ``-Python-2.7.12`` ``intel/2016b`` ``1.3.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` -``1.3.0`` ``-Python-2.7.15`` ``foss/2018b`` -``1.6.0`` ``GCCcore/10.2.0`` +``1.3.0`` ``-Python-2.7.15`` ``foss/2018b`` +``1.6.0`` ``GCCcore/10.2.0`` ========= ================== =============================== @@ -14623,7 +15208,7 @@ Easy to use C API, high performance library to create charts and graphs in PNG, *homepage*: http://users.fred.net/brv/chart ============= ================= -version toolchain +version toolchain ============= ================= ``0.11.5dev`` ``GCCcore/8.2.0`` ============= ================= @@ -14638,15 +15223,16 @@ Grassroots DICOM: Cross-platform DICOM implementation *homepage*: https://sourceforge.net/projects/gdcm -========= ===================================== -version toolchain -========= ===================================== -``2.8.8`` ``GCCcore/6.4.0`` -``2.8.9`` ``GCCcore/7.3.0`` -``3.0.4`` ``GCCcore/8.2.0`` -``3.0.5`` ``GCCcore/8.3.0`` -``3.0.8`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -========= ===================================== +========== ===================================== +version toolchain +========== ===================================== +``2.8.8`` ``GCCcore/6.4.0`` +``2.8.9`` ``GCCcore/7.3.0`` +``3.0.4`` ``GCCcore/8.2.0`` +``3.0.5`` ``GCCcore/8.3.0`` +``3.0.8`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.0.20`` ``GCCcore/11.3.0`` +========== ===================================== .. _list_software_GDGraph_637: @@ -14659,10 +15245,10 @@ GDGraph is a Perl package to generate charts *homepage*: https://metacpan.org/release/GDGraph ======== ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================ =============== ``1.54`` ``-Perl-5.26.1`` ``intel/2018a`` -``1.54`` ``-Perl-5.28.0`` ``foss/2018b`` +``1.54`` ``-Perl-5.28.0`` ``foss/2018b`` ======== ================ =============== @@ -14676,7 +15262,7 @@ The gdist module is a Cython interface to a C++ library (http://code.google.com/ *homepage*: https://pypi.python.org/pypi/gdist ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.0.3`` ``-Python-2.7.11`` ``intel/2016a`` ========= ================== =============== @@ -14692,20 +15278,21 @@ The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It *homepage*: https://docs.gtk.org/gdk-pixbuf/ =========== ==================================================================================== -version toolchain +version toolchain =========== ==================================================================================== -``2.32.3`` ``intel/2016a`` -``2.35.1`` ``foss/2016a``, ``intel/2016a`` -``2.36.0`` ``foss/2016b``, ``intel/2016b`` -``2.36.8`` ``intel/2017a`` -``2.36.10`` ``intel/2017a`` +``2.32.3`` ``intel/2016a`` +``2.35.1`` ``foss/2016a``, ``intel/2016a`` +``2.36.0`` ``foss/2016b``, ``intel/2016b`` +``2.36.8`` ``intel/2017a`` +``2.36.10`` ``intel/2017a`` ``2.36.11`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2018b``, ``intel/2017b``, ``intel/2018a`` -``2.36.12`` ``foss/2018b``, ``fosscuda/2018b`` -``2.38.1`` ``GCCcore/8.2.0`` -``2.38.2`` ``GCCcore/8.3.0`` -``2.40.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``2.42.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``2.42.8`` ``GCCcore/11.3.0`` +``2.36.12`` ``foss/2018b``, ``fosscuda/2018b`` +``2.38.1`` ``GCCcore/8.2.0`` +``2.38.2`` ``GCCcore/8.3.0`` +``2.40.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.42.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.42.8`` ``GCCcore/11.3.0`` +``2.42.10`` ``GCCcore/12.2.0`` =========== ==================================================================================== @@ -14718,15 +15305,15 @@ A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. *homepage*: https://github.com/NVIDIA/gdrcopy -======= ================ ====================================== -version versionsuffix toolchain -======= ================ ====================================== -``2.1`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` -``2.1`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` -``2.1`` ``-CUDA-11.2.1`` ``GCCcore/10.2.0`` +======= ================ ========================================================== +version versionsuffix toolchain +======= ================ ========================================================== +``2.1`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` +``2.1`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` +``2.1`` ``-CUDA-11.2.1`` ``GCCcore/10.2.0`` ``2.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.3`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -======= ================ ====================================== +``2.3`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +======= ================ ========================================================== .. _list_software_Geant4_547: @@ -14739,21 +15326,21 @@ Geant4 is a toolkit for the simulation of the passage of particles through matte *homepage*: https://geant4.cern.ch ============= ================================================================ -version toolchain +version toolchain ============= ================================================================ -``9.5.p02`` ``intel/2016a`` -``9.6.p04`` ``intel/2016a`` -``10.01.p03`` ``intel/2016a`` -``10.02.p01`` ``intel/2016a`` -``10.03.p03`` ``foss/2017b``, ``intel/2017b`` -``10.04`` ``intel/2017b`` +``9.5.p02`` ``intel/2016a`` +``9.6.p04`` ``intel/2016a`` +``10.01.p03`` ``intel/2016a`` +``10.02.p01`` ``intel/2016a`` +``10.03.p03`` ``foss/2017b``, ``intel/2017b`` +``10.04`` ``intel/2017b`` ``10.5`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018b`` -``10.6`` ``foss/2019b`` -``10.6.2`` ``foss/2020a`` -``10.7.1`` ``GCC/10.2.0``, ``GCC/11.2.0`` -``11.0.0`` ``GCC/11.2.0`` -``11.0.1`` ``GCC/11.2.0`` -``11.0.2`` ``GCC/11.2.0`` +``10.6`` ``foss/2019b`` +``10.6.2`` ``foss/2020a`` +``10.7.1`` ``GCC/10.2.0``, ``GCC/11.2.0`` +``11.0.0`` ``GCC/11.2.0`` +``11.0.1`` ``GCC/11.2.0`` +``11.0.2`` ``GCC/11.2.0`` ============= ================================================================ @@ -14767,7 +15354,7 @@ Datasets for Geant4. *homepage*: https://geant4.cern.ch/ ============ ========== -version toolchain +version toolchain ============ ========== ``20201103`` ``system`` ``20210510`` ``system`` @@ -14784,7 +15371,7 @@ Benchmark Suite for Heterogenuous FFT Implementations *homepage*: https://github.com/mpicbg-scicomp/gearshifft ========= ============== -version toolchain +version toolchain ========= ============== ``0.4.0`` ``foss/2019a`` ========= ============== @@ -14800,7 +15387,7 @@ GEGL (Generic Graphics Library) is a data flow based image processing framework, *homepage*: https://www.gegl.org ========== ================== -version toolchain +version toolchain ========== ================== ``0.4.30`` ``GCCcore/10.3.0`` ========== ================== @@ -14816,7 +15403,7 @@ Next-generation sequencing platforms (Illumina/Solexa, ABI/SOLiD, etc.) call f *homepage*: http://algorithms.cnag.cat/wiki/The_GEM_library =================== =============================== ========== -version versionsuffix toolchain +version versionsuffix toolchain =================== =============================== ========== ``20130406-045632`` ``_pre-release-3_Linux-x86_64`` ``system`` =================== =============================== ========== @@ -14832,11 +15419,11 @@ Genome-wide Efficient Mixed Model Association *homepage*: https://github.com/genetics-statistics/GEMMA ========== ============================== -version toolchain +version toolchain ========== ============================== ``0.97`` ``foss/2016b``, ``foss/2017a`` -``0.98.1`` ``foss/2018b`` -``0.98.5`` ``foss/2021b`` +``0.98.1`` ``foss/2018b`` +``0.98.5`` ``foss/2021b`` ========== ============================== @@ -14850,7 +15437,7 @@ Gemmi is a library, accompanied by a set of programs, developed primarily for *homepage*: https://gemmi.readthedocs.io/ ========= ================== -version toolchain +version toolchain ========= ================== ``0.4.5`` ``GCCcore/10.2.0`` ========= ================== @@ -14866,7 +15453,7 @@ This is a bundled install of many software packages for doing variant detection *homepage*: https://nyuad-cgsb.github.io/variant_detection/public/index.html ======= ========== -version toolchain +version toolchain ======= ========== ``1.0`` ``system`` ======= ========== @@ -14882,11 +15469,12 @@ Eukaryotic gene prediction suite with automatic training *homepage*: http://exon.gatech.edu/GeneMark ======== ================== -version toolchain +version toolchain ======== ================== -``4.38`` ``GCCcore/8.2.0`` -``4.57`` ``GCCcore/8.3.0`` +``4.38`` ``GCCcore/8.2.0`` +``4.57`` ``GCCcore/8.3.0`` ``4.65`` ``GCCcore/10.2.0`` +``4.71`` ``GCCcore/11.2.0`` ======== ================== @@ -14900,7 +15488,7 @@ Gengetopt is a tool to write command line option parsing code for C programs. *homepage*: https://www.gnu.org/software/gengetopt/gengetopt.html ======== ========================================================= -version toolchain +version toolchain ======== ========================================================= ``2.23`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ======== ========================================================= @@ -14916,7 +15504,7 @@ Genome Profiler (GeP) is a program to perform whole-genome multilocus sequence *homepage*: https://sourceforge.net/projects/genomeprofiler/ ======= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================ ============== ``2.1`` ``-Perl-5.24.0`` ``foss/2016b`` ======= ================ ============== @@ -14932,7 +15520,7 @@ GenomeMapper is a short read mapping tool designed for accurate read alignments. *homepage*: https://1001genomes.org/software/genomemapper_singleref.html ========= ============== -version toolchain +version toolchain ========= ============== ``0.4.4`` ``foss/2016a`` ========= ============== @@ -14948,7 +15536,7 @@ A toolkit for performing set operations - union, intersection and complement - o *homepage*: https://github.com/bioinfo-ut/GenomeTester4 ======= =============== -version toolchain +version toolchain ======= =============== ``4.0`` ``intel/2018a`` ======= =============== @@ -14964,7 +15552,7 @@ GenomeThreader is a software tool to compute gene structure predictions. *homepage*: http://genomethreader.org ========= ======================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ======================= ========== ``1.7.1`` ``-Linux_x86_64-64bit`` ``system`` ``1.7.3`` ``-Linux_x86_64-64bit`` ``system`` @@ -14981,13 +15569,13 @@ A comprehensive software library for efficient processing of structured genome a *homepage*: http://genometools.org ========== ================== ============================================ -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ============================================ -``1.5.10`` ``foss/2018b`` -``1.5.10`` ``-Python-2.7.15`` ``foss/2018b`` +``1.5.10`` ``foss/2018b`` +``1.5.10`` ``-Python-2.7.15`` ``foss/2018b`` ``1.6.1`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0`` -``1.6.1`` ``-Python-2.7.16`` ``GCC/8.3.0`` -``1.6.2`` ``GCC/10.3.0`` +``1.6.1`` ``-Python-2.7.16`` ``GCC/8.3.0`` +``1.6.2`` ``GCC/10.3.0`` ========== ================== ============================================ @@ -15001,7 +15589,7 @@ SDK for GPU accelerated genome assembly and analysis *homepage*: https://github.com/clara-parabricks/GenomeWorks ============= ================== -version toolchain +version toolchain ============= ================== ``2021.02.2`` ``fosscuda/2020b`` ============= ================== @@ -15017,7 +15605,7 @@ The Genotype Harmonizer is an easy to use command-line tool that allows harmoniz *homepage*: https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer ========== ================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ========== ``1.4.14`` ``-Java-1.7.0_80`` ``system`` ========== ================== ========== @@ -15033,7 +15621,7 @@ Genozip is a compressor for genomic files - it compresses FASTQ, SAM/BAM/CRAM, V *homepage*: https://genozip.com ========== ================== -version toolchain +version toolchain ========== ================== ``13.0.5`` ``GCCcore/11.2.0`` ========== ================== @@ -15049,10 +15637,11 @@ Gensim is a Python library for topic modelling, document indexing and similarity *homepage*: https://radimrehurek.com/gensim ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== -``0.13.2`` ``-Python-2.7.11`` ``foss/2016a`` +``0.13.2`` ``-Python-2.7.11`` ``foss/2016a`` ``3.8.3`` ``foss/2020b``, ``intel/2020b`` +``4.2.0`` ``foss/2021a`` ========== ================== =============================== @@ -15066,7 +15655,7 @@ Tool to convert geopandas vector data into rasterized xarray data. *homepage*: https://corteva.github.io/geocube/latest/ ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.0.14`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================= ============== @@ -15082,14 +15671,15 @@ GeoPandas is a project to add support for geographic data to pandas objects. It *homepage*: https://github.com/geopandas/geopandas ========== ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================== ``0.7.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``0.8.0`` ``-Python-3.7.2`` ``foss/2019a`` -``0.8.1`` ``-Python-3.7.4`` ``intel/2019b`` -``0.8.1`` ``-Python-3.8.2`` ``foss/2020a`` -``0.10.2`` ``foss/2021a`` -``0.11.0`` ``foss/2021b`` +``0.8.0`` ``-Python-3.7.2`` ``foss/2019a`` +``0.8.1`` ``-Python-3.7.4`` ``intel/2019b`` +``0.8.1`` ``-Python-3.8.2`` ``foss/2020a`` +``0.10.2`` ``foss/2021a`` +``0.11.0`` ``foss/2021b`` +``0.12.2`` ``foss/2022a`` ========== ================= ================================== @@ -15103,9 +15693,9 @@ geopy is a Python client for several popular geocoding web services. geopy makes *homepage*: https://geopy.readthedocs.io/en/stable/ ========== ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================== -``1.11.0`` ``-Python-3.6.1`` ``intel/2017a`` +``1.11.0`` ``-Python-3.6.1`` ``intel/2017a`` ``2.1.0`` ``GCCcore/10.2.0`` ========== ================= ================== @@ -15120,7 +15710,7 @@ Georges the lemur opinionated particle accelerator modeling Python package. Also *homepage*: https://github.com/ULB-Metronu/georges ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``2019.2`` ``foss/2021a`` ``2019.2`` ``-Python-3.7.4`` ``foss/2019b`` @@ -15137,26 +15727,26 @@ GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (J *homepage*: https://trac.osgeo.org/geos ========== ================== ======================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ======================================================================= -``3.5.0`` ``-Python-2.7.11`` ``intel/2016a`` -``3.5.0`` ``-Python-2.7.12`` ``intel/2016b`` -``3.6.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.6.1`` ``-Python-2.7.13`` ``intel/2017a`` -``3.6.1`` ``-Python-3.6.1`` ``intel/2017a`` -``3.6.2`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``3.6.2`` ``-Python-2.7.15`` ``foss/2018b`` -``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` -``3.6.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.01`` -``3.6.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` -``3.6.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.7.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` -``3.7.2`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.8.0`` ``GCC/8.3.0`` -``3.8.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``3.8.1`` ``-Python-3.8.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` +``3.5.0`` ``-Python-2.7.11`` ``intel/2016a`` +``3.5.0`` ``-Python-2.7.12`` ``intel/2016b`` +``3.6.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.6.1`` ``-Python-2.7.13`` ``intel/2017a`` +``3.6.1`` ``-Python-3.6.1`` ``intel/2017a`` +``3.6.2`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``3.6.2`` ``-Python-2.7.15`` ``foss/2018b`` +``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` +``3.6.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.01`` +``3.6.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` +``3.6.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.7.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` +``3.7.2`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``3.8.0`` ``GCC/8.3.0`` +``3.8.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``3.8.1`` ``-Python-3.8.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` ``3.9.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304`` -``3.10.3`` ``GCC/11.3.0`` +``3.10.3`` ``GCC/11.3.0`` ========== ================== ======================================================================= @@ -15170,7 +15760,7 @@ Gerris is a Free Software program for the solution of the partial *homepage*: http://gfs.sourceforge.net/wiki/index.php/Main_Page ============ ============== -version toolchain +version toolchain ============ ============== ``20131206`` ``foss/2017b`` ============ ============== @@ -15186,7 +15776,7 @@ GETORB software package contains programs to handle the orbital data records (OD *homepage*: http://www.deos.tudelft.nl/ers/precorbs/tools/getorb_pack.shtml ========= =============== -version toolchain +version toolchain ========= =============== ``2.3.2`` ``intel/2017a`` ========= =============== @@ -15202,7 +15792,7 @@ This toolkit assemblies organelle genome from genomic skimming data. *homepage*: https://github.com/Kinggerm/GetOrganelle ============== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================= ============== ``1.7.2`` ``-Python-3.8.2`` ``foss/2020a`` ``1.7.4-pre2`` ``foss/2020b`` @@ -15221,17 +15811,18 @@ GNU 'gettext' is an important step for the GNU Translation Project, as it is an *homepage*: https://www.gnu.org/software/gettext/ ============ ================== =================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =================================================================================================== -``0.18.2`` ``system`` -``0.19.4`` ``GCC/4.9.2``, ``system`` -``0.19.6`` ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``system`` -``0.19.7`` ``foss/2016a``, ``intel/2016a``, ``system`` +``0.18.2`` ``system`` +``0.19.4`` ``GCC/4.9.2``, ``system`` +``0.19.6`` ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``system`` +``0.19.7`` ``foss/2016a``, ``intel/2016a``, ``system`` ``0.19.8`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016.04``, ``foss/2016b``, ``intel/2016b``, ``system`` -``0.19.8.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` -``0.19.8.1`` ``-libxml2-2.9.7`` ``GCCcore/6.4.0`` -``0.20.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` -``0.21`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` +``0.19.8.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` +``0.19.8.1`` ``-libxml2-2.9.7`` ``GCCcore/6.4.0`` +``0.20.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +``0.21`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` +``0.21.1`` ``GCCcore/12.2.0``, ``system`` ============ ================== =================================================================================================== @@ -15245,7 +15836,7 @@ gexiv2 is a GObject wrapper around the Exiv2 photo metadata library. *homepage*: https://wiki.gnome.org/Projects/gexiv2 ========== ================== -version toolchain +version toolchain ========== ================== ``0.12.2`` ``GCCcore/10.3.0`` ========== ================== @@ -15261,9 +15852,10 @@ GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BL *homepage*: (none) ========= ========== -version toolchain +version toolchain ========= ========== ``2022a`` ``system`` +``2022b`` ``system`` ========= ========== @@ -15277,13 +15869,13 @@ GffCompare provides classification and reference annotation mapping and matchin *homepage*: https://ccb.jhu.edu/software/stringtie/gffcompare.shtml ========== ==================================== -version toolchain +version toolchain ========== ==================================== -``0.10.1`` ``foss/2016b`` -``0.10.6`` ``GCCcore/7.3.0`` +``0.10.1`` ``foss/2016b`` +``0.10.6`` ``GCCcore/7.3.0`` ``0.11.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.12.2`` ``GCC/10.3.0`` -``0.12.6`` ``GCC/11.2.0`` +``0.12.2`` ``GCC/10.3.0`` +``0.12.6`` ``GCC/11.2.0`` ========== ==================================== @@ -15297,11 +15889,11 @@ GFF/GTF parsing utility providing format conversions, region filtering, FASTA se *homepage*: https://github.com/gpertea/gffread ========== ====================================== -version toolchain +version toolchain ========== ====================================== -``0.9.12`` ``foss/2016b`` -``0.10.6`` ``GCCcore/7.3.0`` -``0.11.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.9.12`` ``foss/2016b`` +``0.10.6`` ``GCCcore/7.3.0`` +``0.11.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``0.12.7`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ====================================== @@ -15316,10 +15908,10 @@ The gflags package contains a C++ library that implements commandline flags proc *homepage*: https://github.com/gflags/gflags ========= =================================================================================================================== -version toolchain +version toolchain ========= =================================================================================================================== -``2.1.2`` ``foss/2016a`` -``2.2.1`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` +``2.1.2`` ``foss/2016a`` +``2.2.1`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` ``2.2.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= =================================================================================================================== @@ -15334,7 +15926,7 @@ Generalized fold change for ranking differentially expressed genes from RNA-seq *homepage*: http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html ========= =============== -version toolchain +version toolchain ========= =============== ``1.1.4`` ``intel/2016a`` ========= =============== @@ -15349,11 +15941,12 @@ gh is GitHub on the command line. *homepage*: https://github.com/cli/cli -========= ========== -version toolchain -========= ========== -``1.3.1`` ``system`` -========= ========== +========== ========== +version toolchain +========== ========== +``1.3.1`` ``system`` +``2.20.2`` ``system`` +========== ========== .. _list_software_GHC_210: @@ -15366,7 +15959,7 @@ The Glorious/Glasgow Haskell Compiler *homepage*: https://haskell.org/ghc/ ========== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ========== ``6.12.3`` ``system`` ``8.6.5`` ``-x86_64`` ``system`` @@ -15383,21 +15976,22 @@ Ghostscript is a versatile processor for PostScript data with the ability to ren *homepage*: https://ghostscript.com ========== ================== ================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================================================== -``9.19`` ``intel/2016a``, ``intel/2016b`` -``9.20`` ``foss/2016b``, ``intel/2016b`` -``9.21`` ``intel/2017a`` +``9.19`` ``intel/2016a``, ``intel/2016b`` +``9.20`` ``foss/2016b``, ``intel/2016b`` +``9.21`` ``intel/2017a`` ``9.22`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` -``9.22`` ``-cairo-1.14.12`` ``GCCcore/6.4.0`` -``9.23`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``9.23`` ``-cairo-1.14.12`` ``GCCcore/6.4.0`` -``9.27`` ``GCCcore/8.2.0`` -``9.50`` ``GCCcore/8.3.0`` -``9.52`` ``GCCcore/9.3.0`` -``9.53.3`` ``GCCcore/10.2.0`` -``9.54.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``9.56.1`` ``GCCcore/11.3.0`` +``9.22`` ``-cairo-1.14.12`` ``GCCcore/6.4.0`` +``9.23`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``9.23`` ``-cairo-1.14.12`` ``GCCcore/6.4.0`` +``9.27`` ``GCCcore/8.2.0`` +``9.50`` ``GCCcore/8.3.0`` +``9.52`` ``GCCcore/9.3.0`` +``9.53.3`` ``GCCcore/10.2.0`` +``9.54.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``9.56.1`` ``GCCcore/11.3.0`` +``10.0.0`` ``GCCcore/12.2.0`` ========== ================== ================================================== @@ -15411,7 +16005,7 @@ Gibbs2 is a program for the calculation of thermodynamic properties in periodic *homepage*: https://aoterodelaroza.github.io/gibbs2/ ======= ============== -version toolchain +version toolchain ======= ============== ``1.0`` ``GCC/10.3.0`` ======= ============== @@ -15427,9 +16021,9 @@ giflib is a library for reading and writing gif images. It is API and ABI compat *homepage*: http://giflib.sourceforge.net/ ========= ==================================================================================================================== -version toolchain +version toolchain ========= ==================================================================================================================== -``5.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``5.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``5.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ==================================================================================================================== @@ -15444,9 +16038,9 @@ Gifsicle is a command-line tool for creating, editing, and getting information *homepage*: https://github.com/kohler/gifsicle ======== ================== -version toolchain +version toolchain ======== ================== -``1.92`` ``GCCcore/8.2.0`` +``1.92`` ``GCCcore/8.2.0`` ``1.93`` ``GCCcore/11.3.0`` ======== ================== @@ -15461,7 +16055,7 @@ The GIMIC program calculates magnetically induced currents in molecules. You ne *homepage*: http://gimic.readthedocs.io ============== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================== =============== ``2018.04.20`` ``-Python-2.7.14`` ``intel/2018a`` ============== ================== =============== @@ -15477,7 +16071,7 @@ GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI and MKL *homepage*: (none) ========== ========== -version toolchain +version toolchain ========== ========== ``2.11.5`` ``system`` ``2017a`` ``system`` @@ -15495,7 +16089,7 @@ GIMP is a cross-platform image editor available for GNU/Linux, OS X, Windows and *homepage*: https://www.gimp.org =========== ============== -version toolchain +version toolchain =========== ============== ``2.10.24`` ``GCC/10.3.0`` =========== ============== @@ -15511,7 +16105,7 @@ GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI. *homepage*: (none) ========== ========== -version toolchain +version toolchain ========== ========== ``2.11.5`` ``system`` ``2017a`` ``system`` @@ -15531,7 +16125,7 @@ GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, *homepage*: (none) ========= ========== -version toolchain +version toolchain ========= ========== ``2017b`` ``system`` ========= ========== @@ -15547,10 +16141,10 @@ GIMPS: Great Internet Mersenne Prime Search; it can be useful for limited stres *homepage*: http://www.mersenne.org/ =================== ============= -version toolchain +version toolchain =================== ============= ``p95v279`` ``GCC/4.8.2`` -``p95v279.linux64`` ``system`` +``p95v279.linux64`` ``system`` =================== ============= @@ -15564,7 +16158,7 @@ GNU Compiler Collection (GCC) based compiler toolchain, including IntelMPI for *homepage*: (none) ========= ========== -version toolchain +version toolchain ========= ========== ``2017b`` ``system`` ``2018a`` ``system`` @@ -15581,7 +16175,7 @@ GCC based compiler toolchain __with CUDA support__, and including IntelMPI for *homepage*: (none) ========= ========== -version toolchain +version toolchain ========= ========== ``2017b`` ``system`` ========= ========== @@ -15597,26 +16191,27 @@ Git is a free and open source distributed version control system designed to han *homepage*: http://git-scm.com/ =========== ============= ==================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ============= ==================================== -``1.8.5.6`` ``GCC/4.9.2`` -``2.2.2`` ``GCC/4.9.2`` -``2.4.1`` ``GCC/4.9.2`` -``2.8.0`` ``foss/2016a`` -``2.12.2`` ``foss/2016b`` -``2.13.1`` ``foss/2016b`` -``2.14.1`` ``GCCcore/6.4.0`` -``2.16.1`` ``foss/2018a`` -``2.18.0`` ``GCCcore/7.3.0`` -``2.19.1`` ``GCCcore/7.3.0`` -``2.21.0`` ``GCCcore/8.2.0`` -``2.21.0`` ``-nodocs`` ``GCCcore/8.2.0`` -``2.23.0`` ``GCCcore/8.3.0`` +``1.8.5.6`` ``GCC/4.9.2`` +``2.2.2`` ``GCC/4.9.2`` +``2.4.1`` ``GCC/4.9.2`` +``2.8.0`` ``foss/2016a`` +``2.12.2`` ``foss/2016b`` +``2.13.1`` ``foss/2016b`` +``2.14.1`` ``GCCcore/6.4.0`` +``2.16.1`` ``foss/2018a`` +``2.18.0`` ``GCCcore/7.3.0`` +``2.19.1`` ``GCCcore/7.3.0`` +``2.21.0`` ``GCCcore/8.2.0`` +``2.21.0`` ``-nodocs`` ``GCCcore/8.2.0`` +``2.23.0`` ``GCCcore/8.3.0`` ``2.23.0`` ``-nodocs`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.28.0`` ``-nodocs`` ``GCCcore/10.2.0`` -``2.32.0`` ``-nodocs`` ``GCCcore/10.3.0`` -``2.33.1`` ``-nodocs`` ``GCCcore/11.2.0`` -``2.36.0`` ``-nodocs`` ``GCCcore/11.3.0`` +``2.28.0`` ``-nodocs`` ``GCCcore/10.2.0`` +``2.32.0`` ``-nodocs`` ``GCCcore/10.3.0`` +``2.33.1`` ``-nodocs`` ``GCCcore/11.2.0`` +``2.36.0`` ``-nodocs`` ``GCCcore/11.3.0`` +``2.38.1`` ``-nodocs`` ``GCCcore/12.2.0`` =========== ============= ==================================== @@ -15630,7 +16225,7 @@ Extra useful scripts for git *homepage*: https://github.com/tj/git-extras ========= ============== -version toolchain +version toolchain ========= ============== ``5.1.0`` ``foss/2016a`` ========= ============== @@ -15646,7 +16241,7 @@ Git Large File Storage (LFS) replaces large files such as audio samples, videos *homepage*: https://git-lfs.github.com ========== ========== -version toolchain +version toolchain ========== ========== ``1.1.1`` ``system`` ``2.7.1`` ``system`` @@ -15665,17 +16260,17 @@ GitPython is a python library used to interact with Git repositories *homepage*: https://github.com/gitpython-developers/GitPython ========== ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============================== ``2.1.11`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``2.1.15`` ``system`` -``3.0.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``3.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``3.1.9`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``3.1.14`` ``GCCcore/10.2.0`` -``3.1.18`` ``GCCcore/10.3.0`` -``3.1.24`` ``GCCcore/11.2.0`` -``3.1.27`` ``GCCcore/11.3.0`` +``2.1.15`` ``system`` +``3.0.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``3.1.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``3.1.9`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``3.1.14`` ``GCCcore/10.2.0`` +``3.1.18`` ``GCCcore/10.3.0`` +``3.1.24`` ``GCCcore/11.2.0`` +``3.1.27`` ``GCCcore/11.3.0`` ========== ================= =============================== @@ -15689,7 +16284,7 @@ C++ library for arithmetic and algebraic computations *homepage*: http://givaro.forge.imag.fr/ ========= ============== -version toolchain +version toolchain ========= ============== ``4.0.1`` ``foss/2016a`` ========= ============== @@ -15705,7 +16300,7 @@ Giza is an open, lightweight scientific plotting library built on top of cairo *homepage*: https://danieljprice.github.io/giza/ ========= ============== -version toolchain +version toolchain ========= ============== ``1.1.0`` ``foss/2018b`` ========= ============== @@ -15721,12 +16316,12 @@ GL2PS: an OpenGL to PostScript printing library *homepage*: https://www.geuz.org/gl2ps/ ========= ================ ==================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ==================================================================================================================================== -``1.3.9`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``1.3.9`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` +``1.3.9`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``1.3.9`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` ``1.4.0`` ``GCCcore/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``1.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``1.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ========= ================ ==================================================================================================================================== @@ -15740,12 +16335,12 @@ Glade is a RAD tool to enable quick & easy development of user interfaces for th *homepage*: https://glade.gnome.org/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``3.8.5`` ``-Python-2.7.11`` ``intel/2016a`` ``3.8.5`` ``-Python-2.7.14`` ``intel/2017b`` ``3.8.6`` ``-Python-2.7.14`` ``intel/2018a`` -``3.8.6`` ``-Python-2.7.15`` ``foss/2018b`` +``3.8.6`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== =============== @@ -15759,12 +16354,12 @@ The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C *homepage*: https://github.com/nigels-com/glew ========= ============= =============================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= =============================================================================================================== ``2.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b`` -``2.2.0`` ``-egl`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` -``2.2.0`` ``-glx`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` -``2.2.0`` ``-osmesa`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` +``2.2.0`` ``-egl`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.2.0`` ``-glx`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` +``2.2.0`` ``-osmesa`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` ========= ============= =============================================================================================================== @@ -15778,13 +16373,13 @@ GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan *homepage*: https://www.glfw.org ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``3.2.1`` ``intel/2018a`` -``3.3.2`` ``GCCcore/9.3.0`` -``3.3.3`` ``GCCcore/10.2.0`` +``3.2.1`` ``intel/2018a`` +``3.3.2`` ``GCCcore/9.3.0`` +``3.3.3`` ``GCCcore/10.2.0`` ``3.3.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``3.3.8`` ``GCCcore/11.3.0`` +``3.3.8`` ``GCCcore/11.3.0`` ========= ====================================== @@ -15798,24 +16393,25 @@ GLib is one of the base libraries of the GTK+ project *homepage*: https://www.gtk.org/ ========== ================================================= -version toolchain +version toolchain ========== ================================================= -``2.42.1`` ``GCC/4.9.2`` -``2.44.0`` ``GCC/4.9.2`` +``2.42.1`` ``GCC/4.9.2`` +``2.44.0`` ``GCC/4.9.2`` ``2.47.5`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``2.48.0`` ``foss/2016a``, ``intel/2016a`` -``2.49.5`` ``foss/2016b``, ``intel/2016b`` -``2.52.0`` ``foss/2017a``, ``intel/2017a`` -``2.53.5`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``2.54.2`` ``GCCcore/6.4.0`` -``2.54.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.60.1`` ``GCCcore/8.2.0`` -``2.62.0`` ``GCCcore/8.3.0`` -``2.64.1`` ``GCCcore/9.3.0`` -``2.66.1`` ``GCCcore/10.2.0`` -``2.68.2`` ``GCCcore/10.3.0`` -``2.69.1`` ``GCCcore/11.2.0`` -``2.72.1`` ``GCCcore/11.3.0`` +``2.48.0`` ``foss/2016a``, ``intel/2016a`` +``2.49.5`` ``foss/2016b``, ``intel/2016b`` +``2.52.0`` ``foss/2017a``, ``intel/2017a`` +``2.53.5`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``2.54.2`` ``GCCcore/6.4.0`` +``2.54.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.60.1`` ``GCCcore/8.2.0`` +``2.62.0`` ``GCCcore/8.3.0`` +``2.64.1`` ``GCCcore/9.3.0`` +``2.66.1`` ``GCCcore/10.2.0`` +``2.68.2`` ``GCCcore/10.3.0`` +``2.69.1`` ``GCCcore/11.2.0`` +``2.72.1`` ``GCCcore/11.3.0`` +``2.75.0`` ``GCCcore/12.2.0`` ========== ================================================= @@ -15828,12 +16424,12 @@ Network extensions for GLib *homepage*: https://gitlab.gnome.org/GNOME/glib-networking -========== ================== -version toolchain -========== ================== +========== ====================================== +version toolchain +========== ====================================== ``2.68.1`` ``GCCcore/10.3.0`` -``2.72.1`` ``GCCcore/11.2.0`` -========== ================== +``2.72.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========== ====================================== .. _list_software_glibc_513: @@ -15846,7 +16442,7 @@ The GNU C Library project provides the core libraries for the GNU system and GNU *homepage*: https://www.gnu.org/software/libc/ ======== ================= -version toolchain +version toolchain ======== ================= ``2.17`` ``GCCcore/6.4.0`` ``2.26`` ``GCCcore/6.4.0`` @@ -15864,10 +16460,10 @@ C++ bindings for Glib *homepage*: https://www.gtk.org/ ========== ======================================================= -version toolchain +version toolchain ========== ======================================================= ``2.49.7`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2.66.4`` ``GCCcore/10.3.0`` +``2.66.4`` ``GCCcore/10.3.0`` ========== ======================================================= @@ -15881,7 +16477,7 @@ Glimmer is a system for finding genes in microbial DNA, especially the genomes *homepage*: http://ccb.jhu.edu/software/glimmer/index.shtml ========= ============================== -version toolchain +version toolchain ========= ============================== ``3.02b`` ``foss/2016b``, ``foss/2018b`` ========= ============================== @@ -15897,10 +16493,10 @@ GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. Alt *homepage*: https://ccb.jhu.edu/software/glimmerhmm ========== ============================== -version toolchain +version toolchain ========== ============================== ``3.0.4`` ``foss/2016b``, ``foss/2018b`` -``3.0.4c`` ``GCC/10.2.0``, ``GCC/8.3.0`` +``3.0.4c`` ``GCC/10.2.0``, ``GCC/8.3.0`` ========== ============================== @@ -15913,14 +16509,14 @@ OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics s *homepage*: https://github.com/g-truc/glm -=========== ============================================================================= -version toolchain -=========== ============================================================================= -``0.9.7.6`` ``intel/2016a`` -``0.9.8.3`` ``GCCcore/5.4.0``, ``GCCcore/7.3.0`` -``0.9.9.0`` ``GCCcore/6.4.0`` -``0.9.9.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` -=========== ============================================================================= +=========== ================================================================================================= +version toolchain +=========== ================================================================================================= +``0.9.7.6`` ``intel/2016a`` +``0.9.8.3`` ``GCCcore/5.4.0``, ``GCCcore/7.3.0`` +``0.9.9.0`` ``GCCcore/6.4.0`` +``0.9.9.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` +=========== ================================================================================================= .. _list_software_GLM-AED_471: @@ -15933,7 +16529,7 @@ The General Lake Model (GLM) is a water balance and one-dimensional vertical str *homepage*: https://github.com/AquaticEcoDynamics/glm-aed =========== =============== -version toolchain +version toolchain =========== =============== ``3.3.0a5`` ``gompi/2021b`` =========== =============== @@ -15949,13 +16545,15 @@ Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming mode *homepage*: https://hpc.pnl.gov/globalarrays ========= ============= ================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ================================ -``5.7`` ``intel/2018b`` -``5.7`` ``-peigs`` ``intel/2019a`` -``5.7.2`` ``intel/2019b`` -``5.7.2`` ``-peigs`` ``intel/2019b`` +``5.7`` ``intel/2018b`` +``5.7`` ``-peigs`` ``intel/2019a`` +``5.7.2`` ``intel/2019b`` +``5.7.2`` ``-peigs`` ``intel/2019b`` ``5.8`` ``intel/2020a``, ``intel/2021a`` +``5.8.1`` ``intel/2022a`` +``5.8.2`` ``intel/2022a`` ========= ============= ================================ @@ -15969,9 +16567,9 @@ A Command Line Wrapper over the Globus SDK for Python, which provides an interfa *homepage*: https://docs.globus.org/cli/ ========== ================== -version toolchain +version toolchain ========== ================== -``1.11.0`` ``GCCcore/8.3.0`` +``1.11.0`` ``GCCcore/8.3.0`` ``3.1.1`` ``GCCcore/10.2.0`` ``3.2.0`` ``GCCcore/10.3.0`` ``3.6.0`` ``GCCcore/11.2.0`` @@ -15988,7 +16586,7 @@ Globus Connect Personal turns your laptop or other personal computer into a Glo *homepage*: https://www.globus.org/globus-connect-personal ========= ========== -version toolchain +version toolchain ========= ========== ``2.3.6`` ``system`` ========= ========== @@ -16004,12 +16602,12 @@ A C++ implementation of the Google logging module. *homepage*: https://github.com/google/glog ========= ======================================================= -version toolchain +version toolchain ========= ======================================================= -``0.3.4`` ``foss/2016a`` -``0.3.5`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` +``0.3.4`` ``foss/2016a`` +``0.3.5`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` ``0.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.5.0`` ``GCCcore/10.2.0`` +``0.5.0`` ``GCCcore/10.2.0`` ========= ======================================================= @@ -16023,13 +16621,13 @@ The GLPK (GNU Linear Programming Kit) package is intended for solving large-sca *homepage*: https://www.gnu.org/software/glpk/ ======== ================================================================================================================= -version toolchain +version toolchain ======== ================================================================================================================= -``4.58`` ``foss/2016a``, ``intel/2016a`` -``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` -``4.61`` ``intel/2017a`` +``4.58`` ``foss/2016a``, ``intel/2016a`` +``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` +``4.61`` ``intel/2017a`` ``4.65`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``5.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``5.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ======== ================================================================================================================= @@ -16043,7 +16641,7 @@ X protocol and ancillary headers *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========== ================================================= -version toolchain +version toolchain ========== ================================================= ``1.4.17`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========== ================================================= @@ -16059,7 +16657,7 @@ Glucose is based on a new scoring scheme (well, not so new now, it was introduce *homepage*: https://www.labri.fr/perso/lsimon/glucose/ ======= ============= -version toolchain +version toolchain ======= ============= ``4.1`` ``GCC/9.3.0`` ======= ============= @@ -16075,16 +16673,16 @@ GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: *homepage*: http://research-pub.gene.com/gmap/ ============== =============== -version toolchain +version toolchain ============== =============== -``2016-05-01`` ``foss/2016a`` -``2016-11-07`` ``foss/2016b`` +``2016-05-01`` ``foss/2016a`` +``2016-11-07`` ``foss/2016b`` ``2018-05-11`` ``intel/2018a`` ``2018-07-04`` ``intel/2018a`` -``2019-03-15`` ``foss/2018b`` -``2019-09-12`` ``GCC/8.3.0`` -``2020-12-17`` ``GCC/9.3.0`` -``2021-21-17`` ``GCC/11.2.0`` +``2019-03-15`` ``foss/2018b`` +``2019-09-12`` ``GCC/8.3.0`` +``2020-12-17`` ``GCC/9.3.0`` +``2021-21-17`` ``GCC/11.2.0`` ============== =============== @@ -16098,17 +16696,17 @@ GMP is a free library for arbitrary precision arithmetic, operating on signed i *homepage*: https://gmplib.org/ ========== ===================================================================================================================================================== -version toolchain +version toolchain ========== ===================================================================================================================================================== -``4.3.2`` ``system`` -``5.1.3`` ``GCC/4.8.2`` -``6.0.0`` ``GCC/4.9.2`` -``6.0.0a`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` +``4.3.2`` ``system`` +``5.1.3`` ``GCC/4.8.2`` +``6.0.0`` ``GCC/4.9.2`` +``6.0.0a`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` ``6.1.0`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``6.1.1`` ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``6.1.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b`` -``6.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``6.2.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``6.1.1`` ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` +``6.1.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b`` +``6.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``6.2.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========== ===================================================================================================================================================== @@ -16122,7 +16720,7 @@ gcc and GFortran based compiler toolchain, including MPICH for MPI support. *homepage*: (none) =========== ========== -version toolchain +version toolchain =========== ========== ``2016a`` ``system`` ``2017.08`` ``system`` @@ -16139,7 +16737,7 @@ gcc and GFortran based compiler toolchain, MPICH for MPI support, OpenBLAS (BLA *homepage*: (none) =========== ========== -version toolchain +version toolchain =========== ========== ``2016a`` ``system`` ``2017.10`` ``system`` @@ -16156,16 +16754,16 @@ GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x *homepage*: https://github.com/aleaxit/gmpy =========== ================== ====================================================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ====================================================================== -``2.0.8`` ``-Python-2.7.13`` ``intel/2017a`` -``2.0.8`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.0.8`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.0b4`` ``GCC/8.3.0`` +``2.0.8`` ``-Python-2.7.13`` ``intel/2017a`` +``2.0.8`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2.0.8`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.0b4`` ``GCC/8.3.0`` ``2.1.0b5`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` -``2.1.2`` ``GCC/11.2.0``, ``GCC/11.3.0`` +``2.1.2`` ``GCC/11.2.0``, ``GCC/11.3.0`` =========== ================== ====================================================================== @@ -16179,16 +16777,16 @@ Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-p *homepage*: https://gmsh.info/ ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``3.0.6`` ``-Python-2.7.14`` ``foss/2017b`` -``3.0.6`` ``-Python-3.6.6`` ``foss/2018b`` -``4.2.2`` ``-Python-3.6.6`` ``foss/2018b`` -``4.5.6`` ``-Python-2.7.16`` ``intel/2019b`` -``4.5.6`` ``-Python-3.7.4`` ``foss/2019b`` +``3.0.6`` ``-Python-2.7.14`` ``foss/2017b`` +``3.0.6`` ``-Python-3.6.6`` ``foss/2018b`` +``4.2.2`` ``-Python-3.6.6`` ``foss/2018b`` +``4.5.6`` ``-Python-2.7.16`` ``intel/2019b`` +``4.5.6`` ``-Python-3.7.4`` ``foss/2019b`` ``4.7.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``4.8.4`` ``-Python-3.6.4`` ``foss/2018a`` -``4.9.0`` ``foss/2021a`` +``4.8.4`` ``-Python-3.6.4`` ``foss/2018a`` +``4.9.0`` ``foss/2021a`` ========= ================== =============================== @@ -16202,13 +16800,13 @@ GMT is an open source collection of about 80 command-line tools for manipulating *homepage*: https://www.generic-mapping-tools.org/ ========== =============================== -version toolchain +version toolchain ========== =============================== -``4.5.17`` ``foss/2018a`` -``5.4.1`` ``intel/2017a`` +``4.5.17`` ``foss/2018a`` +``5.4.1`` ``intel/2017a`` ``5.4.3`` ``foss/2018a``, ``intel/2017b`` -``5.4.5`` ``foss/2019a`` -``6.2.0`` ``foss/2019b``, ``foss/2020b`` +``5.4.5`` ``foss/2019a`` +``6.2.0`` ``foss/2019b``, ``foss/2020b`` ========== =============================== @@ -16222,7 +16820,7 @@ GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for *homepage*: (none) ========== ========== -version toolchain +version toolchain ========== ========== ``1.7.20`` ``system`` ``2016a`` ``system`` @@ -16239,7 +16837,7 @@ GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for *homepage*: (none) ========== ========== -version toolchain +version toolchain ========== ========== ``1.7.20`` ``system`` ``2016a`` ``system`` @@ -16256,7 +16854,7 @@ Compiler-only toolchain with GCC and binutils. *homepage*: http://www.gnu.org/software/ ============== ========== -version toolchain +version toolchain ============== ========== ``4.9.2-2.25`` ``system`` ``4.9.3-2.25`` ``system`` @@ -16274,18 +16872,18 @@ Portable interactive, function plotting utility *homepage*: http://gnuplot.sourceforge.net ========= ================================================================ -version toolchain +version toolchain ========= ================================================================ -``5.0.3`` ``foss/2016a``, ``intel/2016a`` -``5.0.5`` ``foss/2016b``, ``intel/2016b`` -``5.0.6`` ``intel/2017a`` +``5.0.3`` ``foss/2016a``, ``intel/2016a`` +``5.0.5`` ``foss/2016b``, ``intel/2016b`` +``5.0.6`` ``intel/2017a`` ``5.2.2`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``5.2.5`` ``foss/2018b`` -``5.2.6`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b`` -``5.2.8`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``5.4.1`` ``GCCcore/10.2.0`` -``5.4.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``5.4.4`` ``GCCcore/11.3.0`` +``5.2.5`` ``foss/2018b`` +``5.2.6`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b`` +``5.2.8`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``5.4.1`` ``GCCcore/10.2.0`` +``5.4.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``5.4.4`` ``GCCcore/11.3.0`` ========= ================================================================ @@ -16299,13 +16897,14 @@ GnuTLS is a secure communications library implementing the SSL, TLS and DTLS pr *homepage*: https://www.gnutls.org ========== ================== -version toolchain +version toolchain ========== ================== -``3.3.21`` ``intel/2016a`` +``3.3.21`` ``intel/2016a`` ``3.4.7`` ``GNU/4.9.3-2.25`` -``3.4.11`` ``foss/2016a`` +``3.4.11`` ``foss/2016a`` ``3.7.2`` ``GCCcore/10.3.0`` ``3.7.3`` ``GCCcore/11.2.0`` +``3.7.8`` ``GCCcore/11.3.0`` ========== ================== @@ -16319,25 +16918,25 @@ Go is an open source programming language that makes it easy to build simple, r *homepage*: http://www.golang.org ========== ================= -version toolchain +version toolchain ========== ================= -``1.2.1`` ``GCC/4.8.2`` -``1.4.2`` ``GCC/4.8.4`` -``1.5`` ``GCC/4.8.4`` -``1.8.1`` ``system`` -``1.11.5`` ``system`` -``1.12`` ``system`` +``1.2.1`` ``GCC/4.8.2`` +``1.4.2`` ``GCC/4.8.4`` +``1.5`` ``GCC/4.8.4`` +``1.8.1`` ``system`` +``1.11.5`` ``system`` +``1.12`` ``system`` ``1.12.1`` ``GCCcore/7.3.0`` -``1.13.1`` ``system`` -``1.14`` ``system`` -``1.14.1`` ``system`` -``1.16.3`` ``system`` -``1.16.5`` ``system`` -``1.16.6`` ``system`` -``1.17.3`` ``system`` -``1.17.6`` ``system`` -``1.18.1`` ``system`` -``1.18.3`` ``system`` +``1.13.1`` ``system`` +``1.14`` ``system`` +``1.14.1`` ``system`` +``1.16.3`` ``system`` +``1.16.5`` ``system`` +``1.16.6`` ``system`` +``1.17.3`` ``system`` +``1.17.6`` ``system`` +``1.18.1`` ``system`` +``1.18.3`` ``system`` ========== ================= @@ -16351,7 +16950,7 @@ Goalign is a set of command line tools to manipulate multiple alignments. *homepage*: https://github.com/evolbioinfo/goalign ========= ========== -version toolchain +version toolchain ========= ========== ``0.3.2`` ``system`` ========= ========== @@ -16367,7 +16966,7 @@ A Python library for Gene Ontology analyses *homepage*: https://github.com/tanghaibao/goatools ========= ============== -version toolchain +version toolchain ========= ============== ``1.1.6`` ``foss/2020b`` ========= ============== @@ -16383,7 +16982,7 @@ GCC and GFortran based compiler toolchain with OpenMPI, BLIS, libFLAME, ScaLAPAC *homepage*: (none) =========== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain =========== ============= ========== ``2020.06`` ``-amd`` ``system`` ``2020.11`` ``system`` @@ -16402,25 +17001,26 @@ GObject introspection is a middleware layer between C libraries (using GObject) *homepage*: https://gi.readthedocs.io/en/latest/ ========== ================== ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ====================================== -``1.47.1`` ``foss/2016a``, ``intel/2016a`` -``1.48.0`` ``foss/2016a``, ``intel/2016a`` -``1.49.1`` ``foss/2016b``, ``intel/2016b`` -``1.52.0`` ``intel/2017a`` -``1.53.5`` ``-Python-2.7.13`` ``intel/2017a`` -``1.53.5`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``1.53.5`` ``-Python-3.6.1`` ``intel/2017a`` -``1.54.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``1.54.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` -``1.54.1`` ``-Python-3.6.6`` ``fosscuda/2018b`` -``1.58.3`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` -``1.60.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``1.63.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``1.64.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``1.66.1`` ``GCCcore/10.2.0`` +``1.47.1`` ``foss/2016a``, ``intel/2016a`` +``1.48.0`` ``foss/2016a``, ``intel/2016a`` +``1.49.1`` ``foss/2016b``, ``intel/2016b`` +``1.52.0`` ``intel/2017a`` +``1.53.5`` ``-Python-2.7.13`` ``intel/2017a`` +``1.53.5`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``1.53.5`` ``-Python-3.6.1`` ``intel/2017a`` +``1.54.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``1.54.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` +``1.54.1`` ``-Python-3.6.6`` ``fosscuda/2018b`` +``1.58.3`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +``1.60.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``1.63.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``1.64.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``1.66.1`` ``GCCcore/10.2.0`` ``1.68.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.72.0`` ``GCCcore/11.3.0`` +``1.72.0`` ``GCCcore/11.3.0`` +``1.74.0`` ``GCCcore/12.2.0`` ========== ================== ====================================== @@ -16434,13 +17034,29 @@ GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for M *homepage*: (none) ========= ========== -version toolchain +version toolchain ========= ========== ``2018b`` ``system`` ``2020b`` ``system`` ========= ========== +.. _list_software_Godon_503: + +*Godon* ++++++++ + +Godon is codon models software written in Go. + +*homepage*: https://bitbucket.org/Davydov/godon/ + +============ ============= ========== +version versionsuffix toolchain +============ ============= ========== +``20210913`` ``-x86_64`` ``system`` +============ ============= ========== + + .. _list_software_gofasta_741: *gofasta* @@ -16451,7 +17067,7 @@ Some functions for dealing with alignments, developed to handle SARS-CoV-2 data *homepage*: https://github.com/cov-ert/gofasta ========= ========== -version toolchain +version toolchain ========= ========== ``0.0.5`` ``system`` ========= ========== @@ -16467,7 +17083,7 @@ GNU Compiler Collection (GCC) based compiler toolchain, including OpenBLAS (BLA *homepage*: (none) ========= ========== -version toolchain +version toolchain ========= ========== ``2018a`` ``system`` ``2020a`` ``system`` @@ -16484,7 +17100,7 @@ GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL *homepage*: (none) ========= ========== -version toolchain +version toolchain ========= ========== ``2018b`` ``system`` ``2019a`` ``system`` @@ -16504,7 +17120,7 @@ GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for M *homepage*: (none) =========== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain =========== ============= ========== ``2016.04`` ``system`` ``2016.06`` ``system`` @@ -16524,7 +17140,9 @@ version versionsuffix toolchain ``2021a`` ``system`` ``2021b`` ``system`` ``2022.05`` ``system`` +``2022.10`` ``system`` ``2022a`` ``system`` +``2022b`` ``system`` ``system`` ``-2.29`` ``system`` =========== ============= ========== @@ -16539,7 +17157,7 @@ GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, *homepage*: (none) ========= ========== -version toolchain +version toolchain ========= ========== ``2017b`` ``system`` ``2018a`` ``system`` @@ -16561,7 +17179,7 @@ Reformats Java source code to comply with Google Java Style. *homepage*: https://github.com/google/google-java-format ======= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= ========== ``1.7`` ``-Java-1.8`` ``system`` ======= ============= ========== @@ -16577,12 +17195,12 @@ Google's framework for writing C++ tests on a variety of platforms *homepage*: https://github.com/google/googletest ========== ===================================================================== -version toolchain +version toolchain ========== ===================================================================== ``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b`` -``1.8.1`` ``GCCcore/8.2.0`` -``1.10.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.11.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.8.1`` ``GCCcore/8.2.0`` +``1.10.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.11.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ===================================================================== @@ -16596,7 +17214,7 @@ GoTree is a set of command line tools to manipulate phylogenetic trees. *homepage*: https://github.com/evolbioinfo/gotree ========= ========== -version toolchain +version toolchain ========= ========== ``0.4.0`` ``system`` ========= ========== @@ -16612,7 +17230,7 @@ The gp2c compiler is a package for translating GP routines into the C programmin *homepage*: http://pari.math.u-bordeaux.fr/pub/pari/manuals/gp2c/gp2c.html ============ ============== -version toolchain +version toolchain ============ ============== ``0.0.9pl5`` ``foss/2016a`` ============ ============== @@ -16628,17 +17246,17 @@ GPAW is a density-functional theory (DFT) Python code based on the projector-aug *homepage*: https://wiki.fysik.dtu.dk/gpaw/ =========== ============================ ================================================================ -version versionsuffix toolchain +version versionsuffix toolchain =========== ============================ ================================================================ -``1.4.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``19.8.1`` ``-ASE-3.18.0-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``19.8.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``20.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``20.10.0`` ``foss/2020b``, ``intel/2020b`` -``20.10.0`` ``-ASE-3.20.1-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``21.1.0`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` -``21.6.0`` ``foss/2021a`` -``21.6.0`` ``-ASE-3.22.0`` ``foss/2020b``, ``intel/2020b`` +``1.4.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``19.8.1`` ``-ASE-3.18.0-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``19.8.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``20.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``20.10.0`` ``foss/2020b``, ``intel/2020b`` +``20.10.0`` ``-ASE-3.20.1-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``21.1.0`` ``-ASE-3.21.1`` ``foss/2020b``, ``intel/2020b`` +``21.6.0`` ``foss/2021a`` +``21.6.0`` ``-ASE-3.22.0`` ``foss/2020b``, ``intel/2020b`` ``22.8.0`` ``foss/2021b``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` =========== ============================ ================================================================ @@ -16653,7 +17271,7 @@ PAW setup for the GPAW Density Functional Theory package. Users can install se *homepage*: https://wiki.fysik.dtu.dk/gpaw/ ============= ========== -version toolchain +version toolchain ============= ========== ``0.8.7929`` ``system`` ``0.9.9672`` ``system`` @@ -16671,12 +17289,12 @@ GNU gperf is a perfect hash function generator. For a given list of strings, it *homepage*: https://www.gnu.org/software/gperf/ -========= ============================================================================================================================================================================= -version toolchain -========= ============================================================================================================================================================================= -``3.0.4`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``3.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -========= ============================================================================================================================================================================= +========= ================================================================================================================================================================================================= +version toolchain +========= ================================================================================================================================================================================================= +``3.0.4`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``3.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +========= ================================================================================================================================================================================================= .. _list_software_gperftools_1093: @@ -16689,14 +17307,14 @@ gperftools is a collection of a high-performance multi-threaded malloc() impleme *homepage*: https://github.com/gperftools/gperftools ========== ========================================================== -version toolchain +version toolchain ========== ========================================================== -``2.5`` ``foss/2016a``, ``intel/2016b`` -``2.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.7.90`` ``GCCcore/8.3.0`` -``2.8`` ``GCCcore/9.3.0`` +``2.5`` ``foss/2016a``, ``intel/2016b`` +``2.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.7.90`` ``GCCcore/8.3.0`` +``2.8`` ``GCCcore/9.3.0`` ``2.9.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``2.10`` ``GCCcore/11.3.0`` +``2.10`` ``GCCcore/11.3.0`` ========== ========================================================== @@ -16710,12 +17328,12 @@ A simple command-line utility for querying and monitoring GPU status *homepage*: https://github.com/wookayin/gpustat =========== ================== ===================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ===================================== -``0.5.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``0.5.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``0.6.0`` ``GCCcore/10.3.0``, ``gcccuda/2020b`` -``0.6.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``1.0.0b1`` ``GCCcore/11.2.0`` +``0.6.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.0.0b1`` ``GCCcore/11.2.0`` =========== ================== ===================================== @@ -16729,7 +17347,7 @@ GPy is a Gaussian Process (GP) framework written in Python *homepage*: https://sheffieldml.github.io/GPy ========== ============== -version toolchain +version toolchain ========== ============== ``1.10.0`` ``foss/2021b`` ========== ============== @@ -16745,7 +17363,7 @@ GPyOpt is a Python open-source library for Bayesian Optimization *homepage*: https://sheffieldml.github.io/GPyOpt ========= =============== -version toolchain +version toolchain ========= =============== ``1.2.6`` ``intel/2020b`` ========= =============== @@ -16761,7 +17379,7 @@ GPyTorch is a Gaussian process library implemented using PyTorch. *homepage*: https://gpytorch.ai ========= ============== -version toolchain +version toolchain ========= ============== ``1.3.0`` ``foss/2020b`` ========= ============== @@ -16777,9 +17395,9 @@ Grace is a WYSIWYG tool to make two-dimensional plots of numerical data. *homepage*: https://plasma-gate.weizmann.ac.il/Grace/ ========== ============= ================================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ================================================================================================================= -``5.1.25`` ``foss/2016a``, ``foss/2021a``, ``foss/2021b``, ``intel/2016a`` +``5.1.25`` ``foss/2016a``, ``foss/2021a``, ``foss/2021b``, ``intel/2016a`` ``5.1.25`` ``-5build1`` ``foss/2017b``, ``foss/2018a``, ``foss/2019a``, ``foss/2019b``, ``intel/2017b``, ``intel/2019a``, ``intel/2019b`` ========== ============= ================================================================================================================= @@ -16794,7 +17412,7 @@ Complete Gradle install. From mobile apps to microservices, from small startups *homepage*: https://gradle.org ========= ========== -version toolchain +version toolchain ========= ========== ``4.5.1`` ``system`` ``6.1.1`` ``system`` @@ -16812,7 +17430,7 @@ Gradient Unwarping. This is the Human Connectome Project fork of the no longer m *homepage*: https://github.com/Washington-University/gradunwarp ========= ====================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ====================== ============== ``1.1.0`` ``-HCP-Python-2.7.15`` ``foss/2019a`` ``1.2.0`` ``-HCP-Python-2.7.15`` ``foss/2019a`` @@ -16830,7 +17448,7 @@ Graph-tool is an efficient Python module for manipulation and statistical analy *homepage*: https://graph-tool.skewed.de/ ======== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================= ============== ``2.26`` ``-Python-3.6.3`` ``foss/2017b`` ``2.27`` ``-Python-3.6.6`` ``foss/2018b`` @@ -16847,9 +17465,9 @@ Graphene is a a thin layer of types for graphic libraries *homepage*: https://ebassi.github.io/graphene/ ========== ================== -version toolchain +version toolchain ========== ================== -``1.6.0`` ``intel/2017a`` +``1.6.0`` ``intel/2017a`` ``1.10.8`` ``GCCcore/11.3.0`` ========== ================== @@ -16864,13 +17482,13 @@ GraphicsMagick is the swiss army knife of image processing. *homepage*: https://www.graphicsmagick.org/ ========== ================================== -version toolchain +version toolchain ========== ================================== -``1.3.23`` ``foss/2016a``, ``intel/2016a`` -``1.3.25`` ``intel/2016b``, ``intel/2017a`` -``1.3.28`` ``foss/2018a`` -``1.3.31`` ``foss/2018b`` -``1.3.34`` ``foss/2019a``, ``foss/2019b`` +``1.3.23`` ``foss/2016a``, ``intel/2016a`` +``1.3.25`` ``intel/2016b``, ``intel/2017a`` +``1.3.28`` ``foss/2018a`` +``1.3.31`` ``foss/2018b`` +``1.3.34`` ``foss/2019a``, ``foss/2019b`` ``1.3.36`` ``GCCcore/11.2.0``, ``foss/2020b`` ========== ================================== @@ -16884,11 +17502,11 @@ Graphite is a "smart font" system developed specifically to handle the complexi *homepage*: https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home -========== ============================================================================= -version toolchain -========== ============================================================================= -``1.3.14`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` -========== ============================================================================= +========== ================================================================================================= +version toolchain +========== ================================================================================================= +``1.3.14`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/8.3.0`` +========== ================================================================================================= .. _list_software_GraPhlAn_749: @@ -16901,7 +17519,7 @@ GraPhlAn is a software tool for producing high-quality circular representations *homepage*: https://segatalab.github.io/tools/graphlan ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``1.1.3`` ``-Python-2.7.16`` ``foss/2019b`` ========= ================== ============== @@ -16917,7 +17535,7 @@ A highly sensitive and accurate mapper for long, error-prone reads *homepage*: https://github.com/isovic/graphmap ========= ============== -version toolchain +version toolchain ========= ============== ``0.5.2`` ``foss/2019b`` ========= ============== @@ -16933,7 +17551,7 @@ A highly sensitive and accurate mapper for long, error-prone reads *homepage*: https://github.com/lbcb-sci/graphmap2 ========= ============== -version toolchain +version toolchain ========= ============== ``0.6.4`` ``foss/2019b`` ========= ============== @@ -16949,20 +17567,20 @@ Graphviz is open source graph visualization software. Graph visualization is a *homepage*: https://www.graphviz.org/ ========== ========================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ========================= =============================== ``2.38.0`` ``foss/2016b``, ``intel/2016b`` ``2.40.1`` ``foss/2018b``, ``intel/2018a`` -``2.40.1`` ``-Python-2.7.15`` ``foss/2018b`` -``2.42.2`` ``foss/2019b`` -``2.42.2`` ``-Java-11`` ``GCCcore/8.3.0`` -``2.42.2`` ``-Python-3.7.4`` ``foss/2019b`` -``2.44.1`` ``-Java-11`` ``GCCcore/9.3.0`` -``2.44.1`` ``-Java-11-Python-3.8.2`` ``GCCcore/9.3.0`` -``2.47.0`` ``-Java-11`` ``GCCcore/10.2.0`` -``2.47.2`` ``GCCcore/10.3.0`` -``2.50.0`` ``GCCcore/11.2.0`` -``5.0.0`` ``GCCcore/11.3.0`` +``2.40.1`` ``-Python-2.7.15`` ``foss/2018b`` +``2.42.2`` ``foss/2019b`` +``2.42.2`` ``-Java-11`` ``GCCcore/8.3.0`` +``2.42.2`` ``-Python-3.7.4`` ``foss/2019b`` +``2.44.1`` ``-Java-11`` ``GCCcore/9.3.0`` +``2.44.1`` ``-Java-11-Python-3.8.2`` ``GCCcore/9.3.0`` +``2.47.0`` ``-Java-11`` ``GCCcore/10.2.0`` +``2.47.2`` ``GCCcore/10.3.0`` +``2.50.0`` ``GCCcore/11.2.0`` +``5.0.0`` ``GCCcore/11.3.0`` ========== ========================= =============================== @@ -16976,11 +17594,11 @@ Simple Python interface for Graphviz *homepage*: https://pypi.python.org/pypi/graphviz ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== ``0.5.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``0.5.1`` ``-Python-3.5.2`` ``intel/2016b`` -``0.8.2`` ``-Python-3.6.4`` ``intel/2018a`` +``0.5.1`` ``-Python-3.5.2`` ``intel/2016b`` +``0.8.2`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================== =============================== @@ -16994,7 +17612,7 @@ The General Relativistic Atomic Structure Package (GRASP) is a set of Fortran 9 *homepage*: https://compas.github.io/grasp/ ======== ============== -version toolchain +version toolchain ======== ============== ``2018`` ``foss/2019b`` ======== ============== @@ -17010,10 +17628,11 @@ The Geographic Resources Analysis Support System - used for geospatial data man *homepage*: https://grass.osgeo.org ========= ================== ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================== -``7.6.0`` ``-Python-2.7.15`` ``foss/2018b`` +``7.6.0`` ``-Python-2.7.15`` ``foss/2018b`` ``7.8.3`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``8.2.0`` ``foss/2021b`` ========= ================== ================== @@ -17027,7 +17646,7 @@ The greenlet package is a spin-off of Stackless, a version of CPython that suppo *homepage*: https://github.com/python-greenlet/greenlet ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``0.4.9`` ``-Python-2.7.11`` ``intel/2016a`` ``0.4.9`` ``-Python-3.5.1`` ``intel/2016a`` @@ -17046,7 +17665,7 @@ The grep command searches one or more input files for lines containing a match t *homepage*: http://www.gnu.org/software/grep/ ======== ============= -version toolchain +version toolchain ======== ============= ``2.21`` ``GCC/4.9.2`` ======== ============= @@ -17062,7 +17681,7 @@ A cross-platform software package for econometric analysis *homepage*: http://gretl.sourceforge.net ========= ============== -version toolchain +version toolchain ========= ============== ``2020a`` ``foss/2019a`` ========= ============== @@ -17078,10 +17697,10 @@ The ECMWF GRIB API is an application program interface accessible from C, FORTRA *homepage*: https://software.ecmwf.int/wiki/display/GRIB/Home ========== ================================================ -version toolchain +version toolchain ========== ================================================ -``1.16.0`` ``intel/2016a`` -``1.21.0`` ``foss/2017a`` +``1.16.0`` ``intel/2016a`` +``1.21.0`` ``foss/2017a`` ``1.24.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ========== ================================================ @@ -17096,7 +17715,7 @@ GRIT - A tool for the integrative analysis of RNA-seq type assays *homepage*: https://github.com/nboley/grit ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``2.0.5`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== @@ -17112,7 +17731,7 @@ XGBoost is an optimized distributed gradient boosting library designed to be hig *homepage*: https://github.com/dmlc/xgboost ============ =================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ =================== =============== ``20171009`` ``-Java-1.8.0_152`` ``intel/2017b`` ============ =================== =============== @@ -17128,7 +17747,7 @@ Groff (GNU troff) is a typesetting system that reads plain text mixed with forma *homepage*: https://www.gnu.org/software/groff ========== =========================================================================================================================================================================== -version toolchain +version toolchain ========== =========================================================================================================================================================================== ``1.22.4`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== =========================================================================================================================================================================== @@ -17144,7 +17763,7 @@ GroIMP (Growth Grammar-related Interactive Modelling Platform) is a 3D-modelling *homepage*: http://www.grogra.de/software/groimp ======= ========== -version toolchain +version toolchain ======= ========== ``1.5`` ``system`` ======= ========== @@ -17160,46 +17779,46 @@ GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the *homepage*: http://www.gromacs.org ========== ============================= ============================================================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========== ============================= ============================================================================================================ -``5.1.2`` ``-hybrid`` ``foss/2016a``, ``intel/2016a`` -``5.1.2`` ``-hybrid-dp`` ``intel/2016a`` -``5.1.2`` ``-mt`` ``foss/2016a`` -``5.1.4`` ``-hybrid`` ``foss/2016b`` -``5.1.4`` ``-mt`` ``foss/2016b`` -``2016`` ``-hybrid`` ``foss/2016b`` -``2016`` ``-mt`` ``foss/2016b`` -``2016.1`` ``-PLUMED`` ``foss/2017a`` -``2016.2`` ``foss/2017a`` -``2016.3`` ``foss/2017a``, ``intel/2017a`` -``2016.3`` ``-GPU-enabled`` ``foss/2016b`` -``2016.4`` ``foss/2017b``, ``fosscuda/2017b``, ``giolf/2017b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` -``2016.5`` ``intel/2018a`` -``2018`` ``foss/2018a`` -``2018.1`` ``-PLUMED`` ``foss/2018b`` +``5.1.2`` ``-hybrid`` ``foss/2016a``, ``intel/2016a`` +``5.1.2`` ``-hybrid-dp`` ``intel/2016a`` +``5.1.2`` ``-mt`` ``foss/2016a`` +``5.1.4`` ``-hybrid`` ``foss/2016b`` +``5.1.4`` ``-mt`` ``foss/2016b`` +``2016`` ``-hybrid`` ``foss/2016b`` +``2016`` ``-mt`` ``foss/2016b`` +``2016.1`` ``-PLUMED`` ``foss/2017a`` +``2016.2`` ``foss/2017a`` +``2016.3`` ``foss/2017a``, ``intel/2017a`` +``2016.3`` ``-GPU-enabled`` ``foss/2016b`` +``2016.4`` ``foss/2017b``, ``fosscuda/2017b``, ``giolf/2017b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` +``2016.5`` ``intel/2018a`` +``2018`` ``foss/2018a`` +``2018.1`` ``-PLUMED`` ``foss/2018b`` ``2018.2`` ``foss/2017b``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018b``, ``intel/2017b``, ``intelcuda/2017b`` -``2018.3`` ``foss/2018b``, ``fosscuda/2018b`` -``2018.4`` ``-PLUMED-2.5.0`` ``foss/2018b``, ``fosscuda/2018b`` -``2019`` ``foss/2018b``, ``fosscuda/2018b`` -``2019.2`` ``fosscuda/2019a`` -``2019.3`` ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019a``, ``fosscuda/2019b`` -``2019.4`` ``foss/2019b`` -``2019.6`` ``fosscuda/2019b`` -``2020`` ``foss/2019b``, ``fosscuda/2019b`` -``2020.1`` ``-Python-3.8.2`` ``foss/2020a`` -``2020.3`` ``fosscuda/2019b`` -``2020.4`` ``-Python-3.8.2`` ``foss/2020a`` -``2020.5`` ``-Python-3.8.2`` ``fosscuda/2020a`` -``2021`` ``foss/2020b``, ``fosscuda/2020b`` -``2021.2`` ``fosscuda/2020b`` -``2021.3`` ``foss/2021a`` -``2021.3`` ``-CUDA-11.3.1`` ``foss/2021a`` -``2021.3`` ``-CUDA-11.3.1-PLUMED-2.7.2`` ``foss/2021a`` -``2021.3`` ``-PLUMED-2.7.2`` ``foss/2021a`` -``2021.5`` ``foss/2021b`` -``2021.5`` ``-CUDA-11.4.1`` ``foss/2021b`` -``2021.5`` ``-CUDA-11.4.1-PLUMED-2.8.0`` ``foss/2021b`` -``2021.5`` ``-PLUMED-2.8.0`` ``foss/2021b`` +``2018.3`` ``foss/2018b``, ``fosscuda/2018b`` +``2018.4`` ``-PLUMED-2.5.0`` ``foss/2018b``, ``fosscuda/2018b`` +``2019`` ``foss/2018b``, ``fosscuda/2018b`` +``2019.2`` ``fosscuda/2019a`` +``2019.3`` ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019a``, ``fosscuda/2019b`` +``2019.4`` ``foss/2019b`` +``2019.6`` ``fosscuda/2019b`` +``2020`` ``foss/2019b``, ``fosscuda/2019b`` +``2020.1`` ``-Python-3.8.2`` ``foss/2020a`` +``2020.3`` ``fosscuda/2019b`` +``2020.4`` ``-Python-3.8.2`` ``foss/2020a`` +``2020.5`` ``-Python-3.8.2`` ``fosscuda/2020a`` +``2021`` ``foss/2020b``, ``fosscuda/2020b`` +``2021.2`` ``fosscuda/2020b`` +``2021.3`` ``foss/2021a`` +``2021.3`` ``-CUDA-11.3.1`` ``foss/2021a`` +``2021.3`` ``-CUDA-11.3.1-PLUMED-2.7.2`` ``foss/2021a`` +``2021.3`` ``-PLUMED-2.7.2`` ``foss/2021a`` +``2021.5`` ``foss/2021b`` +``2021.5`` ``-CUDA-11.4.1`` ``foss/2021b`` +``2021.5`` ``-CUDA-11.4.1-PLUMED-2.8.0`` ``foss/2021b`` +``2021.5`` ``-PLUMED-2.8.0`` ``foss/2021b`` ========== ============================= ============================================================================================================ @@ -17213,7 +17832,7 @@ GromacsWrapper is a python package that wraps system calls to Gromacs tools into *homepage*: https://gromacswrapper.readthedocs.org ========= ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================== ``0.8.0`` ``-Python-3.7.2`` ``fosscuda/2019a`` ========= ================= ================== @@ -17229,7 +17848,7 @@ GroopM is a metagenomic binning toolset. It leverages spatio-temporal dynamics *homepage*: https://ecogenomics.github.io/GroopM/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``0.3.4`` ``-Python-2.7.12`` ``foss/2016b`` ========= ================== ============== @@ -17245,7 +17864,7 @@ Groovy is a powerful, optionally typed and dynamic language, with static-typing *homepage*: https://groovy-lang.org ========= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========== ``2.5.9`` ``-Java-11`` ``system`` ``4.0.3`` ``-Java-11`` ``system`` @@ -17262,7 +17881,7 @@ gRPC is a modern, open source, high-performance remote procedure call (RPC) fram *homepage*: https://grpc.io/ ========== ================== -version toolchain +version toolchain ========== ================== ``1.44.0`` ``GCCcore/11.2.0`` ========== ================== @@ -17278,7 +17897,7 @@ Gene Set Enrichment Analysis (GSEA) is a computational method that determines w *homepage*: https://www.gsea-msigdb.org/gsea/index.jsp ========= ========== -version toolchain +version toolchain ========= ========== ``4.0.3`` ``system`` ========= ========== @@ -17294,7 +17913,7 @@ gsettings-desktop-schemas contains a collection of GSettings schemas for settin *homepage*: https://gitlab.gnome.org/GNOME/gsettings-desktop-schemas ========== ================= -version toolchain +version toolchain ========== ================= ``3.34.0`` ``GCCcore/8.2.0`` ========== ================= @@ -17310,16 +17929,16 @@ The GNU Scientific Library (GSL) is a numerical library for C and C++ programmer *homepage*: https://www.gnu.org/software/gsl/ ========= ============================================================================================================================ -version toolchain +version toolchain ========= ============================================================================================================================ -``1.16`` ``foss/2016a``, ``intel/2016a`` +``1.16`` ``foss/2016a``, ``intel/2016a`` ``2.1`` ``GCC/5.4.0-2.26``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` -``2.2.1`` ``intel/2016a``, ``intel/2016b`` -``2.3`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b``, ``intel/2017a`` -``2.4`` ``GCCcore/6.4.0`` -``2.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2.6`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` -``2.7`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` +``2.2.1`` ``intel/2016a``, ``intel/2016b`` +``2.3`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b``, ``intel/2017a`` +``2.4`` ``GCCcore/6.4.0`` +``2.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2.6`` ``GCC/10.2.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` +``2.7`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ========= ============================================================================================================================ @@ -17333,7 +17952,7 @@ The gSOAP toolkit is a C and C++ software development toolkit for SOAP and REST *homepage*: http://www.cs.fsu.edu/~engelen/soap.html =========== ================= -version toolchain +version toolchain =========== ================= ``2.8.48`` ``GCCcore/6.3.0`` ``2.8.100`` ``GCCcore/8.3.0`` @@ -17350,7 +17969,7 @@ GSPORT command-line tool for accessing GenomeScan Customer Portal *homepage*: https://github.com/genomescan/gsport ========= ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================= ``1.4.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========= ================= ================= @@ -17366,7 +17985,7 @@ GStreamer is a library for constructing graphs of media-handling components. Th *homepage*: https://gstreamer.freedesktop.org/ ========== ============== -version toolchain +version toolchain ========== ============== ``1.20.2`` ``GCC/11.3.0`` ========== ============== @@ -17382,16 +18001,16 @@ GStreamer is a library for constructing graphs of media-handling components. Th *homepage*: https://gstreamer.freedesktop.org/ =========== ================================================================================================================== -version toolchain +version toolchain =========== ================================================================================================================== ``0.10.36`` ``foss/2016a``, ``foss/2017b``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``1.6.4`` ``foss/2016a`` -``1.8.3`` ``foss/2016a`` -``1.16.0`` ``GCC/8.2.0-2.31.1`` -``1.16.2`` ``GCC/8.3.0`` -``1.18.4`` ``GCC/10.2.0``, ``GCC/10.3.0`` -``1.18.5`` ``GCC/11.2.0`` -``1.20.2`` ``GCC/11.3.0`` +``1.6.4`` ``foss/2016a`` +``1.8.3`` ``foss/2016a`` +``1.16.0`` ``GCC/8.2.0-2.31.1`` +``1.16.2`` ``GCC/8.3.0`` +``1.18.4`` ``GCC/10.2.0``, ``GCC/10.3.0`` +``1.18.5`` ``GCC/11.2.0`` +``1.20.2`` ``GCC/11.3.0`` =========== ================================================================================================================== @@ -17405,17 +18024,17 @@ GStreamer is a library for constructing graphs of media-handling components. Th *homepage*: https://gstreamer.freedesktop.org/ =========== ================================================================================================================== -version toolchain +version toolchain =========== ================================================================================================================== ``0.10.36`` ``foss/2016a``, ``foss/2017b``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``1.6.4`` ``foss/2016a`` -``1.8.3`` ``foss/2016a`` -``1.15.1`` ``fosscuda/2018b`` -``1.16.0`` ``GCC/8.2.0-2.31.1`` -``1.16.2`` ``GCC/8.3.0`` -``1.18.4`` ``GCC/10.2.0``, ``GCC/10.3.0`` -``1.18.5`` ``GCC/11.2.0`` -``1.20.2`` ``GCC/11.3.0`` +``1.6.4`` ``foss/2016a`` +``1.8.3`` ``foss/2016a`` +``1.15.1`` ``fosscuda/2018b`` +``1.16.0`` ``GCC/8.2.0-2.31.1`` +``1.16.2`` ``GCC/8.3.0`` +``1.18.4`` ``GCC/10.2.0``, ``GCC/10.3.0`` +``1.18.5`` ``GCC/11.2.0`` +``1.20.2`` ``GCC/11.3.0`` =========== ================================================================================================================== @@ -17429,12 +18048,28 @@ gsutil is a Python application that lets you access Cloud Storage from the comma *homepage*: https://cloud.google.com/storage/docs/gsutil ======== ================== -version toolchain +version toolchain ======== ================== ``5.10`` ``GCCcore/11.2.0`` ======== ================== +.. _list_software_gsw_337: + +*gsw* ++++++ + +This Python implementation of the Thermodynamic Equation of Seawater 2010 (TEOS-10) is based primarily on numpy ufunc wrappers of the GSW-C implementation. This library replaces the original python-gsw pure-python implementation.. The primary reasons for this change are that by building on the C implementation we reduce code duplication and we gain an immediate update to the 75-term equation. Additional benefits include a major increase in speed, a reduction in memory usage, and the inclusion of more functions. The penalty is that a C (or MSVC C++ for Windows) compiler is required to build the package from source. + +*homepage*: https://github.com/TEOS-10/GSW-python + +========== ============== +version toolchain +========== ============== +``3.6.16`` ``foss/2022a`` +========== ============== + + .. _list_software_GTDB-Tk_525: *GTDB-Tk* @@ -17445,15 +18080,15 @@ A toolkit for assigning objective taxonomic classifications to bacterial and arc *homepage*: https://github.com/Ecogenomics/GTDBTk ========= ================== =============================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================================== -``0.2.2`` ``-Python-2.7.15`` ``intel/2018b`` -``0.3.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` -``1.0.2`` ``-Python-3.7.4`` ``intel/2019b`` -``1.3.0`` ``-Python-3.8.2`` ``intel/2020a`` -``1.5.0`` ``intel/2020b`` +``0.2.2`` ``-Python-2.7.15`` ``intel/2018b`` +``0.3.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` +``1.0.2`` ``-Python-3.7.4`` ``intel/2019b`` +``1.3.0`` ``-Python-3.8.2`` ``intel/2020a`` +``1.5.0`` ``intel/2020b`` ``1.7.0`` ``foss/2020b``, ``foss/2021a``, ``intel/2020b`` -``2.0.0`` ``foss/2021a``, ``intel/2021b`` +``2.0.0`` ``foss/2021a``, ``intel/2021b`` ========= ================== =============================================== @@ -17467,18 +18102,18 @@ The GTK+ 2 package contains libraries used for creating graphical user interface *homepage*: https://developer.gnome.org/gtk+/stable/ =========== ================================================================================ -version toolchain +version toolchain =========== ================================================================================ -``2.24.28`` ``intel/2016a`` -``2.24.30`` ``foss/2016a``, ``intel/2016a`` -``2.24.31`` ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``2.24.28`` ``intel/2016a`` +``2.24.30`` ``foss/2016a``, ``intel/2016a`` +``2.24.31`` ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``2.24.32`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` -``2.24.33`` ``GCCcore/10.3.0`` -``3.22.30`` ``fosscuda/2018b`` -``3.24.8`` ``GCCcore/8.2.0`` -``3.24.13`` ``GCCcore/8.3.0`` -``3.24.17`` ``GCCcore/9.3.0`` -``3.24.23`` ``GCCcore/10.2.0`` +``2.24.33`` ``GCCcore/10.3.0`` +``3.22.30`` ``fosscuda/2018b`` +``3.24.8`` ``GCCcore/8.2.0`` +``3.24.13`` ``GCCcore/8.3.0`` +``3.24.17`` ``GCCcore/9.3.0`` +``3.24.23`` ``GCCcore/10.2.0`` =========== ================================================================================ @@ -17492,7 +18127,7 @@ The GTK+ 2 package contains libraries used for creating graphical user interface *homepage*: https://www.gtk.org =========== ====================================== -version toolchain +version toolchain =========== ====================================== ``2.24.33`` ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` =========== ====================================== @@ -17508,11 +18143,12 @@ GTK+ is the primary library used to construct user interfaces in GNOME. It prov *homepage*: https://developer.gnome.org/gtk3/stable/ =========== ================== -version toolchain +version toolchain =========== ================== ``3.24.29`` ``GCCcore/10.3.0`` ``3.24.31`` ``GCCcore/11.2.0`` ``3.24.33`` ``GCCcore/11.3.0`` +``3.24.35`` ``GCCcore/12.2.0`` =========== ================== @@ -17526,7 +18162,7 @@ GTK+ is the primary library used to construct user interfaces in GNOME. It prov *homepage*: https://docs.gtk.org/gtk4/ ========= ============== -version toolchain +version toolchain ========= ============== ``4.7.0`` ``GCC/11.3.0`` ========= ============== @@ -17542,10 +18178,10 @@ GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK+ wi *homepage*: https://wiki.gnome.org/Projects/GtkSourceView =========== ===================================== -version toolchain +version toolchain =========== ===================================== ``3.24.11`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0`` -``4.4.0`` ``GCCcore/8.2.0`` +``4.4.0`` ``GCCcore/8.2.0`` =========== ===================================== @@ -17559,7 +18195,7 @@ GTOOL is a program for transforming sets of genotype data for use with the prog *homepage*: http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html ========= ========== -version toolchain +version toolchain ========= ========== ``0.7.5`` ``system`` ========= ========== @@ -17575,10 +18211,10 @@ GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free *homepage*: http://gts.sourceforge.net/ ============ ======================================================================================================================================================================================================================================================= -version toolchain +version toolchain ============ ======================================================================================================================================================================================================================================================= ``0.7.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``foss/2020a``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` -``20121130`` ``foss/2017b`` +``20121130`` ``foss/2017b`` ============ ======================================================================================================================================================================================================================================================= @@ -17592,7 +18228,7 @@ Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an a *homepage*: https://sanger-pathogens.github.io/gubbins ========= ========== -version toolchain +version toolchain ========= ========== ``2.4.0`` ``system`` ========= ========== @@ -17608,7 +18244,7 @@ guenomu is a software written in C that estimates the species tree for a given s *homepage*: https://bitbucket.org/leomrtns/guenomu ============== ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ============== ============= =============== ``2019.07.05`` ``-mpi`` ``iimpi/2019a`` ============== ============= =============== @@ -17624,15 +18260,15 @@ Guile is a programming language, designed to help programmers create flexible a *homepage*: https://www.gnu.org/software/guile/ ========== ====================================================================================================================================================================================================================== -version toolchain +version toolchain ========== ====================================================================================================================================================================================================================== ``1.8.8`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b`` -``2.0.11`` ``GCC/4.9.3-2.25``, ``foss/2016a`` -``2.2.2`` ``GCCcore/6.4.0`` -``2.2.4`` ``GCCcore/7.3.0``, ``GCCcore/9.3.0`` -``2.2.7`` ``GCCcore/10.3.0`` -``3.0.7`` ``GCCcore/11.2.0`` -``3.0.8`` ``GCCcore/11.3.0`` +``2.0.11`` ``GCC/4.9.3-2.25``, ``foss/2016a`` +``2.2.2`` ``GCCcore/6.4.0`` +``2.2.4`` ``GCCcore/7.3.0``, ``GCCcore/9.3.0`` +``2.2.7`` ``GCCcore/10.3.0`` +``3.0.7`` ``GCCcore/11.2.0`` +``3.0.8`` ``GCCcore/11.3.0`` ========== ====================================================================================================================================================================================================================== @@ -17646,10 +18282,10 @@ GULP is a program for performing a variety of types of simulation on materials *homepage*: https://gulp.curtin.edu.au/gulp/ ======= =============== -version toolchain +version toolchain ======= =============== ``5.1`` ``intel/2019a`` -``6.1`` ``foss/2021b`` +``6.1`` ``foss/2021b`` ======= =============== @@ -17663,25 +18299,25 @@ The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. *homepage*: https://www.gurobi.com ========= ================= ================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================================== -``6.5.1`` ``system`` -``6.5.2`` ``system`` -``7.0.1`` ``system`` -``7.5.2`` ``system`` -``7.5.2`` ``-Python-3.6.4`` ``intel/2018a`` -``8.1.1`` ``system`` -``9.0.0`` ``system`` -``9.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``9.0.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``9.0.1`` ``system`` -``9.0.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``9.0.3`` ``GCCcore/10.2.0``, ``system`` -``9.1.0`` ``system`` -``9.1.1`` ``GCCcore/10.2.0`` +``6.5.1`` ``system`` +``6.5.2`` ``system`` +``7.0.1`` ``system`` +``7.5.2`` ``system`` +``7.5.2`` ``-Python-3.6.4`` ``intel/2018a`` +``8.1.1`` ``system`` +``9.0.0`` ``system`` +``9.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``9.0.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``9.0.1`` ``system`` +``9.0.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``9.0.3`` ``GCCcore/10.2.0``, ``system`` +``9.1.0`` ``system`` +``9.1.1`` ``GCCcore/10.2.0`` ``9.1.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``system`` -``9.5.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``9.5.2`` ``GCCcore/11.3.0`` +``9.5.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``9.5.2`` ``GCCcore/11.3.0`` ========= ================= ================================================== @@ -17695,12 +18331,12 @@ gzip (GNU zip) is a popular data compression program as a replacement for compre *homepage*: http://www.gnu.org/software/gzip/ ======== =================================================================================================================== -version toolchain +version toolchain ======== =================================================================================================================== -``1.8`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``1.9`` ``GCCcore/7.3.0`` +``1.8`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``1.9`` ``GCCcore/7.3.0`` ``1.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.12`` ``GCCcore/11.3.0`` +``1.12`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ======== =================================================================================================================== @@ -17710,7 +18346,7 @@ version toolchain --- -:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_hector_645` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_Highway_721` - :ref:`list_software_HIP_225` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_hiredis_744` - :ref:`list_software_HISAT2_427` - :ref:`list_software_histolab_854` - :ref:`list_software_hivtrace_854` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_how_are_we_stranded_here_2519` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hydra_504` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperopt_891` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` +:ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_HAL_213` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_harmony_766` - :ref:`list_software_HBase_451` - :ref:`list_software_HDBSCAN_499` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF-EOS_486` - :ref:`list_software_HDF-EOS5_539` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_hector_645` - :ref:`list_software_HeFFTe_498` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_hierfstat_970` - :ref:`list_software_hifiasm_737` - :ref:`list_software_HighFive_778` - :ref:`list_software_Highway_721` - :ref:`list_software_HIP_225` - :ref:`list_software_hipify-clang_1211` - :ref:`list_software_HIPS_308` - :ref:`list_software_hipSYCL_636` - :ref:`list_software_hiredis_744` - :ref:`list_software_HISAT2_427` - :ref:`list_software_histolab_854` - :ref:`list_software_hivtrace_854` - :ref:`list_software_hl7apy_597` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_HMMER2_427` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_how_are_we_stranded_here_2519` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_humann_647` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hydra_504` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_HyperQueue_1037` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_HyPo_384` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: @@ -17723,9 +18359,9 @@ The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, a *homepage*: http://www.hdfgroup.org/h4toh5/ ========= ======================== ================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ======================== ================================================ -``2.2.2`` ``-linux-x86_64-static`` ``system`` +``2.2.2`` ``-linux-x86_64-static`` ``system`` ``2.2.3`` ``foss/2018b``, ``gompi/2019b``, ``gompi/2020b`` ========= ======================== ================================================ @@ -17740,7 +18376,7 @@ HDF5 Utility Toolkit: High-Performance I/O Library for Particle-based Simulation *homepage*: https://amas.psi.ch/H5hut/ =========== =============== -version toolchain +version toolchain =========== =============== ``1.99.13`` ``intel/2016b`` =========== =============== @@ -17756,44 +18392,44 @@ HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical *homepage*: https://www.h5py.org/ ========== ===================================== ==================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ===================================== ==================================================================================== -``2.5.0`` ``-Python-2.7.11-HDF5-1.8.16`` ``foss/2016a``, ``intel/2016a`` -``2.5.0`` ``-Python-2.7.11-HDF5-1.8.16-serial`` ``foss/2016a``, ``intel/2016a`` -``2.5.0`` ``-Python-3.5.1-HDF5-1.8.16`` ``foss/2016a`` -``2.6.0`` ``-Python-2.7.11`` ``intel/2016a`` -``2.6.0`` ``-Python-2.7.12-HDF5-1.10.0-patch1`` ``foss/2016b``, ``intel/2016b`` -``2.6.0`` ``-Python-2.7.12-HDF5-1.8.17`` ``foss/2016b``, ``intel/2016b`` -``2.6.0`` ``-Python-2.7.12-HDF5-1.8.18`` ``foss/2016b``, ``intel/2016b`` -``2.6.0`` ``-Python-3.5.2-HDF5-1.10.0-patch1`` ``foss/2016b``, ``intel/2016b`` -``2.6.0`` ``-Python-3.5.2-HDF5-1.8.17`` ``intel/2016b`` -``2.6.0`` ``-Python-3.5.2-HDF5-1.8.18`` ``foss/2016b``, ``intel/2016b`` -``2.7.0`` ``-Python-2.7.12`` ``intel/2016b`` -``2.7.0`` ``-Python-2.7.13`` ``intel/2017a`` -``2.7.0`` ``-Python-2.7.13-HDF5-1.10.1`` ``foss/2017a`` -``2.7.0`` ``-Python-2.7.13-HDF5-1.8.19`` ``foss/2017a`` -``2.7.0`` ``-Python-3.6.1`` ``intel/2017a`` -``2.7.0`` ``-Python-3.6.1-HDF5-1.10.0-patch1`` ``intel/2017a`` -``2.7.0`` ``-Python-3.6.1-HDF5-1.10.1`` ``foss/2017a`` -``2.7.0`` ``-Python-3.6.1-HDF5-1.8.19`` ``foss/2017a`` -``2.7.1`` ``-Python-2.7.13`` ``intel/2017a`` +``2.5.0`` ``-Python-2.7.11-HDF5-1.8.16`` ``foss/2016a``, ``intel/2016a`` +``2.5.0`` ``-Python-2.7.11-HDF5-1.8.16-serial`` ``foss/2016a``, ``intel/2016a`` +``2.5.0`` ``-Python-3.5.1-HDF5-1.8.16`` ``foss/2016a`` +``2.6.0`` ``-Python-2.7.11`` ``intel/2016a`` +``2.6.0`` ``-Python-2.7.12-HDF5-1.10.0-patch1`` ``foss/2016b``, ``intel/2016b`` +``2.6.0`` ``-Python-2.7.12-HDF5-1.8.17`` ``foss/2016b``, ``intel/2016b`` +``2.6.0`` ``-Python-2.7.12-HDF5-1.8.18`` ``foss/2016b``, ``intel/2016b`` +``2.6.0`` ``-Python-3.5.2-HDF5-1.10.0-patch1`` ``foss/2016b``, ``intel/2016b`` +``2.6.0`` ``-Python-3.5.2-HDF5-1.8.17`` ``intel/2016b`` +``2.6.0`` ``-Python-3.5.2-HDF5-1.8.18`` ``foss/2016b``, ``intel/2016b`` +``2.7.0`` ``-Python-2.7.12`` ``intel/2016b`` +``2.7.0`` ``-Python-2.7.13`` ``intel/2017a`` +``2.7.0`` ``-Python-2.7.13-HDF5-1.10.1`` ``foss/2017a`` +``2.7.0`` ``-Python-2.7.13-HDF5-1.8.19`` ``foss/2017a`` +``2.7.0`` ``-Python-3.6.1`` ``intel/2017a`` +``2.7.0`` ``-Python-3.6.1-HDF5-1.10.0-patch1`` ``intel/2017a`` +``2.7.0`` ``-Python-3.6.1-HDF5-1.10.1`` ``foss/2017a`` +``2.7.0`` ``-Python-3.6.1-HDF5-1.8.19`` ``foss/2017a`` +``2.7.1`` ``-Python-2.7.13`` ``intel/2017a`` ``2.7.1`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a`` -``2.7.1`` ``-Python-2.7.14-serial`` ``intel/2018a`` -``2.7.1`` ``-Python-3.6.1`` ``intel/2017a`` -``2.7.1`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b`` -``2.7.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``2.8.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``2.8.0`` ``-Python-2.7.15-serial`` ``intel/2018b`` -``2.8.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``2.9.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``2.10.0`` ``-Python-2.7.18`` ``intel/2020a`` -``2.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` -``2.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` -``2.10.0`` ``-serial-Python-3.7.4`` ``foss/2019b`` -``3.1.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -``3.2.1`` ``foss/2021a`` -``3.6.0`` ``foss/2021b``, ``intel/2021b`` -``3.7.0`` ``foss/2022a`` +``2.7.1`` ``-Python-2.7.14-serial`` ``intel/2018a`` +``2.7.1`` ``-Python-3.6.1`` ``intel/2017a`` +``2.7.1`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b`` +``2.7.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``2.8.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``2.8.0`` ``-Python-2.7.15-serial`` ``intel/2018b`` +``2.8.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``2.9.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` +``2.10.0`` ``-Python-2.7.18`` ``intel/2020a`` +``2.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` +``2.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` +``2.10.0`` ``-serial-Python-3.7.4`` ``foss/2019b`` +``3.1.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +``3.2.1`` ``foss/2021a``, ``gomkl/2021a`` +``3.6.0`` ``foss/2021b``, ``intel/2021b`` +``3.7.0`` ``foss/2022a`` ========== ===================================== ==================================================================================== @@ -17807,16 +18443,16 @@ Hadoop MapReduce by Cloudera *homepage*: https://archive.cloudera.com/cdh5/cdh/5/ =================== ========================== ================== -version versionsuffix toolchain +version versionsuffix toolchain =================== ========================== ================== -``2.4.0`` ``-seagate-722af1-native`` ``system`` -``2.5.0-cdh5.3.1`` ``-native`` ``system`` -``2.6.0-cdh5.4.5`` ``-native`` ``system`` -``2.6.0-cdh5.7.0`` ``-native`` ``system`` -``2.6.0-cdh5.8.0`` ``-native`` ``system`` -``2.6.0-cdh5.12.0`` ``-native`` ``system`` -``2.9.2`` ``-native`` ``GCCcore/7.3.0`` -``2.10.0`` ``-native`` ``GCCcore/8.3.0`` +``2.4.0`` ``-seagate-722af1-native`` ``system`` +``2.5.0-cdh5.3.1`` ``-native`` ``system`` +``2.6.0-cdh5.4.5`` ``-native`` ``system`` +``2.6.0-cdh5.7.0`` ``-native`` ``system`` +``2.6.0-cdh5.8.0`` ``-native`` ``system`` +``2.6.0-cdh5.12.0`` ``-native`` ``system`` +``2.9.2`` ``-native`` ``GCCcore/7.3.0`` +``2.10.0`` ``-native`` ``GCCcore/8.3.0`` ``2.10.0`` ``-native-Java-1.8`` ``GCCcore/10.2.0`` =================== ========================== ================== @@ -17831,7 +18467,7 @@ HAL is a structure to efficiently store and index multiple genome alignments and *homepage*: https://github.com/ComparativeGenomicsToolkit/hal ======= ============== -version toolchain +version toolchain ======= ============== ``2.1`` ``foss/2020b`` ======= ============== @@ -17847,27 +18483,27 @@ HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters ove *homepage*: https://github.com/hpcugent/hanythingondemand ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== -``3.0.0`` ``-cli`` ``system`` -``3.0.1`` ``-cli`` ``system`` -``3.0.2`` ``-cli`` ``system`` -``3.0.3`` ``-cli`` ``system`` -``3.0.4`` ``-cli`` ``system`` +``3.0.0`` ``-cli`` ``system`` +``3.0.1`` ``-cli`` ``system`` +``3.0.2`` ``-cli`` ``system`` +``3.0.3`` ``-cli`` ``system`` +``3.0.4`` ``-cli`` ``system`` ``3.1.0`` ``-Python-2.7.11`` ``intel/2016a`` -``3.1.0`` ``-cli`` ``system`` +``3.1.0`` ``-cli`` ``system`` ``3.1.1`` ``-Python-2.7.11`` ``intel/2016a`` -``3.1.1`` ``-cli`` ``system`` +``3.1.1`` ``-cli`` ``system`` ``3.1.2`` ``-Python-2.7.11`` ``intel/2016a`` -``3.1.2`` ``-cli`` ``system`` +``3.1.2`` ``-cli`` ``system`` ``3.1.3`` ``-Python-2.7.12`` ``intel/2016b`` -``3.1.3`` ``-cli`` ``system`` +``3.1.3`` ``-cli`` ``system`` ``3.1.4`` ``-Python-2.7.12`` ``intel/2016b`` -``3.1.4`` ``-cli`` ``system`` +``3.1.4`` ``-cli`` ``system`` ``3.2.0`` ``-Python-2.7.12`` ``intel/2016b`` -``3.2.0`` ``-cli`` ``system`` +``3.2.0`` ``-cli`` ``system`` ``3.2.2`` ``-Python-2.7.12`` ``intel/2016b`` -``3.2.2`` ``-cli`` ``system`` +``3.2.2`` ``-cli`` ``system`` ========= ================== =============== @@ -17881,7 +18517,7 @@ version versionsuffix toolchain *homepage*: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html ========= ========== -version toolchain +version toolchain ========= ========== ``2.2.0`` ``system`` ========= ========== @@ -17897,22 +18533,23 @@ HarfBuzz is an OpenType text shaping engine. *homepage*: https://www.freedesktop.org/wiki/Software/HarfBuzz ========= ================================================ -version toolchain +version toolchain ========= ================================================ -``1.1.3`` ``foss/2016a``, ``intel/2016a`` -``1.2.7`` ``foss/2016a``, ``intel/2016a`` +``1.1.3`` ``foss/2016a``, ``intel/2016a`` +``1.2.7`` ``foss/2016a``, ``intel/2016a`` ``1.3.1`` ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``1.5.1`` ``intel/2017a`` -``1.7.1`` ``foss/2017b``, ``intel/2017b`` -``1.7.5`` ``foss/2018a``, ``intel/2018a`` -``1.9.0`` ``fosscuda/2018b`` -``2.2.0`` ``foss/2018b``, ``fosscuda/2018b`` -``2.4.0`` ``GCCcore/8.2.0`` -``2.6.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.6.7`` ``GCCcore/10.2.0`` -``2.8.1`` ``GCCcore/10.3.0`` -``2.8.2`` ``GCCcore/11.2.0`` -``4.2.1`` ``GCCcore/11.3.0`` +``1.5.1`` ``intel/2017a`` +``1.7.1`` ``foss/2017b``, ``intel/2017b`` +``1.7.5`` ``foss/2018a``, ``intel/2018a`` +``1.9.0`` ``fosscuda/2018b`` +``2.2.0`` ``foss/2018b``, ``fosscuda/2018b`` +``2.4.0`` ``GCCcore/8.2.0`` +``2.6.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.6.7`` ``GCCcore/10.2.0`` +``2.8.1`` ``GCCcore/10.3.0`` +``2.8.2`` ``GCCcore/11.2.0`` +``4.2.1`` ``GCCcore/11.3.0`` +``5.3.1`` ``GCCcore/12.2.0`` ========= ================================================ @@ -17926,9 +18563,9 @@ Harminv is a free program (and accompanying library) to solve the problem of har *homepage*: https://github.com/stevengj/harminv ========= ================================================================ -version toolchain +version toolchain ========= ================================================================ -``1.4`` ``foss/2016a`` +``1.4`` ``foss/2016a`` ``1.4.1`` ``foss/2017b``, ``foss/2018a``, ``intel/2018a``, ``intel/2020a`` ========= ================================================================ @@ -17943,7 +18580,7 @@ Harmony is a general-purpose R package with an efficient algorithm for integrati *homepage*: https://portals.broadinstitute.org/harmony ================== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ============= ============== ``1.0.0-20200224`` ``-R-4.0.0`` ``foss/2020a`` ================== ============= ============== @@ -17959,7 +18596,7 @@ Apache HBase. is the Hadoop database, a distributed, scalable, big data store. *homepage*: http://hbase.apache.org/ ========= ========== -version toolchain +version toolchain ========= ========== ``1.0.2`` ``system`` ========= ========== @@ -17975,7 +18612,7 @@ The hdbscan library is a suite of tools to use unsupervised learning to find clu *homepage*: http://hdbscan.readthedocs.io/en/latest/ ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.8.24`` ``-Python-3.7.4`` ``foss/2019b`` ``0.8.27`` ``foss/2021a`` @@ -17992,7 +18629,7 @@ HDDM is a Python toolbox for hierarchical Bayesian parameter estimation of the *homepage*: http://ski.clps.brown.edu/hddm_docs ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.6.1`` ``-Python-3.6.6`` ``intel/2018b`` ``0.7.5`` ``-Python-2.7.16`` ``intel/2019b`` @@ -18010,13 +18647,13 @@ HDF (also known as HDF4) is a library and multi-object file format for storing *homepage*: https://www.hdfgroup.org/products/hdf4/ ========== ============== ================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ============== ================================================================================================= -``4.2.11`` ``intel/2016a`` -``4.2.12`` ``intel/2017a`` -``4.2.13`` ``GCCcore/6.4.0`` -``4.2.13`` ``-no-netcdf`` ``intel/2017a`` -``4.2.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``4.2.11`` ``intel/2016a`` +``4.2.12`` ``intel/2017a`` +``4.2.13`` ``GCCcore/6.4.0`` +``4.2.13`` ``-no-netcdf`` ``intel/2017a`` +``4.2.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``4.2.15`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` ========== ============== ================================================================================================= @@ -18031,7 +18668,7 @@ HDF-EOS libraries are software libraries built on HDF libraries. It supports th *homepage*: https://hdfeos.org/ ======== ======================================================== -version toolchain +version toolchain ======== ======================================================== ``2.20`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ======== ======================================================== @@ -18047,7 +18684,7 @@ HDF-EOS libraries are software libraries built on HDF libraries. It supports th *homepage*: https://hdfeos.org/ ======== ================================================ -version toolchain +version toolchain ======== ================================================ ``1.16`` ``foss/2018b``, ``gompi/2019b``, ``gompi/2020b`` ======== ================================================ @@ -18063,34 +18700,34 @@ HDF5 is a data model, library, and file format for storing and managing data. I *homepage*: https://portal.hdfgroup.org/display/support ================= ============= ================================================================================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ================= ============= ================================================================================================================================================================================================================== -``1.8.10`` ``-serial`` ``GCC/4.8.1`` -``1.8.11`` ``-serial`` ``GCC/4.8.1`` -``1.8.12`` ``foss/2018b``, ``intel/2016b`` -``1.8.13`` ``foss/2018b`` -``1.8.16`` ``foss/2016a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``1.8.16`` ``-serial`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``1.8.17`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``1.8.17`` ``-serial`` ``GCC/5.4.0-2.26``, ``foss/2016a``, ``intel/2016b`` -``1.8.18`` ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a`` -``1.8.18`` ``-serial`` ``intel/2017a`` -``1.8.19`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``1.8.20`` ``foss/2018a``, ``gmpolf/2017.10``, ``intel/2017b``, ``intel/2018a`` -``1.10.0-patch1`` ``foss/2016b``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a`` +``1.8.10`` ``-serial`` ``GCC/4.8.1`` +``1.8.11`` ``-serial`` ``GCC/4.8.1`` +``1.8.12`` ``foss/2018b``, ``intel/2016b`` +``1.8.13`` ``foss/2018b`` +``1.8.16`` ``foss/2016a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` +``1.8.16`` ``-serial`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``1.8.17`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``1.8.17`` ``-serial`` ``GCC/5.4.0-2.26``, ``foss/2016a``, ``intel/2016b`` +``1.8.18`` ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a`` +``1.8.18`` ``-serial`` ``intel/2017a`` +``1.8.19`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``1.8.20`` ``foss/2018a``, ``gmpolf/2017.10``, ``intel/2017b``, ``intel/2018a`` +``1.10.0-patch1`` ``foss/2016b``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a`` ``1.10.1`` ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2017b``, ``iomkl/2018a`` -``1.10.2`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``1.10.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompic/2019a``, ``gompic/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpic/2019a``, ``iimpic/2019b``, ``iompi/2019b`` -``1.10.5`` ``-serial`` ``GCCcore/8.3.0`` -``1.10.6`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpic/2020a`` -``1.10.7`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpic/2020b`` -``1.10.8`` ``gompi/2021b`` -``1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` -``1.12.1`` ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021b`` -``1.12.2`` ``gompi/2022a``, ``iimpi/2022a`` -``1.12.2`` ``-serial`` ``GCCcore/11.3.0`` -``1.13.1`` ``gompi/2022a``, ``iimpi/2022a`` -``1.13.1`` ``-serial`` ``GCCcore/11.3.0`` +``1.10.2`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``1.10.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompic/2019a``, ``gompic/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpic/2019a``, ``iimpic/2019b``, ``iompi/2019b`` +``1.10.5`` ``-serial`` ``GCCcore/8.3.0`` +``1.10.6`` ``gompi/2020a``, ``gompic/2020a``, ``iimpi/2020a``, ``iimpic/2020a`` +``1.10.7`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpic/2020b`` +``1.10.8`` ``gompi/2021b``, ``gompi/2022a`` +``1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` +``1.12.1`` ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021b`` +``1.12.2`` ``gompi/2022a``, ``iimpi/2022a`` +``1.12.2`` ``-serial`` ``GCCcore/11.3.0`` +``1.13.1`` ``gompi/2022a``, ``iimpi/2022a`` +``1.13.1`` ``-serial`` ``GCCcore/11.3.0`` ================= ============= ================================================================================================================================================================================================================== @@ -18104,7 +18741,7 @@ This Python package provides high level utilities to read/write a variety of Pyt *homepage*: https://pythonhosted.org/hdf5storage/ ========== ================================== -version toolchain +version toolchain ========== ================================== ``0.1.15`` ``foss/2019a``, ``fosscuda/2019a`` ========== ================================== @@ -18120,7 +18757,7 @@ HDFView is a visual tool for browsing and editing HDF4 and HDF5 files. *homepage*: https://support.hdfgroup.org/products/java/hdfview/ ======== =========================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ======== =========================== ========== ``2.14`` ``-Java-1.8.0_152-centos6`` ``system`` ``2.14`` ``-Java-1.8.0_152-centos7`` ``system`` @@ -18137,7 +18774,7 @@ Hierarchical Equal Area isoLatitude Pixelation of a sphere. *homepage*: http://healpix.sourceforge.net/ ======== ==================================== -version toolchain +version toolchain ======== ==================================== ``3.50`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ======== ==================================== @@ -18153,7 +18790,7 @@ A heap memory profiler for Linux. *homepage*: http://milianw.de/blog/heaptrack-a-heap-memory-profiler-for-linux ========= ============== -version toolchain +version toolchain ========= ============== ``1.1.0`` ``foss/2016b`` ========= ============== @@ -18169,7 +18806,7 @@ This is the repository for Hector, an open source, object-oriented, simple glob *homepage*: https://github.com/JGCRI/hector ========= ============== -version toolchain +version toolchain ========= ============== ``2.5.0`` ``GCC/11.2.0`` ========= ============== @@ -18185,7 +18822,7 @@ Highly Efficient FFT for Exascale (HeFFTe) library *homepage*: https://icl.utk.edu/fft ======= ============== -version toolchain +version toolchain ======= ============== ``1.0`` ``foss/2020a`` ======= ============== @@ -18201,7 +18838,7 @@ The GNU Hello program produces a familiar, friendly greeting. Yes, this is anoth *homepage*: https://www.gnu.org/software/hello/ ======== ================= -version toolchain +version toolchain ======== ================= ``2.10`` ``GCCcore/8.2.0`` ======== ================= @@ -18217,19 +18854,19 @@ help2man produces simple manual pages from the '--help' and '--version' output o *homepage*: https://www.gnu.org/software/help2man/ =========== ================================================================================================================================================================================== -version toolchain +version toolchain =========== ================================================================================================================================================================================== ``1.47.4`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/system``, ``gimkl/2017a``, ``intel/2016b``, ``system`` -``1.47.5`` ``GCCcore/5.5.0`` -``1.47.6`` ``GCCcore/8.1.0`` -``1.47.7`` ``GCCcore/8.2.0`` -``1.47.8`` ``GCCcore/7.4.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0`` -``1.47.10`` ``GCCcore/9.1.0``, ``GCCcore/9.2.0`` -``1.47.12`` ``GCCcore/9.3.0`` -``1.47.15`` ``GCCcore/10.1.0`` -``1.47.16`` ``GCCcore/10.2.0`` -``1.48.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0`` -``1.49.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0`` +``1.47.5`` ``GCCcore/5.5.0`` +``1.47.6`` ``GCCcore/8.1.0`` +``1.47.7`` ``GCCcore/8.2.0`` +``1.47.8`` ``GCCcore/7.4.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0`` +``1.47.10`` ``GCCcore/9.1.0``, ``GCCcore/9.2.0`` +``1.47.12`` ``GCCcore/9.3.0`` +``1.47.15`` ``GCCcore/10.1.0`` +``1.47.16`` ``GCCcore/10.2.0`` +``1.48.3`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/9.4.0`` +``1.49.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0`` =========== ================================================================================================================================================================================== @@ -18243,12 +18880,12 @@ The HH-suite is an open-source software package for sensitive protein sequence *homepage*: https://github.com/soedinglab/hh-suite ============== ================= =================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================= =================================================================================== -``3.0-beta.3`` ``intel/2018a`` -``3.2.0`` ``foss/2019b``, ``fosscuda/2019b`` +``3.0-beta.3`` ``intel/2018a`` +``3.2.0`` ``foss/2019b``, ``fosscuda/2019b`` ``3.3.0`` ``foss/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b`` -``3.3.0`` ``-Python-3.7.4`` ``gompic/2019b`` +``3.3.0`` ``-Python-3.7.4`` ``gompic/2019b`` ============== ================= =================================================================================== @@ -18262,7 +18899,7 @@ HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illu *homepage*: http://nservant.github.io/HiC-Pro ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.9.0`` ``-Python-2.7.12`` ``foss/2016b`` ========= ================== ============== @@ -18278,7 +18915,7 @@ HiCexplorer addresses the common tasks of Hi-C analysis from processing to visua *homepage*: http://hicexplorer.readthedocs.org/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``2.1.1`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================= ============== @@ -18294,7 +18931,7 @@ Estimates hierarchical F-statistics from haploid or diploid genetic data with an *homepage*: https://cran.r-project.org/package=hierfstat ========= ========================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ========================= ============== ``0.5-7`` ``-R-4.0.0-Python-3.8.2`` ``foss/2020a`` ========= ========================= ============== @@ -18310,13 +18947,29 @@ Hifiasm: a haplotype-resolved assembler for accurate Hifi reads. *homepage*: https://github.com/chhylp123/hifiasm ========== ===================================== -version toolchain +version toolchain ========== ===================================== ``0.15.2`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``0.16.1`` ``GCCcore/10.3.0`` +``0.16.1`` ``GCCcore/10.3.0`` ========== ===================================== +.. _list_software_HighFive_778: + +*HighFive* +++++++++++ + +HighFive is a modern header-only C++11 friendly interface for libhdf5. + +*homepage*: https://github.com/BlueBrain/HighFive + +========= =============== +version toolchain +========= =============== +``2.6.2`` ``gompi/2021a`` +========= =============== + + .. _list_software_Highway_721: *Highway* @@ -18327,7 +18980,7 @@ Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. appl *homepage*: https://github.com/google/highway ========== ====================================== -version toolchain +version toolchain ========== ====================================== ``0.12.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========== ====================================== @@ -18343,7 +18996,7 @@ HIP is a C++ Runtime API and Kernel Language that allows developers to create po *homepage*: https://github.com/ROCm-Developer-Tools/HIP ========= ============= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ================== ``4.5.0`` ``-amd`` ``GCCcore/11.2.0`` ========= ============= ================== @@ -18359,7 +19012,7 @@ Hipify-clang is a clang-based tool for translating CUDA sources into HIP sourc *homepage*: https://github.com/ROCm-Developer-Tools/HIPIFY ========= ================= -version toolchain +version toolchain ========= ================= ``4.2.0`` ``gcccuda/2020b`` ========= ================= @@ -18375,7 +19028,7 @@ HIPS (Hierarchical Iterative Parallel Solver) is a scientific library that provi *homepage*: http://hips.gforge.inria.fr/ ============ ============== -version toolchain +version toolchain ============ ============== ``1.2b-rc5`` ``foss/2017b`` ============ ============== @@ -18391,7 +19044,7 @@ hipSYCL is a modern SYCL implementation targeting CPUs and GPUs, with a focus on *homepage*: https://github.com/illuhad/hipSYCL ========= ================================= -version toolchain +version toolchain ========= ================================= ``0.9.1`` ``GCC/10.2.0``, ``gcccuda/2020b`` ========= ================================= @@ -18407,7 +19060,7 @@ Hiredis is a minimalistic C client library for the Redis database. It is minima *homepage*: https://github.com/redis/hiredis ========= ====================================== -version toolchain +version toolchain ========= ====================================== ``1.0.2`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ====================================== @@ -18423,14 +19076,14 @@ HISAT2 is a fast and sensitive alignment program for mapping next-generation seq *homepage*: https://daehwankimlab.github.io/hisat2 ============== ================================================================================= -version toolchain +version toolchain ============== ================================================================================= -``2.0.3-beta`` ``intel/2016a`` -``2.0.4`` ``foss/2016b`` -``2.0.5`` ``intel/2017a`` +``2.0.3-beta`` ``intel/2016a`` +``2.0.4`` ``foss/2016b`` +``2.0.5`` ``intel/2017a`` ``2.1.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``2.2.0`` ``foss/2018b`` -``2.2.1`` ``foss/2019b``, ``foss/2020a``, ``gompi/2020b``, ``gompi/2021b`` +``2.2.0`` ``foss/2018b`` +``2.2.1`` ``foss/2019b``, ``foss/2020a``, ``gompi/2020b``, ``gompi/2021b`` ============== ================================================================================= @@ -18444,7 +19097,7 @@ Library for Digital Pathology Image Processing *homepage*: https://github.com/histolab/histolab ========= ============================== -version toolchain +version toolchain ========= ============================== ``0.4.1`` ``foss/2021a``, ``foss/2021b`` ========= ============================== @@ -18460,7 +19113,7 @@ HIV-TRACE is an application that identifies potential transmission clusters with *homepage*: https://github.com/veg/hivtrace ========= ============== -version toolchain +version toolchain ========= ============== ``0.6.2`` ``foss/2021a`` ========= ============== @@ -18476,7 +19129,7 @@ Python library to parse, create and handle HL7 v2 messages. *homepage*: https://github.com/crs4/hl7apy ========= ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================= ``1.3.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========= ================= ================= @@ -18492,7 +19145,7 @@ HLAminer is a software for HLA predictions from next-generation shotgun (NGS) se *homepage*: http://www.bcgsc.ca/platform/bioinfo/software/hlaminer ======= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================ ============== ``1.4`` ``-Perl-5.28.0`` ``foss/2018b`` ======= ================ ============== @@ -18508,12 +19161,12 @@ HMMER is used for searching sequence databases for homologs of protein sequence *homepage*: http://hmmer.org/ ========= ============================================================================================================================================ -version toolchain +version toolchain ========= ============================================================================================================================================ ``3.1b2`` ``GCC/6.4.0-2.28``, ``foss/2016a``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a``, ``intel/2018a`` -``3.2.1`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iimpi/2019b``, ``intel/2018b`` -``3.3.1`` ``gompi/2020a``, ``iimpi/2020a`` -``3.3.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021b`` +``3.2.1`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iimpi/2019b``, ``intel/2018b`` +``3.3.1`` ``gompi/2020a``, ``iimpi/2020a`` +``3.3.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021b`` ========= ============================================================================================================================================ @@ -18527,7 +19180,7 @@ HMMER is used for searching sequence databases for sequence homologs, and for m *homepage*: http://hmmer.org ========= ============================================= -version toolchain +version toolchain ========= ============================================= ``2.3.2`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0`` ========= ============================================= @@ -18543,7 +19196,7 @@ hmmlearn is a set of algorithms for unsupervised learning and inference of Hidde *homepage*: https://github.com/hmmlearn/hmmlearn ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.2.0`` ``-Python-2.7.14`` ``intel/2017b`` ``0.2.0`` ``-Python-3.6.4`` ``intel/2018a`` @@ -18560,7 +19213,7 @@ HOME (histogram of methylation) is a python package for differential methylation *homepage*: https://github.com/ListerLab/HOME ======= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== ============== ``0.9`` ``-Python-2.7.13`` ``foss/2017a`` ======= ================== ============== @@ -18576,27 +19229,27 @@ Horovod is a distributed training framework for TensorFlow. *homepage*: https://github.com/uber/horovod ========== =================================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== =================================== ================================== -``0.9.10`` ``-Python-3.6.3`` ``intel/2017b`` -``0.18.1`` ``-Python-3.7.2`` ``foss/2019a`` -``0.18.2`` ``-TensorFlow-1.15.0-Python-3.7.4`` ``fosscuda/2019b`` -``0.18.2`` ``-TensorFlow-1.15.2-Python-3.7.4`` ``fosscuda/2019b`` -``0.18.2`` ``-TensorFlow-2.0.0-Python-3.7.4`` ``fosscuda/2019b`` -``0.19.1`` ``-TensorFlow-2.1.0-Python-3.7.4`` ``fosscuda/2019b`` -``0.19.5`` ``-TensorFlow-2.2.0-Python-3.7.4`` ``fosscuda/2019b`` -``0.20.3`` ``-TensorFlow-2.3.1-Python-3.7.4`` ``fosscuda/2019b`` -``0.21.1`` ``-PyTorch-1.7.1-Python-3.7.4`` ``fosscuda/2019b`` -``0.21.1`` ``-TensorFlow-2.4.1`` ``fosscuda/2020b`` -``0.21.1`` ``-TensorFlow-2.4.1-Python-3.7.4`` ``fosscuda/2019b`` -``0.21.3`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` +``0.9.10`` ``-Python-3.6.3`` ``intel/2017b`` +``0.18.1`` ``-Python-3.7.2`` ``foss/2019a`` +``0.18.2`` ``-TensorFlow-1.15.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.18.2`` ``-TensorFlow-1.15.2-Python-3.7.4`` ``fosscuda/2019b`` +``0.18.2`` ``-TensorFlow-2.0.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.19.1`` ``-TensorFlow-2.1.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.19.5`` ``-TensorFlow-2.2.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.20.3`` ``-TensorFlow-2.3.1-Python-3.7.4`` ``fosscuda/2019b`` +``0.21.1`` ``-PyTorch-1.7.1-Python-3.7.4`` ``fosscuda/2019b`` +``0.21.1`` ``-TensorFlow-2.4.1`` ``fosscuda/2020b`` +``0.21.1`` ``-TensorFlow-2.4.1-Python-3.7.4`` ``fosscuda/2019b`` +``0.21.3`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` ``0.21.3`` ``-TensorFlow-2.3.1-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` -``0.22.0`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` -``0.22.1`` ``-CUDA-11.3.1-TensorFlow-2.6.0`` ``foss/2021a`` -``0.22.1`` ``-TensorFlow-2.5.0`` ``fosscuda/2020b`` -``0.22.1`` ``-TensorFlow-2.5.0-Python-3.7.4`` ``fosscuda/2019b`` -``0.23.0`` ``-CUDA-11.3.1-PyTorch-1.10.0`` ``foss/2021a`` -``0.23.0`` ``-TensorFlow-2.5.0`` ``fosscuda/2020b`` +``0.22.0`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` +``0.22.1`` ``-CUDA-11.3.1-TensorFlow-2.6.0`` ``foss/2021a`` +``0.22.1`` ``-TensorFlow-2.5.0`` ``fosscuda/2020b`` +``0.22.1`` ``-TensorFlow-2.5.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.23.0`` ``-CUDA-11.3.1-PyTorch-1.10.0`` ``foss/2021a`` +``0.23.0`` ``-TensorFlow-2.5.0`` ``fosscuda/2020b`` ========== =================================== ================================== @@ -18610,10 +19263,10 @@ HORTON is a Helpful Open-source Research TOol for N-fermion systems, written pr *homepage*: https://theochem.github.io/horton ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== ``2.1.1`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``2.1.1`` ``-Python-2.7.18`` ``intel/2020a`` +``2.1.1`` ``-Python-2.7.18`` ``intel/2020a`` ========= ================== =============================== @@ -18627,7 +19280,7 @@ Python package for testing strandedness of RNA-Seq fastq files *homepage*: https://github.com/signalbash/how_are_we_stranded_here ========= ============== -version toolchain +version toolchain ========= ============== ``1.0.1`` ``foss/2021b`` ========= ============== @@ -18643,9 +19296,9 @@ The HPCG Benchmark project is an effort to create a more relevant metric for ran *homepage*: https://software.sandia.gov/hpcg ======= ================================================================================================= -version toolchain +version toolchain ======= ================================================================================================= -``3.0`` ``foss/2016b``, ``foss/2018b``, ``intel/2018b`` +``3.0`` ``foss/2016b``, ``foss/2018b``, ``intel/2018b`` ``3.1`` ``foss/2018b``, ``foss/2021a``, ``foss/2021b``, ``intel/2018b``, ``intel/2021a``, ``intel/2021b`` ======= ================================================================================================= @@ -18660,7 +19313,7 @@ The Mellanox HPC-X Toolkit is a comprehensive MPI and SHMEM/PGAS software suite *homepage*: http://www.mellanox.com/page/products_dyn?product_family=189&mtag=hpc-x ========= ==================== -version toolchain +version toolchain ========= ==================== ``2.3.0`` ``GCC/8.2.0-2.31.1`` ========= ==================== @@ -18676,7 +19329,7 @@ Highly parallel density based spatial clustering for application with noise *homepage*: https://github.com/Markus-Goetz/hpdbscan ============ ============== -version toolchain +version toolchain ============ ============== ``20171110`` ``foss/2017b`` ``20210826`` ``foss/2020b`` @@ -18692,13 +19345,13 @@ HPL is a software package that solves a (random) dense linear system in double p *homepage*: https://www.netlib.org/benchmark/hpl/ -======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain -======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` +======= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================ +version toolchain +======= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================ +``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``goblf/2018b``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` -``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intel/2022.09``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` -======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== +``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``Fujitsu/21.05``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022.05``, ``foss/2022.10``, ``foss/2022a``, ``foss/2022b``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``gobff/2020.06-amd``, ``gobff/2020.11``, ``gobff/2020b``, ``gobff/2021a``, ``goblf/2020b``, ``gomkl/2019a``, ``gomkl/2020b``, ``gomkl/2021a``, ``iibff/2020b``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intel/2020.06-impi-18.5``, ``intel/2020.12``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022.00``, ``intel/2022.09``, ``intel/2022.11``, ``intel/2022b``, ``intelcuda/2019b``, ``intelcuda/2020a``, ``iomkl/2019.01``, ``iomkl/2021a`` +======= ================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================ .. _list_software_htop_443: @@ -18711,7 +19364,7 @@ An interactive process viewer for Unix *homepage*: https://htop.dev ========= ========== -version toolchain +version toolchain ========= ========== ``2.0.0`` ``system`` ``2.0.1`` ``system`` @@ -18724,25 +19377,26 @@ version toolchain *HTSeq* +++++++ -A framework to process and analyze data from high-throughput sequencing (HTS) assays +HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. -*homepage*: https://www-huber.embl.de/users/anders/HTSeq/ +*homepage*: https://github.com/simon-anders/htseq =========== ================== ================================================ -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ================================================ -``0.6.1p1`` ``-Python-2.7.11`` ``foss/2016a`` -``0.6.1p1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``0.9.1`` ``-Python-2.7.12`` ``foss/2016b`` -``0.9.1`` ``-Python-2.7.13`` ``intel/2017a`` +``0.6.1p1`` ``-Python-2.7.11`` ``foss/2016a`` +``0.6.1p1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``0.9.1`` ``-Python-2.7.12`` ``foss/2016b`` +``0.9.1`` ``-Python-2.7.13`` ``intel/2017a`` ``0.9.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``0.9.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``0.10.0`` ``-Python-2.7.14`` ``foss/2018a`` -``0.11.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``0.11.2`` ``-Python-3.6.6`` ``foss/2018b`` -``0.11.2`` ``-Python-3.7.2`` ``foss/2019a`` -``0.11.2`` ``-Python-3.7.4`` ``foss/2019b`` -``0.11.3`` ``foss/2020b``, ``foss/2021b`` +``0.9.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``0.10.0`` ``-Python-2.7.14`` ``foss/2018a`` +``0.11.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.11.2`` ``-Python-3.6.6`` ``foss/2018b`` +``0.11.2`` ``-Python-3.7.2`` ``foss/2019a`` +``0.11.2`` ``-Python-3.7.4`` ``foss/2019b`` +``0.11.3`` ``foss/2020b``, ``foss/2021b`` +``2.0.2`` ``foss/2022a`` =========== ================== ================================================ @@ -18756,24 +19410,24 @@ PacBio fork of C library for reading/writing high-throughput sequencing data. T *homepage*: https://github.com/PacificBiosciences/htslib ============ ============= =========================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= =========================================================================================================================================================== -``1.2.1`` ``foss/2016b`` -``1.3`` ``foss/2016a``, ``intel/2016a`` -``1.3.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``1.3.2`` ``intel/2016b`` -``1.4`` ``foss/2016b``, ``intel/2016b`` -``1.4.1`` ``foss/2016a``, ``intel/2017a`` -``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` -``1.7`` ``intel/2018a`` -``1.8`` ``GCC/6.4.0-2.28``, ``foss/2018a``, ``intel/2018a`` +``1.2.1`` ``foss/2016b`` +``1.3`` ``foss/2016a``, ``intel/2016a`` +``1.3.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` +``1.3.2`` ``intel/2016b`` +``1.4`` ``foss/2016b``, ``intel/2016b`` +``1.4.1`` ``foss/2016a``, ``intel/2017a`` +``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` +``1.7`` ``intel/2018a`` +``1.8`` ``GCC/6.4.0-2.28``, ``foss/2018a``, ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` -``1.11`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` -``1.14`` ``GCC/11.2.0`` -``1.15.1`` ``GCC/11.3.0`` -``20160107`` ``-PacBio`` ``intel/2017a`` +``1.10.2`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` +``1.11`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` +``1.14`` ``GCC/11.2.0`` +``1.15.1`` ``GCC/11.3.0`` +``20160107`` ``-PacBio`` ``intel/2017a`` ============ ============= =========================================================================================================================================================== @@ -18787,28 +19441,44 @@ hub is a command-line wrapper for git that makes you better at GitHub. *homepage*: https://hub.github.com/ ========= ================ ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ========== ``2.2.2`` ``-linux-amd64`` ``system`` ========= ================ ========== +.. _list_software_humann_647: + +*humann* +++++++++ + +HUMAnN v3 is a pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data. Sequencing a metagenome typically produces millions of short DNA/RNA reads. This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question: What are the microbes in my community-of-interest doing (or capable of doing)? + +*homepage*: http://huttenhower.sph.harvard.edu/humann + +======= ============== +version toolchain +======= ============== +``3.6`` ``foss/2022a`` +======= ============== + + .. _list_software_hunspell_875: *hunspell* ++++++++++ -Hunspell is a spell checker and morphological analyzer library and program designed for languageswith rich morphology and complex word compounding or character encoding. +Hunspell is a spell checker and morphological analyzer library and program designed for languageswith rich morphology and complex word compounding or character encoding. -*homepage*: http://hunspell.github.io/ +*homepage*: https://hunspell.github.io/ -========= ================== -version toolchain -========= ================== -``1.6.1`` ``intel/2017a`` -``1.7.0`` ``GCCcore/8.2.0`` -``1.7.1`` ``GCCcore/11.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.6.1`` ``intel/2017a`` +``1.7.0`` ``GCCcore/8.2.0`` +``1.7.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ====================================== .. _list_software_hwloc_541: @@ -18821,32 +19491,33 @@ The Portable Hardware Locality (hwloc) software package provides a portable abs *homepage*: https://www.open-mpi.org/projects/hwloc/ =========== ===================================================================================================================================================================================================================================================== -version toolchain +version toolchain =========== ===================================================================================================================================================================================================================================================== -``1.7.2`` ``GCC/4.8.2`` -``1.8.1`` ``GCC/4.8.2``, ``GCC/4.8.3`` -``1.9`` ``GCC/4.8.3`` -``1.10.0`` ``GCC/4.9.2`` -``1.10.1`` ``GCC/4.8.4``, ``GNU/4.9.2-2.25`` -``1.11.0`` ``GNU/4.9.3-2.25`` -``1.11.1`` ``GCC/4.9.3`` -``1.11.2`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25`` +``1.7.2`` ``GCC/4.8.2`` +``1.8.1`` ``GCC/4.8.2``, ``GCC/4.8.3`` +``1.9`` ``GCC/4.8.3`` +``1.10.0`` ``GCC/4.9.2`` +``1.10.1`` ``GCC/4.8.4``, ``GNU/4.9.2-2.25`` +``1.11.0`` ``GNU/4.9.3-2.25`` +``1.11.1`` ``GCC/4.9.3`` +``1.11.2`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25`` ``1.11.3`` ``GCC/5.2.0``, ``GCC/5.3.0-2.26``, ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``PGI/16.3-GCC-4.9.3-2.25``, ``PGI/16.4-GCC-5.3.0-2.26``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` -``1.11.4`` ``GCC/6.2.0-2.27``, ``PGI/16.7-GCC-5.4.0-2.26``, ``iccifort/2017.1.132-GCC-5.4.0-2.26`` -``1.11.5`` ``GCC/5.4.0-2.26``, ``GCC/6.3.0-2.27``, ``iccifort/2017.1.132-GCC-6.3.0-2.27`` -``1.11.6`` ``GCC/6.3.0-2.28`` -``1.11.7`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0`` -``1.11.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``intel/2017a`` -``1.11.10`` ``GCCcore/7.3.0`` -``1.11.11`` ``GCCcore/8.2.0`` -``1.11.12`` ``GCCcore/8.3.0`` -``2.0.2`` ``GCCcore/8.2.0`` -``2.0.3`` ``GCCcore/8.3.0`` -``2.1.0`` ``GCCcore/9.2.0`` -``2.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``2.4.1`` ``GCCcore/10.3.0`` -``2.5.0`` ``GCCcore/11.2.0`` -``2.7.1`` ``GCCcore/11.3.0`` +``1.11.4`` ``GCC/6.2.0-2.27``, ``PGI/16.7-GCC-5.4.0-2.26``, ``iccifort/2017.1.132-GCC-5.4.0-2.26`` +``1.11.5`` ``GCC/5.4.0-2.26``, ``GCC/6.3.0-2.27``, ``iccifort/2017.1.132-GCC-6.3.0-2.27`` +``1.11.6`` ``GCC/6.3.0-2.28`` +``1.11.7`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0`` +``1.11.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``intel/2017a`` +``1.11.10`` ``GCCcore/7.3.0`` +``1.11.11`` ``GCCcore/8.2.0`` +``1.11.12`` ``GCCcore/8.3.0`` +``2.0.2`` ``GCCcore/8.2.0`` +``2.0.3`` ``GCCcore/8.3.0`` +``2.1.0`` ``GCCcore/9.2.0`` +``2.2.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.4.1`` ``GCCcore/10.3.0`` +``2.5.0`` ``GCCcore/11.2.0`` +``2.7.1`` ``GCCcore/11.3.0`` +``2.8.0`` ``GCCcore/12.2.0`` =========== ===================================================================================================================================================================================================================================================== @@ -18860,7 +19531,7 @@ Hydra is an open-source Python framework that simplifies the development of rese *homepage*: https://hydra.cc/ ========= ================== -version toolchain +version toolchain ========= ================== ``1.1.1`` ``GCCcore/10.3.0`` ========= ================== @@ -18875,29 +19546,31 @@ hyperopt is a Python library for optimizing over awkward search spaces with real *homepage*: http://hyperopt.github.io/hyperopt/ -========= ================== =============== -version versionsuffix toolchain -========= ================== =============== -``0.1`` ``-Python-2.7.14`` ``intel/2017b`` -``0.1.1`` ``-Python-3.6.6`` ``intel/2018b`` -========= ================== =============== +========= ========================== ================== +version versionsuffix toolchain +========= ========================== ================== +``0.1`` ``-Python-2.7.14`` ``intel/2017b`` +``0.1.1`` ``-Python-3.6.6`` ``intel/2018b`` +``0.2.4`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` +``0.2.5`` ``fosscuda/2020b`` +``0.2.7`` ``foss/2021a`` +========= ========================== ================== -.. _list_software_hyperopt_891: +.. _list_software_HyperQueue_1037: -*hyperopt* -++++++++++ +*HyperQueue* +++++++++++++ -Distributed Asynchronous Hyperparameter Optimization in Python +HyperQueue lets you build a computation plan consisting of a large amount of tasks and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs and distributes them to fully utilize allocated nodes. You thus do not have to manually aggregate your tasks into SLURM/PBS jobs. -*homepage*: https://github.com/hyperopt/hyperopt +*homepage*: https://it4innovations.github.io/hyperqueue/ -========= ========================== ================== -version versionsuffix toolchain -========= ========================== ================== -``0.2.4`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` -``0.2.5`` ``fosscuda/2020b`` -========= ========================== ================== +========== ========== +version toolchain +========== ========== +``0.13.0`` ``system`` +========== ========== .. _list_software_hyperspy_900: @@ -18910,7 +19583,7 @@ HyperSpy is an open source Python library which provides tools to facilitate the *homepage*: https://hyperspy.org/ ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``1.1.1`` ``-Python-3.5.2`` ``intel/2016b`` ========= ================= =============== @@ -18926,9 +19599,9 @@ HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package *homepage*: https://veg.github.io/hyphy-site/ ========== =============== -version toolchain +version toolchain ========== =============== -``2.3.13`` ``foss/2016b`` +``2.3.13`` ``foss/2016b`` ``2.5.1`` ``gompi/2019a`` ``2.5.33`` ``gompi/2021a`` ========== =============== @@ -18944,7 +19617,7 @@ HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies *homepage*: https://github.com/kensung-lab/hypo ========= ================= ============= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============= ``1.0.3`` ``-Python-3.7.4`` ``GCC/8.3.0`` ========= ================= ============= @@ -18960,21 +19633,21 @@ Hypothesis is an advanced testing library for Python. It lets you write tests wh *homepage*: https://github.com/HypothesisWorks/hypothesis ========== ================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================================== ``4.5.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``4.23.4`` ``GCCcore/8.2.0`` -``4.39.3`` ``-Python-3.6.4`` ``intel/2018a`` -``4.44.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``4.53.1`` ``GCCcore/10.2.0`` -``4.57.1`` ``-Python-2.7.18`` ``GCCcore/11.2.0`` -``5.6.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``5.41.2`` ``GCCcore/10.2.0`` -``5.41.5`` ``GCCcore/10.2.0`` -``6.7.0`` ``GCCcore/10.2.0`` -``6.13.1`` ``GCCcore/10.3.0`` -``6.14.6`` ``GCCcore/11.2.0`` -``6.46.7`` ``GCCcore/11.3.0`` +``4.23.4`` ``GCCcore/8.2.0`` +``4.39.3`` ``-Python-3.6.4`` ``intel/2018a`` +``4.44.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``4.53.1`` ``GCCcore/10.2.0`` +``4.57.1`` ``-Python-2.7.18`` ``GCCcore/11.2.0`` +``5.6.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``5.41.2`` ``GCCcore/10.2.0`` +``5.41.5`` ``GCCcore/10.2.0`` +``6.7.0`` ``GCCcore/10.2.0`` +``6.13.1`` ``GCCcore/10.3.0`` +``6.14.6`` ``GCCcore/11.2.0`` +``6.46.7`` ``GCCcore/11.3.0`` ========== ================== ================================== @@ -18988,16 +19661,16 @@ Hypre is a library for solving large, sparse linear systems of equations on mass *homepage*: https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods ========== ================================================================ -version toolchain +version toolchain ========== ================================================================ -``2.11.1`` ``foss/2016a``, ``intel/2016a`` -``2.14.0`` ``foss/2018a``, ``intel/2018a`` -``2.15.1`` ``foss/2019a``, ``intel/2019a`` +``2.11.1`` ``foss/2016a``, ``intel/2016a`` +``2.14.0`` ``foss/2018a``, ``intel/2018a`` +``2.15.1`` ``foss/2019a``, ``intel/2019a`` ``2.18.2`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` -``2.20.0`` ``foss/2020b``, ``intel/2020b`` -``2.21.0`` ``foss/2021a``, ``fosscuda/2020b`` -``2.24.0`` ``intel/2021b`` -``2.25.0`` ``foss/2022a`` +``2.20.0`` ``foss/2020b``, ``intel/2020b`` +``2.21.0`` ``foss/2021a``, ``fosscuda/2020b`` +``2.24.0`` ``intel/2021b`` +``2.25.0`` ``foss/2022a`` ========== ================================================================ @@ -19007,7 +19680,7 @@ version toolchain --- -:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_i7z_282` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_Imath_499` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_indicators_1072` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_InterProScan_data_1713` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intervaltree-python_2020` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_Iris_407` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_IsoNet_594` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` +:ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_i7z_282` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_ichorCNA_743` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_idemux_652` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IgBLAST_550` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_igv-reports_1154` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iibff_512` - :ref:`list_software_iimkl_534` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_IJulia_574` - :ref:`list_software_ILAMB_357` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imagecodecs_1140` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_Imath_499` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_imkl-FFTW_785` - :ref:`list_software_Imlib2_543` - :ref:`list_software_immunedeconv_1290` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_InChI_427` - :ref:`list_software_indicators_1072` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_inferCNV_763` - :ref:`list_software_infercnvpy_1092` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inline_639` - :ref:`list_software_InParanoid_997` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_intel-compilers_1559` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelDAAL_782` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_InterProScan_data_1713` - :ref:`list_software_intervaltree_1301` - :ref:`list_software_intervaltree-python_2020` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_ioapi_530` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_IPM_230` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_Iris_407` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISA-L_342` - :ref:`list_software_ISL_232` - :ref:`list_software_isoCirc_716` - :ref:`list_software_IsoNet_594` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_itpp_445` - :ref:`list_software_ITSTool_654` - :ref:`list_software_ITSx_360` - :ref:`list_software_iVar_402` .. _list_software_i-cisTarget_1084: @@ -19020,7 +19693,7 @@ An integrative genomics method for the prediction of regulatory features and cis *homepage*: https://gbiomed.kuleuven.be/apps/lcb/i-cisTarget ============ ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============== ``20160602`` ``-Python-2.7.11`` ``intel/2016a`` ============ ================== =============== @@ -19036,7 +19709,7 @@ A Python wrapper for (ab initio) (path integrals) molecular dynamics *homepage*: https://github.com/i-pi/i-pi ================ ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ================ ================== =============== ``1.0-20160213`` ``-Python-2.7.11`` ``intel/2016a`` ================ ================== =============== @@ -19052,7 +19725,7 @@ I-TASSER is a set of pre-compiled binaries and scripts for protein structure and *homepage*: http://zhanglab.ccmb.med.umich.edu/I-TASSER/ ======= ========== -version toolchain +version toolchain ======= ========== ``4.0`` ``system`` ``4.2`` ``system`` @@ -19070,7 +19743,7 @@ A better i7 (and now i3, i5) reporting tool for Linux *homepage*: https://github.com/ajaiantilal/i7z ============ ================== -version toolchain +version toolchain ============ ================== ``20131012`` ``GCCcore/11.2.0`` ============ ================== @@ -19086,7 +19759,7 @@ ICA-AROMA (i.e. 'ICA-based Automatic Removal Of Motion Artifacts') concerns a da *homepage*: https://github.com/maartenmennes/ICA-AROMA ============== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================= ============== ``0.4.4-beta`` ``-Python-3.6.6`` ``foss/2018b`` ============== ================= ============== @@ -19102,7 +19775,7 @@ C and C++ compiler from Intel *homepage*: http://software.intel.com/en-us/intel-compilers/ ============== ===================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ============== ===================== ========== ``2016.0.109`` ``system`` ``2016.0.109`` ``-GCC-4.9.3-2.25`` ``system`` @@ -19143,7 +19816,7 @@ Intel C, C++ & Fortran compilers *homepage*: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ ============== ===================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ============== ===================== ========== ``2016.0.109`` ``system`` ``2016.0.109`` ``-GCC-4.9.3-2.25`` ``system`` @@ -19188,7 +19861,7 @@ Intel C, C++ & Fortran compilers with CUDA toolkit *homepage*: (none) ============== =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ============== =================== ========== ``2016.10`` ``system`` ``2017.4.196`` ``-GCC-6.4.0-2.28`` ``system`` @@ -19209,7 +19882,7 @@ ichorCNA is a tool for estimating the fraction of tumor in cell-free DNA from ul *homepage*: https://github.com/broadinstitute/ichorCNA/wiki ================== ============== -version toolchain +version toolchain ================== ============== ``0.2.0`` ``foss/2019b`` ``0.3.2-20191219`` ``foss/2020a`` @@ -19226,7 +19899,7 @@ Icmake is a hybrid between a 'make' utility and a 'shell script' language. Origi *homepage*: http://icmake.sourceforge.net/ =========== ============== -version toolchain +version toolchain =========== ============== ``7.23.02`` ``foss/2016a`` =========== ============== @@ -19242,7 +19915,7 @@ iCount: protein-RNA interaction analysis is a Python module and associated comm *homepage*: https://github.com/tomazc/iCount ============ ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ============== ``20180820`` ``-Python-3.6.6`` ``foss/2018b`` ============ ================= ============== @@ -19258,15 +19931,16 @@ ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode a *homepage*: https://icu.unicode.org ======== ====================================== -version toolchain +version toolchain ======== ====================================== -``61.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``64.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``65.1`` ``GCCcore/8.3.0`` -``66.1`` ``GCCcore/9.3.0`` -``67.1`` ``GCCcore/10.2.0`` +``61.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``64.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``65.1`` ``GCCcore/8.3.0`` +``66.1`` ``GCCcore/9.3.0`` +``67.1`` ``GCCcore/10.2.0`` ``69.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``71.1`` ``GCCcore/11.3.0`` +``71.1`` ``GCCcore/11.3.0`` +``72.1`` ``GCCcore/12.2.0`` ======== ====================================== @@ -19279,11 +19953,11 @@ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequen *homepage*: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/ -========= ================================================================================================================== -version toolchain -========= ================================================================================================================== -``1.1.3`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` -========= ================================================================================================================== +========= ================================================================================================================================== +version toolchain +========= ================================================================================================================================== +``1.1.3`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` +========= ================================================================================================================================== .. _list_software_idemux_652: @@ -19296,7 +19970,7 @@ idemux - inline barcode demultiplexing Idemux is a command line tool designed to *homepage*: https://github.com/Lexogen-Tools/idemux ========= ================== -version toolchain +version toolchain ========= ================== ``0.1.6`` ``GCCcore/10.2.0`` ========= ================== @@ -19312,7 +19986,7 @@ IEEG.ORG is a collaborative initiative funded by the National Institutes of Neu *homepage*: https://www.ieeg.org/ =========== ========== -version toolchain +version toolchain =========== ========== ``1.14.56`` ``system`` =========== ========== @@ -19328,7 +20002,7 @@ Fortran compiler from Intel *homepage*: http://software.intel.com/en-us/intel-compilers/ ============== ===================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ============== ===================== ========== ``2016.0.109`` ``system`` ``2016.0.109`` ``-GCC-4.9.3-2.25`` ``system`` @@ -19369,7 +20043,7 @@ IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable *homepage*: https://ncbi.github.io/igblast ========== ============== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============== ========== ``1.15.0`` ``-x64-linux`` ``system`` ``1.18.0`` ``-x64-linux`` ``system`` @@ -19386,10 +20060,10 @@ IGMPlot is a free open-source program developed to identify molecular interactio *homepage*: http://igmplot.univ-reims.fr ========== ====================================== -version toolchain +version toolchain ========== ====================================== ``2.4.2`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``2.6.9b`` ``GCC/11.2.0`` +``2.6.9b`` ``GCC/11.2.0`` ========== ====================================== @@ -19403,15 +20077,15 @@ igraph is a collection of network analysis tools with the emphasis on efficiency *homepage*: https://igraph.org ========= ================================================ -version toolchain +version toolchain ========= ================================================ ``0.7.1`` ``foss/2018b``, ``intel/2016b``, ``intel/2017b`` -``0.8.0`` ``foss/2019b`` -``0.8.2`` ``foss/2020a`` -``0.8.5`` ``foss/2020b`` -``0.9.1`` ``foss/2020b``, ``fosscuda/2020b`` -``0.9.4`` ``foss/2021a`` -``0.9.5`` ``foss/2021b`` +``0.8.0`` ``foss/2019b`` +``0.8.2`` ``foss/2020a`` +``0.8.5`` ``foss/2020b`` +``0.9.1`` ``foss/2020b``, ``fosscuda/2020b`` +``0.9.4`` ``foss/2021a`` +``0.9.5`` ``foss/2021b`` ========= ================================================ @@ -19425,7 +20099,7 @@ This package contains command line utilities for preprocessing, computing featu *homepage*: https://www.broadinstitute.org/software/igv/ ========== ================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ========== ``2.3.68`` ``-Java-1.7.0_80`` ``system`` ``2.3.80`` ``-Java-1.7.0_80`` ``system`` @@ -19446,7 +20120,7 @@ Python application to generate self-contained igv.js pages that can be opened wi *homepage*: https://github.com/igvteam/igv-reports ========= ================= ============= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============= ``0.9.8`` ``-Python-3.7.4`` ``GCC/8.3.0`` ========= ================= ============= @@ -19462,7 +20136,7 @@ This package contains command line utilities for preprocessing, computing feat *homepage*: https://software.broadinstitute.org/software/igv/igvtools ========== ================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ========== ``2.3.68`` ``-Java-1.7.0_80`` ``system`` ``2.3.72`` ``-Java-1.7.0_80`` ``system`` @@ -19481,7 +20155,7 @@ GCC and GFortran based compiler toolchain with OpenMPI, BLIS, libFLAME, ScaLAPAC *homepage*: (none) ========= ========== -version toolchain +version toolchain ========= ========== ``2020b`` ``system`` ========= ========== @@ -19497,9 +20171,10 @@ Intel C/C++ and Fortran compilers, alongside Intel Math Kernel Library (MKL). *homepage*: https://software.intel.com/en-us/intel-cluster-toolkit-compiler/ ========= ========== -version toolchain +version toolchain ========= ========== ``2018a`` ``system`` +``2022b`` ``system`` ========= ========== @@ -19513,7 +20188,7 @@ Intel C/C++ and Fortran compilers, alongside Intel MPI. *homepage*: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ ===================== ==================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ===================== ==================== ========== ``8.1.5`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.00`` ``-GCC-4.9.3-2.25`` ``system`` @@ -19552,7 +20227,9 @@ version versionsuffix toolchain ``2022.00`` ``system`` ``2022.05`` ``system`` ``2022.09`` ``system`` +``2022.11`` ``system`` ``2022a`` ``system`` +``2022b`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ===================== ==================== ========== @@ -19567,7 +20244,7 @@ Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA. *homepage*: (none) =========== ========== -version toolchain +version toolchain =========== ========== ``2016.10`` ``system`` ``2017b`` ``system`` @@ -19578,6 +20255,22 @@ version toolchain =========== ========== +.. _list_software_IJulia_574: + +*IJulia* +++++++++ + +Julia kernel for Jupyter + +*homepage*: https://github.com/JuliaLang/IJulia.jl + +========== ================ ========== +version versionsuffix toolchain +========== ================ ========== +``1.23.3`` ``-Julia-1.6.7`` ``system`` +========== ================ ========== + + .. _list_software_ILAMB_357: *ILAMB* @@ -19588,7 +20281,7 @@ The International Land Model Benchmarking (ILAMB) project is a model-data interc *homepage*: https://www.ilamb.org/ ======= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= ============== ``2.5`` ``-Python-3.8.2`` ``foss/2020a`` ======= ================= ============== @@ -19604,7 +20297,7 @@ IMa2 is a progam for population genetic analysis that can handle two or more pop *homepage*: https://bio.cst.temple.edu/~hey/software/software.htm#IMa2 =========== ============== -version toolchain +version toolchain =========== ============== ``8.27.12`` ``foss/2016a`` =========== ============== @@ -19620,9 +20313,9 @@ IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC *homepage*: https://github.com/arunsethuraman/ima2p ============ =============== -version toolchain +version toolchain ============ =============== -``20151123`` ``foss/2016a`` +``20151123`` ``foss/2016a`` ``20160804`` ``intel/2016b`` ============ =============== @@ -19637,9 +20330,10 @@ Imagecodecs is a Python library that provides block-oriented, in-memory buffer t *homepage*: https://github.com/cgohlke/imagecodecs ============= ============== -version toolchain +version toolchain ============= ============== ``2021.8.26`` ``foss/2020b`` +``2022.9.26`` ``foss/2021a`` ============= ============== @@ -19653,14 +20347,15 @@ Imageio is a Python library that provides an easy interface to read and write a *homepage*: https://imageio.github.io ========== ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================== -``2.3.0`` ``-Python-3.6.4`` ``intel/2018a`` -``2.5.0`` ``foss/2019a`` +``2.3.0`` ``-Python-3.6.4`` ``intel/2018a`` +``2.5.0`` ``foss/2019a`` ``2.9.0`` ``foss/2020b``, ``fosscuda/2020b`` -``2.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``2.10.5`` ``foss/2021a`` -``2.13.5`` ``foss/2021b`` +``2.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``2.10.5`` ``foss/2021a`` +``2.13.5`` ``foss/2021b`` +``2.22.2`` ``foss/2022a`` ========== ================= ================================== @@ -19674,7 +20369,7 @@ Image Processing and Analysis in Java *homepage*: https://imagej.nih.gov/ij ========= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========== ``1.51a`` ``system`` ``1.51i`` ``system`` @@ -19693,30 +20388,31 @@ ImageMagick is a software suite to create, edit, compose, or convert bitmap imag *homepage*: https://www.imagemagick.org/ ============= =================================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ============= =================================== =============================== -``6.9.4-8`` ``intel/2016a`` -``7.0.1-6`` ``intel/2016a`` -``7.0.1-9`` ``intel/2016a`` -``7.0.2-9`` ``intel/2016a`` -``7.0.3-1`` ``intel/2016b`` -``7.0.5-4`` ``intel/2017a`` -``7.0.5-10`` ``foss/2016b`` -``7.0.7-8`` ``-JasPer-1.900.1`` ``intel/2017a`` +``6.9.4-8`` ``intel/2016a`` +``7.0.1-6`` ``intel/2016a`` +``7.0.1-9`` ``intel/2016a`` +``7.0.2-9`` ``intel/2016a`` +``7.0.3-1`` ``intel/2016b`` +``7.0.5-4`` ``intel/2017a`` +``7.0.5-10`` ``foss/2016b`` +``7.0.7-8`` ``-JasPer-1.900.1`` ``intel/2017a`` ``7.0.7-14`` ``foss/2017b``, ``intel/2017b`` -``7.0.7-15`` ``GCCcore/6.4.0`` -``7.0.7-26`` ``foss/2018a`` -``7.0.7-30`` ``GCCcore/6.4.0`` -``7.0.7-30`` ``-Ghostscript-9.22-cairo-1.14.12`` ``GCCcore/6.4.0`` -``7.0.7-39`` ``-Ghostscript-9.23-cairo-1.14.12`` ``GCCcore/6.4.0`` -``7.0.8-11`` ``GCCcore/7.3.0`` -``7.0.8-46`` ``GCCcore/8.2.0`` -``7.0.9-5`` ``GCCcore/8.3.0`` -``7.0.10-1`` ``GCCcore/9.3.0`` -``7.0.10-35`` ``GCCcore/10.2.0`` -``7.0.11-14`` ``GCCcore/10.3.0`` -``7.1.0-4`` ``GCCcore/11.2.0`` -``7.1.0-37`` ``GCCcore/11.3.0`` +``7.0.7-15`` ``GCCcore/6.4.0`` +``7.0.7-26`` ``foss/2018a`` +``7.0.7-30`` ``GCCcore/6.4.0`` +``7.0.7-30`` ``-Ghostscript-9.22-cairo-1.14.12`` ``GCCcore/6.4.0`` +``7.0.7-39`` ``-Ghostscript-9.23-cairo-1.14.12`` ``GCCcore/6.4.0`` +``7.0.8-11`` ``GCCcore/7.3.0`` +``7.0.8-46`` ``GCCcore/8.2.0`` +``7.0.9-5`` ``GCCcore/8.3.0`` +``7.0.10-1`` ``GCCcore/9.3.0`` +``7.0.10-35`` ``GCCcore/10.2.0`` +``7.0.11-14`` ``GCCcore/10.3.0`` +``7.1.0-4`` ``GCCcore/11.2.0`` +``7.1.0-37`` ``GCCcore/11.3.0`` +``7.1.0-53`` ``GCCcore/12.2.0`` ============= =================================== =============================== @@ -19730,9 +20426,9 @@ imake is a Makefile-generator that is intended to make it easier to develop soft *homepage*: https://www.x.org/ ========= ========================================================== -version toolchain +version toolchain ========= ========================================================== -``1.0.7`` ``intel/2016a`` +``1.0.7`` ``intel/2016a`` ``1.0.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ========================================================== @@ -19747,7 +20443,7 @@ Imath is a C++ and python library of 2D and 3D vector, matrix, and math operatio *homepage*: https://imath.readthedocs.io/en/latest/ ========= ================== -version toolchain +version toolchain ========= ================== ``3.1.5`` ``GCCcore/11.3.0`` ========= ================== @@ -19763,12 +20459,12 @@ The Intel MPI Benchmarks perform a set of MPI performance measurements for point *homepage*: https://software.intel.com/en-us/articles/intel-mpi-benchmarks ========== ================================================================== -version toolchain +version toolchain ========== ================================================================== ``4.1`` ``foss/2016a``, ``foss/2017a``, ``intel/2017.02``, ``intel/2017a`` -``2018.1`` ``intel/2017a`` -``2019.3`` ``gompi/2019a``, ``iimpi/2019a`` -``2021.3`` ``gompi/2021b`` +``2018.1`` ``intel/2017a`` +``2019.3`` ``gompi/2019a``, ``iimpi/2019a`` +``2021.3`` ``gompi/2021b`` ========== ================================================================== @@ -19782,13 +20478,14 @@ imbalanced-learn is a Python package offering a number of re-sampling techniques *homepage*: https://github.com/scikit-learn-contrib/imbalanced-learn ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.2.1`` ``-Python-2.7.12`` ``intel/2016b`` ``0.2.1`` ``-Python-3.5.2`` ``intel/2016b`` -``0.3.3`` ``-Python-3.6.4`` ``foss/2018a`` -``0.4.3`` ``-Python-3.6.6`` ``foss/2018b`` -``0.7.0`` ``foss/2020b`` +``0.3.3`` ``-Python-3.6.4`` ``foss/2018a`` +``0.4.3`` ``-Python-3.6.6`` ``foss/2018b`` +``0.7.0`` ``foss/2020b`` +``0.9.0`` ``foss/2021b`` ========= ================== =============== @@ -19801,15 +20498,16 @@ This python library helps you with augmenting images for your machine learning p *homepage*: https://imgaug.readthedocs.io/en/latest/ -========= ================= ============================== -version versionsuffix toolchain -========= ================= ============================== -``0.2.8`` ``-Python-3.6.6`` ``foss/2018b`` -``0.4.0`` ``foss/2021a``, ``foss/2021b`` -``0.4.0`` ``-CUDA-11.3.1`` ``foss/2021a`` -``0.4.0`` ``-CUDA-11.4.1`` ``foss/2021b`` -``0.4.0`` ``-Python-3.7.4`` ``foss/2019b`` -========= ================= ============================== +========= ================= ============================================== +version versionsuffix toolchain +========= ================= ============================================== +``0.2.8`` ``-Python-3.6.6`` ``foss/2018b`` +``0.4.0`` ``foss/2021a``, ``foss/2021b``, ``foss/2022a`` +``0.4.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``0.4.0`` ``-CUDA-11.4.1`` ``foss/2021b`` +``0.4.0`` ``-CUDA-11.7.0`` ``foss/2022a`` +``0.4.0`` ``-Python-3.7.4`` ``foss/2019b`` +========= ================= ============================================== .. _list_software_imkl_429: @@ -19822,39 +20520,40 @@ Intel oneAPI Math Kernel Library *homepage*: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html ============== ============= ====================================================================================================================================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ============== ============= ====================================================================================================================================================================================================================================================================== -``11.2.3.187`` ``gimpi/2.11.5`` -``11.3.0.109`` ``iimpi/2016.00-GCC-4.9.3-2.25`` -``11.3.1.150`` ``iimpi/2016.01-GCC-4.9.3-2.25``, ``iimpi/8.1.5-GCC-4.9.3-2.25`` -``11.3.2.181`` ``iimpi/2016.02-GCC-4.9.3-2.25``, ``iimpi/2016.02-GCC-5.3.0-2.26``, ``pompi/2016.03`` +``11.2.3.187`` ``gimpi/2.11.5`` +``11.3.0.109`` ``iimpi/2016.00-GCC-4.9.3-2.25`` +``11.3.1.150`` ``iimpi/2016.01-GCC-4.9.3-2.25``, ``iimpi/8.1.5-GCC-4.9.3-2.25`` +``11.3.2.181`` ``iimpi/2016.02-GCC-4.9.3-2.25``, ``iimpi/2016.02-GCC-5.3.0-2.26``, ``pompi/2016.03`` ``11.3.3.210`` ``iimpi/2016.03-GCC-4.9.3-2.25``, ``iimpi/2016.03-GCC-5.3.0-2.26``, ``iimpi/2016.03-GCC-5.4.0-2.26``, ``iimpi/2016b``, ``iimpic/2016.10``, ``iompi/2016.07``, ``iompi/2016.09-GCC-4.9.3-2.25``, ``iompi/2016.09-GCC-5.4.0-2.26``, ``pompi/2016.04``, ``pompi/2016.09`` -``2017.0.098`` ``iimpi/2017.00-GCC-5.4.0-2.26`` -``2017.1.132`` ``gimpi/2017a``, ``iimpi/2017.01-GCC-5.4.0-2.26``, ``iimpi/2017a``, ``iompi/2017.01``, ``iompi/2017a`` -``2017.2.174`` ``iimpi/2017.02-GCC-6.3.0-2.27`` -``2017.3.196`` ``gompi/2017b``, ``iimpi/2017b``, ``iimpic/2017b``, ``iompi/2017b`` -``2017.4.239`` ``iimpi/2017.09`` -``2018.0.128`` ``iimpi/2018.00`` -``2018.1.163`` ``iimpi/2018.01``, ``iimpi/2018a``, ``iompi/2018a`` -``2018.1.163`` ``-serial`` ``iccifort/2018.1.163-GCC-6.4.0-2.28`` -``2018.2.199`` ``iimpi/2018.02``, ``iompi/2018.02`` -``2018.3.222`` ``gimpi/2018b``, ``gompi/2018b``, ``iimpi/2018b``, ``iompi/2018b`` -``2018.4.274`` ``iimpi/2018.04`` -``2019.0.117`` ``iimpi/2019.00`` -``2019.1.144`` ``gompi/2019a``, ``iimpi/2019.01``, ``iimpi/2019a``, ``iimpic/2019a``, ``iompi/2019.01`` -``2019.2.187`` ``iimpi/2019.02`` -``2019.3.199`` ``iimpi/2019.03`` -``2019.5.281`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b``, ``iompi/2019b`` -``2020.0.166`` ``iimpi/2020.00`` -``2020.1.217`` ``gompi/2020a``, ``iimpi/2020.06-impi-18.5``, ``iimpi/2020a``, ``iimpic/2020a``, ``iompi/2020a`` -``2020.4.304`` ``NVHPC/21.2``, ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpic/2020b``, ``iompi/2020b`` -``2021.1.1`` ``iimpi/2020.12`` -``2021.2.0`` ``gompi/2021a``, ``iimpi/2021a``, ``iompi/2021a`` -``2021.3.0`` ``gompi/2021a`` -``2021.4.0`` ``system`` -``2022.0.1`` ``system`` -``2022.1.0`` ``system`` -``2022.2.0`` ``system`` +``2017.0.098`` ``iimpi/2017.00-GCC-5.4.0-2.26`` +``2017.1.132`` ``gimpi/2017a``, ``iimpi/2017.01-GCC-5.4.0-2.26``, ``iimpi/2017a``, ``iompi/2017.01``, ``iompi/2017a`` +``2017.2.174`` ``iimpi/2017.02-GCC-6.3.0-2.27`` +``2017.3.196`` ``gompi/2017b``, ``iimpi/2017b``, ``iimpic/2017b``, ``iompi/2017b`` +``2017.4.239`` ``iimpi/2017.09`` +``2018.0.128`` ``iimpi/2018.00`` +``2018.1.163`` ``iimpi/2018.01``, ``iimpi/2018a``, ``iompi/2018a`` +``2018.1.163`` ``-serial`` ``iccifort/2018.1.163-GCC-6.4.0-2.28`` +``2018.2.199`` ``iimpi/2018.02``, ``iompi/2018.02`` +``2018.3.222`` ``gimpi/2018b``, ``gompi/2018b``, ``iimpi/2018b``, ``iompi/2018b`` +``2018.4.274`` ``iimpi/2018.04`` +``2019.0.117`` ``iimpi/2019.00`` +``2019.1.144`` ``gompi/2019a``, ``iimpi/2019.01``, ``iimpi/2019a``, ``iimpic/2019a``, ``iompi/2019.01`` +``2019.2.187`` ``iimpi/2019.02`` +``2019.3.199`` ``iimpi/2019.03`` +``2019.5.281`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b``, ``iompi/2019b`` +``2020.0.166`` ``iimpi/2020.00`` +``2020.1.217`` ``gompi/2020a``, ``iimpi/2020.06-impi-18.5``, ``iimpi/2020a``, ``iimpic/2020a``, ``iompi/2020a`` +``2020.4.304`` ``NVHPC/21.2``, ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpic/2020b``, ``iompi/2020b`` +``2021.1.1`` ``iimpi/2020.12`` +``2021.2.0`` ``gompi/2021a``, ``iimpi/2021a``, ``iompi/2021a`` +``2021.3.0`` ``gompi/2021a`` +``2021.4.0`` ``system`` +``2022.0.1`` ``system`` +``2022.1.0`` ``system`` +``2022.2.0`` ``system`` +``2022.2.1`` ``system`` ============== ============= ====================================================================================================================================================================================================================================================================== @@ -19868,12 +20567,13 @@ FFTW interfaces using Intel oneAPI Math Kernel Library *homepage*: https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html ============ ================================== -version toolchain +version toolchain ============ ================================== -``2021.4.0`` ``gompi/2021b``, ``iimpi/2021b`` -``2022.0.1`` ``iimpi/2022.00`` +``2021.4.0`` ``gompi/2021b``, ``iimpi/2021b`` +``2022.0.1`` ``iimpi/2022.00`` ``2022.1.0`` ``iimpi/2022.05``, ``iimpi/2022a`` -``2022.2.0`` ``iimpi/2022.09`` +``2022.2.0`` ``iimpi/2022.09`` +``2022.2.1`` ``iimpi/2022.11``, ``iimpi/2022b`` ============ ================================== @@ -19887,7 +20587,7 @@ This is the Imlib 2 library - a library that does image file loading and saving *homepage*: https://docs.enlightenment.org/api/imlib2/html/ ========= ================= -version toolchain +version toolchain ========= ================= ``1.5.1`` ``GCCcore/6.4.0`` ========= ================= @@ -19903,7 +20603,7 @@ immunedeconv is an R package for unified access to computational methods for est *homepage*: https://github.com/icbi-lab/immunedeconv ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``2.0.2`` ``-R-4.0.0`` ``foss/2020a`` ========= ============= ============== @@ -19919,9 +20619,9 @@ IMOD is a set of image processing, modeling and display programs used for tomogr *homepage*: http://bio3d.colorado.edu/imod/ ========== ===================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ===================== ================================== -``4.7.15`` ``_RHEL6-64_CUDA6.0`` ``system`` +``4.7.15`` ``_RHEL6-64_CUDA6.0`` ``system`` ``4.11.5`` ``foss/2020b``, ``fosscuda/2020b`` ========== ===================== ================================== @@ -19936,49 +20636,50 @@ The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing librar *homepage*: http://software.intel.com/en-us/intel-mpi-library/ =============== ============= ================================================================================================================================================================================================================================ -version versionsuffix toolchain +version versionsuffix toolchain =============== ============= ================================================================================================================================================================================================================================ -``3.2.2.006`` ``system`` -``4.0.0.028`` ``system`` -``4.0.0.028`` ``-32bit`` ``system`` -``4.0.2.003`` ``system`` -``4.1.0.027`` ``system`` -``4.1.0.030`` ``system`` -``4.1.1.036`` ``system`` -``4.1.2.040`` ``system`` -``4.1.3.045`` ``system`` -``4.1.3.049`` ``GCC/4.8.3``, ``system`` -``5.0.3.048`` ``GCC/4.9.3`` -``5.1.1.109`` ``iccifort/2016.0.109-GCC-4.9.3-2.25`` -``5.1.2.150`` ``iccifort/2016.1.150-GCC-4.9.3-2.25`` +``3.2.2.006`` ``system`` +``4.0.0.028`` ``system`` +``4.0.0.028`` ``-32bit`` ``system`` +``4.0.2.003`` ``system`` +``4.1.0.027`` ``system`` +``4.1.0.030`` ``system`` +``4.1.1.036`` ``system`` +``4.1.2.040`` ``system`` +``4.1.3.045`` ``system`` +``4.1.3.049`` ``GCC/4.8.3``, ``system`` +``5.0.3.048`` ``GCC/4.9.3`` +``5.1.1.109`` ``iccifort/2016.0.109-GCC-4.9.3-2.25`` +``5.1.2.150`` ``iccifort/2016.1.150-GCC-4.9.3-2.25`` ``5.1.3.181`` ``iccifort/2016.2.181-GCC-4.9.3-2.25``, ``iccifort/2016.2.181-GCC-5.3.0-2.26``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.3.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``iccifortcuda/2016.10`` -``2017.0.098`` ``iccifort/2017.0.098-GCC-5.4.0-2.26`` -``2017.1.132`` ``GCC/5.4.0-2.26``, ``iccifort/2017.1.132-GCC-5.4.0-2.26``, ``iccifort/2017.1.132-GCC-6.3.0-2.27`` -``2017.2.174`` ``iccifort/2017.2.174-GCC-6.3.0-2.27`` -``2017.3.196`` ``GCC/6.4.0-2.28``, ``gcccuda/2017b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifortcuda/2017.4.196-GCC-6.4.0-2.28`` -``2017.4.239`` ``iccifort/2017.5.239-GCC-6.4.0-2.28`` -``2018.0.128`` ``iccifort/2018.0.128-GCC-6.4.0-2.28`` -``2018.1.163`` ``GCC/6.4.0-2.28``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` -``2018.2.199`` ``iccifort/2018.2.199-GCC-6.4.0-2.28`` -``2018.3.222`` ``GCC/7.3.0-2.30``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` -``2018.4.274`` ``iccifort/2018.5.274-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifortcuda/2019a`` -``2018.5.288`` ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifortcuda/2019b`` -``2019.0.117`` ``iccifort/2019.0.117-GCC-8.2.0-2.31.1`` -``2019.1.144`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2019.2.187`` ``iccifort/2019.2.187-GCC-8.2.0-2.31.1`` -``2019.3.199`` ``iccifort/2019.3.199-GCC-8.3.0-2.32`` -``2019.6.166`` ``iccifort/2020.0.166-GCC-9.2.0`` -``2019.7.217`` ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` -``2019.9.304`` ``iccifort/2020.4.304``, ``iccifortcuda/2020b`` -``2019.12.320`` ``iccifort/2020.4.304`` -``2021.1.1`` ``intel-compilers/2021.1.2`` -``2021.2.0`` ``intel-compilers/2021.2.0`` -``2021.3.0`` ``intel-compilers/2021.3.0`` -``2021.4.0`` ``intel-compilers/2021.4.0`` -``2021.5.0`` ``intel-compilers/2022.0.1`` -``2021.6.0`` ``intel-compilers/2022.1.0`` -``2021.7.0`` ``intel-compilers/2022.2.0`` -``system`` ``iccifort/system-GCC-system-2.29`` +``2017.0.098`` ``iccifort/2017.0.098-GCC-5.4.0-2.26`` +``2017.1.132`` ``GCC/5.4.0-2.26``, ``iccifort/2017.1.132-GCC-5.4.0-2.26``, ``iccifort/2017.1.132-GCC-6.3.0-2.27`` +``2017.2.174`` ``iccifort/2017.2.174-GCC-6.3.0-2.27`` +``2017.3.196`` ``GCC/6.4.0-2.28``, ``gcccuda/2017b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifortcuda/2017.4.196-GCC-6.4.0-2.28`` +``2017.4.239`` ``iccifort/2017.5.239-GCC-6.4.0-2.28`` +``2018.0.128`` ``iccifort/2018.0.128-GCC-6.4.0-2.28`` +``2018.1.163`` ``GCC/6.4.0-2.28``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` +``2018.2.199`` ``iccifort/2018.2.199-GCC-6.4.0-2.28`` +``2018.3.222`` ``GCC/7.3.0-2.30``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` +``2018.4.274`` ``iccifort/2018.5.274-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifortcuda/2019a`` +``2018.5.288`` ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifortcuda/2019b`` +``2019.0.117`` ``iccifort/2019.0.117-GCC-8.2.0-2.31.1`` +``2019.1.144`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``2019.2.187`` ``iccifort/2019.2.187-GCC-8.2.0-2.31.1`` +``2019.3.199`` ``iccifort/2019.3.199-GCC-8.3.0-2.32`` +``2019.6.166`` ``iccifort/2020.0.166-GCC-9.2.0`` +``2019.7.217`` ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` +``2019.9.304`` ``iccifort/2020.4.304``, ``iccifortcuda/2020b`` +``2019.12.320`` ``iccifort/2020.4.304`` +``2021.1.1`` ``intel-compilers/2021.1.2`` +``2021.2.0`` ``intel-compilers/2021.2.0`` +``2021.3.0`` ``intel-compilers/2021.3.0`` +``2021.4.0`` ``intel-compilers/2021.4.0`` +``2021.5.0`` ``intel-compilers/2022.0.1`` +``2021.6.0`` ``intel-compilers/2022.1.0`` +``2021.7.0`` ``intel-compilers/2022.2.0`` +``2021.7.1`` ``intel-compilers/2022.2.1`` +``system`` ``iccifort/system-GCC-system-2.29`` =============== ============= ================================================================================================================================================================================================================================ @@ -19992,7 +20693,7 @@ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotyp *homepage*: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html ========= =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= =================== ========== ``2.3.0`` ``_x86_64_dynamic`` ``system`` ``2.3.0`` ``_x86_64_static`` ``system`` @@ -20011,7 +20712,7 @@ The IUPAC International Chemical Identifier (InChI TM) is a non-proprietary iden *homepage*: https://www.inchi-trust.org/ ======== ============== -version toolchain +version toolchain ======== ============== ``1.06`` ``GCC/10.3.0`` ======== ============== @@ -20027,7 +20728,7 @@ version toolchain *homepage*: https://github.com/p-ranav/indicators ======= ================== -version toolchain +version toolchain ======= ================== ``2.2`` ``GCCcore/11.3.0`` ======= ================== @@ -20043,7 +20744,7 @@ Python package for eigenchannels, vibrations and inelastic electron transport ba *homepage*: https://github.com/tfrederiksen/inelastica ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.3.5`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============== @@ -20059,16 +20760,32 @@ InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence *homepage*: https://github.com/broadinstitute/inferCNV/wiki ========== ========================= ============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ========================= ============================== -``1.0.4`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` -``1.2.1`` ``-Python-3.7.4`` ``foss/2019b`` +``1.0.4`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` +``1.2.1`` ``-Python-3.7.4`` ``foss/2019b`` ``1.3.3`` ``foss/2020b``, ``foss/2021a`` -``1.3.3`` ``-Python-3.8.2`` ``foss/2020a`` -``1.10.1`` ``-R-4.1.2`` ``foss/2021b`` +``1.3.3`` ``-Python-3.8.2`` ``foss/2020a`` +``1.10.1`` ``-R-4.1.2`` ``foss/2021b`` ========== ========================= ============================== +.. _list_software_infercnvpy_1092: + +*infercnvpy* +++++++++++++ + +Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy. + +*homepage*: https://github.com/icbi-lab/infercnvpy + +========= ============== +version toolchain +========= ============== +``0.4.0`` ``foss/2021b`` +========= ============== + + .. _list_software_Infernal_815: *Infernal* @@ -20079,10 +20796,10 @@ Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases *homepage*: http://eddylab.org/infernal/ ========= ================================================================ -version toolchain +version toolchain ========= ================================================================ ``1.1.2`` ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018b`` -``1.1.4`` ``foss/2020b``, ``foss/2021b`` +``1.1.4`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` ========= ================================================================ @@ -20096,7 +20813,7 @@ Multi-level network clustering based on the Map equation. *homepage*: https://www.mapequation.org/code.html#Linux ============ ==================== -version toolchain +version toolchain ============ ==================== ``20190308`` ``GCC/8.2.0-2.31.1`` ============ ==================== @@ -20112,12 +20829,28 @@ Functionality to dynamically define R functions and S4 methods with 'inlined' C *homepage*: https://cran.r-project.org/web/packages/inline ========== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ============== ``0.3.19`` ``-R-4.0.4`` ``foss/2020b`` ========== ============= ============== +.. _list_software_InParanoid_997: + +*InParanoid* +++++++++++++ + +InParanoid: ortholog groups with inparalogs. + +*homepage*: https://inparanoid.sbc.su.se + +================ ============== +version toolchain +================ ============== +``5.0-20220607`` ``GCC/10.3.0`` +================ ============== + + .. _list_software_inputproto_1124: *inputproto* @@ -20128,10 +20861,10 @@ X.org InputProto protocol headers. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= -version toolchain +version toolchain ========= ================================================= ``2.3.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``2.3.2`` ``intel/2016a`` +``2.3.2`` ``intel/2016a`` ========= ================================================= @@ -20145,7 +20878,7 @@ Intel Inspector is a dynamic memory and threading error checking tool for users *homepage*: https://software.intel.com/en-us/inspector ================ ========== -version toolchain +version toolchain ================ ========== ``2013_update6`` ``system`` ``2013_update7`` ``system`` @@ -20173,7 +20906,7 @@ Efficient RNA-RNA interaction prediction incorporating accessibility and seeding *homepage*: https://github.com/BackofenLab/IntaRNA ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.3.1`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== ============== @@ -20189,7 +20922,7 @@ INTEGRATE is a tool calling gene fusions with exact fusion junctions and genomic *homepage*: https://sourceforge.net/p/integrate-fusion/wiki/Home/ ========= ================= -version toolchain +version toolchain ========= ================= ``0.2.6`` ``GCCcore/8.2.0`` ========= ================= @@ -20205,7 +20938,7 @@ INTEGRATE-Neo is a gene fusion neoantigen discovering tool using next-generation *homepage*: ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.2.1`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== @@ -20221,7 +20954,7 @@ Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Li *homepage*: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain ===================== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ===================== ============= ========== ``2016.00`` ``system`` ``2016.01`` ``system`` @@ -20260,7 +20993,9 @@ version versionsuffix toolchain ``2022.00`` ``system`` ``2022.05`` ``system`` ``2022.09`` ``system`` +``2022.11`` ``system`` ``2022a`` ``system`` +``2022b`` ``system`` ===================== ============= ========== @@ -20274,7 +21009,7 @@ Intel C, C++ & Fortran compilers (classic and oneAPI) *homepage*: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html ============ ========== -version toolchain +version toolchain ============ ========== ``2021.1.2`` ``system`` ``2021.2.0`` ``system`` @@ -20284,6 +21019,7 @@ version toolchain ``2022.0.2`` ``system`` ``2022.1.0`` ``system`` ``2022.2.0`` ``system`` +``2022.2.1`` ``system`` ============ ========== @@ -20297,7 +21033,7 @@ Intel Cluster Checker verifies the configuration and performance of Linux OS-ba *homepage*: https://software.intel.com/en-us/cluster-checker ============== ========== -version toolchain +version toolchain ============== ========== ``2017.1.016`` ``system`` ``2021.5.0`` ``system`` @@ -20314,7 +21050,7 @@ Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compiler *homepage*: (none) =========== ========== -version toolchain +version toolchain =========== ========== ``2016.10`` ``system`` ``2017b`` ``system`` @@ -20335,7 +21071,7 @@ Intel® Data Analytics Acceleration Library (Intel® DAAL) is the library of In *homepage*: https://software.intel.com/en-us/daal ============== ========== -version toolchain +version toolchain ============== ========== ``2019.4.007`` ``system`` ============== ========== @@ -20351,7 +21087,7 @@ Intel® Distribution for Python. Powered by Anaconda. Accelerating Python* perf *homepage*: https://software.intel.com/en-us/intel-distribution-for-python ========== =============== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== =============== ========== ``2.7.15`` ``-2019.2.066`` ``system`` ``3.6.8`` ``-2019.2.066`` ``system`` @@ -20368,13 +21104,13 @@ InterProScan is a sequence analysis application (nucleotide and protein sequence *homepage*: https://www.ebi.ac.uk/interpro/ ============= ================== -version toolchain +version toolchain ============= ================== -``5.26-65.0`` ``intel/2017b`` -``5.27-66.0`` ``intel/2017b`` -``5.28-67.0`` ``intel/2018a`` +``5.26-65.0`` ``intel/2017b`` +``5.27-66.0`` ``intel/2017b`` +``5.28-67.0`` ``intel/2018a`` ``5.52-86.0`` ``GCCcore/10.3.0`` -``5.55-88.0`` ``foss/2021a`` +``5.55-88.0`` ``foss/2021a`` ============= ================== @@ -20388,7 +21124,7 @@ InterProScan is a sequence analysis application (nucleotide and protein sequence *homepage*: https://www.ebi.ac.uk/interpro/ ============= ============== -version toolchain +version toolchain ============= ============== ``5.55-88.0`` ``foss/2021a`` ============= ============== @@ -20404,7 +21140,7 @@ An interval tree can be used to efficiently find a set of numeric intervals ove *homepage*: https://github.com/ekg/intervaltree ======= ============================================================================= -version toolchain +version toolchain ======= ============================================================================= ``0.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ======= ============================================================================= @@ -20420,9 +21156,9 @@ A mutable, self-balancing interval tree. Queries may be by point, by range over *homepage*: https://github.com/chaimleib/intervaltree ========= ================= ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ====================================== -``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` +``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` ``3.1.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ================= ====================================== @@ -20436,18 +21172,18 @@ intltool is a set of tools to centralize translation of many different file for *homepage*: http://freedesktop.org/wiki/Software/intltool/ -========== ================ ======================================================================================================================================= -version versionsuffix toolchain -========== ================ ======================================================================================================================================= -``0.51.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.51.0`` ``-Perl-5.20.3`` ``intel/2016a`` -``0.51.0`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` -``0.51.0`` ``-Perl-5.24.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` -``0.51.0`` ``-Perl-5.24.1`` ``GCCcore/6.3.0``, ``intel/2017a`` -``0.51.0`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` -``0.51.0`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``0.51.0`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -========== ================ ======================================================================================================================================= +========== ================ =========================================================================================================================================================== +version versionsuffix toolchain +========== ================ =========================================================================================================================================================== +``0.51.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.51.0`` ``-Perl-5.20.3`` ``intel/2016a`` +``0.51.0`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` +``0.51.0`` ``-Perl-5.24.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` +``0.51.0`` ``-Perl-5.24.1`` ``GCCcore/6.3.0``, ``intel/2017a`` +``0.51.0`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` +``0.51.0`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``0.51.0`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +========== ================ =========================================================================================================================================================== .. _list_software_io_lib_622: @@ -20460,7 +21196,7 @@ Io_lib is a library of file reading and writing code to provide a general purpos *homepage*: http://sourceforge.net/projects/staden/files/io_lib/ ========== ============== -version toolchain +version toolchain ========== ============== ``1.14.8`` ``foss/2016a`` ========== ============== @@ -20476,7 +21212,7 @@ The Models-3/EDSS Input/Output Applications Programming Interface (I/O API) prov *homepage*: https://www.cmascenter.org/ioapi/ =============== ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain =============== ============= =============== ``3.2-2020111`` ``-nocpl`` ``gompi/2019b`` =============== ============= =============== @@ -20492,7 +21228,7 @@ Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Lib *homepage*: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html ========================== ========== -version toolchain +version toolchain ========================== ========== ``2016.07`` ``system`` ``2016.09-GCC-4.9.3-2.25`` ``system`` @@ -20521,7 +21257,7 @@ Intel C/C++ and Fortran compilers, alongside Open MPI. *homepage*: https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html ========================== ========== -version toolchain +version toolchain ========================== ========== ``2016.07`` ``system`` ``2016.09-GCC-4.9.3-2.25`` ``system`` @@ -20549,13 +21285,13 @@ The IOR software is used for benchmarking parallel file systems using POSIX, MPI *homepage*: https://github.com/hpc/ior -========= ============= ================================ -version versionsuffix toolchain -========= ============= ================================ -``3.0.1`` ``-mpiio`` ``foss/2016a`` -``3.2.1`` ``gompi/2019b`` -``3.3.0`` ``gompi/2020b``, ``gompi/2021a`` -========= ============= ================================ +========= ============= ================================================= +version versionsuffix toolchain +========= ============= ================================================= +``3.0.1`` ``-mpiio`` ``foss/2016a`` +``3.2.1`` ``gompi/2019b`` +``3.3.0`` ``gompi/2020b``, ``gompi/2021a``, ``gompi/2022a`` +========= ============= ================================================= .. _list_software_IOzone_596: @@ -20568,7 +21304,7 @@ IOzone is a filesystem benchmark tool. The benchmark generates and measures a va *homepage*: http://www.iozone.org/ ========= ============== -version toolchain +version toolchain ========= ============== ``3.434`` ``foss/2016a`` ========= ============== @@ -20584,7 +21320,7 @@ IPM is a portable profiling infrastructure for parallel codes. It provides a lo *homepage*: https://github.com/nerscadmin/IPM ========= =================================================================================== -version toolchain +version toolchain ========= =================================================================================== ``2.0.6`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iompi/2020a`` ========= =================================================================================== @@ -20600,9 +21336,9 @@ IPOPT (Interior Point Optimizer, pronounced Eye-Pea-Opt) is an open source soft *homepage*: https://projects.coin-or.org/Ipopt =========== =============== -version toolchain +version toolchain =========== =============== -``3.12.9`` ``foss/2017b`` +``3.12.9`` ``foss/2017b`` ``3.12.13`` ``intel/2019a`` =========== =============== @@ -20617,7 +21353,7 @@ Intel Integrated Performance Primitives (Intel IPP) is an extensive library of *homepage*: https://software.intel.com/en-us/articles/intel-ipp/ ============== ========== -version toolchain +version toolchain ============== ========== ``7.0.5.233`` ``system`` ``8.1.0.144`` ``system`` @@ -20636,7 +21372,7 @@ Class and tools for handling of IPv4 and IPv6 addresses and networks *homepage*: https://pypi.python.org/pypi/IPy ======== ========== -version toolchain +version toolchain ======== ========== ``0.83`` ``system`` ======== ========== @@ -20652,7 +21388,7 @@ ipyparallel is a Python package and collection of CLI scripts for controlling c *homepage*: https://ipyparallel.readthedocs.io ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``6.2.2`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================= ============== @@ -20668,7 +21404,7 @@ ipyrad is an interactive toolkit for assembly and analysis of restriction-site a *homepage*: https://ipyrad.readthedocs.io ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``0.6.15`` ``-Python-2.7.13`` ``intel/2017a`` ========== ================== =============== @@ -20684,33 +21420,33 @@ IPython provides a rich architecture for interactive computing with: Powerful i *homepage*: https://ipython.org/index.html ========== ================== ======================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ======================================================================================= -``3.2.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``4.2.0`` ``-Python-2.7.11`` ``intel/2016a`` -``5.0.0`` ``-Python-2.7.11`` ``foss/2016a`` -``5.0.0`` ``-Python-3.5.1`` ``foss/2016a`` -``5.1.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``5.1.0`` ``-Python-3.5.2`` ``intel/2016b`` -``5.2.2`` ``-Python-2.7.12`` ``intel/2016b`` -``5.3.0`` ``-Python-2.7.13`` ``intel/2017a`` -``5.7.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``5.8.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``3.2.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``4.2.0`` ``-Python-2.7.11`` ``intel/2016a`` +``5.0.0`` ``-Python-2.7.11`` ``foss/2016a`` +``5.0.0`` ``-Python-3.5.1`` ``foss/2016a`` +``5.1.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``5.1.0`` ``-Python-3.5.2`` ``intel/2016b`` +``5.2.2`` ``-Python-2.7.12`` ``intel/2016b`` +``5.3.0`` ``-Python-2.7.13`` ``intel/2017a`` +``5.7.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``5.8.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``5.8.0`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``fosscuda/2018b``, ``fosscuda/2019a``, ``intel/2018b`` -``5.8.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``5.10.0`` ``-Python-2.7.18`` ``foss/2021b`` -``6.2.1`` ``-Python-3.6.4`` ``foss/2017a`` -``6.3.1`` ``-Python-3.6.4`` ``intel/2018a`` -``6.4.0`` ``-Python-3.6.4`` ``foss/2018a`` -``7.2.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``7.7.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` -``7.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``7.13.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``7.15.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``7.18.1`` ``GCCcore/10.2.0`` -``7.25.0`` ``GCCcore/10.3.0`` -``7.26.0`` ``GCCcore/11.2.0`` -``8.5.0`` ``GCCcore/11.3.0`` +``5.8.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``5.10.0`` ``-Python-2.7.18`` ``foss/2021b`` +``6.2.1`` ``-Python-3.6.4`` ``foss/2017a`` +``6.3.1`` ``-Python-3.6.4`` ``intel/2018a`` +``6.4.0`` ``-Python-3.6.4`` ``foss/2018a`` +``7.2.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``7.7.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` +``7.9.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``7.13.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``7.15.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``7.18.1`` ``GCCcore/10.2.0`` +``7.25.0`` ``GCCcore/10.3.0`` +``7.26.0`` ``GCCcore/11.2.0`` +``8.5.0`` ``GCCcore/11.3.0`` ========== ================== ======================================================================================= @@ -20724,14 +21460,14 @@ Efficient phylogenomic software by maximum likelihood *homepage*: http://www.iqtree.org/ ========== ============= =============================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= =============================================== -``1.5.5`` ``-omp-mpi`` ``foss/2016a`` -``1.6.6`` ``intel/2018a`` +``1.5.5`` ``-omp-mpi`` ``foss/2016a`` +``1.6.6`` ``intel/2018a`` ``1.6.12`` ``foss/2018b``, ``foss/2020a``, ``intel/2019b`` -``2.1.2`` ``foss/2020a``, ``gompi/2020b`` -``2.1.3`` ``gompi/2021a`` -``2.2.1`` ``gompi/2021b`` +``2.1.2`` ``foss/2020a``, ``gompi/2020b`` +``2.1.3`` ``gompi/2021a`` +``2.2.1`` ``gompi/2021b`` ========== ============= =============================================== @@ -20745,7 +21481,7 @@ A module for improving the insertion sequences of structural variant calls *homepage*: https://github.com/mkirsche/Iris ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.0.5`` ``-Java-15`` ``GCC/11.2.0`` ========= ============= ============== @@ -20761,14 +21497,14 @@ The R kernel for the 'Jupyter' environment executes R code which the front-end *homepage*: https://irkernel.github.io ========== ========================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ========================== ================================== -``0.8.15`` ``-R-3.4.3-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``0.8.15`` ``-R-3.4.3-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.1`` ``-R-3.6.2-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``1.1`` ``-R-3.6.3-Python-3.8.2`` ``foss/2020a`` -``1.2`` ``-R-4.0.0-Python-3.8.2`` ``foss/2020a`` -``1.2`` ``-R-4.1.0`` ``foss/2021a`` -``1.3`` ``-R-4.2.0`` ``foss/2021b`` +``1.1`` ``-R-3.6.3-Python-3.8.2`` ``foss/2020a`` +``1.2`` ``-R-4.0.0-Python-3.8.2`` ``foss/2020a`` +``1.2`` ``-R-4.1.0`` ``foss/2021a`` +``1.3`` ``-R-4.2.0`` ``foss/2021b`` ========== ========================== ================================== @@ -20782,7 +21518,7 @@ IronPython is an open-source implementation of the Python programming language *homepage*: http://ironpython.net/ ======= =============== -version toolchain +version toolchain ======= =============== ``2.7`` ``intel/2016b`` ======= =============== @@ -20798,7 +21534,7 @@ Intelligent Storage Acceleration Library *homepage*: https://github.com/intel/isa-l ========== ============================================================================== -version toolchain +version toolchain ========== ============================================================================== ``2.30.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ============================================================================== @@ -20814,14 +21550,14 @@ isl is a library for manipulating sets and relations of integer points bounded b *homepage*: http://isl.gforge.inria.fr/ ======== ========================================================= -version toolchain +version toolchain ======== ========================================================= -``0.14`` ``GCC/4.9.2`` -``0.15`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a`` -``0.16`` ``GCC/4.9.3-2.25`` -``0.17`` ``foss/2016a`` +``0.14`` ``GCC/4.9.2`` +``0.15`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a`` +``0.16`` ``GCC/4.9.3-2.25`` +``0.17`` ``foss/2016a`` ``0.23`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``0.24`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``0.24`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ======== ========================================================= @@ -20835,7 +21571,7 @@ isoCirc: computational pipeline to identify high-confidence BSJs and full-length *homepage*: https://github.com/Xinglab/isoCirc ========= ============== -version toolchain +version toolchain ========= ============== ``1.0.4`` ``foss/2020b`` ========= ============== @@ -20851,7 +21587,7 @@ IsoNet stands for for ISOtropic reconstructioN of Electron Tomography. It trains *homepage*: https://github.com/Heng-Z/IsoNet =========================== ================== -version toolchain +version toolchain =========================== ================== ``0.1_20210822_04_674f67f`` ``fosscuda/2020b`` =========================== ================== @@ -20867,7 +21603,7 @@ Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD *homepage*: http://ispc.github.io/ , https://github.com/ispc/ispc/ ========== ========== -version toolchain +version toolchain ========== ========== ``1.6.0`` ``system`` ``1.10.0`` ``system`` @@ -20886,7 +21622,7 @@ The Intel Trace Collector is a low-overhead tracing library that performs event *homepage*: https://software.intel.com/en-us/intel-trace-analyzer/ ============== ========== -version toolchain +version toolchain ============== ========== ``8.0.0.011`` ``system`` ``8.1.4.045`` ``system`` @@ -20911,24 +21647,24 @@ Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite *homepage*: https://itk.org -========== ================== ============================================== -version versionsuffix toolchain -========== ================== ============================================== -``4.12.2`` ``-Python-2.7.12`` ``foss/2016b`` -``4.13.0`` ``-Python-2.7.14`` ``foss/2018a`` -``4.13.0`` ``-Python-3.6.4`` ``foss/2018a`` -``4.13.1`` ``-Python-2.7.14`` ``foss/2018a`` -``4.13.1`` ``-Python-2.7.15`` ``foss/2018b`` -``4.13.1`` ``-Python-3.6.4`` ``foss/2018a`` -``4.13.1`` ``-Python-3.6.6`` ``foss/2018b`` -``4.13.1`` ``-Python-3.7.4`` ``foss/2019b`` -``5.0.1`` ``-Python-3.7.2`` ``foss/2019a`` -``5.0.1`` ``-Python-3.7.4`` ``foss/2019b`` -``5.0b01`` ``-Python-3.6.6`` ``foss/2018b`` -``5.1.2`` ``foss/2020a``, ``fosscuda/2020a`` -``5.1.2`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` -``5.2.1`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` -========== ================== ============================================== +========== ================== ============================================================== +version versionsuffix toolchain +========== ================== ============================================================== +``4.12.2`` ``-Python-2.7.12`` ``foss/2016b`` +``4.13.0`` ``-Python-2.7.14`` ``foss/2018a`` +``4.13.0`` ``-Python-3.6.4`` ``foss/2018a`` +``4.13.1`` ``-Python-2.7.14`` ``foss/2018a`` +``4.13.1`` ``-Python-2.7.15`` ``foss/2018b`` +``4.13.1`` ``-Python-3.6.4`` ``foss/2018a`` +``4.13.1`` ``-Python-3.6.6`` ``foss/2018b`` +``4.13.1`` ``-Python-3.7.4`` ``foss/2019b`` +``5.0.1`` ``-Python-3.7.2`` ``foss/2019a`` +``5.0.1`` ``-Python-3.7.4`` ``foss/2019b`` +``5.0b01`` ``-Python-3.6.6`` ``foss/2018b`` +``5.1.2`` ``foss/2020a``, ``fosscuda/2020a`` +``5.1.2`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``5.2.1`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a`` +========== ================== ============================================================== .. _list_software_itpp_445: @@ -20941,7 +21677,7 @@ IT++ is a C++ library of mathematical, signal processing and communication clas *homepage*: https://sourceforge.net/projects/itpp/ ========= ============== -version toolchain +version toolchain ========= ============== ``4.3.1`` ``foss/2019b`` ========= ============== @@ -20957,10 +21693,10 @@ ITS Tool allows you to translate your XML documents with PO files *homepage*: http://itstool.org/ ========= ================== ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================= -``2.0.5`` ``-Python-2.7.14`` ``intel/2018a`` -``2.0.5`` ``-Python-2.7.15`` ``foss/2018b`` +``2.0.5`` ``-Python-2.7.14`` ``intel/2018a`` +``2.0.5`` ``-Python-2.7.15`` ``foss/2018b`` ``2.0.6`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========= ================== ================= @@ -20975,9 +21711,9 @@ ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal *homepage*: https://microbiology.se/software/itsx/ ========= ================== -version toolchain +version toolchain ========= ================== -``1.1.2`` ``GCCcore/9.3.0`` +``1.1.2`` ``GCCcore/9.3.0`` ``1.1.3`` ``GCCcore/10.3.0`` ========= ================== @@ -20992,9 +21728,9 @@ iVar is a computational package that contains functions broadly useful for viral *homepage*: https://github.com/andersen-lab/ivar ========= ============================= -version toolchain +version toolchain ========= ============================= -``1.0.1`` ``foss/2018b`` +``1.0.1`` ``foss/2018b`` ``1.3.1`` ``GCC/10.2.0``, ``GCC/9.3.0`` ========= ============================= @@ -21005,7 +21741,7 @@ version toolchain --- -:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_Jasmine_711` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_JavaFX_544` - :ref:`list_software_jax_323` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_Jorg_402` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_json-fortran_1251` - :ref:`list_software_JSON-GLib_709` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyter-matlab-proxy_2080` - :ref:`list_software_jupyter-resource-usage_2282` - :ref:`list_software_jupyter-server-proxy_2118` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` - :ref:`list_software_jxrlib_651` +:ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_Jasmine_711` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_JavaFX_544` - :ref:`list_software_jax_323` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_Jorg_402` - :ref:`list_software_joypy_571` - :ref:`list_software_jq_219` - :ref:`list_software_json-c_586` - :ref:`list_software_json-fortran_1251` - :ref:`list_software_JSON-GLib_709` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyter-matlab-proxy_2080` - :ref:`list_software_jupyter-resource-usage_2282` - :ref:`list_software_jupyter-server_1495` - :ref:`list_software_jupyter-server-proxy_2118` - :ref:`list_software_JupyterHub_1042` - :ref:`list_software_JupyterLab_1026` - :ref:`list_software_JWM_238` - :ref:`list_software_jxrlib_651` .. _list_software_JAGS_293: @@ -21018,9 +21754,9 @@ JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian *homepage*: http://mcmc-jags.sourceforge.net/ ========= =================================================================================================================================================================== -version toolchain +version toolchain ========= =================================================================================================================================================================== -``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` +``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` ``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2020b``, ``intel/2017b`` ========= =================================================================================================================================================================== @@ -21035,11 +21771,11 @@ Jansson is a C library for encoding, decoding and manipulating JSON data. Its m *homepage*: http://www.digip.org/jansson/ ========== ============================== -version toolchain +version toolchain ========== ============================== -``2.6`` ``GCC/4.8.3`` +``2.6`` ``GCC/4.8.3`` ``2.13.1`` ``GCC/10.2.0``, ``GCC/11.2.0`` -``2.14`` ``GCC/11.3.0`` +``2.14`` ``GCC/11.3.0`` ========== ============================== @@ -21053,7 +21789,7 @@ SV Merging Across Samples *homepage*: https://github.com/mkirsche/Jasmine ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.1.4`` ``-Java-15`` ``GCC/11.2.0`` ========= ============= ============== @@ -21069,16 +21805,17 @@ The JasPer Project is an open-source initiative to provide a free software-base *homepage*: https://www.ece.uvic.ca/~frodo/jasper/ =========== ========================================================================================================================================================== -version toolchain +version toolchain =========== ========================================================================================================================================================== ``1.900.1`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``2.0.10`` ``intel/2016b`` -``2.0.12`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` -``2.0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.0.16`` ``GCCcore/9.3.0`` -``2.0.24`` ``GCCcore/10.2.0`` -``2.0.28`` ``GCCcore/10.3.0`` -``2.0.33`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.0.10`` ``intel/2016b`` +``2.0.12`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` +``2.0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.0.16`` ``GCCcore/9.3.0`` +``2.0.24`` ``GCCcore/10.2.0`` +``2.0.28`` ``GCCcore/10.3.0`` +``2.0.33`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.0.0`` ``GCCcore/12.2.0`` =========== ========================================================================================================================================================== @@ -21092,7 +21829,7 @@ Java Platform, Standard Edition (Java SE) lets you develop and deploy Java appli *homepage*: https://java.com/ ============= ======================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ============= ======================== ========== ``1.6.0_24`` ``system`` ``1.7.0_10`` ``system`` @@ -21170,7 +21907,7 @@ OpenJFX is an open source, next generation client application platform for deskt *homepage*: https://openjfx.io/ ========== ====================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ====================== ========== ``11.0.2`` ``_linux-x64_bin-sdk`` ``system`` ========== ====================== ========== @@ -21186,15 +21923,17 @@ Composable transformations of Python+NumPy programs: differentiate, vectorize, J *homepage*: https://pypi.python.org/pypi/jax ========== ================ ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================ ================================== ``0.2.19`` ``foss/2020b``, ``fosscuda/2020b`` -``0.2.20`` ``foss/2021a`` -``0.2.24`` ``foss/2021a`` -``0.2.24`` ``-CUDA-11.3.1`` ``foss/2021a`` -``0.3.9`` ``foss/2021a`` -``0.3.9`` ``-CUDA-11.3.1`` ``foss/2021a`` -``0.3.14`` ``-CUDA-11.7.0`` ``foss/2022a`` +``0.2.20`` ``foss/2021a`` +``0.2.24`` ``foss/2021a`` +``0.2.24`` ``-CUDA-11.3.1`` ``foss/2021a`` +``0.3.9`` ``foss/2021a`` +``0.3.9`` ``-CUDA-11.3.1`` ``foss/2021a`` +``0.3.14`` ``-CUDA-11.7.0`` ``foss/2022a`` +``0.3.23`` ``foss/2022a`` +``0.3.23`` ``-CUDA-11.4.1`` ``foss/2021b`` ========== ================ ================================== @@ -21208,7 +21947,7 @@ JAXFront is a technology to generate graphical user interfaces on multiple chan *homepage*: http://www.jaxfront.org/pages/free_community_edition.html ======== ========== -version toolchain +version toolchain ======== ========== ``2.75`` ``system`` ======== ========== @@ -21223,11 +21962,11 @@ JBIG-KIT is a software implementation of the JBIG1 data compression standard (I *homepage*: https://www.cl.cam.ac.uk/~mgk25/jbigkit/ -======= ========================================================================================================================================================== -version toolchain -======= ========================================================================================================================================================== -``2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= ========================================================================================================================================================== +======= ============================================================================================================================================================================== +version toolchain +======= ============================================================================================================================================================================== +``2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ============================================================================================================================================================================== .. _list_software_Jellyfish_938: @@ -21240,12 +21979,12 @@ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. *homepage*: http://www.genome.umd.edu/jellyfish.html ========== =================================================================== -version toolchain +version toolchain ========== =================================================================== -``1.1.11`` ``foss/2016a``, ``foss/2016b`` -``1.1.12`` ``foss/2018b``, ``intel/2018a`` -``2.2.6`` ``foss/2016b``, ``intel/2017a`` -``2.2.10`` ``foss/2018b``, ``intel/2018a`` +``1.1.11`` ``foss/2016a``, ``foss/2016b`` +``1.1.12`` ``foss/2018b``, ``intel/2018a`` +``2.2.6`` ``foss/2016b``, ``intel/2017a`` +``2.2.10`` ``foss/2018b``, ``intel/2018a`` ``2.3.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` ========== =================================================================== @@ -21260,17 +21999,17 @@ jemalloc is a general purpose malloc(3) implementation that emphasizes fragmenta *homepage*: http://jemalloc.net ========= ================================================================================================ -version toolchain +version toolchain ========= ================================================================================================ -``4.1.0`` ``intel/2016a`` -``4.2.0`` ``foss/2016a``, ``intel/2016a`` -``4.2.1`` ``intel/2016b`` -``4.5.0`` ``intel/2017a`` -``5.0.1`` ``GCCcore/6.4.0`` -``5.1.0`` ``GCCcore/7.3.0`` -``5.2.0`` ``GCCcore/8.2.0`` +``4.1.0`` ``intel/2016a`` +``4.2.0`` ``foss/2016a``, ``intel/2016a`` +``4.2.1`` ``intel/2016b`` +``4.5.0`` ``intel/2017a`` +``5.0.1`` ``GCCcore/6.4.0`` +``5.1.0`` ``GCCcore/7.3.0`` +``5.2.0`` ``GCCcore/8.2.0`` ``5.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``5.3.0`` ``GCCcore/11.3.0`` +``5.3.0`` ``GCCcore/11.3.0`` ========= ================================================================================================ @@ -21284,7 +22023,7 @@ JHBuild allows you to automatically download and compile “modules” (i.e. sou *homepage*: https://wiki.gnome.org/action/show/Projects/Jhbuild =========== ================= -version toolchain +version toolchain =========== ================= ``3.15.92`` ``GCCcore/4.9.3`` =========== ================= @@ -21300,10 +22039,10 @@ Just-in-time compilation for ordinary/delay/stochastic differential equations (D *homepage*: https://jitcde-common.readthedocs.io ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``1.3.2`` ``-Python-3.6.4`` ``intel/2018a`` -``1.4.0`` ``-Python-3.7.2`` ``foss/2019a`` +``1.4.0`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= =============== @@ -21317,7 +22056,7 @@ jModelTest is a tool to carry out statistical selection of best-fit models of nu *homepage*: https://github.com/ddarriba/jmodeltest2 =================== ================== ========== -version versionsuffix toolchain +version versionsuffix toolchain =================== ================== ========== ``2.1.10r20160303`` ``-Java-1.8.0_92`` ``system`` =================== ================== ========== @@ -21333,7 +22072,7 @@ A MAG Circularization Method By Lauren Lui, Torben Nielsen, and Adam Arkin *homepage*: https://github.com/lmlui/Jorg ========= ============== -version toolchain +version toolchain ========= ============== ``1.0.1`` ``foss/2020b`` ========= ============== @@ -21349,7 +22088,7 @@ Joyplots in Python with matplotlib & pandas *homepage*: https://github.com/sbebo/joypy ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.2.2`` ``-Python-3.7.4`` ``intel/2019b`` ``0.2.4`` ``intel/2020b`` @@ -21366,9 +22105,9 @@ jq is a lightweight and flexible command-line JSON processor. *homepage*: https://stedolan.github.io/jq/ ======= ========================================================== -version toolchain +version toolchain ======= ========================================================== -``1.5`` ``GCCcore/6.4.0`` +``1.5`` ``GCCcore/6.4.0`` ``1.6`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ======= ========================================================== @@ -21383,10 +22122,10 @@ JSON-C implements a reference counting object model that allows you to easily co *homepage*: https://github.com/json-c/json-c ======== ========================================================== -version toolchain +version toolchain ======== ========================================================== ``0.15`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``0.16`` ``GCCcore/11.3.0`` +``0.16`` ``GCCcore/11.3.0`` ======== ========================================================== @@ -21400,7 +22139,7 @@ JSON-Fortran: A Modern Fortran JSON API *homepage*: https://github.com/jacobwilliams/json-fortran ========= ================== -version toolchain +version toolchain ========= ================== ``8.3.0`` ``GCCcore/11.2.0`` ========= ================== @@ -21416,7 +22155,7 @@ JSON-GLib implements a full JSON parser and generator using GLib and GObject, a *homepage*: https://wiki.gnome.org/Projects/JsonGlib ========= ================== -version toolchain +version toolchain ========= ================== ``1.6.2`` ``GCCcore/10.3.0`` ========= ================== @@ -21432,12 +22171,12 @@ JsonCpp is a C++ library that allows manipulating JSON values, including serial *homepage*: https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html ========== ============================================================================= -version toolchain +version toolchain ========== ============================================================================= -``0.10.7`` ``GCCcore/8.2.0`` -``1.9.3`` ``GCCcore/8.3.0`` +``0.10.7`` ``GCCcore/8.2.0`` +``1.9.3`` ``GCCcore/8.3.0`` ``1.9.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``1.9.5`` ``GCCcore/11.3.0`` +``1.9.5`` ``GCCcore/11.3.0`` ========== ============================================================================= @@ -21451,7 +22190,7 @@ The JUBE benchmarking environment provides a script based framework to easily cr *homepage*: https://www.fz-juelich.de/jsc/jube ========= ========== -version toolchain +version toolchain ========= ========== ``2.0.3`` ``system`` ``2.0.4`` ``system`` @@ -21472,7 +22211,7 @@ A C library that implements a dynamic array. *homepage*: http://judy.sourceforge.net/ ========= ==================================================================================================================== -version toolchain +version toolchain ========= ==================================================================================================================== ``1.0.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ==================================================================================================================== @@ -21488,7 +22227,7 @@ Julia is a high-level, high-performance dynamic programming language for numeric *homepage*: https://julialang.org ========= ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ========== ``1.1.1`` ``-linux-x86_64`` ``system`` ``1.2.0`` ``-linux-x86_64`` ``system`` @@ -21523,7 +22262,7 @@ A programmer-oriented testing framework for Java. *homepage*: http://sourceforge.net/projects/junit ======== =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ======== =================== ========== ``4.10`` ``-Java-1.7.0_10`` ``system`` ``4.10`` ``-Java-1.7.0_21`` ``system`` @@ -21556,7 +22295,7 @@ MATLAB Integration for Jupyter *homepage*: https://github.com/mathworks/jupyter-matlab-proxy ========= ================== -version toolchain +version toolchain ========= ================== ``0.3.4`` ``GCCcore/10.3.0`` ========= ================== @@ -21572,12 +22311,28 @@ Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or *homepage*: https://github.com/jupyter-server/jupyter-resource-usage ========= ================== -version toolchain +version toolchain ========= ================== ``0.6.1`` ``GCCcore/10.3.0`` ========= ================== +.. _list_software_jupyter-server_1495: + +*jupyter-server* +++++++++++++++++ + +The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila. + +*homepage*: https://jupyter.org/ + +========== ================== +version toolchain +========== ================== +``1.21.0`` ``GCCcore/11.3.0`` +========== ================== + + .. _list_software_jupyter-server-proxy_2118: *jupyter-server-proxy* @@ -21588,7 +22343,7 @@ Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, *homepage*: https://github.com/jupyterhub/jupyter-server-proxy ========= ================== -version toolchain +version toolchain ========= ================== ``3.2.1`` ``GCCcore/10.3.0`` ========= ================== @@ -21604,10 +22359,10 @@ JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed fo *homepage*: https://jupyter.org ========= ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================== -``0.6.1`` ``-Python-3.5.1`` ``foss/2016a`` -``0.8.1`` ``-Python-3.6.4`` ``foss/2017a`` +``0.6.1`` ``-Python-3.5.1`` ``foss/2016a`` +``0.8.1`` ``-Python-3.6.4`` ``foss/2017a`` ``1.1.0`` ``GCCcore/10.2.0`` ``1.4.1`` ``GCCcore/10.3.0`` ========= ================= ================== @@ -21623,13 +22378,14 @@ JupyterLab is the next-generation user interface for Project Jupyter offering al *homepage*: https://jupyter.org/ ========== ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================== ``1.2.5`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``2.2.8`` ``GCCcore/10.2.0`` -``3.0.16`` ``GCCcore/10.3.0`` -``3.1.6`` ``GCCcore/11.2.0`` -``3.2.8`` ``GCCcore/10.3.0`` +``2.2.8`` ``GCCcore/10.2.0`` +``3.0.16`` ``GCCcore/10.3.0`` +``3.1.6`` ``GCCcore/11.2.0`` +``3.2.8`` ``GCCcore/10.3.0`` +``3.5.0`` ``GCCcore/11.3.0`` ========== ================= ================================== @@ -21643,7 +22399,7 @@ JWM is a light-weight window manager for the X11 Window System. *homepage*: https://joewing.net/projects/jwm/ ========= =============== -version toolchain +version toolchain ========= =============== ``2.3.5`` ``intel/2016a`` ========= =============== @@ -21658,11 +22414,11 @@ Open source implementation of jpegxr *homepage*: https://github.com/4creators/jxrlib -======= ================== -version toolchain -======= ================== -``1.1`` ``GCCcore/10.2.0`` -======= ================== +======= ====================================== +version toolchain +======= ====================================== +``1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +======= ====================================== .. _list_software_letter_k: @@ -21671,7 +22427,23 @@ version toolchain --- -:ref:`list_software_Kaiju_500` - :ref:`list_software_Kaleido_697` - :ref:`list_software_Kalign_598` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_kedro_533` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_king_425` - :ref:`list_software_kma_313` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` +:ref:`list_software_KaHIP_397` - :ref:`list_software_Kaiju_500` - :ref:`list_software_Kaleido_697` - :ref:`list_software_Kalign_598` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_kedro_533` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_king_425` - :ref:`list_software_KITE_301` - :ref:`list_software_kma_313` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` + + +.. _list_software_KaHIP_397: + +*KaHIP* ++++++++ + +The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning. + +*homepage*: https://kahip.github.io/ + +======== =============== +version toolchain +======== =============== +``3.14`` ``gompi/2022a`` +======== =============== .. _list_software_Kaiju_500: @@ -21684,7 +22456,7 @@ Kaiju is a program for sensitive taxonomic classification of high-throughput seq *homepage*: http://kaiju.binf.ku.dk/ ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``1.5.0`` ``intel/2016b`` ``1.7.2`` ``-Python-3.7.2`` ``iimpi/2019a`` @@ -21702,7 +22474,7 @@ Fast static image export for web-based visualization libraries with zero depende *homepage*: https://github.com/plotly/Kaleido ========= ================== -version toolchain +version toolchain ========= ================== ``0.1.0`` ``GCCcore/10.2.0`` ``0.2.1`` ``GCCcore/10.3.0`` @@ -21719,11 +22491,11 @@ Kalign is a fast multiple sequence alignment program for biological sequences. *homepage*: https://github.com/TimoLassmann/kalign ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``2.0.4`` ``GCCcore/10.2.0`` +``2.0.4`` ``GCCcore/10.2.0`` ``3.3.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``3.3.2`` ``GCCcore/11.2.0`` +``3.3.2`` ``GCCcore/11.2.0`` ========= ====================================== @@ -21737,18 +22509,18 @@ kallisto is a program for quantifying abundances of transcripts from RNA-Seq dat *homepage*: https://pachterlab.github.io/kallisto/ ========== ================================================ -version toolchain +version toolchain ========== ================================================ -``0.42.5`` ``foss/2016a`` -``0.43.0`` ``intel/2016b`` +``0.42.5`` ``foss/2016a`` +``0.43.0`` ``intel/2016b`` ``0.43.1`` ``foss/2016b``, ``intel/2017a``, ``intel/2017b`` -``0.44.0`` ``foss/2016b``, ``intel/2018a`` -``0.45.0`` ``foss/2018b`` -``0.45.1`` ``foss/2019a`` -``0.46.0`` ``intel/2019a`` +``0.44.0`` ``foss/2016b``, ``intel/2018a`` +``0.45.0`` ``foss/2018b`` +``0.45.1`` ``foss/2019a`` +``0.46.0`` ``intel/2019a`` ``0.46.1`` ``foss/2019b``, ``iimpi/2020a``, ``iimpi/2020b`` -``0.46.2`` ``foss/2020b`` -``0.48.0`` ``gompi/2021b`` +``0.46.2`` ``foss/2020b`` +``0.48.0`` ``gompi/2021b`` ========== ================================================ @@ -21762,7 +22534,7 @@ The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and com *homepage*: https://www.earlham.ac.uk/kat-tools ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``2.4.2`` ``-Python-3.6.4`` ``foss/2018a`` ``2.4.2`` ``-Python-3.7.2`` ``foss/2019a`` @@ -21779,7 +22551,7 @@ X.org KBProto protocol headers. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================================== -version toolchain +version toolchain ========= ================================================================== ``1.0.7`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017b`` ========= ================================================================== @@ -21795,7 +22567,7 @@ Kedro is an open-source Python framework that applies software engineering best- *homepage*: https://github.com/quantumblacklabs/kedro ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.16.5`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================= ============== @@ -21811,16 +22583,16 @@ Kent utilities: collection of tools used by the UCSC genome browser. *homepage*: https://genome.cse.ucsc.edu/ ============ ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= =============== ``401`` ``gompi/2019b`` -``411`` ``GCC/10.2.0`` -``418`` ``GCC/10.3.0`` -``422`` ``GCC/11.2.0`` -``20130806`` ``-linux.x86_64`` ``system`` -``20171107`` ``-linux.x86_64`` ``system`` -``20180716`` ``-linux.x86_64`` ``system`` -``20190326`` ``-linux.x86_64`` ``system`` +``411`` ``GCC/10.2.0`` +``418`` ``GCC/10.3.0`` +``422`` ``GCC/11.2.0`` +``20130806`` ``-linux.x86_64`` ``system`` +``20171107`` ``-linux.x86_64`` ``system`` +``20180716`` ``-linux.x86_64`` ``system`` +``20190326`` ``-linux.x86_64`` ``system`` ============ ================= =============== @@ -21834,28 +22606,28 @@ Keras is a deep learning API written in Python, running on top of the machine le *homepage*: https://keras.io/ ========= ================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================================== -``1.0.8`` ``-Python-3.5.2`` ``intel/2016b`` -``1.1.0`` ``-Python-3.5.2`` ``intel/2016b`` -``2.0.4`` ``-Python-2.7.13`` ``intel/2017a`` -``2.0.4`` ``-Python-3.6.1`` ``intel/2017a`` -``2.0.5`` ``-Python-3.6.1`` ``intel/2017a`` -``2.0.8`` ``-Python-3.6.1`` ``intel/2017a`` -``2.1.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.1.1`` ``-Python-3.6.3`` ``intel/2017b`` -``2.1.2`` ``-Python-2.7.14`` ``intel/2017b`` -``2.1.2`` ``-Python-3.6.3`` ``foss/2017b`` -``2.1.3`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.2.0`` ``-Python-2.7.14`` ``fosscuda/2017b`` -``2.2.0`` ``-Python-3.6.3`` ``fosscuda/2017b`` -``2.2.0`` ``-Python-3.6.4`` ``foss/2018a`` -``2.2.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``2.2.4`` ``-Python-3.6.4`` ``intel/2018a`` +``1.0.8`` ``-Python-3.5.2`` ``intel/2016b`` +``1.1.0`` ``-Python-3.5.2`` ``intel/2016b`` +``2.0.4`` ``-Python-2.7.13`` ``intel/2017a`` +``2.0.4`` ``-Python-3.6.1`` ``intel/2017a`` +``2.0.5`` ``-Python-3.6.1`` ``intel/2017a`` +``2.0.8`` ``-Python-3.6.1`` ``intel/2017a`` +``2.1.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.1.1`` ``-Python-3.6.3`` ``intel/2017b`` +``2.1.2`` ``-Python-2.7.14`` ``intel/2017b`` +``2.1.2`` ``-Python-3.6.3`` ``foss/2017b`` +``2.1.3`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.2.0`` ``-Python-2.7.14`` ``fosscuda/2017b`` +``2.2.0`` ``-Python-3.6.3`` ``fosscuda/2017b`` +``2.2.0`` ``-Python-3.6.4`` ``foss/2018a`` +``2.2.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``2.2.4`` ``-Python-3.6.4`` ``intel/2018a`` ``2.2.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``2.2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``2.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``2.3.1`` ``-Python-3.8.2`` ``foss/2020a`` +``2.3.1`` ``-Python-3.8.2`` ``foss/2020a`` ``2.4.3`` ``foss/2020b``, ``fosscuda/2020b`` ========= ================== ================================== @@ -21870,9 +22642,9 @@ In-memory nucleotide sequence k-mer counting, filtering, graph traversal and mor *homepage*: https://github.com/ged-lab/khmer/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== -``1.4.1`` ``-Python-2.7.12`` ``foss/2016b`` +``1.4.1`` ``-Python-2.7.12`` ``foss/2016b`` ``2.1.1`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== @@ -21887,12 +22659,12 @@ Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collec *homepage*: https://openkim.org/ ========= ================================================================ -version toolchain +version toolchain ========= ================================================================ -``2.1.2`` ``foss/2019a``, ``intel/2019a`` +``2.1.2`` ``foss/2019a``, ``intel/2019a`` ``2.1.3`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b``, ``intel/2020a`` -``2.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.3.0`` ``GCCcore/11.2.0`` +``2.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.3.0`` ``GCCcore/11.2.0`` ========= ================================================================ @@ -21906,13 +22678,29 @@ KING is a toolset that makes use of high-throughput SNP data typically seen in *homepage*: https://kingrelatedness.com/ ========= ========== -version toolchain +version toolchain ========= ========== ``2.2.4`` ``system`` ``2.2.7`` ``system`` ========= ========== +.. _list_software_KITE_301: + +*KITE* +++++++ + +KITE is an open-source Python/C++ software suite for efficient real-space tight-binding (TB) simulations of electronic structure and bulk quantum transport properties of disordered systems scalable to multi billions of atomic orbitals. + +*homepage*: https://github.com/quantum-kite/kite + +======= =============== +version toolchain +======= =============== +``1.1`` ``gompi/2022a`` +======= =============== + + .. _list_software_kma_313: *kma* @@ -21923,7 +22711,7 @@ KMA is a mapping method designed to map raw reads directly against redundant dat *homepage*: https://bitbucket.org/genomicepidemiology/kma ========== =============== -version toolchain +version toolchain ========== =============== ``1.2.22`` ``intel/2019b`` ========== =============== @@ -21939,12 +22727,12 @@ KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/F *homepage*: http://sun.aei.polsl.pl/kmc ============ ================= ============================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ============================== ``3.1.0`` ``foss/2018a``, ``foss/2018b`` -``3.1.1`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` -``3.1.2rc1`` ``-Python-3.7.4`` ``GCC/8.3.0`` -``3.2.1`` ``GCC/11.2.0`` +``3.1.1`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` +``3.1.2rc1`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``3.2.1`` ``GCC/11.2.0`` ============ ================= ============================== @@ -21958,7 +22746,7 @@ KmerGenie estimates the best k-mer length for genome de novo assembly. *homepage*: http://kmergenie.bx.psu.edu/ ========== =============== -version toolchain +version toolchain ========== =============== ``1.7044`` ``intel/2017a`` ``1.7048`` ``intel/2018a`` @@ -21975,7 +22763,7 @@ KNIME Analytics Platform is the open source software for creating data science a *homepage*: https://www.knime.com/ ========= ========== -version toolchain +version toolchain ========= ========== ``3.6.2`` ``system`` ========= ========== @@ -21991,7 +22779,7 @@ Kernel PC (kPC) algorithm for causal structure learning and causal inference us *homepage*: https://cran.r-project.org/package=kpcalg ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.0.1`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== @@ -22007,14 +22795,14 @@ Kraken is a system for assigning taxonomic labels to short DNA sequences, usual *homepage*: https://ccb.jhu.edu/software/kraken/ =============== ================ ========================================================= -version versionsuffix toolchain +version versionsuffix toolchain =============== ================ ========================================================= -``0.10.5-beta`` ``-Perl-5.22.1`` ``foss/2016a`` -``0.10.5-beta`` ``-Perl-5.24.0`` ``foss/2016b`` -``1.0`` ``-Perl-5.26.1`` ``intel/2018a`` -``1.1`` ``-Perl-5.28.0`` ``foss/2018b`` +``0.10.5-beta`` ``-Perl-5.22.1`` ``foss/2016a`` +``0.10.5-beta`` ``-Perl-5.24.0`` ``foss/2016b`` +``1.0`` ``-Perl-5.26.1`` ``intel/2018a`` +``1.1`` ``-Perl-5.28.0`` ``foss/2018b`` ``1.1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``1.1.1`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``1.1.1`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` =============== ================ ========================================================= @@ -22028,14 +22816,14 @@ Kraken is a system for assigning taxonomic labels to short DNA sequences, usual *homepage*: https://github.com/DerrickWood/kraken2/wiki ============== ================ ================================ -version versionsuffix toolchain +version versionsuffix toolchain ============== ================ ================================ -``2.0.6-beta`` ``-Perl-5.26.1`` ``foss/2018a`` -``2.0.7-beta`` ``-Perl-5.28.0`` ``foss/2018b`` -``2.0.8-beta`` ``-Perl-5.30.0`` ``gompi/2019b`` -``2.0.9-beta`` ``-Perl-5.28.0`` ``foss/2018b`` -``2.0.9-beta`` ``-Perl-5.30.2`` ``gompi/2020a`` -``2.1.1`` ``gompi/2020b`` +``2.0.6-beta`` ``-Perl-5.26.1`` ``foss/2018a`` +``2.0.7-beta`` ``-Perl-5.28.0`` ``foss/2018b`` +``2.0.8-beta`` ``-Perl-5.30.0`` ``gompi/2019b`` +``2.0.9-beta`` ``-Perl-5.28.0`` ``foss/2018b`` +``2.0.9-beta`` ``-Perl-5.30.2`` ``gompi/2020a`` +``2.1.1`` ``gompi/2020b`` ``2.1.2`` ``gompi/2021a``, ``gompi/2021b`` ============== ================ ================================ @@ -22050,7 +22838,7 @@ Kratos Multiphysics (A.K.A Kratos) is a framework for building parallel multi-di *homepage*: https://www.cimne.com/kratos ======= ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= =============================== ``6.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ======= ================= =============================== @@ -22065,14 +22853,14 @@ Krona Tools is a set of scripts to create Krona charts from several Bioinformat *homepage*: https://github.com/marbl/Krona/wiki/KronaTools -========= ================================== -version toolchain -========= ================================== -``2.7`` ``GCCcore/7.3.0`` -``2.7.1`` ``GCCcore/8.2.0`` +========= ====================================== +version toolchain +========= ====================================== +``2.7`` ``GCCcore/7.3.0`` +``2.7.1`` ``GCCcore/8.2.0`` ``2.8`` ``GCC/10.3.0``, ``GCCcore/10.2.0`` -``2.8.1`` ``GCCcore/11.2.0`` -========= ================================== +``2.8.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ====================================== .. _list_software_kwant_549: @@ -22085,7 +22873,7 @@ Kwant is a free (open source), powerful, and easy to use Python package for nu *homepage*: https://kwant-project.org/ ========= ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============================== ``1.4.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ========= ================= =============================== @@ -22101,7 +22889,7 @@ The Kitware Information Macro Library *homepage*: https://gitlab.kitware.com/utils/kwiml ============ ================= -version toolchain +version toolchain ============ ================= ``20180201`` ``GCCcore/6.4.0`` ============ ================= @@ -22117,7 +22905,7 @@ This software implements a de novo, alignment free measure of sample genetic di *homepage*: https://github.com/kdmurray91/kWIP ========= ================= -version toolchain +version toolchain ========= ================= ``0.2.0`` ``GCCcore/6.4.0`` ========= ================= @@ -22133,7 +22921,7 @@ Kyoto Cabinet is a library of routines for managing a database. *homepage*: https://fallabs.com/kyotocabinet ========== ==================================== -version toolchain +version toolchain ========== ==================================== ``1.2.77`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ========== ==================================== @@ -22145,7 +22933,7 @@ version toolchain --- -:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LBFGS++_452` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_LERC_294` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaec_608` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libavif_733` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libde265_669` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libev_530` - :ref:`list_software_libevent_857` - :ref:`list_software_libexif_739` - :ref:`list_software_libfabric_926` - :ref:`list_software_libfdf_615` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgdiplus_1071` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libheif_723` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_LibLZF_515` - :ref:`list_software_libmad_617` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libmbd_618` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libnsl_644` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libopus_766` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libplinkio_1069` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpspio_866` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libSBML_613` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libtree_743` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_longread_umi_1270` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPeg_360` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_LuaJIT2-OpenResty_1553` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` +:ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LADR_291` - :ref:`list_software_lagrangian-filtering_2053` - :ref:`list_software_LAME_287` - :ref:`list_software_LAMMPS_458` - :ref:`list_software_lancet_631` - :ref:`list_software_LAPACK_428` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LBFGS++_452` - :ref:`list_software_LCov_372` - :ref:`list_software_LDC_211` - :ref:`list_software_lDDT_328` - :ref:`list_software_LeadIT_531` - :ref:`list_software_leidenalg_933` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_LERC_294` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_LHAPDF_431` - :ref:`list_software_libaec_608` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libav_526` - :ref:`list_software_libavif_733` - :ref:`list_software_libBigWig_880` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcdms_734` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcint_741` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libde265_669` - :ref:`list_software_libdeflate_1036` - :ref:`list_software_libdivsufsort_1424` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdrs_640` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libev_530` - :ref:`list_software_libevent_857` - :ref:`list_software_libexif_739` - :ref:`list_software_libfabric_926` - :ref:`list_software_libfdf_615` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgdiplus_1071` - :ref:`list_software_libGDSII_679` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libgit2_685` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libGridXC_856` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libheif_723` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_libidn2_676` - :ref:`list_software_Libint_610` - :ref:`list_software_LiBis_467` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libjxl_645` - :ref:`list_software_LibLZF_515` - :ref:`list_software_libmad_617` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libmbd_618` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libmicrohttpd_1397` - :ref:`list_software_libmo_unpack_1268` - :ref:`list_software_libmypaint_1081` - :ref:`list_software_libnsl_644` - :ref:`list_software_libobjcryst_1191` - :ref:`list_software_libogg_628` - :ref:`list_software_libopus_766` - :ref:`list_software_libosmium_977` - :ref:`list_software_libpci_627` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libplinkio_1069` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libPSML_627` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpspio_866` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librosa_748` - :ref:`list_software_librsb_638` - :ref:`list_software_librsvg_761` - :ref:`list_software_librttopo_991` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libSBML_613` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_libStatGen_1005` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_libtecla_832` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libtree_743` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libuv_546` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libvorbis_972` - :ref:`list_software_libwebp_741` - :ref:`list_software_libwpe_643` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzeep_747` - :ref:`list_software_libzip_650` - :ref:`list_software_lie_learn_939` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_liknorm_764` - :ref:`list_software_likwid_644` - :ref:`list_software_limix_547` - :ref:`list_software_LinBox_588` - :ref:`list_software_line_profiler_1386` - :ref:`list_software_Lingeling_921` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLDB_286` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LncLOOM_596` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_logaddexp_952` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_longestrunsubsequence_2292` - :ref:`list_software_longread_umi_1270` - :ref:`list_software_Longshot_846` - :ref:`list_software_loompy_672` - :ref:`list_software_LPeg_360` - :ref:`list_software_LPJmL_415` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSD2_277` - :ref:`list_software_LSMS_319` - :ref:`list_software_LTR_retriever_1321` - :ref:`list_software_LtrDetector_1132` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_LuaJIT2-OpenResty_1553` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: @@ -22158,7 +22946,7 @@ L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to sc *homepage*: http://www.fishbrowser.org/software/L_RNA_scaffolder/ ============ ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================ =============== ``20141124`` ``-Perl-5.24.0`` ``intel/2016b`` ============ ================ =============== @@ -22174,12 +22962,28 @@ Prover9, Mace4, and several related programs come packaged in a system called L *homepage*: https://www.cs.unm.edu/~mccune/mace4/download ============ ================== -version toolchain +version toolchain ============ ================== ``2009-11A`` ``GCCcore/10.2.0`` ============ ================== +.. _list_software_lagrangian-filtering_2053: + +*lagrangian-filtering* +++++++++++++++++++++++ + +Temporal filtering of data in a Lagrangian frame of reference. + +*homepage*: https://github.com/angus-g/lagrangian-filtering + +========= ============== +version toolchain +========= ============== +``0.8.3`` ``foss/2022a`` +========= ============== + + .. _list_software_LAME_287: *LAME* @@ -22190,9 +22994,9 @@ LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGP *homepage*: http://lame.sourceforge.net/ ========== ============================================================================================================================================================================================== -version toolchain +version toolchain ========== ============================================================================================================================================================================================== -``3.99.5`` ``foss/2016b``, ``intel/2017a`` +``3.99.5`` ``foss/2016b``, ``intel/2017a`` ``3.100`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017b`` ========== ============================================================================================================================================================================================== @@ -22207,15 +23011,15 @@ LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale At *homepage*: https://lammps.sandia.gov/ ============= ============================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ============= ============================= =============================== ``3Mar2020`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` ``3Mar2020`` ``-Python-3.8.2-kokkos`` ``foss/2020a``, ``intel/2020a`` ``7Aug2019`` ``-Python-3.7.4-kokkos`` ``foss/2019b``, ``intel/2019b`` -``7Aug2019`` ``-Python-3.7.4-kokkos-OCTP`` ``intel/2019b`` -``23Jun2022`` ``-kokkos`` ``foss/2021a``, ``foss/2021b`` -``23Jun2022`` ``-kokkos-CUDA-11.3.1`` ``foss/2021a`` -``23Jun2022`` ``-kokkos-CUDA-11.4.1`` ``foss/2021b`` +``7Aug2019`` ``-Python-3.7.4-kokkos-OCTP`` ``intel/2019b`` +``23Jun2022`` ``-kokkos`` ``foss/2021a``, ``foss/2021b`` +``23Jun2022`` ``-kokkos-CUDA-11.3.1`` ``foss/2021a`` +``23Jun2022`` ``-kokkos-CUDA-11.4.1`` ``foss/2021b`` ============= ============================= =============================== @@ -22229,7 +23033,7 @@ Lancet is a somatic variant caller (SNVs and indels) for short read data. *homepage*: https://github.com/nygenome/lancet ========= ======================= -version toolchain +version toolchain ========= ======================= ``1.1.0`` ``iccifort/2019.5.281`` ========= ======================= @@ -22245,10 +23049,10 @@ LAPACK is written in Fortran90 and provides routines for solving systems of sim *homepage*: https://www.netlib.org/lapack/ ========== ============================== -version toolchain +version toolchain ========== ============================== -``3.8.0`` ``GCC/7.3.0-2.30`` -``3.9.1`` ``GCC/10.2.0`` +``3.8.0`` ``GCC/7.3.0-2.30`` +``3.9.1`` ``GCC/10.2.0`` ``3.10.1`` ``GCC/11.2.0``, ``GCC/11.3.0`` ========== ============================== @@ -22263,12 +23067,12 @@ LAST finds similar regions between sequences. *homepage*: http://last.cbrc.jp/ ======== =============== -version toolchain +version toolchain ======== =============== ``869`` ``intel/2017a`` ``914`` ``intel/2017b`` ``1045`` ``intel/2019b`` -``1179`` ``GCC/10.2.0`` +``1179`` ``GCC/10.2.0`` ======== =============== @@ -22282,7 +23086,7 @@ LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally de *homepage*: https://www.bx.psu.edu/~rsharris/lastz/ =========== ============== -version toolchain +version toolchain =========== ============== ``1.02.00`` ``foss/2016a`` ``1.04.03`` ``foss/2019b`` @@ -22299,11 +23103,11 @@ Fit a variety of latent variable models, including confirmatory factor analysis, *homepage*: https://cran.r-project.org/web/packages/lavaan ============== ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ============== ============= =============== ``0.6-2`` ``-R-3.4.4`` ``intel/2018a`` -``0.6-4.1433`` ``-R-3.6.0`` ``foss/2019a`` -``0.6-9`` ``-R-4.1.0`` ``foss/2021a`` +``0.6-4.1433`` ``-R-3.6.0`` ``foss/2019a`` +``0.6-9`` ``-R-4.1.0`` ``foss/2021a`` ============== ============= =============== @@ -22317,7 +23121,7 @@ A header-only C++ library for L-BFGS and L-BFGS-B algorithms *homepage*: https://lbfgspp.statr.me ========= ========== -version toolchain +version toolchain ========= ========== ``0.1.0`` ``system`` ========= ========== @@ -22333,7 +23137,7 @@ LCOV - the LTP GCOV extension *homepage*: http://ltp.sourceforge.net/coverage/lcov.php ======== ================= -version toolchain +version toolchain ======== ================= ``1.13`` ``GCCcore/7.2.0`` ======== ================= @@ -22349,10 +23153,10 @@ The LLVM-based D Compiler *homepage*: https://wiki.dlang.org/LDC ========== ============= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ================== -``0.17.6`` ``-x86_64`` ``system`` -``1.24.0`` ``-x86_64`` ``system`` +``0.17.6`` ``-x86_64`` ``system`` +``1.24.0`` ``-x86_64`` ``system`` ``1.25.1`` ``GCCcore/10.2.0`` ``1.26.0`` ``GCCcore/10.3.0`` ``1.30.0`` ``GCCcore/11.3.0`` @@ -22369,7 +23173,7 @@ The local Distance Difference Test (lDDT) is a superposition-free score which ev *homepage*: https://openstructure.org ======= ========== -version toolchain +version toolchain ======= ========== ``1.2`` ``system`` ======= ========== @@ -22385,7 +23189,7 @@ Visually Informed LeadOpt *homepage*: http://www.biosolveit.de/LeadIT/index.html ========= ========== -version toolchain +version toolchain ========= ========== ``2.1.9`` ``system`` ========= ========== @@ -22401,12 +23205,12 @@ Implementation of the Leiden algorithm for various quality functions to be used *homepage*: https://github.com/vtraag/leidenalg ========= ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================== -``0.8.2`` ``-Python-3.8.2`` ``foss/2020a`` +``0.8.2`` ``-Python-3.8.2`` ``foss/2020a`` ``0.8.3`` ``foss/2020b``, ``fosscuda/2020b`` -``0.8.7`` ``foss/2021a`` -``0.8.8`` ``foss/2021b`` +``0.8.7`` ``foss/2021a`` +``0.8.8`` ``foss/2021b`` ========= ================= ================================== @@ -22420,7 +23224,7 @@ LEMON stands for Library for Efficient Modeling and Optimization in Networks. I *homepage*: https://lemon.cs.elte.hu ========= ==================== -version toolchain +version toolchain ========= ==================== ``1.3.1`` ``GCC/8.2.0-2.31.1`` ========= ==================== @@ -22436,11 +23240,12 @@ Leptonica is a collection of pedagogically-oriented open source software that i *homepage*: http://www.leptonica.org ========== ================== -version toolchain +version toolchain ========== ================== -``1.77.0`` ``GCCcore/7.3.0`` -``1.78.0`` ``GCCcore/8.2.0`` +``1.77.0`` ``GCCcore/7.3.0`` +``1.78.0`` ``GCCcore/8.2.0`` ``1.82.0`` ``GCCcore/10.3.0`` +``1.83.0`` ``GCCcore/11.3.0`` ========== ================== @@ -22453,11 +23258,11 @@ LERC is an open-source image or raster format which supports rapid encoding and *homepage*: https://github.com/Esri/lerc -======= ================== -version toolchain -======= ================== -``3.0`` ``GCCcore/10.2.0`` -======= ================== +======= ====================================== +version toolchain +======= ====================================== +``3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +======= ====================================== .. _list_software_less_439: @@ -22470,7 +23275,7 @@ Less is a free, open-source file pager. It can be found on most versions of Linu *homepage*: http://www.greenwoodsoftware.com/less/ ======= ============= -version toolchain +version toolchain ======= ============= ``458`` ``GCC/4.8.2`` ======= ============= @@ -22486,11 +23291,11 @@ LevelDB is a fast key-value storage library written at Google that provides an *homepage*: https://github.com/google/leveldb ======== ================================================ -version toolchain +version toolchain ======== ================================================ ``1.18`` ``foss/2016a``, ``intel/2017a``, ``intel/2017b`` -``1.20`` ``GCCcore/7.3.0`` -``1.22`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +``1.20`` ``GCCcore/7.3.0`` +``1.22`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` ======== ================================================ @@ -22504,14 +23309,30 @@ LFTP is a sophisticated ftp/http client, and a file transfer program supporting *homepage*: https://lftp.yar.ru ========= ================== -version toolchain +version toolchain ========= ================== ``4.6.4`` ``GNU/4.9.3-2.25`` -``4.8.4`` ``GCCcore/6.4.0`` +``4.8.4`` ``GCCcore/6.4.0`` ``4.9.2`` ``GCCcore/11.2.0`` ========= ================== +.. _list_software_LHAPDF_431: + +*LHAPDF* +++++++++ + +Les Houches Parton Density Function LHAPDF is the standard tool for evaluating parton distribution functions (PDFs) in high-energy physics. + +*homepage*: http://lhapdf.hepforge.org/ + +========= ============== +version toolchain +========= ============== +``6.5.3`` ``GCC/11.3.0`` +========= ============== + + .. _list_software_libaec_608: *libaec* @@ -22521,11 +23342,11 @@ Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsig *homepage*: https://gitlab.dkrz.de/k202009/libaec -========= ========================================================== -version toolchain -========= ========================================================== -``1.0.6`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -========= ========================================================== +========= ============================================================================== +version toolchain +========= ============================================================================== +``1.0.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ============================================================================== .. _list_software_libaio_624: @@ -22538,9 +23359,9 @@ Asynchronous input/output library that uses the kernels native interface. *homepage*: https://pagure.io/libaio =========== ============================================================================== -version toolchain +version toolchain =========== ============================================================================== -``0.3.111`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.3.111`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``0.3.112`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` =========== ============================================================================== @@ -22555,13 +23376,13 @@ Multi-format archive and compression library *homepage*: https://www.libarchive.org/ ========= ========================================================= -version toolchain +version toolchain ========= ========================================================= -``3.4.0`` ``GCCcore/8.2.0`` -``3.4.2`` ``GCCcore/9.3.0`` -``3.4.3`` ``GCCcore/10.2.0`` +``3.4.0`` ``GCCcore/8.2.0`` +``3.4.2`` ``GCCcore/9.3.0`` +``3.4.3`` ``GCCcore/10.2.0`` ``3.5.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` -``3.6.1`` ``GCCcore/11.3.0`` +``3.6.1`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========= ========================================================= @@ -22575,7 +23396,7 @@ Libav is a friendly and community-driven effort to provide its users with a set *homepage*: https://libav.org/ ========= ================= -version toolchain +version toolchain ========= ================= ``11.10`` ``GCCcore/6.4.0`` ========= ================= @@ -22590,11 +23411,12 @@ This library aims to be a friendly, portable C implementation of the AV1 Image F *homepage*: https://github.com/AOMediaCodec/libavif -========= ============== -version toolchain -========= ============== -``0.9.0`` ``foss/2020b`` -========= ============== +========== ============== +version toolchain +========== ============== +``0.9.0`` ``foss/2020b`` +``0.11.1`` ``foss/2021a`` +========== ============== .. _list_software_libBigWig_880: @@ -22607,9 +23429,9 @@ A C library for handling bigWig files *homepage*: https://github.com/dpryan79/libBigWig ========= ================== -version toolchain +version toolchain ========= ================== -``0.4.4`` ``GCCcore/8.3.0`` +``0.4.4`` ``GCCcore/8.3.0`` ``0.4.6`` ``GCCcore/11.2.0`` ========= ================== @@ -22624,7 +23446,7 @@ libbitmask provides a convenient, powerful bitmask data type *homepage*: http://oss.sgi.com/projects/cpusets/ ======= ========== -version toolchain +version toolchain ======= ========== ``2.0`` ``system`` ======= ========== @@ -22640,7 +23462,7 @@ Climate Data Management System Library. *homepage*: https://github.com/CDAT/libcdms/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``3.1.2`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -22656,17 +23478,17 @@ libcerf is a self-contained numeric library that provides an efficient and accu *homepage*: https://jugit.fz-juelich.de/mlz/libcerf ======== ========================================================================================================= -version toolchain +version toolchain ======== ========================================================================================================= -``1.4`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` +``1.4`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` ``1.5`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``1.7`` ``GCCcore/7.3.0`` -``1.11`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.14`` ``GCCcore/10.2.0`` -``1.15`` ``GCCcore/10.3.0`` -``1.17`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``2.1`` ``GCCcore/11.3.0`` +``1.7`` ``GCCcore/7.3.0`` +``1.11`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.14`` ``GCCcore/10.2.0`` +``1.15`` ``GCCcore/10.3.0`` +``1.17`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.1`` ``GCCcore/11.3.0`` ======== ========================================================================================================= @@ -22679,12 +23501,12 @@ libcint is an open source library for analytical Gaussian integrals. *homepage*: https://github.com/sunqm/libcint -========= ============================== -version toolchain -========= ============================== -``4.4.0`` ``foss/2020b``, ``foss/2021a`` -``5.1.6`` ``foss/2022a`` -========= ============================== +========= =============================================== +version toolchain +========= =============================================== +``4.4.0`` ``foss/2020b``, ``foss/2021a``, ``gomkl/2021a`` +``5.1.6`` ``foss/2022a`` +========= =============================================== .. _list_software_libcircle_937: @@ -22697,9 +23519,9 @@ An API to provide an efficient distributed queue on a cluster. libcircle is an *homepage*: https://github.com/hpc/libcircle/ ============== ================================================= -version toolchain +version toolchain ============== ================================================= -``0.2.1-rc.1`` ``gompi/2019a``, ``iimpi/2019a`` +``0.2.1-rc.1`` ``gompi/2019a``, ``iimpi/2019a`` ``0.3`` ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020a`` ============== ================================================= @@ -22714,7 +23536,7 @@ libcmaes is a multithreaded C++11 library for high performance blackbox stochast *homepage*: http://beniz.github.io/libcmaes/ ========= ============== -version toolchain +version toolchain ========= ============== ``0.9.5`` ``foss/2016a`` ========= ============== @@ -22729,14 +23551,14 @@ Libconfig is a simple library for processing structured configuration files *homepage*: https://hyperrealm.github.io/libconfig -========= ================== -version toolchain -========= ================== -``1.5`` ``intel/2016b`` -``1.7.1`` ``GCCcore/6.4.0`` -``1.7.2`` ``GCCcore/7.3.0`` -``1.7.3`` ``GCCcore/10.3.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.5`` ``intel/2016b`` +``1.7.1`` ``GCCcore/6.4.0`` +``1.7.2`` ``GCCcore/7.3.0`` +``1.7.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +========= ====================================== .. _list_software_libcpuset_971: @@ -22749,7 +23571,7 @@ libcpuset provides full access to cpuset capabilities *homepage*: http://oss.sgi.com/projects/cpusets/ ======= ========== -version toolchain +version toolchain ======= ========== ``1.0`` ``system`` ======= ========== @@ -22765,9 +23587,9 @@ Libcroco is a standalone css2 parsing and manipulation library. *homepage*: https://github.com/GNOME/libcroco ========== ============================== -version toolchain +version toolchain ========== ============================== -``0.6.11`` ``intel/2016a`` +``0.6.11`` ``intel/2016a`` ``0.6.13`` ``GCC/10.2.0``, ``foss/2019a`` ========== ============================== @@ -22782,10 +23604,10 @@ libctl is a free Guile-based library implementing flexible control files for sci *homepage*: https://libctl.readthedocs.io/en/latest/ ========= ================= -version toolchain +version toolchain ========= ================= -``3.2.2`` ``foss/2016a`` -``4.0.0`` ``intel/2020a`` +``3.2.2`` ``foss/2016a`` +``4.0.0`` ``intel/2020a`` ``4.1.3`` ``GCCcore/6.4.0`` ========= ================= @@ -22799,18 +23621,19 @@ A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes *homepage*: https://www.opendap.org/software/libdap -========== ================== ========================================================= -version versionsuffix toolchain -========== ================== ========================================================= -``3.18.1`` ``intel/2017a`` -``3.18.1`` ``-Python-2.7.11`` ``foss/2016a`` -``3.19.1`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` -``3.20.3`` ``GCCcore/7.3.0`` -``3.20.4`` ``GCCcore/8.2.0`` -``3.20.6`` ``GCCcore/8.3.0`` -``3.20.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``3.20.8`` ``GCCcore/11.2.0`` -========== ================== ========================================================= +=========== ================== ========================================================= +version versionsuffix toolchain +=========== ================== ========================================================= +``3.18.1`` ``intel/2017a`` +``3.18.1`` ``-Python-2.7.11`` ``foss/2016a`` +``3.19.1`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` +``3.20.3`` ``GCCcore/7.3.0`` +``3.20.4`` ``GCCcore/8.2.0`` +``3.20.6`` ``GCCcore/8.3.0`` +``3.20.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``3.20.8`` ``GCCcore/11.2.0`` +``3.20.11`` ``GCCcore/11.3.0`` +=========== ================== ========================================================= .. _list_software_libde265_669: @@ -22822,11 +23645,11 @@ libde265 is an open source implementation of the h.265 video codec *homepage*: https://github.com/strukturag/libde265 -========= ============== -version toolchain -========= ============== -``1.0.8`` ``GCC/11.2.0`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``1.0.8`` ``GCC/10.3.0``, ``GCC/11.2.0`` +========= ============================== .. _list_software_libdeflate_1036: @@ -22839,12 +23662,13 @@ Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. *homepage*: https://github.com/ebiggers/libdeflate ======== ========================================================= -version toolchain +version toolchain ======== ========================================================= -``1.5`` ``GCCcore/7.3.0`` +``1.5`` ``GCCcore/7.3.0`` ``1.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``1.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.10`` ``GCCcore/11.3.0`` +``1.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.10`` ``GCCcore/11.3.0`` +``1.15`` ``GCCcore/12.2.0`` ======== ========================================================= @@ -22858,7 +23682,7 @@ libdivsufsort is a software library that implements a lightweight suffix array *homepage*: https://github.com/y-256/libdivsufsort ========= ============== -version toolchain +version toolchain ========= ============== ``2.0.1`` ``foss/2018b`` ========= ============== @@ -22874,22 +23698,23 @@ Direct Rendering Manager runtime library. *homepage*: https://dri.freedesktop.org =========== ================================================== -version toolchain +version toolchain =========== ================================================== -``2.4.67`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``2.4.68`` ``foss/2016a``, ``intel/2016a`` +``2.4.67`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``2.4.68`` ``foss/2016a``, ``intel/2016a`` ``2.4.70`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` -``2.4.76`` ``GCCcore/6.3.0``, ``intel/2017a`` -``2.4.88`` ``GCCcore/6.4.0`` -``2.4.91`` ``GCCcore/6.4.0`` -``2.4.92`` ``GCCcore/7.3.0`` -``2.4.97`` ``GCCcore/8.2.0`` -``2.4.99`` ``GCCcore/8.3.0`` -``2.4.100`` ``GCCcore/9.3.0`` -``2.4.102`` ``GCCcore/10.2.0`` -``2.4.106`` ``GCCcore/10.3.0`` -``2.4.107`` ``GCCcore/11.2.0`` -``2.4.110`` ``GCCcore/11.3.0`` +``2.4.76`` ``GCCcore/6.3.0``, ``intel/2017a`` +``2.4.88`` ``GCCcore/6.4.0`` +``2.4.91`` ``GCCcore/6.4.0`` +``2.4.92`` ``GCCcore/7.3.0`` +``2.4.97`` ``GCCcore/8.2.0`` +``2.4.99`` ``GCCcore/8.3.0`` +``2.4.100`` ``GCCcore/9.3.0`` +``2.4.102`` ``GCCcore/10.2.0`` +``2.4.106`` ``GCCcore/10.3.0`` +``2.4.107`` ``GCCcore/11.2.0`` +``2.4.110`` ``GCCcore/11.3.0`` +``2.4.114`` ``GCCcore/12.2.0`` =========== ================================================== @@ -22903,7 +23728,7 @@ PCMDI's old DRS format implementation *homepage*: https://github.com/CDAT/libdrs/ ========= ============== -version toolchain +version toolchain ========= ============== ``3.1.2`` ``foss/2020a`` ========= ============== @@ -22919,15 +23744,15 @@ The DWARF Debugging Information Format is of interest to programmers working on *homepage*: https://www.prevanders.net/dwarf.html ============ =================================================== -version toolchain +version toolchain ============ =================================================== -``0.4.1`` ``GCCcore/11.3.0`` -``20140805`` ``GCC/4.9.2`` +``0.4.1`` ``GCCcore/11.3.0`` +``20140805`` ``GCC/4.9.2`` ``20150310`` ``GCC/4.9.2``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0`` -``20190529`` ``GCCcore/8.2.0`` -``20201201`` ``GCCcore/10.2.0`` -``20210305`` ``GCCcore/10.3.0`` -``20210528`` ``GCCcore/11.2.0`` +``20190529`` ``GCCcore/8.2.0`` +``20201201`` ``GCCcore/10.2.0`` +``20210305`` ``GCCcore/10.3.0`` +``20210528`` ``GCCcore/11.2.0`` ============ =================================================== @@ -22941,11 +23766,11 @@ This BSD-style licensed command line editor library provides generic line editin *homepage*: https://thrysoee.dk/editline/ ============ ================== -version toolchain +version toolchain ============ ================== ``20150325`` ``GNU/4.9.3-2.25`` -``20180525`` ``GCCcore/6.4.0`` -``20191231`` ``GCCcore/9.3.0`` +``20180525`` ``GCCcore/6.4.0`` +``20191231`` ``GCCcore/9.3.0`` ``20210910`` ``GCCcore/11.2.0`` ============ ================== @@ -22960,7 +23785,7 @@ libelf is a free ELF object file access library *homepage*: https://directory.fsf.org/wiki/Libelf ========== ======================================================================================================================================================================================== -version toolchain +version toolchain ========== ======================================================================================================================================================================================== ``0.8.13`` ``GCC/4.8.3``, ``GCC/4.9.2``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` ========== ======================================================================================================================================================================================== @@ -22976,13 +23801,13 @@ Epoxy is a library for handling OpenGL function pointer management for you *homepage*: https://github.com/anholt/libepoxy ========== ======================================================== -version toolchain +version toolchain ========== ======================================================== -``1.5.2`` ``foss/2018a`` -``1.5.3`` ``GCCcore/8.2.0``, ``fosscuda/2018b`` +``1.5.2`` ``foss/2018a`` +``1.5.3`` ``GCCcore/8.2.0``, ``fosscuda/2018b`` ``1.5.4`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.5.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.5.10`` ``GCCcore/11.3.0`` +``1.5.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.5.10`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========== ======================================================== @@ -22991,15 +23816,15 @@ version toolchain *libev* +++++++ -A full-featured and high-performance (see benchmark) event loop that is loosely modelled after libevent, but without its limitations and bugs. It is used in GNU Virtual Private Ethernet, rxvt-unicode, auditd, the Deliantra MORPG Server and Client, and many other programs. +A full-featured and high-performance (see benchmark) event loop that is loosely modelled after libevent, but without its limitations and bugs. It is used in GNU Virtual Private Ethernet, rxvt-unicode, auditd, the Deliantra MORPG Server and Client, and many other programs. *homepage*: http://software.schmorp.de/pkg/libev.html -======== ============== -version toolchain -======== ============== -``4.33`` ``GCC/11.2.0`` -======== ============== +======== ============================== +version toolchain +======== ============================== +``4.33`` ``GCC/11.2.0``, ``GCC/11.3.0`` +======== ============================== .. _list_software_libevent_857: @@ -23011,14 +23836,14 @@ The libevent API provides a mechanism to execute a callback function when a spec *homepage*: http://libevent.org/ -========== ========================================================================================== -version toolchain -========== ========================================================================================== -``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` -``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` -``2.1.11`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.1.12`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` -========== ========================================================================================== +========== ============================================================================================================== +version toolchain +========== ============================================================================================================== +``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` +``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` +``2.1.11`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.1.12`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` +========== ============================================================================================================== .. _list_software_libexif_739: @@ -23031,7 +23856,7 @@ A library for parsing, editing, and saving EXIF data. *homepage*: https://libexif.github.io/ ========== ================== -version toolchain +version toolchain ========== ================== ``0.6.24`` ``GCCcore/11.2.0`` ========== ================== @@ -23047,16 +23872,17 @@ Libfabric is a core component of OFI. It is the library that defines and exports *homepage*: https://ofiwg.github.io/libfabric/ ========== ===================================== -version toolchain +version toolchain ========== ===================================== -``1.9.1`` ``GCCcore/9.3.0`` -``1.10.1`` ``GCCcore/9.3.0`` +``1.9.1`` ``GCCcore/9.3.0`` +``1.10.1`` ``GCCcore/9.3.0`` ``1.11.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``1.12.1`` ``GCCcore/10.3.0`` -``1.13.0`` ``GCCcore/11.2.0`` -``1.13.1`` ``GCCcore/11.2.0`` -``1.13.2`` ``GCCcore/11.2.0`` -``1.15.1`` ``GCCcore/11.3.0`` +``1.12.1`` ``GCCcore/10.3.0`` +``1.13.0`` ``GCCcore/11.2.0`` +``1.13.1`` ``GCCcore/11.2.0`` +``1.13.2`` ``GCCcore/11.2.0`` +``1.15.1`` ``GCCcore/11.3.0`` +``1.16.1`` ``GCCcore/12.2.0`` ========== ===================================== @@ -23069,11 +23895,11 @@ LibFDF provides a Fortran API to parse files in the Flexible Data Format (FDF). *homepage*: https://launchpad.net/libfdf -========= ============= ======================================= -version versionsuffix toolchain -========= ============= ======================================= -``0.2.2`` ``-serial`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -========= ============= ======================================= +========= ============= =================================================================================================================================== +version versionsuffix toolchain +========= ============= =================================================================================================================================== +``0.2.2`` ``-serial`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` +========= ============= =================================================================================================================================== .. _list_software_libffcall_927: @@ -23086,11 +23912,11 @@ GNU Libffcall is a collection of four libraries which can be used to build fore *homepage*: https://www.gnu.org/software/libffcall/ ======== ==================================== -version toolchain +version toolchain ======== ==================================== -``1.13`` ``GCCcore/6.4.0`` +``1.13`` ``GCCcore/6.4.0`` ``2.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.4`` ``GCCcore/10.2.0`` +``2.4`` ``GCCcore/10.2.0`` ======== ==================================== @@ -23104,11 +23930,12 @@ The libffi library provides a portable, high level programming interface to var *homepage*: https://sourceware.org/libffi/ ========= ============================================================================================================================================================================================================================================================================================================= -version toolchain +version toolchain ========= ============================================================================================================================================================================================================================================================================================================= ``3.2.1`` ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``system`` -``3.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``3.4.2`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``3.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``3.4.2`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``3.4.4`` ``GCCcore/12.2.0`` ========= ============================================================================================================================================================================================================================================================================================================= @@ -23122,10 +23949,10 @@ libFLAME is a portable library for dense matrix computations, providing much of *homepage*: https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame ========= ============= ========================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========================================================================= -``1.0`` ``-amd`` ``GCC/7.3.0-2.30`` -``2.2`` ``-amd`` ``GCCcore/9.3.0`` +``1.0`` ``-amd`` ``GCC/7.3.0-2.30`` +``2.2`` ``-amd`` ``GCCcore/9.3.0`` ``5.2.0`` ``GCC/10.3.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ========= ============= ========================================================================= @@ -23140,7 +23967,7 @@ X11 font encoding library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs/ ========= ================================================= -version toolchain +version toolchain ========= ================================================= ``1.1.3`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= @@ -23156,13 +23983,13 @@ Libgcrypt is a general purpose cryptographic library originally based on code fr *homepage*: https://gnupg.org/related_software/libgcrypt/index.html ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``1.6.5`` ``intel/2016a`` -``1.8.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.8.5`` ``GCCcore/8.3.0`` +``1.6.5`` ``intel/2016a`` +``1.8.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.8.5`` ``GCCcore/8.3.0`` ``1.9.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``1.9.3`` ``GCCcore/11.2.0`` +``1.9.3`` ``GCCcore/11.2.0`` ========= ====================================== @@ -23176,15 +24003,15 @@ GD is an open source code library for the dynamic creation of images by programm *homepage*: https://libgd.github.io ========= ============================================================================================================ -version toolchain +version toolchain ========= ============================================================================================================ -``2.1.1`` ``foss/2016a``, ``intel/2016a`` -``2.2.3`` ``foss/2016b``, ``intel/2016b`` -``2.2.4`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` +``2.1.1`` ``foss/2016a``, ``intel/2016a`` +``2.2.3`` ``foss/2016b``, ``intel/2016b`` +``2.2.4`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` ``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b``, ``intel/2018a`` -``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``2.3.1`` ``GCCcore/10.3.0`` -``2.3.3`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.3.1`` ``GCCcore/10.3.0`` +``2.3.3`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ============================================================================================================ @@ -23198,7 +24025,7 @@ Libgdiplus is the Mono library that provides a GDI+-compatible API on non-Windo *homepage*: https://www.mono-project.com/docs/gui/libgdiplus ======= ================== -version toolchain +version toolchain ======= ================== ``6.1`` ``GCCcore/11.2.0`` ======= ================== @@ -23214,7 +24041,7 @@ libGDSII is a C++ library for working with GDSII binary data files, intended pr *homepage*: https://github.com/HomerReid/libGDSII ======== ================= -version toolchain +version toolchain ======== ================= ``0.21`` ``GCCcore/6.4.0`` ======== ================= @@ -23230,13 +24057,13 @@ Library for reading and writing coordinate system information from/to GeoTIFF fi *homepage*: https://directory.fsf.org/wiki/Libgeotiff ========= ======================================================= -version toolchain +version toolchain ========= ======================================================= -``1.4.2`` ``foss/2018a``, ``foss/2018b``, ``intel/2018b`` +``1.4.2`` ``foss/2018a``, ``foss/2018b``, ``intel/2018b`` ``1.5.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``1.7.0`` ``GCCcore/11.2.0`` -``1.7.1`` ``GCCcore/11.3.0`` +``1.6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.7.0`` ``GCCcore/11.2.0`` +``1.7.1`` ``GCCcore/11.3.0`` ========= ======================================================= @@ -23250,12 +24077,12 @@ libgit2 is a portable, pure C implementation of the Git core methods provided as *homepage*: https://libgit2.org/ ========= ========================================================= -version toolchain +version toolchain ========= ========================================================= -``1.0.0`` ``GCCcore/8.3.0`` +``1.0.0`` ``GCCcore/8.3.0`` ``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``1.1.1`` ``GCCcore/11.2.0`` -``1.4.3`` ``GCCcore/11.3.0`` +``1.1.1`` ``GCCcore/11.2.0`` +``1.4.3`` ``GCCcore/11.3.0`` ========= ========================================================= @@ -23269,7 +24096,7 @@ Libglade is a library for constructing user interfaces dynamically from XML desc *homepage*: https://developer.gnome.org/libglade/ ========= ================================================================= -version toolchain +version toolchain ========= ================================================================= ``2.6.4`` ``foss/2018b``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a`` ========= ================================================================= @@ -23285,12 +24112,12 @@ The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. *homepage*: https://mesa.freedesktop.org/archive/glu/ ========= ================ =========================================================================================================================================================================================================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =========================================================================================================================================================================================================================================================================================================================================== ``9.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b``, ``iomkl/2018a`` -``9.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` -``9.0.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``9.0.2`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``9.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` +``9.0.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``9.0.2`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========= ================ =========================================================================================================================================================================================================================================================================================================================================== @@ -23304,12 +24131,13 @@ libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls bet *homepage*: https://gitlab.freedesktop.org/glvnd/libglvnd ========= ======================================================= -version toolchain +version toolchain ========= ======================================================= ``1.2.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.3.2`` ``GCCcore/10.2.0`` -``1.3.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.4.0`` ``GCCcore/11.3.0`` +``1.3.2`` ``GCCcore/10.2.0`` +``1.3.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.4.0`` ``GCCcore/11.3.0`` +``1.6.0`` ``GCCcore/12.2.0`` ========= ======================================================= @@ -23323,14 +24151,15 @@ Libgpg-error is a small library that defines common error values for all GnuPG c *homepage*: https://gnupg.org/related_software/libgpg-error/index.html ======== ====================================== -version toolchain +version toolchain ======== ====================================== -``1.21`` ``intel/2016a`` -``1.35`` ``GCCcore/7.3.0`` -``1.36`` ``GCCcore/8.2.0`` -``1.38`` ``GCCcore/8.3.0`` -``1.41`` ``GCCcore/10.2.0`` +``1.21`` ``intel/2016a`` +``1.35`` ``GCCcore/7.3.0`` +``1.36`` ``GCCcore/8.2.0`` +``1.38`` ``GCCcore/8.3.0`` +``1.41`` ``GCCcore/10.2.0`` ``1.42`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.46`` ``GCCcore/11.3.0`` ======== ====================================== @@ -23344,14 +24173,14 @@ Library to manipulate tensors on the GPU. *homepage*: http://deeplearning.net/software/libgpuarray/ ========= ================== ======================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ======================================================== -``0.7.5`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``0.7.5`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` ``0.7.5`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``0.7.6`` ``fosscuda/2019a``, ``fosscuda/2020b`` -``0.7.6`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``0.7.6`` ``-Python-3.6.6`` ``fosscuda/2018b`` -``0.7.6`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``0.7.6`` ``fosscuda/2019a``, ``fosscuda/2020b`` +``0.7.6`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``0.7.6`` ``-Python-3.6.6`` ``fosscuda/2018b`` +``0.7.6`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ================== ======================================================== @@ -23365,9 +24194,9 @@ A library to compute the exchange and correlation energy and potential in spher *homepage*: https://gitlab.com/siesta-project/libraries/libgridxc ========= ==================================================================================================== -version toolchain +version toolchain ========= ==================================================================================================== -``0.8.5`` ``iimpi/2019b`` +``0.8.5`` ``iimpi/2019b`` ``0.9.6`` ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b`` ========= ==================================================================================================== @@ -23382,7 +24211,7 @@ ligtextutils is a dependency of fastx-toolkit and is provided via the same upstr *homepage*: http://hannonlab.cshl.edu/fastx_toolkit/ ======= ================================================================== -version toolchain +version toolchain ======= ================================================================== ``0.7`` ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2018a`` ======= ================================================================== @@ -23398,7 +24227,7 @@ libHaru is a free, cross platform, open source library for generating PDF files. *homepage*: http://libharu.org/ ========= ===================================================================================================================================================================================================================== -version toolchain +version toolchain ========= ===================================================================================================================================================================================================================== ``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2021a``, ``foss/2021b``, ``intel/2017a``, ``intel/2018b`` ========= ===================================================================================================================================================================================================================== @@ -23413,11 +24242,11 @@ libheif is an HEIF and AVIF file format decoder and encoder *homepage*: https://github.com/strukturag/libheif -========== ============== -version toolchain -========== ============== -``1.12.0`` ``GCC/11.2.0`` -========== ============== +========== ============================== +version toolchain +========== ============================== +``1.12.0`` ``GCC/10.3.0``, ``GCC/11.2.0`` +========== ============================== .. _list_software_libibmad_820: @@ -23430,7 +24259,7 @@ libibmad is a convenience library to encode, decode, and dump IB MAD packets. It *homepage*: http://www.openfabrics.org ========== ================== -version toolchain +version toolchain ========== ================== ``1.3.12`` ``GCC/4.9.3-2.25`` ========== ================== @@ -23446,7 +24275,7 @@ libibumad is the umad kernel interface library. *homepage*: http://www.openfabrics.org ============ ================== -version toolchain +version toolchain ============ ================== ``1.3.10.2`` ``GCC/4.9.3-2.25`` ============ ================== @@ -23462,7 +24291,7 @@ X Inter-Client Exchange library for freedesktop.org *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= -version toolchain +version toolchain ========= ================================================= ``1.0.9`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= @@ -23478,11 +24307,11 @@ Libiconv converts from one character encoding to another through Unicode convers *homepage*: https://www.gnu.org/software/libiconv ======== =================================================================================================================== -version toolchain +version toolchain ======== =================================================================================================================== -``1.15`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``1.15`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``1.16`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.17`` ``GCCcore/11.3.0`` +``1.17`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ======== =================================================================================================================== @@ -23496,13 +24325,14 @@ GNU Libidn is a fully documented implementation of the Stringprep, Punycode and *homepage*: http://www.gnu.org/software/libidn ======== ====================================================================================== -version toolchain +version toolchain ======== ====================================================================================== ``1.32`` ``GCCcore/5.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` -``1.34`` ``GCCcore/6.4.0`` -``1.35`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.36`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``1.38`` ``GCCcore/11.2.0`` +``1.34`` ``GCCcore/6.4.0`` +``1.35`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.36`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.38`` ``GCCcore/11.2.0`` +``1.41`` ``GCCcore/11.3.0`` ======== ====================================================================================== @@ -23516,10 +24346,10 @@ Libidn2 implements the revised algorithm for internationalized domain names call *homepage*: http://www.gnu.org/software/libidn2 ========= ===================================================================================================================================== -version toolchain +version toolchain ========= ===================================================================================================================================== ``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.3.2`` ``GCCcore/11.2.0`` +``2.3.2`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ===================================================================================================================================== @@ -23533,16 +24363,16 @@ Libint library is used to evaluate the traditional (electron repulsion) and cert *homepage*: https://github.com/evaleev/libint ========= ================ =================================================================================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =================================================================================================================================================================================================================== -``1.1.4`` ``intel/2016a`` +``1.1.4`` ``intel/2016a`` ``1.1.6`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018a``, ``foss/2020a``, ``foss/2020b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` -``2.0.3`` ``foss/2018b``, ``gompi/2019a``, ``intel/2018b`` -``2.1.0`` ``intel/2016b`` -``2.4.2`` ``intel/2018a`` -``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` -``2.6.0`` ``-lmax-6-cp2k`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a``, ``iimpi/2021a`` -``2.7.2`` ``-lmax-6-cp2k`` ``GCC/11.3.0`` +``2.0.3`` ``foss/2018b``, ``gompi/2019a``, ``intel/2018b`` +``2.1.0`` ``intel/2016b`` +``2.4.2`` ``intel/2018a`` +``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` +``2.6.0`` ``-lmax-6-cp2k`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``gompi/2020a``, ``iccifort/2020.4.304``, ``iimpi/2020a``, ``iimpi/2021a`` +``2.7.2`` ``-lmax-6-cp2k`` ``GCC/11.3.0`` ========= ================ =================================================================================================================================================================================================================== @@ -23556,7 +24386,7 @@ An ultrasensitive alignment method for low input bisulfite sequencing *homepage*: https://github.com/Dangertrip/LiBis ============ ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ============== ``20200428`` ``-Python-3.7.4`` ``foss/2019b`` ============ ================= ============== @@ -23572,21 +24402,22 @@ libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelera *homepage*: https://sourceforge.net/projects/libjpeg-turbo/ ========= ================= ================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================================================== -``1.4.2`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` -``1.4.2`` ``-NASM-2.12.01`` ``foss/2016a``, ``intel/2016a`` +``1.4.2`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` +``1.4.2`` ``-NASM-2.12.01`` ``foss/2016a``, ``intel/2016a`` ``1.5.0`` ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``1.5.1`` ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``1.5.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``1.5.3`` ``GCCcore/6.4.0`` -``2.0.0`` ``GCCcore/7.3.0`` -``2.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``2.0.3`` ``GCCcore/8.3.0`` -``2.0.4`` ``GCCcore/9.3.0`` -``2.0.5`` ``GCCcore/10.2.0`` -``2.0.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``2.1.3`` ``GCCcore/11.3.0`` +``1.5.1`` ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``1.5.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``1.5.3`` ``GCCcore/6.4.0`` +``2.0.0`` ``GCCcore/7.3.0`` +``2.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``2.0.3`` ``GCCcore/8.3.0`` +``2.0.4`` ``GCCcore/9.3.0`` +``2.0.5`` ``GCCcore/10.2.0`` +``2.0.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.1.3`` ``GCCcore/11.3.0`` +``2.1.4`` ``GCCcore/12.2.0`` ========= ================= ================================================================== @@ -23600,7 +24431,7 @@ JPEG XL image format reference implementation *homepage*: https://github.com/libjxl/libjxl ========= ================== -version toolchain +version toolchain ========= ================== ``0.5`` ``GCCcore/10.3.0`` ``0.6.1`` ``GCCcore/10.2.0`` @@ -23617,9 +24448,10 @@ LibLZF is a very small data compression library. It consists of only two .c and *homepage*: http://oldhome.schmorp.de/marc/liblzf.html ======= ================== -version toolchain +version toolchain ======= ================== ``3.4`` ``GCCcore/10.2.0`` +``3.6`` ``GCCcore/10.3.0`` ======= ================== @@ -23633,7 +24465,7 @@ MAD is a high-quality MPEG audio decoder. *homepage*: https://www.underbit.com/products/mad/ =========== ================== -version toolchain +version toolchain =========== ================== ``0.15.1b`` ``GCCcore/11.3.0`` =========== ================== @@ -23649,7 +24481,7 @@ GNU libmatheval is a library (callable from C and Fortran) to parse and evaluat *homepage*: http://www.gnu.org/software/libmatheval/ ========== =============================================================================================================================================================== -version toolchain +version toolchain ========== =============================================================================================================================================================== ``1.1.11`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b`` ========== =============================================================================================================================================================== @@ -23665,7 +24497,7 @@ libmaus2 is a collection of data structures and algorithms. *homepage*: https://github.com/gt1/libmaus2 =========== =============== -version toolchain +version toolchain =========== =============== ``2.0.453`` ``intel/2018a`` =========== =============== @@ -23681,7 +24513,7 @@ Libmbd implements the many-body dispersion (MBD) method in several programming l *homepage*: https://libmbd.github.io/index.html ========== ================================================================ -version toolchain +version toolchain ========== ================================================================ ``0.10.4`` ``foss/2020b``, ``foss/2021a``, ``intel/2020b``, ``intel/2021a`` ========== ================================================================ @@ -23697,7 +24529,7 @@ libMemcached is an open source C/C++ client library and tools for the memcached *homepage*: https://memcached.org ========== ==================================== -version toolchain +version toolchain ========== ==================================== ``1.0.18`` ``GCCcore/6.4.0``, ``GCCcore/9.3.0`` ========== ==================================== @@ -23713,9 +24545,9 @@ GNU libmicrohttpd is a small C library that is supposed to make it easy to run *homepage*: https://www.gnu.org/software/libmicrohttpd/ ========== ======================================================== -version toolchain +version toolchain ========== ======================================================== -``0.9.71`` ``GCCcore/9.3.0`` +``0.9.71`` ``GCCcore/9.3.0`` ``0.9.73`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========== ======================================================== @@ -23730,7 +24562,7 @@ A library for handling the WGDOS and RLE compression schemes used in UM files. *homepage*: https://github.com/SciTools/libmo_unpack ========= ================= -version toolchain +version toolchain ========= ================= ``3.1.2`` ``GCCcore/6.4.0`` ========= ================= @@ -23746,7 +24578,7 @@ libmypaint, a.k.a. "brushlib", is a library for making brushstrokes which is use *homepage*: https://github.com/mypaint/libmypaint ========= ================== -version toolchain +version toolchain ========= ================== ``1.6.1`` ``GCCcore/10.3.0`` ========= ================== @@ -23762,7 +24594,7 @@ The libnsl package contains the public client interface for NIS(YP). *homepage*: https://github.com/thkukuk/libnsl ========= ================== -version toolchain +version toolchain ========= ================== ``1.3.0`` ``GCCcore/10.3.0`` ========= ================== @@ -23778,10 +24610,10 @@ ObjCryst++ is Object-Oriented Crystallographic Library for C++ *homepage*: https://github.com/diffpy/libobjcryst ============ =============== -version toolchain +version toolchain ============ =============== ``2017.2.3`` ``intel/2020a`` -``2021.1.2`` ``foss/2021b`` +``2021.1.2`` ``foss/2021b`` ============ =============== @@ -23795,7 +24627,7 @@ Ogg is a multimedia container format, and the native file and stream format for *homepage*: https://xiph.org/ogg/ ========= ====================================== -version toolchain +version toolchain ========= ====================================== ``1.3.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.3.5`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` @@ -23812,7 +24644,7 @@ Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unma *homepage*: https://www.opus-codec.org/ ========= ================== -version toolchain +version toolchain ========= ================== ``1.3.1`` ``GCCcore/11.3.0`` ========= ================== @@ -23828,7 +24660,7 @@ A fast and flexible C++ library for working with OpenStreetMap data. The Osmium *homepage*: https://osmcode.org/libosmium/ ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``2.15.4`` ``-Python-3.6.6`` ``foss/2018b`` ``2.15.6`` ``-Python-3.7.4`` ``foss/2019b`` @@ -23845,7 +24677,7 @@ Library for portable access to PCI bus configuration registers from PCI Utils. *homepage*: https://github.com/pciutils/pciutils ========= ============================================================================= -version toolchain +version toolchain ========= ============================================================================= ``3.7.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0`` ========= ============================================================================= @@ -23861,11 +24693,12 @@ Generic PCI access library. *homepage*: https://cgit.freedesktop.org/xorg/lib/libpciaccess/ ========== ==================================================================================================================== -version toolchain +version toolchain ========== ==================================================================================================================== -``0.13.4`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` -``0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.13.4`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` +``0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``0.16`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``0.17`` ``GCCcore/12.2.0`` ========== ==================================================================================================================== @@ -23879,7 +24712,7 @@ A small C and Python library for reading PLINK genotype files. *homepage*: https://github.com/mfranberg/libplinkio ========= ================= -version toolchain +version toolchain ========= ================= ``0.9.8`` ``GCCcore/9.3.0`` ========= ================= @@ -23895,22 +24728,23 @@ libpng is the official PNG reference library *homepage*: http://www.libpng.org/pub/png/libpng.html ========== ==================================================================================================================== -version toolchain +version toolchain ========== ==================================================================================================================== -``1.2.58`` ``system`` -``1.2.59`` ``system`` -``1.5.30`` ``system`` -``1.6.21`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``1.6.23`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``1.6.24`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` -``1.6.26`` ``foss/2016b``, ``intel/2016b`` -``1.6.27`` ``intel/2016b`` -``1.6.28`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``gimkl/2017a`` -``1.6.29`` ``GCCcore/6.3.0`` -``1.6.32`` ``GCCcore/6.4.0`` -``1.6.34`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.6.36`` ``GCCcore/8.2.0`` +``1.2.58`` ``system`` +``1.2.59`` ``system`` +``1.5.30`` ``system`` +``1.6.21`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``1.6.23`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` +``1.6.24`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` +``1.6.26`` ``foss/2016b``, ``intel/2016b`` +``1.6.27`` ``intel/2016b`` +``1.6.28`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``gimkl/2017a`` +``1.6.29`` ``GCCcore/6.3.0`` +``1.6.32`` ``GCCcore/6.4.0`` +``1.6.34`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.6.36`` ``GCCcore/8.2.0`` ``1.6.37`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.6.38`` ``GCCcore/12.2.0`` ========== ==================================================================================================================== @@ -23923,13 +24757,13 @@ C library for the Public Suffix List *homepage*: https://rockdaboot.github.io/libpsl -========== ========================================================== -version toolchain -========== ========================================================== -``0.20.2`` ``GCCcore/7.3.0`` -``0.21.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``0.21.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -========== ========================================================== +========== ============================================================================== +version toolchain +========== ============================================================================== +``0.20.2`` ``GCCcore/7.3.0`` +``0.21.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``0.21.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========== ============================================================================== .. _list_software_libPSML_627: @@ -23942,7 +24776,7 @@ A library to handle PSML, the pseudopotential markup language. *homepage*: https://launchpad.net/libpsml ========= ======================= -version toolchain +version toolchain ========= ======================= ``1.1.8`` ``iccifort/2019.5.281`` ========= ======================= @@ -23958,9 +24792,9 @@ LibPSML provides a Fortran API to parse files in the PSeudopotential Markup Lan *homepage*: https://launchpad.net/libpsml ========== =================================================================================================================================== -version toolchain +version toolchain ========== =================================================================================================================================== -``1.1.7`` ``foss/2016b``, ``foss/2017a`` +``1.1.7`` ``foss/2016b``, ``foss/2017a`` ``1.1.10`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ========== =================================================================================================================================== @@ -23975,7 +24809,7 @@ PSORT family of programs for subcellular localization prediction as well as othe *homepage*: http://psort.org/ ======= ============== -version toolchain +version toolchain ======= ============== ``1.0`` ``foss/2016a`` ======= ============== @@ -23991,7 +24825,7 @@ libpspio is a library to read and write pseudopotentials in multiple formats. *homepage*: https://gitlab.e-cam2020.eu/esl/pspio/ ========= ======================================================= -version toolchain +version toolchain ========= ======================================================= ``0.2.4`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` ========= ======================================================= @@ -24007,10 +24841,10 @@ The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a s *homepage*: http://xcb.freedesktop.org/ ======= ===================================================================================================== -version toolchain +version toolchain ======= ===================================================================================================== ``0.3`` ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` -``0.4`` ``GCCcore/6.4.0`` +``0.4`` ``GCCcore/6.4.0`` ======= ===================================================================================================== @@ -24024,13 +24858,13 @@ libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D v *homepage*: http://libqglviewer.com/ ========= ================ =============================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =============================================== ``2.6.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``2.6.3`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` -``2.6.4`` ``intel/2016b`` -``2.7.1`` ``intel/2018a`` -``2.8.0`` ``GCCcore/10.3.0`` +``2.6.3`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` +``2.6.4`` ``intel/2016b`` +``2.7.1`` ``intel/2018a`` +``2.8.0`` ``GCCcore/10.3.0`` ========= ================ =============================================== @@ -24044,14 +24878,14 @@ The GNU Readline library provides a set of functions for use by applications th *homepage*: https://tiswww.case.edu/php/chet/readline/rltop.html ========= =================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain +version toolchain ========= =================================================================================================================================================================================================================================================================================================================================================================================== ``6.3`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``7.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``8.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` -``8.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``8.1.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0`` -``8.2`` ``GCCcore/12.2.0`` +``7.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``8.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +``8.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``8.1.2`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0`` +``8.2`` ``GCCcore/12.2.0`` ========= =================================================================================================================================================================================================================================================================================================================================================================================== @@ -24065,10 +24899,10 @@ The routines supporting the distribution and special functions in R and a few ot *homepage*: https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library ========= ================== -version toolchain +version toolchain ========= ================== -``3.6.0`` ``foss/2018b`` -``4.0.0`` ``GCCcore/9.3.0`` +``3.6.0`` ``foss/2018b`` +``4.0.0`` ``GCCcore/9.3.0`` ``4.1.0`` ``GCCcore/10.2.0`` ``4.1.2`` ``GCCcore/11.2.0`` ``4.2.0`` ``GCCcore/10.3.0`` @@ -24085,7 +24919,7 @@ Python module for audio and music processing *homepage*: https://librosa.github.io ========= ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================== ``0.7.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========= ================= ================================== @@ -24101,7 +24935,7 @@ A shared memory parallel sparse matrix computations library for the Recursive Sp *homepage*: https://sourceforge.net/projects/librsb/ ============ ============== -version toolchain +version toolchain ============ ============== ``1.2.0.9`` ``GCC/10.2.0`` ``1.2.0.10`` ``GCC/10.2.0`` @@ -24121,15 +24955,32 @@ Librsvg is a library to render SVG files using cairo. *homepage*: https://wiki.gnome.org/Projects/LibRsvg =========== ================== -version toolchain +version toolchain =========== ================== -``2.40.15`` ``intel/2016a`` -``2.48.4`` ``foss/2019a`` +``2.40.15`` ``intel/2016a`` +``2.48.4`` ``foss/2019a`` ``2.51.2`` ``GCCcore/10.3.0`` ``2.52.8`` ``GCCcore/11.2.0`` +``2.55.1`` ``GCCcore/11.3.0`` =========== ================== +.. _list_software_librttopo_991: + +*librttopo* ++++++++++++ + +The RT Topology Library exposes an API to create and manage standard (ISO 13249 aka SQL/MM) topologies using user-provided data stores. + +*homepage*: https://git.osgeo.org/gitea/rttopo/librttopo + +========= ============== +version toolchain +========= ============== +``1.1.0`` ``GCC/11.2.0`` +========= ============== + + .. _list_software_libsamplerate_1381: *libsamplerate* @@ -24140,7 +24991,7 @@ Secret Rabbit Code (aka libsamplerate) is a Sample Rate Converter for audio. *homepage*: http://www.mega-nerd.com/libsamplerate ========= ================= -version toolchain +version toolchain ========= ================= ``0.1.9`` ``GCCcore/8.2.0`` ========= ================= @@ -24156,7 +25007,7 @@ libSBML (Systems Biology Markup Language library) is a free, open-source program *homepage*: http://sbml.org/Software/libSBML ========== ============== -version toolchain +version toolchain ========== ============== ``5.19.0`` ``GCC/10.3.0`` ========== ============== @@ -24172,12 +25023,12 @@ The libsigc++ package implements a typesafe callback system for standard C++. *homepage*: https://libsigcplusplus.github.io/libsigcplusplus/ ========== ==================================== -version toolchain +version toolchain ========== ==================================== -``2.10.0`` ``GCCcore/6.4.0`` -``2.10.1`` ``GCCcore/7.3.0`` +``2.10.0`` ``GCCcore/6.4.0`` +``2.10.1`` ``GCCcore/7.3.0`` ``2.10.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2.10.8`` ``GCCcore/10.3.0`` +``2.10.8`` ``GCCcore/10.3.0`` ========== ==================================== @@ -24191,10 +25042,10 @@ GNU libsigsegv is a library for handling page faults in user mode. *homepage*: https://www.gnu.org/software/libsigsegv/ ======== ================== -version toolchain +version toolchain ======== ================== -``2.11`` ``GCCcore/6.4.0`` -``2.12`` ``GCCcore/9.3.0`` +``2.11`` ``GCCcore/6.4.0`` +``2.12`` ``GCCcore/9.3.0`` ``2.13`` ``GCCcore/10.2.0`` ======== ================== @@ -24209,7 +25060,7 @@ X11 Session Management library, which allows for applications to both manage ses *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= -version toolchain +version toolchain ========= ================================================= ``1.2.2`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= @@ -24225,11 +25076,11 @@ Libsndfile is a C library for reading and writing files containing sampled sound *homepage*: http://www.mega-nerd.com/libsndfile ========== ================================================================================================================================== -version toolchain +version toolchain ========== ================================================================================================================================== ``1.0.28`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a`` -``1.0.31`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.1.0`` ``GCCcore/11.3.0`` +``1.0.31`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.1.0`` ``GCCcore/11.3.0`` ========== ================================================================================================================================== @@ -24243,15 +25094,15 @@ Sodium is a modern, easy-to-use software library for encryption, decryption, sig *homepage*: https://doc.libsodium.org/ ========== ==================================================================================================================== -version toolchain +version toolchain ========== ==================================================================================================================== -``1.0.6`` ``intel/2016a`` -``1.0.8`` ``foss/2016a`` -``1.0.11`` ``foss/2016b``, ``intel/2016b`` -``1.0.12`` ``GCCcore/6.4.0``, ``intel/2017a`` -``1.0.13`` ``GCCcore/6.4.0``, ``foss/2017a`` -``1.0.16`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.0.17`` ``GCCcore/8.2.0`` +``1.0.6`` ``intel/2016a`` +``1.0.8`` ``foss/2016a`` +``1.0.11`` ``foss/2016b``, ``intel/2016b`` +``1.0.12`` ``GCCcore/6.4.0``, ``intel/2017a`` +``1.0.13`` ``GCCcore/6.4.0``, ``foss/2017a`` +``1.0.16`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.0.17`` ``GCCcore/8.2.0`` ``1.0.18`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ==================================================================================================================== @@ -24266,13 +25117,14 @@ libsoup is an HTTP client/server library for GNOME. It uses GObjects and the gli *homepage*: https://wiki.gnome.org/Projects/libsoup ========== ================== -version toolchain +version toolchain ========== ================== -``2.66.1`` ``GCCcore/8.2.0`` -``2.70.0`` ``GCCcore/8.3.0`` +``2.66.1`` ``GCCcore/8.2.0`` +``2.70.0`` ``GCCcore/8.3.0`` ``2.72.0`` ``GCCcore/10.2.0`` ``2.74.0`` ``GCCcore/10.3.0`` -``3.0.7`` ``GCC/11.2.0`` +``3.0.7`` ``GCC/11.2.0`` +``3.0.8`` ``GCC/11.3.0`` ========== ================== @@ -24286,10 +25138,10 @@ C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API *homepage*: https://libspatialindex.org ========= ====================================================================================== -version toolchain +version toolchain ========= ====================================================================================== ``1.8.5`` ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2018a`` -``1.9.3`` ``GCCcore/11.2.0`` +``1.9.3`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ====================================================================================== @@ -24303,11 +25155,12 @@ SpatiaLite is an open source library intended to extend the SQLite core to suppo *homepage*: https://www.gaia-gis.it/fossil/libspatialite/home ========== ================= =============================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============================================== ``4.3.0a`` ``foss/2016b``, ``foss/2018b``, ``intel/2016b`` -``4.3.0a`` ``-Python-3.7.2`` ``foss/2019a`` -``4.3.0a`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``4.3.0a`` ``-Python-3.7.2`` ``foss/2019a`` +``4.3.0a`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``5.0.1`` ``GCC/11.2.0`` ========== ================= =============================================== @@ -24321,7 +25174,7 @@ Multiplatform C library implementing the SSHv2 protocol on client and server sid *homepage*: https://www.libssh.org ========= ================= -version toolchain +version toolchain ========= ================= ``0.9.0`` ``GCCcore/6.4.0`` ========= ================= @@ -24337,10 +25190,10 @@ Useful set of classes for creating statistical genetic programs. *homepage*: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen ============ ================== -version toolchain +version toolchain ============ ================== ``1.0.15`` ``GCCcore/10.2.0`` -``20190330`` ``GCCcore/6.4.0`` +``20190330`` ``GCCcore/6.4.0`` ============ ================== @@ -24354,13 +25207,13 @@ LIBSVM is an integrated software for support vector classification, (C-SVC, nu-S *homepage*: https://www.csie.ntu.edu.tw/~cjlin/libsvm/ ======== ========================================================== -version toolchain +version toolchain ======== ========================================================== -``3.22`` ``intel/2016b``, ``intel/2017b`` -``3.23`` ``foss/2018b``, ``intel/2018b`` -``3.24`` ``GCCcore/9.3.0`` +``3.22`` ``intel/2016b``, ``intel/2017b`` +``3.23`` ``foss/2018b``, ``intel/2018b`` +``3.24`` ``GCCcore/9.3.0`` ``3.25`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``3.30`` ``GCCcore/11.3.0`` +``3.30`` ``GCCcore/11.3.0`` ======== ========================================================== @@ -24374,7 +25227,7 @@ C library for manipulating POSIX tar files *homepage*: https://repo.or.cz/libtar.git ========== ==================================== -version toolchain +version toolchain ========== ==================================== ``1.2.20`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ========== ==================================== @@ -24390,14 +25243,15 @@ Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages *homepage*: https://www.gnu.org/software/libtasn1/ ========== =================================================== -version toolchain +version toolchain ========== =================================================== ``4.7`` ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` -``4.12`` ``GCCcore/5.4.0`` -``4.13`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``4.16.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` -``4.17.0`` ``GCCcore/10.3.0`` -``4.18.0`` ``GCCcore/11.2.0`` +``4.12`` ``GCCcore/5.4.0`` +``4.13`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``4.16.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` +``4.17.0`` ``GCCcore/10.3.0`` +``4.18.0`` ``GCCcore/11.2.0`` +``4.19.0`` ``GCCcore/11.3.0`` ========== =================================================== @@ -24411,7 +25265,7 @@ The tecla library provides UNIX and LINUX programs with interactive command line *homepage*: https://sites.astro.caltech.edu/~mcs/tecla/ ========= ================== -version toolchain +version toolchain ========= ================== ``1.6.3`` ``GCCcore/10.2.0`` ========= ================== @@ -24424,19 +25278,20 @@ version toolchain tiff: Library and tools for reading and writing TIFF data files -*homepage*: https://libtiff.maptools.org/ +*homepage*: https://libtiff.gitlab.io/libtiff/ ========== ========================================================================================================= -version toolchain +version toolchain ========== ========================================================================================================= -``4.0.6`` ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``4.0.7`` ``foss/2016b``, ``intel/2017a`` -``4.0.8`` ``intel/2017a``, ``intel/2017b`` +``4.0.6`` ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``4.0.7`` ``foss/2016b``, ``intel/2017a`` +``4.0.8`` ``intel/2017a``, ``intel/2017b`` ``4.0.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018b`` -``4.0.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``4.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.2.0`` ``GCCcore/10.3.0`` -``4.3.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.0.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``4.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.2.0`` ``GCCcore/10.3.0`` +``4.3.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.4.0`` ``GCCcore/12.2.0`` ========== ========================================================================================================= @@ -24450,11 +25305,11 @@ Libtirpc is a port of Suns Transport-Independent RPC library to Linux. *homepage*: https://sourceforge.net/projects/libtirpc/ ========= ========================================================== -version toolchain +version toolchain ========= ========================================================== -``1.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.2.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.3.1`` ``GCCcore/10.2.0`` +``1.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.2.6`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.3.1`` ``GCCcore/10.2.0`` ``1.3.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ========================================================== @@ -24469,12 +25324,12 @@ GNU libtool is a generic library support script. Libtool hides the complexity o *homepage*: https://www.gnu.org/software/libtool ========= ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain +version toolchain ========= ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` -``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` +``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` ``2.4.6`` ``FCC/4.5.0``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``2.4.7`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` +``2.4.7`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``system`` ========= ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -24488,10 +25343,10 @@ libtree is a tool that turns ldd into a tree, explains why shared libraries are *homepage*: https://github.com/haampie/libtree ========= ================== -version toolchain +version toolchain ========= ================== ``2.0.0`` ``GCCcore/10.3.0`` -``3.0.3`` ``system`` +``3.0.3`` ``system`` ========= ================== @@ -24505,13 +25360,13 @@ This library provides functions for manipulating Unicode strings and for manipu *homepage*: https://www.gnu.org/software/libunistring/ ========== ============================================================================================== -version toolchain +version toolchain ========== ============================================================================================== -``0.9.3`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` -``0.9.6`` ``GCCcore/5.4.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016b`` -``0.9.7`` ``GCCcore/6.4.0`` +``0.9.3`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` +``0.9.6`` ``GCCcore/5.4.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016b`` +``0.9.7`` ``GCCcore/6.4.0`` ``0.9.10`` ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ============================================================================================== @@ -24525,14 +25380,14 @@ The primary goal of libunwind is to define a portable and efficient C programmin *homepage*: https://www.nongnu.org/libunwind/ ========= ======================================================================= -version toolchain +version toolchain ========= ======================================================================= -``1.1`` ``GCC/4.9.2``, ``foss/2016a``, ``intel/2016b`` +``1.1`` ``GCC/4.9.2``, ``foss/2016a``, ``intel/2016b`` ``1.2.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016b`` -``1.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.4.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``1.5.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.6.2`` ``GCCcore/11.3.0`` +``1.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.4.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.5.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.6.2`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========= ======================================================================= @@ -24546,7 +25401,7 @@ libutempter is library that provides an interface for terminal emulators such a *homepage*: http://git.altlinux.org/people/ldv/packages/?p=libutempter.git =========== ================== -version toolchain +version toolchain =========== ================== ``1.1.6.2`` ``GCC/6.4.0-2.28`` =========== ================== @@ -24562,7 +25417,7 @@ Portable uuid C library *homepage*: http://sourceforge.net/projects/libuuid/ ========= ============================================================================================================================ -version toolchain +version toolchain ========= ============================================================================================================================ ``1.0.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``intel/2017a``, ``intel/2017b`` ========= ============================================================================================================================ @@ -24578,7 +25433,7 @@ libuv is a multi-platform support library with a focus on asynchronous I/O. *homepage*: https://libuv.org ========== ================= -version toolchain +version toolchain ========== ================= ``1.37.0`` ``GCCcore/8.3.0`` ========== ================= @@ -24594,9 +25449,9 @@ libvdwxc is a general library for evaluating energy and potential for exchange-c *homepage*: https://libvdwxc.org ========= ================================================================================================================================================================= -version toolchain +version toolchain ========= ================================================================================================================================================================= -``0.3.2`` ``foss/2018b`` +``0.3.2`` ``foss/2018b`` ``0.4.0`` ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` ========= ================================================================================================================================================================= @@ -24611,7 +25466,7 @@ Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-pu *homepage*: https://xiph.org/vorbis/ ========= ============================================================================== -version toolchain +version toolchain ========= ============================================================================== ``1.3.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ============================================================================== @@ -24627,16 +25482,32 @@ WebP is a modern image format that provides superior lossless and lossy compress *homepage*: https://developers.google.com/speed/webp/ ========= ======================================================== -version toolchain +version toolchain ========= ======================================================== -``1.0.0`` ``foss/2018b`` -``1.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``1.0.0`` ``foss/2018b`` +``1.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.2.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.2.4`` ``GCCcore/11.3.0`` +``1.2.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.2.4`` ``GCCcore/11.3.0`` ========= ======================================================== +.. _list_software_libwpe_643: + +*libwpe* +++++++++ + +WPE is the reference WebKit port for embedded and low-consumption computer devices. It has been designed from the ground-up with performance, small footprint, accelerated content rendering, and simplicity of deployment in mind, bringing the excellence of the WebKit engine to countless platforms and target devices. + +*homepage*: https://webkit.org/wpe + +========== ================== +version toolchain +========== ================== +``1.13.3`` ``GCCcore/11.2.0`` +========== ================== + + .. _list_software_libX11_497: *libX11* @@ -24647,7 +25518,7 @@ X11 client-side library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= -version toolchain +version toolchain ========= ================================================= ``1.6.3`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= @@ -24663,7 +25534,7 @@ The libXau package contains a library implementing the X11 Authorization Protoco *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ==================================================================== -version toolchain +version toolchain ========= ==================================================================== ``1.0.8`` ``GCCcore/6.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ==================================================================== @@ -24679,21 +25550,21 @@ Libxc is a library of exchange-correlation functionals for density-functional th *homepage*: https://www.tddft.org/programs/libxc ========= =================================================================================================================================================================================================================================================================================== -version toolchain +version toolchain ========= =================================================================================================================================================================================================================================================================================== -``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` -``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` -``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``foss/2020b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` -``4.0.1`` ``foss/2017b``, ``intel/2017b`` -``4.0.3`` ``foss/2016b``, ``foss/2017a`` -``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` +``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` +``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` +``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``foss/2020b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b``, ``intel/2020a`` +``4.0.1`` ``foss/2017b``, ``intel/2017b`` +``4.0.3`` ``foss/2016b``, ``foss/2017a`` +``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` ``4.3.4`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` -``5.1.2`` ``GCC/10.2.0`` -``5.1.3`` ``GCC/10.2.0`` -``5.1.5`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` -``5.1.6`` ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` -``5.2.3`` ``GCC/11.3.0``, ``intel-compilers/2022.1.0`` +``5.1.2`` ``GCC/10.2.0`` +``5.1.3`` ``GCC/10.2.0`` +``5.1.5`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` +``5.1.6`` ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` +``5.2.3`` ``GCC/11.3.0``, ``intel-compilers/2022.1.0`` ========= =================================================================================================================================================================================================================================================================================== @@ -24707,10 +25578,10 @@ The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a sm *homepage*: https://xcb.freedesktop.org/ ========== ================================================= -version toolchain +version toolchain ========== ================================================= ``1.11.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``1.13`` ``GCCcore/6.4.0`` +``1.13`` ``GCCcore/6.4.0`` ========== ================================================= @@ -24724,7 +25595,7 @@ X Cursor management library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========== =============================== -version toolchain +version toolchain ========== =============================== ``1.1.14`` ``foss/2016a``, ``intel/2016a`` ========== =============================== @@ -24740,7 +25611,7 @@ X Damage extension library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= -version toolchain +version toolchain ========= ================================================= ``1.1.4`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= @@ -24756,7 +25627,7 @@ The libXdmcp package contains a library implementing the X Display Manager Contr *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ==================================================================== -version toolchain +version toolchain ========= ==================================================================== ``1.1.2`` ``GCCcore/6.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ==================================================================== @@ -24772,7 +25643,7 @@ Common X Extensions library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= -version toolchain +version toolchain ========= ================================================= ``1.3.3`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= @@ -24788,10 +25659,10 @@ X Fixes extension library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= -version toolchain +version toolchain ========= ================================================= ``5.0.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``5.0.2`` ``intel/2016a`` +``5.0.2`` ``intel/2016a`` ========= ================================================= @@ -24805,10 +25676,10 @@ X font libary *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =================== ================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========= =================== ================================================= ``1.5.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``1.5.1`` ``-freetype-2.6.3`` ``foss/2016a``, ``intel/2016a`` +``1.5.1`` ``-freetype-2.6.3`` ``foss/2016a``, ``intel/2016a`` ========= =================== ================================================= @@ -24822,11 +25693,11 @@ X11 client-side library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ======================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ======================= =============================== ``2.3.2`` ``foss/2016a``, ``intel/2016a`` -``2.3.2`` ``-fontconfig-2.11.95`` ``intel/2016a`` -``2.3.2`` ``-freetype-2.6.3`` ``foss/2016a`` +``2.3.2`` ``-fontconfig-2.11.95`` ``intel/2016a`` +``2.3.2`` ``-freetype-2.6.3`` ``foss/2016a`` ========= ======================= =============================== @@ -24840,7 +25711,7 @@ LibXi provides an X Window System client interface to the XINPUT extension to th *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== -version toolchain +version toolchain ========= =============================== ``1.7.6`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -24856,7 +25727,7 @@ Xinerama multiple monitor library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== -version toolchain +version toolchain ========= =============================== ``1.1.3`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -24872,7 +25743,7 @@ xkbcommon is a library to handle keyboard descriptions, including loading them *homepage*: http://xkbcommon.org/ ========= =============================== -version toolchain +version toolchain ========= =============================== ``0.6.1`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -24888,10 +25759,10 @@ libxml++ is a C++ wrapper for the libxml XML parser library. *homepage*: http://libxmlplusplus.sourceforge.net ========== ======================================================= -version toolchain +version toolchain ========== ======================================================= ``2.40.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2.42.1`` ``GCC/10.3.0`` +``2.42.1`` ``GCC/10.3.0`` ========== ======================================================= @@ -24905,21 +25776,22 @@ Libxml2 is the XML C parser and toolchain developed for the Gnome project (but *homepage*: http://xmlsoft.org/ ========== ================== ================================================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================================================================================================================================================================================== -``2.9.2`` ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25`` -``2.9.3`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``2.9.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``2.9.2`` ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25`` +``2.9.3`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``2.9.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``2.9.4`` ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` -``2.9.4`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.9.4`` ``-Python-2.7.13`` ``intel/2017a`` -``2.9.5`` ``GCCcore/6.3.0`` -``2.9.6`` ``GCCcore/6.4.0`` -``2.9.7`` ``GCCcore/6.4.0`` -``2.9.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``2.9.9`` ``GCCcore/8.3.0`` -``2.9.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -``2.9.13`` ``GCCcore/11.3.0`` +``2.9.4`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``2.9.4`` ``-Python-2.7.13`` ``intel/2017a`` +``2.9.5`` ``GCCcore/6.3.0`` +``2.9.6`` ``GCCcore/6.4.0`` +``2.9.7`` ``GCCcore/6.4.0`` +``2.9.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``2.9.9`` ``GCCcore/8.3.0`` +``2.9.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``2.9.13`` ``GCCcore/11.3.0`` +``2.10.3`` ``GCCcore/12.2.0`` ========== ================== ================================================================================================================================================================================== @@ -24932,13 +25804,14 @@ Libxml2 is the XML C parser and toolchain developed for the Gnome project (but *homepage*: http://xmlsoft.org/ -========= ================== ================= -version versionsuffix toolchain -========= ================== ================= -``2.9.7`` ``-Python-2.7.14`` ``intel/2018a`` -``2.9.8`` ``-Python-2.7.15`` ``foss/2018b`` -``2.9.8`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -========= ================== ================= +========== ================== ================== +version versionsuffix toolchain +========== ================== ================== +``2.9.7`` ``-Python-2.7.14`` ``intel/2018a`` +``2.9.8`` ``-Python-2.7.15`` ``foss/2018b`` +``2.9.8`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``2.9.13`` ``GCCcore/11.3.0`` +========== ================== ================== .. _list_software_libXmu_625: @@ -24951,7 +25824,7 @@ libXmu provides a set of miscellaneous utility convenience functions for X libra *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== -version toolchain +version toolchain ========= =============================== ``1.1.2`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -24967,7 +25840,7 @@ libXp provides the X print library. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============== -version toolchain +version toolchain ========= =============== ``1.0.3`` ``intel/2016a`` ========= =============== @@ -24983,7 +25856,7 @@ libXp provides the X print library. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========== =============================== -version toolchain +version toolchain ========== =============================== ``3.5.11`` ``foss/2016a``, ``intel/2016a`` ========== =============================== @@ -24999,7 +25872,7 @@ X Resize, Rotate and Reflection extension library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== -version toolchain +version toolchain ========= =============================== ``1.5.0`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -25015,7 +25888,7 @@ X11 client-side library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= -version toolchain +version toolchain ========= ================================================= ``0.9.9`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= @@ -25031,14 +25904,14 @@ Libxslt is the XSLT C library developed for the GNOME project (but usable outsi *homepage*: http://xmlsoft.org/ ========== ================== ==================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ==================================================================================================================== -``1.1.28`` ``foss/2016a``, ``intel/2016a`` -``1.1.28`` ``-Python-2.7.11`` ``intel/2016a`` -``1.1.29`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``1.1.30`` ``GCCcore/6.3.0`` -``1.1.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``1.1.33`` ``GCCcore/8.2.0`` +``1.1.28`` ``foss/2016a``, ``intel/2016a`` +``1.1.28`` ``-Python-2.7.11`` ``intel/2016a`` +``1.1.29`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``1.1.30`` ``GCCcore/6.3.0`` +``1.1.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.1.33`` ``GCCcore/8.2.0`` ``1.1.34`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ================== ==================================================================================================================== @@ -25053,17 +25926,17 @@ LIBXSMM is a library for small dense and small sparse matrix-matrix multiplicati *homepage*: https://github.com/hfp/libxsmm ========== =============================================================================================== -version toolchain +version toolchain ========== =============================================================================================== -``1.4`` ``intel/2016a`` -``1.4.4`` ``foss/2016b``, ``intel/2016b`` -``1.6.4`` ``foss/2016b``, ``intel/2016b`` -``1.8.2`` ``intel/2017b`` -``1.8.3`` ``foss/2018a``, ``intel/2018a`` +``1.4`` ``intel/2016a`` +``1.4.4`` ``foss/2016b``, ``intel/2016b`` +``1.6.4`` ``foss/2016b``, ``intel/2016b`` +``1.8.2`` ``intel/2017b`` +``1.8.3`` ``foss/2018a``, ``intel/2018a`` ``1.10`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``1.16.1`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` -``1.16.2`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` -``1.17`` ``GCC/11.2.0`` +``1.16.1`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` +``1.16.2`` ``GCC/10.3.0``, ``intel-compilers/2021.2.0`` +``1.17`` ``GCC/11.2.0`` ========== =============================================================================================== @@ -25077,7 +25950,7 @@ libXt provides the X Toolkit Intrinsics, an abstract widget library upon which o *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= -version toolchain +version toolchain ========= ================================================= ``1.1.5`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= @@ -25093,7 +25966,7 @@ X11 XFree86 video mode extension library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== -version toolchain +version toolchain ========= =============================== ``1.1.4`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -25108,15 +25981,15 @@ LibYAML is a YAML parser and emitter written in C. *homepage*: https://pyyaml.org/wiki/LibYAML -========= ============================================================================== -version toolchain -========= ============================================================================== -``0.1.6`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``0.1.7`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``system`` -``0.2.1`` ``GCCcore/7.3.0``, ``system`` -``0.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -========= ============================================================================== +========= ================================================================================================== +version toolchain +========= ================================================================================================== +``0.1.6`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``0.1.7`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``system`` +``0.2.1`` ``GCCcore/7.3.0``, ``system`` +``0.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +========= ================================================================================================== .. _list_software_libzeep_747: @@ -25129,7 +26002,7 @@ Libzeep was originally developed to make it easy to create SOAP servers. *homepage*: https://github.com/mhekkel/libzeep ========= =============== -version toolchain +version toolchain ========= =============== ``5.0.1`` ``gompi/2019b`` ========= =============== @@ -25145,11 +26018,11 @@ libzip is a C library for reading, creating, and modifying zip archives. *homepage*: https://libzip.org/ ========= ========================================================== -version toolchain +version toolchain ========= ========================================================== -``1.5.2`` ``GCCcore/8.2.0`` +``1.5.2`` ``GCCcore/8.2.0`` ``1.7.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.9.2`` ``GCCcore/11.3.0`` +``1.9.2`` ``GCCcore/11.3.0`` ========= ========================================================== @@ -25163,7 +26036,7 @@ lie_learn is a python package that knows how to do various tricky computations r *homepage*: https://github.com/AMLab-Amsterdam/lie_learn =============== ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain =============== ================= ================== ``0.0.1.post1`` ``-Python-3.7.4`` ``fosscuda/2019b`` =============== ================= ================== @@ -25179,7 +26052,7 @@ lifelines is a complete survival analysis library, written in pure Python. *homepage*: https://lifelines.readthedocs.io/en/latest/ ========== ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================== ``0.22.8`` ``-Python-3.7.2`` ``fosscuda/2019a`` ``0.26.3`` ``fosscuda/2020b`` @@ -25196,9 +26069,9 @@ Fast and memory-efficient sequencing error corrector *homepage*: https://github.com/mourisl/Lighter ========= ============================== -version toolchain +version toolchain ========= ============================== -``1.1.1`` ``foss/2018a`` +``1.1.1`` ``foss/2018a`` ``1.1.2`` ``GCC/11.2.0``, ``foss/2018b`` ========= ============================== @@ -25213,7 +26086,7 @@ Moments of the product of an exponential-family likelihood with a Normal distrib *homepage*: https://github.com/limix/liknorm ========= ================= -version toolchain +version toolchain ========= ================= ``1.5.2`` ``GCCcore/7.3.0`` ========= ================= @@ -25229,17 +26102,17 @@ Likwid stands for Like I knew what I am doing. This project contributes easy to *homepage*: https://github.com/RRZE-HPC/likwid ========= ===================================================================================================== -version toolchain +version toolchain ========= ===================================================================================================== -``4.0.1`` ``GNU/4.9.3-2.25`` -``4.1.0`` ``GCCcore/4.9.3`` -``4.2.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2017a``, ``intel/2017a`` -``4.3.2`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``5.0.1`` ``GCCcore/8.3.0`` -``5.1.0`` ``GCCcore/9.3.0`` +``4.0.1`` ``GNU/4.9.3-2.25`` +``4.1.0`` ``GCCcore/4.9.3`` +``4.2.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2017a``, ``intel/2017a`` +``4.3.2`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``5.0.1`` ``GCCcore/8.3.0`` +``5.1.0`` ``GCCcore/9.3.0`` ``5.2.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0`` -``5.2.1`` ``GCC/11.2.0`` -``5.2.2`` ``GCC/11.3.0`` +``5.2.1`` ``GCC/11.2.0`` +``5.2.2`` ``GCC/11.3.0`` ========= ===================================================================================================== @@ -25253,7 +26126,7 @@ Limix is a flexible and efficient linear mixed model library with interfaces to *homepage*: https://github.com/limix/limix ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``2.0.4`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== @@ -25269,7 +26142,7 @@ C++ library for exact, high-performance linear algebra *homepage*: http://linalg.org/ ========= ============== -version toolchain +version toolchain ========= ============== ``1.4.0`` ``foss/2016a`` ========= ============== @@ -25285,10 +26158,11 @@ line_profiler is a module for doing line-by-line profiling of functions. kernpro *homepage*: https://github.com/pyutils/line_profiler ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``3.1.0`` ``-Python-3.8.2`` ``foss/2020a`` ``3.5.1`` ``foss/2021b`` +``4.0.0`` ``foss/2022a`` ========= ================= ============== @@ -25302,7 +26176,7 @@ One of the design principles of the state-of-the-art SAT solver Lingeling is to *homepage*: http://fmv.jku.at/lingeling/ ======= ============= -version toolchain +version toolchain ======= ============= ``bcp`` ``GCC/9.3.0`` ======= ============= @@ -25318,14 +26192,15 @@ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, *homepage*: http://www.littlecms.com/ ========== ============================================================================================================================================== -version toolchain +version toolchain ========== ============================================================================================================================================== -``2.7`` ``intel/2016a`` -``2.8`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``2.7`` ``intel/2016a`` +``2.8`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``2.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` -``2.11`` ``GCCcore/10.2.0`` -``2.12`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``2.13.1`` ``GCCcore/11.3.0`` +``2.11`` ``GCCcore/10.2.0`` +``2.12`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.13.1`` ``GCCcore/11.3.0`` +``2.14`` ``GCCcore/12.2.0`` ========== ============================================================================================================================================== @@ -25339,7 +26214,7 @@ The debugger component of the LLVM project *homepage*: https://lldb.llvm.org/ ========== ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================= ``11.0.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========== ================= ================= @@ -25355,29 +26230,30 @@ The LLVM Core libraries provide a modern source- and target-independent optimiz *homepage*: https://llvm.org/ ========== ======================================================================== -version toolchain +version toolchain ========== ======================================================================== -``3.7.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``3.8.0`` ``foss/2016a``, ``intel/2016a`` -``3.8.1`` ``GCCcore/4.9.3``, ``foss/2016b``, ``intel/2016b`` -``3.9.0`` ``foss/2016b``, ``intel/2016b`` -``3.9.1`` ``foss/2017a`` -``4.0.0`` ``foss/2017a``, ``intel/2017a`` -``4.0.1`` ``intel/2017a``, ``intel/2017b`` +``3.7.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``3.8.0`` ``foss/2016a``, ``intel/2016a`` +``3.8.1`` ``GCCcore/4.9.3``, ``foss/2016b``, ``intel/2016b`` +``3.9.0`` ``foss/2016b``, ``intel/2016b`` +``3.9.1`` ``foss/2017a`` +``4.0.0`` ``foss/2017a``, ``intel/2017a`` +``4.0.1`` ``intel/2017a``, ``intel/2017b`` ``5.0.0`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``5.0.1`` ``GCCcore/6.4.0`` -``6.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``7.0.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``7.0.1`` ``GCCcore/8.2.0`` -``8.0.1`` ``GCCcore/8.3.0`` -``9.0.0`` ``GCCcore/8.3.0`` -``9.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``10.0.0`` ``GCCcore/8.3.0`` -``10.0.1`` ``GCCcore/10.2.0`` -``11.0.0`` ``GCCcore/10.2.0`` -``11.1.0`` ``GCCcore/10.3.0`` -``12.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``14.0.3`` ``GCCcore/11.3.0`` +``5.0.1`` ``GCCcore/6.4.0`` +``6.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``7.0.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``7.0.1`` ``GCCcore/8.2.0`` +``8.0.1`` ``GCCcore/8.3.0`` +``9.0.0`` ``GCCcore/8.3.0`` +``9.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``10.0.0`` ``GCCcore/8.3.0`` +``10.0.1`` ``GCCcore/10.2.0`` +``11.0.0`` ``GCCcore/10.2.0`` +``11.1.0`` ``GCCcore/10.3.0`` +``12.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``14.0.3`` ``GCCcore/11.3.0`` +``15.0.5`` ``GCCcore/12.2.0`` ========== ======================================================================== @@ -25391,15 +26267,15 @@ LMDB is a fast, memory-efficient database. With memory-mapped files, it has the *homepage*: https://symas.com/lmdb ========== ======================================================== -version toolchain +version toolchain ========== ======================================================== -``0.9.18`` ``foss/2016a`` -``0.9.21`` ``GCCcore/6.4.0``, ``intel/2017a`` -``0.9.22`` ``GCCcore/7.3.0`` -``0.9.23`` ``GCCcore/8.2.0`` +``0.9.18`` ``foss/2016a`` +``0.9.21`` ``GCCcore/6.4.0``, ``intel/2017a`` +``0.9.22`` ``GCCcore/7.3.0`` +``0.9.23`` ``GCCcore/8.2.0`` ``0.9.24`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.9.28`` ``GCCcore/10.3.0`` -``0.9.29`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``0.9.28`` ``GCCcore/10.3.0`` +``0.9.29`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ======================================================== @@ -25413,13 +26289,13 @@ Lmfit provides a high-level interface to non-linear optimization and curve fitti *homepage*: https://lmfit.github.io/lmfit-py ========== ================== =============================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================================== -``0.9.9`` ``-Python-3.6.4`` ``intel/2018a`` -``0.9.14`` ``-Python-2.7.15`` ``intel/2018b`` -``1.0.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.0.1`` ``-Python-3.8.2`` ``foss/2020a`` -``1.0.2`` ``foss/2020b``, ``intel/2020b`` +``0.9.9`` ``-Python-3.6.4`` ``intel/2018a`` +``0.9.14`` ``-Python-2.7.15`` ``intel/2018b`` +``1.0.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.0.1`` ``-Python-3.8.2`` ``foss/2020a`` +``1.0.2`` ``foss/2020b``, ``intel/2020b`` ``1.0.3`` ``foss/2021a``, ``foss/2022a``, ``intel/2022a`` ========== ================== =============================================== @@ -25434,22 +26310,22 @@ Lmod is a Lua based module system. Modules allow for dynamic modification of a *homepage*: http://sourceforge.net/projects/lmod/ ========= ============================ -version toolchain +version toolchain ========= ============================ -``5.2`` ``GCC/4.8.2`` -``5.2.5`` ``GCC/4.8.2`` -``5.3`` ``GCC/4.8.2`` -``5.4`` ``GCC/4.8.2`` -``5.4.2`` ``GCC/4.8.2`` -``5.5`` ``GCC/4.8.2`` -``5.5.1`` ``GCC/4.8.2`` -``5.6`` ``GCC/4.8.2`` -``5.7`` ``GCC/4.8.2`` -``5.8`` ``GCC/4.8.2`` -``5.8.5`` ``GCC/4.8.2`` +``5.2`` ``GCC/4.8.2`` +``5.2.5`` ``GCC/4.8.2`` +``5.3`` ``GCC/4.8.2`` +``5.4`` ``GCC/4.8.2`` +``5.4.2`` ``GCC/4.8.2`` +``5.5`` ``GCC/4.8.2`` +``5.5.1`` ``GCC/4.8.2`` +``5.6`` ``GCC/4.8.2`` +``5.7`` ``GCC/4.8.2`` +``5.8`` ``GCC/4.8.2`` +``5.8.5`` ``GCC/4.8.2`` ``5.9`` ``GCC/4.8.2``, ``GCC/4.8.4`` -``6.4.2`` ``system`` -``7.3`` ``system`` +``6.4.2`` ``system`` +``7.3`` ``system`` ========= ============================ @@ -25463,7 +26339,7 @@ LncLOOM is a graph-based framework that uses integer programming to identify com *homepage*: https://github.com/lncLOOM/lncLOOMv2/ ======= ============== -version toolchain +version toolchain ======= ============== ``2.0`` ``foss/2020b`` ======= ============== @@ -25479,7 +26355,7 @@ LocARNA is a collection of alignment tools for the structural analysis of RNA. *homepage*: http://www.bioinf.uni-freiburg.de/Software/LocARNA/ =========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================= ============== ``1.9.2`` ``foss/2016b`` ``1.9.2.2`` ``-Python-3.6.6`` ``foss/2018b`` @@ -25497,9 +26373,9 @@ Fast and sensitive variant calling from next-gen sequencing data *homepage*: http://csb5.github.io/lofreq =========== ================== ================================================ -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ================================================ -``2.1.2`` ``-Python-2.7.12`` ``intel/2016b`` +``2.1.2`` ``-Python-2.7.12`` ``intel/2016b`` ``2.1.3.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` =========== ================== ================================================ @@ -25514,7 +26390,7 @@ Log4perl *homepage*: https://metacpan.org/pod/Log::Log4perl ======== ============== -version toolchain +version toolchain ======== ============== ``1.47`` ``foss/2016a`` ======== ============== @@ -25530,7 +26406,7 @@ C library that implements the logarithm of the sum of exponentiations. Inspired *homepage*: https://github.com/horta/logaddexp ========= ================= -version toolchain +version toolchain ========= ================= ``1.0.3`` ``GCCcore/7.3.0`` ========= ================= @@ -25546,7 +26422,7 @@ LOHHLA, Loss Of Heterozygosity in Human Leukocyte Antigen, a computational tool *homepage*: https://bitbucket.org/mcgranahanlab/lohhla ============== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============== ============= ============== ``2018.11.05`` ``-R-3.5.1`` ``foss/2018b`` ============== ============= ============== @@ -25562,7 +26438,7 @@ Loki is a C++ library of designs, containing flexible implementations of common *homepage*: http://loki-lib.sourceforge.net/ ========= ================================================================================= -version toolchain +version toolchain ========= ================================================================================= ``0.1.7`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` ========= ================================================================================= @@ -25578,7 +26454,7 @@ Implementation of a solver for the Longest Run Subsequence Problem. Given a seq *homepage*: https://pypi.org/project/longestrunsubsequence/ ========= ================== -version toolchain +version toolchain ========= ================== ``1.0.1`` ``GCCcore/10.3.0`` ========= ================== @@ -25594,7 +26470,7 @@ A collection of scripts for processing longread UMI data. *homepage*: https://github.com/SorenKarst/longread_umi ========= ============== -version toolchain +version toolchain ========= ============== ``0.3.2`` ``foss/2020b`` ========= ============== @@ -25610,11 +26486,11 @@ Longshot is a variant calling tool for diploid genomes using long error prone re *homepage*: https://github.com/pjedge/longshot ========= ===================================== -version toolchain +version toolchain ========= ===================================== -``0.3.4`` ``GCCcore/8.2.0`` +``0.3.4`` ``GCCcore/8.2.0`` ``0.4.1`` ``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` -``0.4.3`` ``GCCcore/10.2.0`` +``0.4.3`` ``GCCcore/10.2.0`` ========= ===================================== @@ -25628,9 +26504,9 @@ Python implementation of the Loom file format, an efficient file format for larg *homepage*: https://loompy.org/ ========= =============================== -version toolchain +version toolchain ========= =============================== -``3.0.6`` ``intel/2020b`` +``3.0.6`` ``intel/2020b`` ``3.0.7`` ``foss/2021b``, ``intel/2021b`` ========= =============================== @@ -25645,7 +26521,7 @@ LPeg is a new pattern-matching library for Lua, based on Parsing Expression Gram *homepage*: http://www.inf.puc-rio.br/~roberto/lpeg/ ========= ================== -version toolchain +version toolchain ========= ================== ``1.0.2`` ``GCCcore/10.2.0`` ========= ================== @@ -25661,7 +26537,7 @@ Dynamic global vegetation model with managed land and river routing *homepage*: https://github.com/PIK-LPJmL/LPJmL =========== =============== -version toolchain +version toolchain =========== =============== ``4.0.003`` ``iimpi/2020b`` =========== =============== @@ -25677,10 +26553,10 @@ Mixed Integer Linear Programming (MILP) solver *homepage*: https://sourceforge.net/projects/lpsolve/ ============ ============================================================================================================================================================================================== -version toolchain +version toolchain ============ ============================================================================================================================================================================================== ``5.5.2.5`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifort/2019.5.281``, ``intel/2017a``, ``intel/2018b`` -``5.5.2.11`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` +``5.5.2.11`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` ============ ============================================================================================================================================================================================== @@ -25694,7 +26570,7 @@ lrslib is a self-contained ANSI C implementation of the reverse search algorithm *homepage*: http://cgm.cs.mcgill.ca/~avis/C/lrs.html ======== =============== -version toolchain +version toolchain ======== =============== ``6.2`` ``intel/2018b`` ``7.0a`` ``gompi/2019a`` @@ -25711,7 +26587,7 @@ LS-PrePost is an advanced pre and post-processor that is delivered free with LS- *homepage*: http://lstc.com/products/ls-prepost ========== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ========== ``4.6`` ``-centos6`` ``system`` ``4.6`` ``-centos7`` ``system`` @@ -25731,10 +26607,10 @@ Least-squares methods to estimate rates and dates from phylogenies *homepage*: https://github.com/tothuhien/lsd2 ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``1.9.7`` ``GCCcore/9.3.0`` -``2.2`` ``GCCcore/10.2.0`` +``1.9.7`` ``GCCcore/9.3.0`` +``2.2`` ``GCCcore/10.2.0`` ``2.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ====================================== @@ -25749,7 +26625,7 @@ LSMS benchmark, part of CORAL suite *homepage*: https://asc.llnl.gov/CORAL-benchmarks/#lsms ============ ============== -version toolchain +version toolchain ============ ============== ``3_rev237`` ``foss/2016a`` ============ ============== @@ -25765,7 +26641,7 @@ LTR_retriever is a highly accurate and sensitive program for identification of *homepage*: https://github.com/oushujun/LTR_retriever ========= ============== -version toolchain +version toolchain ========= ============== ``2.9.0`` ``foss/2020b`` ========= ============== @@ -25781,7 +26657,7 @@ A modern tool-suite for detectinglong terminal repeat retrotransposons de-novo o *homepage*: https://github.com/TulsaBioinformaticsToolsmith/LtrDetector ======= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= =============== ``1.0`` ``-Python-3.7.4`` ``intel/2019b`` ======= ================= =============== @@ -25797,17 +26673,17 @@ Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combin *homepage*: https://www.lua.org/ =========== ======================================================================================= -version toolchain +version toolchain =========== ======================================================================================= -``5.1.4-5`` ``GCC/4.8.2`` -``5.1.4-8`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``system`` -``5.1.5`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` -``5.2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``5.3.4`` ``GCCcore/7.2.0``, ``system`` +``5.1.4-5`` ``GCC/4.8.2`` +``5.1.4-8`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``system`` +``5.1.5`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +``5.2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``5.3.4`` ``GCCcore/7.2.0``, ``system`` ``5.3.5`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` -``5.4.2`` ``GCCcore/10.2.0`` -``5.4.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``5.4.4`` ``GCCcore/11.3.0`` +``5.4.2`` ``GCCcore/10.2.0`` +``5.4.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``5.4.4`` ``GCCcore/11.3.0`` =========== ======================================================================================= @@ -25821,7 +26697,7 @@ LuaJIT is a Just-In-Time Compiler (JIT) for the Lua programming language. Lua is *homepage*: http://luajit.org/ ========= ============= -version toolchain +version toolchain ========= ============= ``2.0.2`` ``GCC/4.9.2`` ========= ============= @@ -25837,7 +26713,7 @@ openresty/luajit2 - OpenResty's maintained branch of LuaJIT. LuaJIT is a Just-In *homepage*: https://github.com/openresty/luajit2 ================ ============= -version toolchain +version toolchain ================ ============= ``2.1-20220411`` ``GCC/9.3.0`` ================ ============= @@ -25853,7 +26729,7 @@ A command line gazetteer built around the Geonames.org dataset, that uses the Ap *homepage*: https://github.com/chrismattmann/lucene-geo-gazetteer ============ ========== -version toolchain +version toolchain ============ ========== ``20170718`` ``system`` ============ ========== @@ -25869,7 +26745,7 @@ A probabilistic framework for structural variant discovery. *homepage*: https://github.com/arq5x/lumpy-sv ========== ============== -version toolchain +version toolchain ========== ============== ``0.2.13`` ``foss/2016b`` ``0.3.1`` ``foss/2020b`` @@ -25886,7 +26762,7 @@ Luscus is the program for graphical display and editing of molecular systems. *homepage*: https://sourceforge.net/projects/luscus/ ========= =============================== -version toolchain +version toolchain ========= =============================== ``0.8.6`` ``foss/2018b``, ``intel/2018a`` ========= =============================== @@ -25902,10 +26778,10 @@ The light-weight group library defines data structures and collective operations *homepage*: https://github.com/LLNL/lwgrp ========= ================================================================== -version toolchain +version toolchain ========= ================================================================== ``1.0.2`` ``gompi/2019a``, ``gompi/2020a``, ``iimpi/2019a``, ``iimpi/2020a`` -``1.0.3`` ``gompi/2020b`` +``1.0.3`` ``gompi/2020b`` ========= ================================================================== @@ -25919,23 +26795,23 @@ The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxs *homepage*: https://lxml.de/ ========= ================== ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ====================================== -``3.5.0`` ``-Python-2.7.11`` ``intel/2016a`` -``3.6.0`` ``-Python-2.7.11`` ``intel/2016a`` -``3.6.4`` ``-Python-2.7.12`` ``intel/2016b`` -``4.0.0`` ``-Python-2.7.13`` ``intel/2017a`` -``4.1.1`` ``-Python-2.7.14`` ``intel/2017b`` -``4.2.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``4.2.0`` ``-Python-3.6.4`` ``intel/2018a`` -``4.2.5`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``4.2.5`` ``-Python-3.6.6`` ``foss/2018b`` -``4.3.3`` ``GCCcore/8.2.0`` -``4.4.2`` ``GCCcore/8.3.0`` -``4.5.2`` ``GCCcore/9.3.0`` -``4.6.2`` ``GCCcore/10.2.0`` +``3.5.0`` ``-Python-2.7.11`` ``intel/2016a`` +``3.6.0`` ``-Python-2.7.11`` ``intel/2016a`` +``3.6.4`` ``-Python-2.7.12`` ``intel/2016b`` +``4.0.0`` ``-Python-2.7.13`` ``intel/2017a`` +``4.1.1`` ``-Python-2.7.14`` ``intel/2017b`` +``4.2.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``4.2.0`` ``-Python-3.6.4`` ``intel/2018a`` +``4.2.5`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``4.2.5`` ``-Python-3.6.6`` ``foss/2018b`` +``4.3.3`` ``GCCcore/8.2.0`` +``4.4.2`` ``GCCcore/8.3.0`` +``4.5.2`` ``GCCcore/9.3.0`` +``4.6.2`` ``GCCcore/10.2.0`` ``4.6.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``4.9.1`` ``GCCcore/11.3.0`` +``4.9.1`` ``GCCcore/11.3.0`` ========= ================== ====================================== @@ -25949,7 +26825,7 @@ lynx is an alphanumeric display oriented World-Wide Web Client *homepage*: http://lynx.browser.org/ ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``2.8.9`` ``-develop`` ``foss/2016b`` ========= ============= ============== @@ -25965,13 +26841,14 @@ LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s p *homepage*: https://lz4.github.io/lz4/ ========= ========================================================== -version toolchain +version toolchain ========= ========================================================== -``1.8.2`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0`` -``1.9.0`` ``GCCcore/7.3.0`` -``1.9.1`` ``GCCcore/8.2.0`` -``1.9.2`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.8.2`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0`` +``1.9.0`` ``GCCcore/7.3.0`` +``1.9.1`` ``GCCcore/8.2.0`` +``1.9.2`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.9.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.9.4`` ``GCCcore/12.2.0`` ========= ========================================================== @@ -25985,9 +26862,9 @@ Portable lossless data compression library *homepage*: http://www.oberhumer.com/opensource/lzo/ ======== ================================================================================================================================================================================================================================================================================================== -version toolchain +version toolchain ======== ================================================================================================================================================================================================================================================================================================== -``2.09`` ``intel/2016b``, ``intel/2017b`` +``2.09`` ``intel/2016b``, ``intel/2017b`` ``2.10`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` ======== ================================================================================================================================================================================================================================================================================================== @@ -25998,7 +26875,7 @@ version toolchain --- -:ref:`list_software_M1QN3_336` - :ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_MAGeCK_456` - :ref:`list_software_magick_620` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_Mamba_478` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_matplotlib-inline_1764` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_MEGAN_360` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaMorpheus_1242` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mgltools_881` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_Miller_613` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_miniasm_750` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_Minipolish_1052` - :ref:`list_software_MiniSat_693` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_mm-common_912` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MNE-Python_911` - :ref:`list_software_MOABS_370` - :ref:`list_software_ModelTest-NG_1107` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_MONA_299` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MuJoCo_557` - :ref:`list_software_mujoco-py_931` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_muMerge_722` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` +:ref:`list_software_M1QN3_336` - :ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_MACSE_361` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_MAGeCK_456` - :ref:`list_software_magick_620` - :ref:`list_software_Magics_596` - :ref:`list_software_MAGMA_355` - :ref:`list_software_magma_515` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_makeinfo_842` - :ref:`list_software_Mako_392` - :ref:`list_software_Mamba_478` - :ref:`list_software_manta_529` - :ref:`list_software_mapDamage_893` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_MARS_307` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matlab-proxy_1248` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_matplotlib-inline_1764` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maude_492` - :ref:`list_software_mauveAligner_1248` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_maze_429` - :ref:`list_software_MbedTLS_619` - :ref:`list_software_MBROLA_445` - :ref:`list_software_mbuffer_743` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_mcu_325` - :ref:`list_software_MDAnalysis_981` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_MDSplus-Java_1111` - :ref:`list_software_MDSplus-Python_1367` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_medImgProc_999` - :ref:`list_software_MedPy_479` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Megalodon_918` - :ref:`list_software_MEGAN_360` - :ref:`list_software_Meld_386` - :ref:`list_software_MEM_223` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_MEMOTE_455` - :ref:`list_software_memtester_982` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_Mesa-demos_971` - :ref:`list_software_meshalyzer_1092` - :ref:`list_software_meshio_645` - :ref:`list_software_meshtool_875` - :ref:`list_software_Meson_514` - :ref:`list_software_meson-python_1265` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MESS_312` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_metaerg_741` - :ref:`list_software_MetaEuk_684` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metagenome-Atlas_1572` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaMorpheus_1242` - :ref:`list_software_MetaPhlAn_858` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mgltools_881` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_mhcnuggets_1077` - :ref:`list_software_MicrobeAnnotator_1655` - :ref:`list_software_microctools_1198` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_Miller_613` - :ref:`list_software_mimalloc_846` - :ref:`list_software_MINC_295` - :ref:`list_software_MinCED_496` - :ref:`list_software_Mini-XML_683` - :ref:`list_software_miniasm_750` - :ref:`list_software_minibar_738` - :ref:`list_software_MiniCARD_679` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_Minipolish_1052` - :ref:`list_software_MiniSat_693` - :ref:`list_software_minizip_768` - :ref:`list_software_MINPACK_515` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_Mish-Cuda_827` - :ref:`list_software_misha_530` - :ref:`list_software_MITgcmutils_1106` - :ref:`list_software_MITObim_625` - :ref:`list_software_MitoZ_499` - :ref:`list_software_MiXCR_419` - :ref:`list_software_MixMHC2pred_995` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_mkl_fft_739` - :ref:`list_software_MLC_220` - :ref:`list_software_MLxtend_700` - :ref:`list_software_mm-common_912` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_mmtf-cpp_804` - :ref:`list_software_MNE-Python_911` - :ref:`list_software_MOABS_370` - :ref:`list_software_ModelTest-NG_1107` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_mold_428` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_MONA_299` - :ref:`list_software_MONAI_372` - :ref:`list_software_mongolite_974` - :ref:`list_software_Mono_409` - :ref:`list_software_Monocle3_768` - :ref:`list_software_moonjit_768` - :ref:`list_software_MOOSE_387` - :ref:`list_software_mordecai_836` - :ref:`list_software_MoreRONN_720` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_motionSegmentation_1924` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPB_223` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_mrcfile_738` - :ref:`list_software_MRChem_540` - :ref:`list_software_MRCPP_386` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_msgpack-c_886` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_mstore_666` - :ref:`list_software_MTL4_289` - :ref:`list_software_MuJoCo_557` - :ref:`list_software_mujoco-py_931` - :ref:`list_software_multichoose_1196` - :ref:`list_software_MultilevelEstimators_2126` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_muMerge_722` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_muparserx_999` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MUST_329` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_mxml_446` - :ref:`list_software_mxmlplus_898` - :ref:`list_software_MXNet_460` - :ref:`list_software_MyCC_332` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_Myokit_637` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M1QN3_336: @@ -26011,7 +26888,7 @@ A solver of large-scale unconstrained minimization problems *homepage*: https://who.rocq.inria.fr/Jean-Charles.Gilbert/modulopt/optimization-routines/m1qn3/m1qn3.html ======= ============== -version toolchain +version toolchain ======= ============== ``3.3`` ``GCC/10.3.0`` ======= ============== @@ -26027,12 +26904,12 @@ GNU M4 is an implementation of the traditional Unix macro processor. It is most *homepage*: https://www.gnu.org/software/m4/m4.html ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain +version toolchain ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``1.4.16`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` +``1.4.16`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.4.18`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` -``1.4.19`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``system`` +``1.4.18`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/system``, ``system`` +``1.4.19`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.4.0``, ``GCCcore/9.5.0``, ``system`` ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -26046,7 +26923,7 @@ MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or *homepage*: http://csg.sph.umich.edu/abecasis/MACH/ ========== ========== -version toolchain +version toolchain ========== ========== ``1.0.18`` ``system`` ========== ========== @@ -26062,13 +26939,13 @@ Model Based Analysis for ChIP-Seq data *homepage*: https://github.com/taoliu/MACS ================== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ================== ================== =============================== -``2.1.1.20160309`` ``-Python-2.7.14`` ``intel/2017b`` +``2.1.1.20160309`` ``-Python-2.7.14`` ``intel/2017b`` ``2.1.2.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.1.2.1`` ``-Python-2.7.15`` ``intel/2019a`` -``2.2.5`` ``-Python-3.6.6`` ``foss/2018b`` -``2.2.7.1`` ``foss/2021b`` +``2.1.2.1`` ``-Python-2.7.15`` ``intel/2019a`` +``2.2.5`` ``-Python-3.6.6`` ``foss/2018b`` +``2.2.7.1`` ``foss/2021b`` ================== ================== =============================== @@ -26082,7 +26959,7 @@ MACSE aligns coding NT sequences with respect to their AA translation while allo *homepage*: https://bioweb.supagro.inra.fr/macse/index.php ======== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ======== ============= ========== ``2.06`` ``-Java-15`` ``system`` ======== ============= ========== @@ -26098,9 +26975,9 @@ maeparser is a parser for Schrodinger Maestro files. *homepage*: https://github.com/schrodinger/maeparser ========= ================================================================== -version toolchain +version toolchain ========= ================================================================== -``1.2.2`` ``gompi/2019a``, ``iimpi/2019a`` +``1.2.2`` ``gompi/2019a``, ``iimpi/2019a`` ``1.3.0`` ``gompi/2019b``, ``gompi/2021a``, ``gompi/2022a``, ``iimpi/2020a`` ========= ================================================================== @@ -26115,18 +26992,18 @@ MAFFT is a multiple sequence alignment program for unix-like operating systems. *homepage*: https://mafft.cbrc.jp/alignment/software/ ========= ==================== ======================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ==================== ======================================================================================= -``7.305`` ``-with-extensions`` ``foss/2016b`` -``7.397`` ``-with-extensions`` ``intel/2018a`` -``7.427`` ``-with-extensions`` ``foss/2018b``, ``intel/2018b`` -``7.429`` ``-with-extensions`` ``GCC/8.2.0-2.31.1`` +``7.305`` ``-with-extensions`` ``foss/2016b`` +``7.397`` ``-with-extensions`` ``intel/2018a`` +``7.427`` ``-with-extensions`` ``foss/2018b``, ``intel/2018b`` +``7.429`` ``-with-extensions`` ``GCC/8.2.0-2.31.1`` ``7.453`` ``-with-extensions`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``gompi/2020a``, ``iccifort/2019.5.281``, ``iimpi/2020a`` -``7.470`` ``-with-extensions`` ``GCC/9.3.0``, ``gompi/2020a`` -``7.471`` ``-with-extensions`` ``iimpi/2020a`` -``7.475`` ``-with-extensions`` ``GCC/10.2.0``, ``gompi/2020b`` -``7.487`` ``-with-extensions`` ``gompi/2021a`` -``7.490`` ``-with-extensions`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``gompi/2021b`` +``7.470`` ``-with-extensions`` ``GCC/9.3.0``, ``gompi/2020a`` +``7.471`` ``-with-extensions`` ``iimpi/2020a`` +``7.475`` ``-with-extensions`` ``GCC/10.2.0``, ``gompi/2020b`` +``7.487`` ``-with-extensions`` ``gompi/2021a`` +``7.490`` ``-with-extensions`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``gompi/2021b`` ========= ==================== ======================================================================================= @@ -26140,7 +27017,7 @@ Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computati *homepage*: https://sourceforge.net/p/mageck/wiki/Home/ =========== ============== -version toolchain +version toolchain =========== ============== ``0.5.9.4`` ``foss/2021a`` =========== ============== @@ -26156,12 +27033,28 @@ R bindings to the open-source image processing library ImageMagick *homepage*: https://cran.r-project.org/web/packages/magick/ ======= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= ============== ``2.0`` ``-R-3.5.1`` ``foss/2018b`` ======= ============= ============== +.. _list_software_Magics_596: + +*Magics* +++++++++ + +Magics is ECMWF's meteorological plotting software and can be either accessed directly through its Python or Fortran interfaces or by using Metview. + +*homepage*: https://confluence.ecmwf.int/display/MAGP/ + +========== =============== +version toolchain +========== =============== +``4.13.0`` ``gompi/2022a`` +========== =============== + + .. _list_software_MAGMA_355: *MAGMA* @@ -26172,10 +27065,10 @@ MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data *homepage*: https://ctg.cncr.nl/software/magma ========== ============== -version toolchain +version toolchain ========== ============== ``1.07b`` ``foss/2018b`` -``1.07bb`` ``GCC/8.3.0`` +``1.07bb`` ``GCC/8.3.0`` ``1.09b`` ``GCC/11.2.0`` ========== ============== @@ -26190,17 +27083,17 @@ The MAGMA project aims to develop a dense linear algebra library similar to LAP *homepage*: https://icl.cs.utk.edu/magma/ ========= ================ ======================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ======================================================================================================================== -``2.3.0`` ``fosscuda/2017b``, ``intelcuda/2017b`` -``2.3.0`` ``-CUDA-9.1.85`` ``foss/2018a`` -``2.4.0`` ``fosscuda/2018b`` -``2.5.0`` ``fosscuda/2018b`` -``2.5.1`` ``fosscuda/2019a``, ``fosscuda/2019b`` +``2.3.0`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``2.3.0`` ``-CUDA-9.1.85`` ``foss/2018a`` +``2.4.0`` ``fosscuda/2018b`` +``2.5.0`` ``fosscuda/2018b`` +``2.5.1`` ``fosscuda/2019a``, ``fosscuda/2019b`` ``2.5.4`` ``fosscuda/2019a``, ``fosscuda/2019b``, ``fosscuda/2020a``, ``fosscuda/2020b``, ``intelcuda/2019b``, ``intelcuda/2020b`` -``2.6.1`` ``-CUDA-11.3.1`` ``foss/2021a`` -``2.6.2`` ``-CUDA-11.4.1`` ``foss/2021b`` -``2.6.2`` ``-CUDA-11.7.0`` ``foss/2022a`` +``2.6.1`` ``-CUDA-11.3.1`` ``foss/2021a`` +``2.6.2`` ``-CUDA-11.4.1`` ``foss/2021b`` +``2.6.2`` ``-CUDA-11.7.0`` ``foss/2022a`` ========= ================ ======================================================================================================================== @@ -26214,7 +27107,7 @@ MagresPython is a Python library for parsing the CCP-NC ab-initio magnetic reson *homepage*: http://tfgg.me/magres-python ============ ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ============== ``20160329`` ``-Python-2.7.15`` ``foss/2018b`` ============ ================== ============== @@ -26230,7 +27123,7 @@ Mahotas is a computer vision and image processing library for Python *homepage*: https://mahotas.readthedocs.io/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.4.3`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== @@ -26246,7 +27139,7 @@ MAJIQ and Voila are two software packages that together detect, quantify, and vi *homepage*: https://majiq.biociphers.org ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``1.1.1`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== @@ -26261,14 +27154,14 @@ GNU version of make utility *homepage*: https://www.gnu.org/software/make/make.html -========= ============================================================================= -version toolchain -========= ============================================================================= -``3.82`` ``GCC/4.8.2`` -``4.1`` ``GCC/4.9.2`` -``4.2.1`` ``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` -``4.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -========= ============================================================================= +========= ================================================================================================= +version toolchain +========= ================================================================================================= +``3.82`` ``GCC/4.8.2`` +``4.1`` ``GCC/4.9.2`` +``4.2.1`` ``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` +``4.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +========= ================================================================================================= .. _list_software_makedepend_1038: @@ -26281,10 +27174,11 @@ The makedepend package contains a C-preprocessor like utility to determine build *homepage*: https://linux.die.net/man/1/makedepend ========= =============================================================================================== -version toolchain +version toolchain ========= =============================================================================================== -``1.0.5`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``1.0.5`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``1.0.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.0.7`` ``GCCcore/11.3.0`` ========= =============================================================================================== @@ -26298,7 +27192,7 @@ Makedepf90 is a program for automatic creation of Makefile-style dependency lis *homepage*: https://linux.die.net/man/1/makedepf90 ========= ============== -version toolchain +version toolchain ========= ============== ``2.8.8`` ``foss/2017a`` ========= ============== @@ -26314,11 +27208,11 @@ makeinfo is part of the Texinfo project, the official documentation format of th *homepage*: https://www.gnu.org/software/texinfo/ ======= ============= =========================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= =========================================================================================== ``6.7`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``6.7`` ``-minimal`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``6.8`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``6.7`` ``-minimal`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``6.8`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ======= ============= =========================================================================================== @@ -26332,20 +27226,21 @@ A super-fast templating language that borrows the best ideas from the existing t *homepage*: https://www.makotemplates.org ========= ================== ================================================================================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================================================================================================================================================================= -``1.0.4`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.0.6`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``1.0.4`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``1.0.6`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` ``1.0.7`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2018a`` -``1.0.7`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``1.0.7`` ``-Python-3.6.4`` ``intel/2018a`` -``1.0.7`` ``-Python-3.6.6`` ``fosscuda/2018b`` -``1.0.8`` ``GCCcore/8.2.0`` -``1.1.0`` ``GCCcore/8.3.0`` -``1.1.2`` ``GCCcore/9.3.0`` -``1.1.3`` ``GCCcore/10.2.0`` -``1.1.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.2.0`` ``GCCcore/11.3.0`` +``1.0.7`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``1.0.7`` ``-Python-3.6.4`` ``intel/2018a`` +``1.0.7`` ``-Python-3.6.6`` ``fosscuda/2018b`` +``1.0.8`` ``GCCcore/8.2.0`` +``1.1.0`` ``GCCcore/8.3.0`` +``1.1.2`` ``GCCcore/9.3.0`` +``1.1.3`` ``GCCcore/10.2.0`` +``1.1.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.2.0`` ``GCCcore/11.3.0`` +``1.2.4`` ``GCCcore/12.2.0`` ========= ================== ================================================================================================================================================================= @@ -26359,7 +27254,7 @@ Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, *homepage*: https://mamba.readthedocs.io/ ============ ========== -version toolchain +version toolchain ============ ========== ``4.14.0-0`` ``system`` ============ ========== @@ -26375,11 +27270,11 @@ Manta calls structural variants (SVs) and indels from mapped paired-end sequenci *homepage*: https://github.com/Illumina/manta ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``1.1.1`` ``system`` -``1.6.0`` ``system`` -``1.6.0`` ``-Python-2.7.16`` ``gompi/2019b`` +``1.1.1`` ``system`` +``1.6.0`` ``system`` +``1.6.0`` ``-Python-2.7.16`` ``gompi/2019b`` ``1.6.0`` ``-Python-2.7.18`` ``GCC/10.2.0``, ``gompi/2020a`` ========= ================== =============================== @@ -26394,7 +27289,7 @@ mapDamage2 is a computational framework written in Python and R, which track *homepage*: https://ginolhac.github.io/mapDamage/ ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``2.2.1`` ``foss/2021b`` ``2.2.1`` ``-R-4.0.4`` ``foss/2020b`` @@ -26412,7 +27307,7 @@ Maple combines the world's most powerful mathematical computation engine with an *homepage*: http://www.maplesoft.com/products/maple/ ========== ========== -version toolchain +version toolchain ========== ========== ``15`` ``system`` ``2017.2`` ``system`` @@ -26429,9 +27324,9 @@ MapSplice is a software for mapping RNA-seq data to reference genome for splice *homepage*: http://www.netlab.uky.edu/p/bioinfo/MapSplice2 ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== -``2.2.1`` ``-Python-2.7.12`` ``foss/2016b`` +``2.2.1`` ``-Python-2.7.12`` ``foss/2016b`` ``2.2.1`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============== @@ -26446,7 +27341,7 @@ Maq is a software that builds mapping assemblies from short reads generated by t *homepage*: http://maq.sourceforge.net/maq-man.shtml ========= ========== -version toolchain +version toolchain ========= ========== ``0.7.0`` ``system`` ========= ========== @@ -26462,21 +27357,21 @@ MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, *homepage*: https://mariadb.org/ =========== =============================== -version toolchain +version toolchain =========== =============================== -``10.0.21`` ``GNU/4.9.3-2.25`` -``10.1.13`` ``intel/2016a`` +``10.0.21`` ``GNU/4.9.3-2.25`` +``10.1.13`` ``intel/2016a`` ``10.1.14`` ``foss/2016a``, ``intel/2016a`` -``10.1.17`` ``intel/2016b`` -``10.1.24`` ``intel/2017a`` +``10.1.17`` ``intel/2016b`` +``10.1.24`` ``intel/2017a`` ``10.2.11`` ``foss/2017b``, ``intel/2017b`` -``10.3.7`` ``intel/2018a`` -``10.3.10`` ``foss/2018b`` -``10.3.14`` ``foss/2019a`` -``10.4.13`` ``gompi/2019b`` -``10.5.8`` ``GCC/10.2.0`` -``10.6.4`` ``GCC/10.3.0``, ``GCC/11.2.0`` -``10.9.3`` ``GCC/11.3.0`` +``10.3.7`` ``intel/2018a`` +``10.3.10`` ``foss/2018b`` +``10.3.14`` ``foss/2019a`` +``10.4.13`` ``gompi/2019b`` +``10.5.8`` ``GCC/10.2.0`` +``10.6.4`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``10.9.3`` ``GCC/11.3.0`` =========== =============================== @@ -26490,14 +27385,14 @@ MariaDB Connector/C is used to connect applications developed in C/C++ to MariaD *homepage*: https://downloads.mariadb.org/connector-c/ ========== ==================================================== -version toolchain +version toolchain ========== ==================================================== -``2.3.4`` ``foss/2017b``, ``intel/2017b`` -``2.3.5`` ``intel/2018a``, ``iomkl/2018a`` +``2.3.4`` ``foss/2017b``, ``intel/2017b`` +``2.3.5`` ``intel/2018a``, ``iomkl/2018a`` ``2.3.7`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` -``3.1.7`` ``GCCcore/9.3.0`` -``3.1.11`` ``GCCcore/10.2.0`` -``3.2.2`` ``GCCcore/10.3.0`` +``3.1.7`` ``GCCcore/9.3.0`` +``3.1.11`` ``GCCcore/10.2.0`` +``3.2.2`` ``GCCcore/10.3.0`` ========== ==================================================== @@ -26511,7 +27406,7 @@ improving Multiple circular sequence Alignment using Refined Sequences *homepage*: https://github.com/lorrainea/MARS ============ ================= -version toolchain +version toolchain ============ ================= ``20191101`` ``GCCcore/8.3.0`` ============ ================= @@ -26527,11 +27422,11 @@ Fast genome and metagenome distance estimation using MinHash *homepage*: http://mash.readthedocs.org ======= ============================================================ -version toolchain +version toolchain ======= ============================================================ -``2.0`` ``foss/2018a`` -``2.1`` ``foss/2018b`` -``2.2`` ``GCC/9.3.0`` +``2.0`` ``foss/2018a`` +``2.1`` ``foss/2018b`` +``2.2`` ``GCC/9.3.0`` ``2.3`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.4.0`` ======= ============================================================ @@ -26546,7 +27441,7 @@ MaSuRCA is whole genome assembly software. It combines the efficiency of the de *homepage*: https://www.genome.umd.edu/masurca.html ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``3.2.2`` ``foss/2016a`` ``3.2.2`` ``-Perl-5.26.0`` ``foss/2017b`` @@ -26568,7 +27463,7 @@ Mathematica is a computational software program used in many scientific, enginee *homepage*: http://www.wolfram.com/mathematica ========== ========== -version toolchain +version toolchain ========== ========== ``9.0.1`` ``system`` ``10.0.2`` ``system`` @@ -26593,7 +27488,7 @@ MathGL is ... a library for making high-quality scientific graphics under Linux *homepage*: http://mathgl.sourceforge.net/doc_en/Main.html ========= ============== -version toolchain +version toolchain ========= ============== ``2.4.1`` ``foss/2018a`` ========= ============== @@ -26609,13 +27504,13 @@ matio is an C library for reading and writing Matlab MAT files. *homepage*: http://sourceforge.net/projects/matio/ ========== ================== -version toolchain +version toolchain ========== ================== -``1.5.9`` ``GCCcore/5.4.0`` -``1.5.11`` ``foss/2017b`` -``1.5.12`` ``GCCcore/6.4.0`` -``1.5.17`` ``GCCcore/8.3.0`` -``1.5.19`` ``GCCcore/9.3.0`` +``1.5.9`` ``GCCcore/5.4.0`` +``1.5.11`` ``foss/2017b`` +``1.5.12`` ``GCCcore/6.4.0`` +``1.5.17`` ``GCCcore/8.3.0`` +``1.5.19`` ``GCCcore/9.3.0`` ``1.5.21`` ``GCCcore/10.2.0`` ========== ================== @@ -26630,7 +27525,7 @@ MATLAB is a high-level language and interactive environment that enables you to *homepage*: https://www.mathworks.com/products/matlab ========= ========== -version toolchain +version toolchain ========= ========== ``2012b`` ``system`` ``2013b`` ``system`` @@ -26655,13 +27550,31 @@ The MATLAB Engine API for Python provides a package for Python to call MATLAB a *homepage*: https://www.mathworks.com/help/matlab/matlab-engine-for-python.html -========= ================== =============================== -version versionsuffix toolchain -========= ================== =============================== -``2018b`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2018b`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2019b`` ``GCCcore/8.3.0`` -========= ================== =============================== +================= ================== =============================== +version versionsuffix toolchain +================= ================== =============================== +``2018b`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2018b`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2019b`` ``GCCcore/8.3.0`` +``2021a-9.10.1`` ``GCCcore/10.2.0`` +``2021b-9.11.19`` ``GCCcore/11.2.0`` +================= ================== =============================== + + +.. _list_software_matlab-proxy_1248: + +*matlab-proxy* +++++++++++++++ + +A Python package which enables you to launch MATLAB and access it from a web browser. + +*homepage*: https://github.com/mathworks/matlab-proxy + +========= ================== +version toolchain +========= ================== +``0.5.4`` ``GCCcore/11.3.0`` +========= ================== .. _list_software_matplotlib_1080: @@ -26674,49 +27587,49 @@ matplotlib is a python 2D plotting library which produces publication quality fi *homepage*: https://matplotlib.org ========= ================================= =================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================================= =================================================================================== -``1.4.3`` ``-Python-2.7.12`` ``intel/2016b`` -``1.5.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``1.5.1`` ``-Python-2.7.11-freetype-2.6.3`` ``foss/2016a``, ``intel/2016a`` -``1.5.1`` ``-Python-2.7.12`` ``intel/2016b`` -``1.5.1`` ``-Python-3.5.1`` ``foss/2016a``, ``intel/2016a`` -``1.5.1`` ``-Python-3.5.2`` ``intel/2016b`` -``1.5.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.5.2`` ``-Python-3.5.2`` ``intel/2016b`` -``1.5.3`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.5.3`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``2.0.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.0.0`` ``-Python-2.7.13`` ``intel/2017a`` -``2.0.1`` ``-Python-3.6.1`` ``intel/2017a`` -``2.0.2`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` -``2.0.2`` ``-Python-2.7.13-Qt-4.8.7`` ``intel/2017a`` -``2.0.2`` ``-Python-2.7.13-libpng-1.6.29`` ``intel/2017a`` -``2.0.2`` ``-Python-3.6.1`` ``foss/2017a`` -``2.0.2`` ``-Python-3.6.1-libpng-1.6.29`` ``intel/2017a`` -``2.1.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``2.1.0`` ``-Python-3.6.2`` ``foss/2017b`` -``2.1.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``2.1.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.1.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.2`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``2.1.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018.02``, ``iomkl/2018a`` -``2.2.3`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``2.2.3`` ``-Python-3.6.6`` ``intel/2018b`` -``2.2.4`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``2.2.4`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``2.2.5`` ``-Python-2.7.16`` ``foss/2019b`` +``1.4.3`` ``-Python-2.7.12`` ``intel/2016b`` +``1.5.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``1.5.1`` ``-Python-2.7.11-freetype-2.6.3`` ``foss/2016a``, ``intel/2016a`` +``1.5.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.5.1`` ``-Python-3.5.1`` ``foss/2016a``, ``intel/2016a`` +``1.5.1`` ``-Python-3.5.2`` ``intel/2016b`` +``1.5.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``1.5.2`` ``-Python-3.5.2`` ``intel/2016b`` +``1.5.3`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``1.5.3`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``2.0.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``2.0.0`` ``-Python-2.7.13`` ``intel/2017a`` +``2.0.1`` ``-Python-3.6.1`` ``intel/2017a`` +``2.0.2`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``2.0.2`` ``-Python-2.7.13-Qt-4.8.7`` ``intel/2017a`` +``2.0.2`` ``-Python-2.7.13-libpng-1.6.29`` ``intel/2017a`` +``2.0.2`` ``-Python-3.6.1`` ``foss/2017a`` +``2.0.2`` ``-Python-3.6.1-libpng-1.6.29`` ``intel/2017a`` +``2.1.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``2.1.0`` ``-Python-3.6.2`` ``foss/2017b`` +``2.1.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``2.1.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.1.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.1.2`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``2.1.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018.02``, ``iomkl/2018a`` +``2.2.3`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``2.2.3`` ``-Python-3.6.6`` ``intel/2018b`` +``2.2.4`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` +``2.2.4`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2.2.5`` ``-Python-2.7.16`` ``foss/2019b`` ``2.2.5`` ``-Python-2.7.18`` ``foss/2020a``, ``foss/2020b``, ``foss/2021b``, ``fosscuda/2020a``, ``intel/2020a`` -``3.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` -``3.0.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` -``3.2.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` -``3.3.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -``3.4.2`` ``foss/2021a``, ``intel/2021a`` -``3.4.3`` ``foss/2021b``, ``intel/2021b`` -``3.5.1`` ``foss/2020b``, ``intel/2020b`` -``3.5.2`` ``foss/2022a``, ``intel/2022a`` +``3.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` +``3.0.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` +``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` +``3.2.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` +``3.3.3`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` +``3.4.2`` ``foss/2021a``, ``gomkl/2021a``, ``intel/2021a`` +``3.4.3`` ``foss/2021b``, ``intel/2021b`` +``3.5.1`` ``foss/2020b``, ``intel/2020b`` +``3.5.2`` ``foss/2021b``, ``foss/2022a``, ``intel/2022a`` ========= ================================= =================================================================================== @@ -26730,7 +27643,7 @@ Matplotlib Inline Back-end for IPython and Jupyter. *homepage*: https://github.com/ipython/matplotlib-inline ========= ================== -version toolchain +version toolchain ========= ================== ``0.1.3`` ``GCCcore/10.2.0`` ========= ================== @@ -26746,9 +27659,9 @@ MATSim is an open-source framework to implement large-scale agent-based transpor *homepage*: https://www.matsim.org/ ========= =================== ============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =================== ============================== -``0.8.1`` ``-Java-1.8.0_112`` ``intel/2016b`` +``0.8.1`` ``-Java-1.8.0_112`` ``intel/2016b`` ``14.0`` ``-Java-11`` ``GCCcore/11.2.0``, ``system`` ========= =================== ============================== @@ -26763,7 +27676,7 @@ Maude is a high-performance reflective language and system supporting both equat *homepage*: https://maude.cs.illinois.edu/w/index.php/The_Maude_System ======= ================== -version toolchain +version toolchain ======= ================== ``3.1`` ``GCCcore/10.2.0`` ======= ================== @@ -26779,7 +27692,7 @@ Mauve is a system for constructing multiple genome alignments in the presence of *homepage*: https://darlinglab.org/mauve/mauve.html ======== =============== -version toolchain +version toolchain ======== =============== ``4736`` ``gompi/2020a`` ======== =============== @@ -26795,7 +27708,7 @@ Binary maven install, Apache Maven is a software project management and comprehe *homepage*: https://maven.apache.org/index.html ========= ========== -version toolchain +version toolchain ========= ========== ``3.2.3`` ``system`` ``3.3.3`` ``system`` @@ -26817,9 +27730,9 @@ mawk is an interpreter for the AWK Programming Language. *homepage*: https://invisible-island.net/mawk/ ================== ================================================================================================= -version toolchain +version toolchain ================== ================================================================================================= -``1.3.4-20141206`` ``GCC/4.9.2`` +``1.3.4-20141206`` ``GCC/4.9.2`` ``1.3.4-20171017`` ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2018a``, ``intel/2018b``, ``intel/2019a`` ================== ================================================================================================= @@ -26833,13 +27746,13 @@ MaxBin is software for binning assembled metagenomic sequences based on an Expec *homepage*: https://sourceforge.net/projects/maxbin/ -========= ================ ================================ -version versionsuffix toolchain -========= ================ ================================ -``2.2.6`` ``-Perl-5.28.0`` ``foss/2018b`` -``2.2.7`` ``gompi/2020b``, ``gompi/2021b`` -``2.2.7`` ``-Perl-5.28.1`` ``GCC/8.2.0-2.31.1`` -========= ================ ================================ +========= ================ ================================================= +version versionsuffix toolchain +========= ================ ================================================= +``2.2.6`` ``-Perl-5.28.0`` ``foss/2018b`` +``2.2.7`` ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b`` +``2.2.7`` ``-Perl-5.28.1`` ``GCC/8.2.0-2.31.1`` +========= ================ ================================================= .. _list_software_MaxQuant_815: @@ -26852,9 +27765,9 @@ MaxQuant is a quantitative proteomics software package designed for analyzing la *homepage*: https://maxquant.org/maxquant ============= ================== -version toolchain +version toolchain ============= ================== -``1.6.10.43`` ``foss/2018b`` +``1.6.10.43`` ``foss/2018b`` ``2.0.3.0`` ``GCCcore/11.2.0`` ============= ================== @@ -26869,13 +27782,13 @@ The Mayavi scientific data 3-dimensional visualizer *homepage*: http://code.enthought.com/projects/mayavi/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``4.4.4`` ``-Python-2.7.11`` ``intel/2016a`` -``4.6.2`` ``-Python-3.6.6`` ``foss/2018b`` -``4.7.1`` ``-Python-2.7.15`` ``foss/2019a`` -``4.7.1`` ``-Python-3.7.2`` ``foss/2019a`` -``4.7.4`` ``foss/2021b`` +``4.6.2`` ``-Python-3.6.6`` ``foss/2018b`` +``4.7.1`` ``-Python-2.7.15`` ``foss/2019a`` +``4.7.1`` ``-Python-3.7.2`` ``foss/2019a`` +``4.7.4`` ``foss/2021b`` ========= ================== =============== @@ -26889,7 +27802,7 @@ In a similar manner to dot plots, maze highlights local sequence similarity betw *homepage*: https://github.com/dellytools/maze ============ ============== -version toolchain +version toolchain ============ ============== ``20170124`` ``foss/2020b`` ============ ============== @@ -26905,7 +27818,7 @@ An open source, portable, easy to use, readable and flexible SSL library. *homepage*: https://tls.mbed.org/ ========== ================== -version toolchain +version toolchain ========== ================== ``2.26.0`` ``GCCcore/10.2.0`` ========== ================== @@ -26921,7 +27834,7 @@ MBROLA is a speech synthesizer based on the concatenation of diphones. It takes *homepage*: ['https://github.com/numediart/MBROLA', 'https://github.com/numediart/MBROLA-voices'] ======= ==================== ================= -version versionsuffix toolchain +version versionsuffix toolchain ======= ==================== ================= ``3.3`` ``-voices-20200330`` ``GCCcore/9.3.0`` ======= ==================== ================= @@ -26937,7 +27850,7 @@ mbuffer is a tool for buffering data streams with a large set of unique features *homepage*: https://www.maier-komor.de/mbuffer.html ============ ================= -version toolchain +version toolchain ============ ================= ``20191016`` ``GCCcore/9.3.0`` ============ ================= @@ -26953,7 +27866,7 @@ mc-4.6.1: User-friendly file manager and visual shell *homepage*: https://www.midnight-commander.org/ ========== ============= -version toolchain +version toolchain ========== ============= ``4.8.13`` ``GCC/4.9.2`` ========== ============= @@ -26969,12 +27882,12 @@ The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable *homepage*: http://micans.org/mcl/ ========== ================ ============================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================ ============================================================================================================= -``02.063`` ``intel/2016b`` +``02.063`` ``intel/2016b`` ``14.137`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``intel/2016b`` -``14.137`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``14.137`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``14.137`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``14.137`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` ========== ================ ============================================================================================================= @@ -26988,7 +27901,7 @@ The MATLAB Runtime is a standalone set of shared libraries that enables the exe *homepage*: https://www.mathworks.com/products/compiler/mcr/ ========== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ========== ``R2013a`` ``system`` ``R2013b`` ``system`` @@ -27014,6 +27927,22 @@ version versionsuffix toolchain ========== ============= ========== +.. _list_software_mcu_325: + +*mcu* ++++++ + +A package for periodic wavefunction and crystallography analysis. mcu is designed to support large scale analysis and topological descriptions for periodic wavefunction. + +*homepage*: https://hungqpham.com/mcu/ + +============== =============== +version toolchain +============== =============== +``2021-04-06`` ``gomkl/2021a`` +============== =============== + + .. _list_software_MDAnalysis_981: *MDAnalysis* @@ -27023,14 +27952,14 @@ MDAnalysis is an object-oriented Python library to analyze trajectories from mol *homepage*: https://www.mdanalysis.org/ -========== ================= =============================== -version versionsuffix toolchain -========== ================= =============================== +========== ================= =============================================== +version versionsuffix toolchain +========== ================= =============================================== ``0.20.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.1.1`` ``foss/2020b`` -``2.0.0`` ``foss/2021b``, ``intel/2021b`` -``2.2.0`` ``foss/2022a`` -========== ================= =============================== +``1.1.1`` ``foss/2020b`` +``2.0.0`` ``foss/2021a``, ``foss/2021b``, ``intel/2021b`` +``2.2.0`` ``foss/2022a`` +========== ================= =============================================== .. _list_software_MDBM_288: @@ -27043,7 +27972,7 @@ MDBM is a super-fast memory-mapped key/value store *homepage*: https://github.com/yahoo/mdbm ========== ==================================== -version toolchain +version toolchain ========== ==================================== ``4.13.0`` ``GCCcore/6.4.0``, ``GCCcore/9.3.0`` ========== ==================================== @@ -27059,10 +27988,10 @@ MDSplus is a set of software tools for data acquisition and storage and a method *homepage*: https://mdsplus.org/ =========== ================================ ================= -version versionsuffix toolchain +version versionsuffix toolchain =========== ================================ ================= -``7.0.67`` ``-Java-1.7.0_79-Python-2.7.11`` ``foss/2016a`` -``7.46.1`` ``foss/2018a`` +``7.0.67`` ``-Java-1.7.0_79-Python-2.7.11`` ``foss/2016a`` +``7.46.1`` ``foss/2018a`` ``7.96.8`` ``GCCcore/9.3.0`` ``7.96.12`` ``GCCcore/9.3.0`` =========== ================================ ================= @@ -27078,7 +28007,7 @@ MDSplus is a set of software tools for data acquisition and storage and a method *homepage*: https://mdsplus.org =========== ============= ================= -version versionsuffix toolchain +version versionsuffix toolchain =========== ============= ================= ``7.96.12`` ``-Java-13`` ``GCCcore/9.3.0`` =========== ============= ================= @@ -27094,7 +28023,7 @@ MDSplus is a set of software tools for data acquisition and storage and a method *homepage*: https://mdsplus.org =========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================= ============== ``7.96.12`` ``-Python-3.8.2`` ``foss/2020a`` =========== ================= ============== @@ -27110,7 +28039,7 @@ mdtest is an MPI-coordinated metadata benchmark test that performs open/stat/c *homepage*: http://sourceforge.net/projects/mdtest/ ========= =============== -version toolchain +version toolchain ========= =============== ``1.9.3`` ``intel/2017a`` ========= =============== @@ -27126,13 +28055,13 @@ Read, write and analyze MD trajectories with only a few lines of Python code. *homepage*: https://mdtraj.org ========= ================= ================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================================================ -``1.9.1`` ``-Python-3.6.3`` ``intel/2017b`` -``1.9.2`` ``-Python-3.6.6`` ``intel/2018b`` -``1.9.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.9.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.9.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``1.9.1`` ``-Python-3.6.3`` ``intel/2017b`` +``1.9.2`` ``-Python-3.6.6`` ``intel/2018b`` +``1.9.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.9.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.9.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.9.7`` ``foss/2021a``, ``foss/2022a``, ``intel/2021b``, ``intel/2022a`` ========= ================= ================================================================ @@ -27147,7 +28076,7 @@ medaka is a tool to create a consensus sequence from nanopore sequencing data. *homepage*: https://github.com/nanoporetech/medaka ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.4.3`` ``-Python-3.6.6`` ``foss/2018b`` ``0.11.4`` ``-Python-3.6.6`` ``foss/2018b`` @@ -27172,7 +28101,7 @@ Motion correction, explicit spatio-temporal regularization of motion tracking, r *homepage*: https://github.com/WeiXuanChan/motionSegmentation ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``2.5.7`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -27188,7 +28117,7 @@ MedPy is a library and script collection for medical image processing in Python, *homepage*: https://pypi.org/project/MedPy/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.4.0`` ``foss/2020b`` ``0.4.0`` ``-Python-3.7.4`` ``foss/2019b`` @@ -27205,10 +28134,10 @@ Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation softwar *homepage*: https://meep.readthedocs.io/en/latest/ ========= ================== =============================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================================== -``1.3`` ``foss/2016a`` -``1.4.3`` ``intel/2020a`` +``1.3`` ``foss/2016a`` +``1.4.3`` ``intel/2020a`` ``1.6.0`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2018a`` ========= ================== =============================================== @@ -27223,7 +28152,7 @@ MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an inte *homepage*: http://www.megasoftware.net/ ============ ========== -version toolchain +version toolchain ============ ========== ``7.0.20-1`` ``system`` ``10.0.5`` ``system`` @@ -27241,7 +28170,7 @@ MEGA-Computing Core - Sophisticated and user-friendly software suite for analyzi *homepage*: http://www.megasoftware.net ============ ========== -version toolchain +version toolchain ============ ========== ``7.0.18-1`` ``system`` ============ ========== @@ -27256,18 +28185,18 @@ An ultra-fast single-node solution for large and complex metagenomics assembly *homepage*: https://github.com/voutcn/megahit -========= ================== ===================================================== -version versionsuffix toolchain -========= ================== ===================================================== -``1.1.2`` ``-Python-2.7.14`` ``foss/2018a`` -``1.1.3`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a`` -``1.1.3`` ``-Python-3.6.3`` ``foss/2017b`` -``1.1.4`` ``-Python-2.7.15`` ``foss/2018b`` -``1.1.4`` ``-Python-3.6.6`` ``foss/2018b`` -``1.2.8`` ``GCCcore/8.2.0`` -``1.2.9`` ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``foss/2018b`` -``1.2.9`` ``-Python-2.7.18`` ``GCCcore/10.2.0`` -========= ================== ===================================================== +========= ================== ========================================================================= +version versionsuffix toolchain +========= ================== ========================================================================= +``1.1.2`` ``-Python-2.7.14`` ``foss/2018a`` +``1.1.3`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a`` +``1.1.3`` ``-Python-3.6.3`` ``foss/2017b`` +``1.1.4`` ``-Python-2.7.15`` ``foss/2018b`` +``1.1.4`` ``-Python-3.6.6`` ``foss/2018b`` +``1.2.8`` ``GCCcore/8.2.0`` +``1.2.9`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``foss/2018b`` +``1.2.9`` ``-Python-2.7.18`` ``GCCcore/10.2.0`` +========= ================== ========================================================================= .. _list_software_Megalodon_918: @@ -27280,11 +28209,11 @@ Megalodon is a research command line tool to extract high accuracy modified base *homepage*: https://github.com/nanoporetech/megalodon ========= ================ ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ================================== ``2.3.5`` ``foss/2020b``, ``fosscuda/2020b`` -``2.5.0`` ``foss/2021a`` -``2.5.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``2.5.0`` ``foss/2021a`` +``2.5.0`` ``-CUDA-11.3.1`` ``foss/2021a`` ========= ================ ================================== @@ -27298,7 +28227,7 @@ MEGAN is a comprehensive toolbox for interactively analyzing microbiome data *homepage*: http://megan.informatik.uni-tuebingen.de/ ========== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ========== ``6.22.0`` ``-Java-17`` ``system`` ========== ============= ========== @@ -27314,7 +28243,7 @@ Meld is a visual diff and merge tool targeted at developers. Meld helps you co *homepage*: https://meldmerge.org/ ========== ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================= ``3.20.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================= ================= @@ -27330,7 +28259,7 @@ Marker Enrichment Modeling (MEM) is a tool designed to calculate enrichment scor *homepage*: https://github.com/cytolab/mem ============ ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= ============== ``20191023`` ``foss/2019b`` ``20191023`` ``-R-4.0.0`` ``foss/2020a`` @@ -27347,14 +28276,14 @@ The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or *homepage*: https://meme-suite.org/meme/index.html ========= ============================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============================== =============================== ``5.0.4`` ``-Perl-5.26.0-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``5.0.4`` ``-Perl-5.26.0-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``5.1.1`` ``-Python-3.6.6`` ``foss/2018b`` +``5.1.1`` ``-Python-3.6.6`` ``foss/2018b`` ``5.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``5.4.1`` ``GCC/10.3.0``, ``gompi/2021b`` -``5.4.1`` ``-Python-2.7.18`` ``gompi/2021b`` +``5.4.1`` ``-Python-2.7.18`` ``gompi/2021b`` ========= ============================== =============================== @@ -27368,7 +28297,7 @@ User Extensible Heap Manager built on top of jemalloc which enables control of m *homepage*: http://memkind.github.io ========= ================= -version toolchain +version toolchain ========= ================= ``1.5.0`` ``GCCcore/5.4.0`` ========= ================= @@ -27384,12 +28313,44 @@ memory-profiler is a Python module for monitoring memory consumption of a proces *homepage*: https://pypi.org/project/memory-profiler ========== =============================== -version toolchain +version toolchain ========== =============================== ``0.55.0`` ``foss/2019a``, ``intel/2019a`` ========== =============================== +.. _list_software_MEMOTE_455: + +*MEMOTE* +++++++++ + +The genome-scale metabolic model test suite + +*homepage*: https://github.com/opencobra/memote + +========== ============== +version toolchain +========== ============== +``0.13.0`` ``foss/2021a`` +========== ============== + + +.. _list_software_memtester_982: + +*memtester* ++++++++++++ + +A userspace utility for testing the memory subsystem for faults + +*homepage*: https://pyropus.ca./software/memtester/ + +========= ================== +version toolchain +========= ================== +``4.5.1`` ``GCCcore/11.3.0`` +========= ================== + + .. _list_software_meRanTK_658: *meRanTK* @@ -27400,7 +28361,7 @@ meRanTK is a versatile high performance toolkit for complete analysis of methyla *homepage*: http://www.icbi.at/index.html ========== ========== -version toolchain +version toolchain ========== ========== ``1.1.1b`` ``system`` ========== ========== @@ -27416,7 +28377,7 @@ Multilingual Entity/Resource Combiner & Knowledge eXtractor *homepage*: https://github.com/madewild/MERCKX ============ ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============== ``20170330`` ``-Python-2.7.13`` ``intel/2017a`` ============ ================== =============== @@ -27432,11 +28393,11 @@ Mercurial is a free, distributed source control management tool. It efficiently *homepage*: https://www.mercurial-scm.org ========= ================== ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================== -``3.8.3`` ``-Python-2.7.11`` ``foss/2016a`` +``3.8.3`` ``-Python-2.7.11`` ``foss/2016a`` ``5.7.1`` ``GCCcore/10.2.0`` -``5.7.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``5.7.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``5.8`` ``GCCcore/10.3.0`` ``6.2`` ``GCCcore/11.3.0`` ========= ================== ================== @@ -27452,24 +28413,25 @@ Mesa is an open-source implementation of the OpenGL specification - a system fo *homepage*: https://www.mesa3d.org/ ========== ==================================================================== -version toolchain +version toolchain ========== ==================================================================== -``11.1.2`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``11.2.1`` ``foss/2016a``, ``intel/2016a`` -``12.0.2`` ``foss/2016b``, ``intel/2016b`` -``17.0.2`` ``foss/2017a``, ``intel/2017a`` -``17.2.4`` ``intel/2017b``, ``intelcuda/2017b`` -``17.2.5`` ``foss/2017b``, ``fosscuda/2017b`` +``11.1.2`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``11.2.1`` ``foss/2016a``, ``intel/2016a`` +``12.0.2`` ``foss/2016b``, ``intel/2016b`` +``17.0.2`` ``foss/2017a``, ``intel/2017a`` +``17.2.4`` ``intel/2017b``, ``intelcuda/2017b`` +``17.2.5`` ``foss/2017b``, ``fosscuda/2017b`` ``17.3.6`` ``foss/2018a``, ``fosscuda/2018a``, ``intel/2018a``, ``iomkl/2018a`` -``18.1.1`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``19.0.1`` ``GCCcore/8.2.0`` -``19.1.7`` ``GCCcore/8.3.0`` -``19.2.1`` ``GCCcore/8.3.0`` -``20.0.2`` ``GCCcore/9.3.0`` -``20.2.1`` ``GCCcore/10.2.0`` -``21.1.1`` ``GCCcore/10.3.0`` -``21.1.7`` ``GCCcore/11.2.0`` -``22.0.3`` ``GCCcore/11.3.0`` +``18.1.1`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``19.0.1`` ``GCCcore/8.2.0`` +``19.1.7`` ``GCCcore/8.3.0`` +``19.2.1`` ``GCCcore/8.3.0`` +``20.0.2`` ``GCCcore/9.3.0`` +``20.2.1`` ``GCCcore/10.2.0`` +``21.1.1`` ``GCCcore/10.3.0`` +``21.1.7`` ``GCCcore/11.2.0`` +``22.0.3`` ``GCCcore/11.3.0`` +``22.2.4`` ``GCCcore/12.2.0`` ========== ==================================================================== @@ -27483,7 +28445,7 @@ Mesa utility and demo programs, including glxinfo and eglinfo. *homepage*: https://www.mesa3d.org/ ========= ================== -version toolchain +version toolchain ========= ================== ``8.4.0`` ``GCCcore/10.3.0`` ========= ================== @@ -27499,7 +28461,7 @@ Graphical program for display time dependent data on 3D finite element meshes *homepage*: https://git.opencarp.org/openCARP/meshalyzer ============ ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ============== ``2.0`` ``-Python-3.8.2`` ``foss/2020a`` ``2.2`` ``foss/2020b`` @@ -27517,7 +28479,7 @@ meshio is a tool for reading/writing various mesh formats representing unstructu *homepage*: https://github.com/nschloe/meshio ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.7.1`` ``-Python-2.7.12`` ``intel/2016b`` ``2.0.2`` ``-Python-2.7.14`` ``intel/2018a`` @@ -27535,7 +28497,7 @@ Meshtool is a comand-line tool written in C++. It is designed to apply various m *homepage*: https://bitbucket.org/aneic/meshtool ======= ============================= -version toolchain +version toolchain ======= ============================= ``16`` ``GCC/10.2.0``, ``GCC/9.3.0`` ======= ============================= @@ -27551,25 +28513,42 @@ Meson is a cross-platform build system designed to be both as fast and as user f *homepage*: https://mesonbuild.com ========== ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================== -``0.43.0`` ``-Python-3.6.3`` ``intel/2017b`` -``0.46.1`` ``-Python-3.6.4`` ``foss/2018a`` -``0.48.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.43.0`` ``-Python-3.6.3`` ``intel/2017b`` +``0.46.1`` ``-Python-3.6.4`` ``foss/2018a`` +``0.48.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``0.48.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``0.50.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``0.51.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``0.53.1`` ``-Python-3.6.3`` ``intel/2017b`` -``0.53.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``0.55.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``0.55.3`` ``GCCcore/10.2.0`` -``0.58.0`` ``GCCcore/10.3.0`` -``0.58.2`` ``GCCcore/11.2.0`` -``0.59.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``0.62.1`` ``GCCcore/11.3.0`` +``0.50.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``0.51.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.53.1`` ``-Python-3.6.3`` ``intel/2017b`` +``0.53.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``0.55.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``0.55.3`` ``GCCcore/10.2.0`` +``0.58.0`` ``GCCcore/10.3.0`` +``0.58.2`` ``GCCcore/11.2.0`` +``0.59.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.62.1`` ``GCCcore/11.3.0`` +``0.64.0`` ``GCCcore/12.2.0`` ========== ================= ================================== +.. _list_software_meson-python_1265: + +*meson-python* +++++++++++++++ + +Python build backend (PEP 517) for Meson projects + +*homepage*: https://github.com/mesonbuild/meson-python + +========== ================== +version toolchain +========== ================== +``0.11.0`` ``GCCcore/12.2.0`` +========== ================== + + .. _list_software_Mesquite_845: *Mesquite* @@ -27580,7 +28559,7 @@ Mesh-Quality Improvement Library *homepage*: https://software.sandia.gov/mesquite/ ========= ======================================================================================== -version toolchain +version toolchain ========= ======================================================================================== ``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017a`` ========= ======================================================================================== @@ -27596,7 +28575,7 @@ Master Equation System Solver (MESS) *homepage*: https://github.com/PACChem/MESS ========= ============== -version toolchain +version toolchain ========= ============== ``0.1.6`` ``foss/2019b`` ========= ============== @@ -27611,14 +28590,14 @@ An efficient tool for accurately reconstructing single genomes from complex micr *homepage*: https://bitbucket.org/berkeleylab/metabat -========== ================== =============== -version versionsuffix toolchain -========== ================== =============== -``2.12.1`` ``-Python-2.7.15`` ``foss/2018b`` +========== ================== ================================ +version versionsuffix toolchain +========== ================== ================================ +``2.12.1`` ``-Python-2.7.15`` ``foss/2018b`` ``2.14`` ``gompi/2019a`` -``2.15`` ``gompi/2021b`` +``2.15`` ``gompi/2021a``, ``gompi/2021b`` ``2.15`` ``-Python-2.7.18`` ``gompi/2020b`` -========== ================== =============== +========== ================== ================================ .. _list_software_MetaboAnalystR_1414: @@ -27631,7 +28610,7 @@ MetaboAnalystR contains the R functions and libraries underlying the popular Met *homepage*: https://www.metaboanalyst.ca ================== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ============= ============== ``2.0.1-20190827`` ``-R-3.6.0`` ``foss/2019a`` ================== ============= ============== @@ -27647,7 +28626,7 @@ MetaErg is a stand-alone and fully automated metagenomic and metaproteomic data *homepage*: https://github.com/xiaoli-dong/metaerg ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.2.3`` ``-Python-2.7.16`` ``intel/2019b`` ========= ================== =============== @@ -27663,7 +28642,7 @@ MetaEuk is a modular toolkit designed for large-scale gene discovery and annotat *homepage*: https://metaeuk.soedinglab.org ======= ============== -version toolchain +version toolchain ======= ============== ``4`` ``GCC/10.2.0`` ``5`` ``GCC/10.3.0`` @@ -27681,7 +28660,7 @@ MetaGeneAnnotator is a gene-finding program for prokaryote and phage. *homepage*: http://metagene.nig.ac.jp/ ============ ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= ========== ``20080819`` ``-x86-64`` ``system`` ============ ============= ========== @@ -27697,7 +28676,7 @@ Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It h *homepage*: https://github.com/metagenome-atlas/atlas ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``2.4.3`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================= =============== @@ -27713,7 +28692,7 @@ Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta- *homepage*: http://csg.sph.umich.edu/abecasis/Metal/ ============== ============== -version toolchain +version toolchain ============== ============== ``2011-03-25`` ``foss/2016a`` ``2020-05-05`` ``GCC/10.2.0`` @@ -27730,7 +28709,7 @@ MetaMorpheus is a bottom-up proteomics database search software with integrated *homepage*: https://github.com/smith-chem-wisc/MetaMorpheus =========== ================== -version toolchain +version toolchain =========== ================== ``0.0.320`` ``GCCcore/10.3.0`` =========== ================== @@ -27746,7 +28725,7 @@ MetaPhlAn is a computational tool for profiling the composition of microbial co *homepage*: https://github.com/biobakery/MetaPhlAn ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``3.0.9`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -27762,7 +28741,7 @@ MetaPhlAn is a computational tool for profiling the composition of microbial co *homepage*: https://bitbucket.org/biobakery/metaphlan2/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.7.8`` ``-Python-2.7.12`` ``foss/2016b`` ``2.7.8`` ``-Python-3.6.6`` ``foss/2018b`` @@ -27780,7 +28759,7 @@ MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes t *homepage*: https://github.com/bxlab/metaWRAP ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``1.2`` ``-Python-2.7.15`` ``foss/2018b`` ``1.2.2`` ``-Python-2.7.15`` ``foss/2019a`` @@ -27798,7 +28777,7 @@ Metaxa2 -- Identifies Small Subunit (SSU) rRNAs and classifies them taxonomicall *homepage*: https://microbiology.se/software/metaxa2/ ======= =============== -version toolchain +version toolchain ======= =============== ``2.2`` ``gompi/2019a`` ======= =============== @@ -27814,11 +28793,11 @@ A (mostly) universal methylation extractor for BS-seq experiments. *homepage*: https://github.com/dpryan79/MethylDackel ========= ======================================== -version toolchain +version toolchain ========= ======================================== ``0.4.0`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``0.5.0`` ``iccifort/2019.5.281`` -``0.6.1`` ``GCC/11.2.0`` +``0.5.0`` ``iccifort/2019.5.281`` +``0.6.1`` ``GCC/11.2.0`` ========= ======================================== @@ -27832,7 +28811,7 @@ Bisulfite sequencing data processing and differential methylation analysis. *homepage*: https://pypi.python.org/pypi/methylpy ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``1.1.9`` ``-Python-2.7.13`` ``foss/2017a`` ``1.2.9`` ``foss/2021b`` @@ -27849,11 +28828,11 @@ METIS is a set of serial programs for partitioning graphs, partitioning finite e *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview ========= ============= ================================================================================================================================================================================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ================================================================================================================================================================================================================================================================================================================== -``5.0.2`` ``gimkl/2.11.5`` +``5.0.2`` ``gimkl/2.11.5`` ``5.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``5.1.0`` ``-32bitIDX`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``5.1.0`` ``-32bitIDX`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ============= ================================================================================================================================================================================================================================================================================================================== @@ -27867,7 +28846,7 @@ The MGLTools software suite can be used for visualization and analysis of mo *homepage*: https://ccsb.scripps.edu/mgltools/ ========= ========== -version toolchain +version toolchain ========= ========== ``1.5.7`` ``system`` ========= ========== @@ -27883,7 +28862,7 @@ MHCflurry implements class I peptide/MHC binding affinity prediction. By defaul *homepage*: https://github.com/openvax/mhcflurry ========= ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================== ``1.2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ========= ================= ================================== @@ -27899,7 +28878,7 @@ MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II. *homepage*: https://github.com/KarchinLab/mhcnuggets ======= ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= ================================== ``2.3`` ``foss/2020b``, ``fosscuda/2020b`` ``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` @@ -27916,7 +28895,7 @@ Easy-to-use pipeline for the comprehensive metabolic annotation of microbial gen *homepage*: https://github.com/cruizperez/MicrobeAnnotator ========= ============== -version toolchain +version toolchain ========= ============== ``2.0.5`` ``foss/2021a`` ========= ============== @@ -27932,7 +28911,7 @@ Various worker functions for microclimc package *homepage*: https://github.com/ilyamaclean/microctools ================== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ============= ============== ``0.1.0-20201209`` ``-R-4.0.4`` ``foss/2020b`` ================== ============= ============== @@ -27948,7 +28927,7 @@ MIGEC is a software pipeline that facilitates processing and analysis of immun *homepage*: https://milaboratory.com/software/migec/ ========= =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= =================== ========== ``1.2.8`` ``-Java-1.8.0_162`` ``system`` ``1.2.9`` ``-Java-1.8`` ``system`` @@ -27962,13 +28941,14 @@ version versionsuffix toolchain Migrate estimates population parameters, effective population sizes and migration rates of n populations, using genetic data. It uses a coalescent theory approach taking into account history of mutations and uncertainty of the genealogy. -*homepage*: http://popgen.sc.fsu.edu/Migrate/Migrate-n.html +*homepage*: https://peterbeerli.com/migrate-html5/index.html ========== ============== -version toolchain +version toolchain ========== ============== ``4.2.8`` ``foss/2016a`` ``4.2.14`` ``foss/2018a`` +``5.0.4`` ``foss/2021b`` ========== ============== @@ -27982,7 +28962,7 @@ Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, *homepage*: https://miller.readthedocs.io/ ========= ========== -version toolchain +version toolchain ========= ========== ``6.4.0`` ``system`` ========= ========== @@ -27998,7 +28978,7 @@ mimalloc is a general purpose allocator with excellent performance characteristi *homepage*: https://microsoft.github.io/mimalloc/ ========= ====================================== -version toolchain +version toolchain ========= ====================================== ``1.7.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ====================================== @@ -28014,7 +28994,7 @@ Medical Image NetCDF or MINC isn't netCDF. *homepage*: https://github.com/BIC-MNI/libminc ========== =============================================== -version toolchain +version toolchain ========== =============================================== ``2.4.03`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` ========== =============================================== @@ -28030,7 +29010,7 @@ Mining CRISPRs in Environmental Datasets *homepage*: https://github.com/ctSkennerton/minced ========= ============= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ================= ``0.4.2`` ``-Java-11`` ``GCCcore/8.3.0`` ========= ============= ================= @@ -28046,10 +29026,10 @@ Mini-XML is a small XML parsing library that you can use to read XML data files *homepage*: https://www.msweet.org/mxml ========= ================== -version toolchain +version toolchain ========= ================== -``2.9`` ``GCCcore/8.2.0`` -``2.12`` ``GCCcore/9.3.0`` +``2.9`` ``GCCcore/8.2.0`` +``2.12`` ``GCCcore/9.3.0`` ``3.2`` ``GCCcore/10.3.0`` ``3.3.1`` ``GCCcore/11.2.0`` ========= ================== @@ -28065,7 +29045,7 @@ Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It take *homepage*: https://github.com/lh3/minimap2 ================ ====================================== -version toolchain +version toolchain ================ ====================================== ``0.3-20191007`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ================ ====================================== @@ -28081,7 +29061,7 @@ Dual barcode and primer demultiplexing for MinION sequenced reads *homepage*: https://github.com/calacademy-research/minibar ============ ================= ======================= -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ======================= ``20200326`` ``-Python-3.7.4`` ``iccifort/2019.5.281`` ``20200326`` ``-Python-3.8.2`` ``iccifort/2020.1.217`` @@ -28098,7 +29078,7 @@ MiniCARD is a *cardinality solver* based on MiniSAT [www.minisat.se]. MiniCARD *homepage*: https://github.com/liffiton/minicard ======= ============= -version toolchain +version toolchain ======= ============= ``1.2`` ``GCC/9.3.0`` ======= ============= @@ -28114,7 +29094,7 @@ Miniconda is a free minimal installer for conda. It is a small, bootstrap versi *homepage*: https://docs.conda.io/en/latest/miniconda.html ========== ========== -version toolchain +version toolchain ========== ========== ``4.3.21`` ``system`` ``4.6.14`` ``system`` @@ -28132,7 +29112,7 @@ Miniconda is a free minimal installer for conda. It is a small, bootstrap versi *homepage*: https://docs.conda.io/en/latest/miniconda.html ========== ========== -version toolchain +version toolchain ========== ========== ``4.4.10`` ``system`` ``4.5.12`` ``system`` @@ -28140,6 +29120,7 @@ version toolchain ``4.7.10`` ``system`` ``4.8.3`` ``system`` ``4.9.2`` ``system`` +``4.12.0`` ``system`` ========== ========== @@ -28153,12 +29134,12 @@ A small wrapper for core parts of EIgen, c++ library for linear algebra. *homepage*: https://launchpad.net/minieigen/ ========= =============================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =============================== =============================== ``0.5.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``0.5.3`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``0.5.3`` ``-Python-2.7.12-Boost-1.63.0`` ``intel/2016b`` -``0.5.4`` ``-Python-2.7.14`` ``intel/2018a`` +``0.5.3`` ``-Python-2.7.12-Boost-1.63.0`` ``intel/2016b`` +``0.5.4`` ``-Python-2.7.14`` ``intel/2018a`` ========= =============================== =============================== @@ -28172,7 +29153,7 @@ Minimac4 is a latest version in the series of genotype imputation software - pr *homepage*: https://genome.sph.umich.edu/wiki/Minimac4 ========= ============== -version toolchain +version toolchain ========= ============== ``1.0.0`` ``foss/2018a`` ========= ============== @@ -28188,18 +29169,18 @@ Minimap2 is a fast sequence mapping and alignment program that can find overlaps *homepage*: https://github.com/lh3/minimap2 ========== ====================================================== -version toolchain +version toolchain ========== ====================================================== -``2.0rc1`` ``foss/2016b`` -``2.10`` ``foss/2018a`` -``2.11`` ``intel/2018a`` -``2.12`` ``foss/2018a`` -``2.13`` ``foss/2018b`` +``2.0rc1`` ``foss/2016b`` +``2.10`` ``foss/2018a`` +``2.11`` ``intel/2018a`` +``2.12`` ``foss/2018a`` +``2.13`` ``foss/2018b`` ``2.17`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCCcore/9.3.0`` -``2.18`` ``GCCcore/10.2.0`` -``2.20`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.22`` ``GCCcore/11.2.0`` -``2.24`` ``GCCcore/11.2.0`` +``2.18`` ``GCCcore/10.2.0`` +``2.20`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.22`` ``GCCcore/11.2.0`` +``2.24`` ``GCCcore/11.2.0`` ========== ====================================================== @@ -28213,7 +29194,7 @@ A tool for Racon polishing of miniasm assemblies *homepage*: https://github.com/rrwick/Minipolish ========= ============== -version toolchain +version toolchain ========= ============== ``0.1.3`` ``GCC/11.2.0`` ========= ============== @@ -28229,13 +29210,29 @@ MiniSat is a minimalistic, open-source SAT solver, developed to help researchers *homepage*: http://minisat.se/ ============ ============= -version toolchain +version toolchain ============ ============= ``2.2.0`` ``GCC/9.3.0`` ``20130925`` ``GCC/9.3.0`` ============ ============= +.. _list_software_minizip_768: + +*minizip* ++++++++++ + +Mini zip and unzip based on zlib + +*homepage*: https://www.winimage.com/zLibDll/minizip.html + +======= ================== +version toolchain +======= ================== +``1.1`` ``GCCcore/11.2.0`` +======= ================== + + .. _list_software_MINPACK_515: *MINPACK* @@ -28246,7 +29243,7 @@ Minpack includes software for solving nonlinear equations and nonlinear least s *homepage*: https://www.netlib.org/minpack/ ============ ============== -version toolchain +version toolchain ============ ============== ``19961126`` ``GCC/10.3.0`` ============ ============== @@ -28262,11 +29259,11 @@ MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway *homepage*: https://omics.informatics.indiana.edu/MinPath ======= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== =============================== ``1.4`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``1.4`` ``-Python-2.7.16`` ``intel/2019b`` -``1.6`` ``GCCcore/11.2.0`` +``1.4`` ``-Python-2.7.16`` ``intel/2019b`` +``1.6`` ``GCCcore/11.2.0`` ======= ================== =============================== @@ -28280,12 +29277,12 @@ MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solex *homepage*: https://sourceforge.net/p/mira-assembler/wiki/Home/ ========== ================== ================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================================================ ``4.0.2`` ``foss/2018b``, ``gompi/2019b``, ``intel/2017b`` -``4.0.2`` ``-Python-2.7.11`` ``foss/2016a`` -``4.9.6`` ``intel/2017b`` -``5.0rc2`` ``foss/2020b`` +``4.0.2`` ``-Python-2.7.11`` ``foss/2016a`` +``4.9.6`` ``intel/2017b`` +``5.0rc2`` ``foss/2020b`` ========== ================== ================================================ @@ -28299,9 +29296,9 @@ miRDeep2 is a completely overhauled tool which discovers microRNA genes by analy *homepage*: https://www.mdc-berlin.de/8551903/en/ =========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================= =============== -``0.1.1`` ``-Python-3.6.6`` ``foss/2018b`` +``0.1.1`` ``-Python-3.6.6`` ``foss/2018b`` ``2.0.0.8`` ``intel/2016b`` =========== ================= =============== @@ -28316,7 +29313,7 @@ Mish-Cuda: Self Regularized Non-Monotonic Activation Function *homepage*: https://github.com/JunnYu/mish-cuda ============ ================== ================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ================== ``20210309`` ``-PyTorch-1.9.0`` ``fosscuda/2020b`` ============ ================== ================== @@ -28332,12 +29329,28 @@ The misha package is intended to help users to efficiently analyze genomic data *homepage*: https://github.com/tanaylab/misha ========== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ============== ``4.0.10`` ``-R-4.0.0`` ``foss/2020a`` ========== ============= ============== +.. _list_software_MITgcmutils_1106: + +*MITgcmutils* ++++++++++++++ + +A numerical model designed for study of the atmosphere, ocean, and climate, MITgcm’s flexible non-hydrostatic formulation enables it to efficiently simulate fluid phenomena over a wide range of scales; its adjoint capabilities enable it to be applied to sensitivity questions and to parameter and state estimation problems. By employing fluid equation isomorphisms, a single dynamical kernel can be used to simulate flow of both the atmosphere and ocean. The model is developed to perform efficiently on a wide variety of computational platforms. + +*homepage*: https://mitgcm.org/ + +========= ============== +version toolchain +========= ============== +``0.1.2`` ``foss/2022a`` +========= ============== + + .. _list_software_MITObim_625: *MITObim* @@ -28348,7 +29361,7 @@ The MITObim procedure (mitochondrial baiting and iterative mapping) represents *homepage*: https://github.com/chrishah/MITObim ========= =============================== -version toolchain +version toolchain ========= =============================== ``1.9.1`` ``foss/2018b``, ``gompi/2019b`` ========= =============================== @@ -28364,7 +29377,7 @@ MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw *homepage*: https://github.com/linzhi2013/MitoZ ======= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= ============== ``2.3`` ``-Python-3.6.6`` ``foss/2018b`` ======= ================= ============== @@ -28380,7 +29393,7 @@ MiXCR processes big immunome data from raw sequences to quantitated clonotypes *homepage*: https://milaboratory.com/software/mixcr/ ========== =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== =================== ========== ``2.1.9`` ``-Java-1.8.0_162`` ``system`` ``3.0.3`` ``-Java-1.8`` ``system`` @@ -28399,7 +29412,7 @@ MixMHC2pred is a predictor of HLA class II ligands and epitopes. It is describe *homepage*: https://github.com/GfellerLab/MixMHC2pred ======= ========== -version toolchain +version toolchain ======= ========== ``1.2`` ``system`` ======= ========== @@ -28415,12 +29428,12 @@ Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN) *homepage*: https://01.org/mkl-dnn ========== =============================== -version toolchain +version toolchain ========== =============================== -``0.11`` ``intel/2017b`` -``0.13`` ``intel/2018a`` +``0.11`` ``intel/2017b`` +``0.13`` ``intel/2018a`` ``0.16`` ``foss/2018b``, ``intel/2018b`` -``0.17.2`` ``foss/2018a`` +``0.17.2`` ``foss/2018a`` ========== =============================== @@ -28434,11 +29447,11 @@ Python hooks for Intel(R) Math Kernel Library runtime control settings. *homepage*: https://github.com/IntelPython/mkl-service ========= ================= ================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================ -``2.0.2`` ``intel/2019a`` +``2.0.2`` ``intel/2019a`` ``2.3.0`` ``intel/2020b``, ``intel/2021b`` -``2.3.0`` ``-Python-3.7.4`` ``intel/2019b`` +``2.3.0`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================= ================================ @@ -28452,7 +29465,7 @@ NumPy-based Python interface to Intel(R) MKL FFT functionality *homepage*: https://github.com/IntelPython/mkl_fft ========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============== ``1.0.14`` ``-Python-3.6.6`` ``intel/2018b`` ========== ================= =============== @@ -28468,7 +29481,7 @@ Intel Memory Latency Checker (Intel MLC) is a tool used to measure memory latenc *homepage*: https://software.intel.com/en-us/articles/intelr-memory-latency-checker ======= ========== -version toolchain +version toolchain ======= ========== ``3.0`` ``system`` ======= ========== @@ -28484,7 +29497,7 @@ Mlxtend (machine learning extensions) is a Python library of useful tools for th *homepage*: https://rasbt.github.io/mlxtend/ ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.17.3`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================= ============== @@ -28500,7 +29513,7 @@ The mm-common module provides the build infrastructure and utilities shared amon *homepage*: https://gitlab.gnome.org/GNOME/mm-common ========= ================== -version toolchain +version toolchain ========= ================== ``1.0.4`` ``GCCcore/10.3.0`` ========= ================== @@ -28516,9 +29529,9 @@ Mmg is an open source software for simplicial remeshing. It provides 3 applicati *homepage*: https://www.mmgtools.org/ ========= ================================ -version toolchain +version toolchain ========= ================================ -``5.3.9`` ``foss/2017b`` +``5.3.9`` ``foss/2017b`` ``5.6.0`` ``gompi/2021a``, ``gompi/2021b`` ========= ================================ @@ -28533,7 +29546,7 @@ The MMSEQ package contains a collection of statistical tools for analysing RNA- *homepage*: https://github.com/eturro/mmseq ========= =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= =================== ========== ``1.0.8`` ``-linux64-static`` ``system`` ========= =================== ========== @@ -28549,16 +29562,16 @@ MMseqs2: ultra fast and sensitive search and clustering suite *homepage*: https://mmseqs.com ===================== ================================================= -version toolchain +version toolchain ===================== ================================================= -``1-c7a89`` ``foss/2016b`` -``5-9375b`` ``intel/2018a`` -``8-fac81`` ``intel/2018b`` -``10-6d92c`` ``gompi/2019b``, ``iimpi/2019b`` -``11-e1a1c`` ``iimpi/2019b`` +``1-c7a89`` ``foss/2016b`` +``5-9375b`` ``intel/2018a`` +``8-fac81`` ``intel/2018b`` +``10-6d92c`` ``gompi/2019b``, ``iimpi/2019b`` +``11-e1a1c`` ``iimpi/2019b`` ``13-45111`` ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b`` -``13-45111-20211006`` ``gompi/2020b`` -``13-45111-20211019`` ``gompi/2020b`` +``13-45111-20211006`` ``gompi/2020b`` +``13-45111-20211019`` ``gompi/2020b`` ===================== ================================================= @@ -28572,7 +29585,7 @@ The Macromolecular Transmission Format (MMTF) is a new compact binary format to *homepage*: https://mmtf.rcsb.org/ ========= ================== -version toolchain +version toolchain ========= ================== ``1.0.0`` ``GCCcore/10.2.0`` ========= ================== @@ -28588,7 +29601,7 @@ MNE-Python software is an open-source Python package for exploring, visualizing, *homepage*: https://mne.tools/stable/index.html ========== ============== -version toolchain +version toolchain ========== ============== ``0.24.1`` ``foss/2021a`` ========== ============== @@ -28604,7 +29617,7 @@ MOABS: MOdel based Analysis of Bisulfite Sequencing data *homepage*: https://github.com/sunnyisgalaxy/moabs =========== =============== -version toolchain +version toolchain =========== =============== ``1.3.9.6`` ``gompi/2019b`` =========== =============== @@ -28620,7 +29633,7 @@ ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and *homepage*: https://github.com/ddarriba/modeltest ========= =============== -version toolchain +version toolchain ========= =============== ``0.1.7`` ``gompi/2021b`` ========= =============== @@ -28636,7 +29649,7 @@ Compute modal decompositions and reduced-order models, easily, efficiently, and *homepage*: https://pypi.python.org/pypi/modred/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``2.0.2`` ``-Python-3.5.2`` ``foss/2016b`` ========= ================= ============== @@ -28652,7 +29665,7 @@ Molcas is an ab initio quantum chemistry software package developed by scientist *homepage*: http://www.molcas.org ================ ====================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ================ ====================== ========== ``8.0-15.06.18`` ``_CentOS_6.6_x86_64`` ``system`` ``8.2`` ``-centos-mkl-par`` ``system`` @@ -28670,12 +29683,13 @@ mold is a high-performance drop-in replacement for existing Unix linkers. *homepage*: https://github.com/rui314/mold ========= ================== -version toolchain +version toolchain ========= ================== ``0.9.6`` ``GCCcore/11.2.0`` ``1.0.0`` ``GCCcore/11.2.0`` ``1.2.1`` ``GCCcore/11.3.0`` ``1.3.0`` ``GCCcore/11.3.0`` +``1.7.1`` ``GCCcore/12.2.0`` ========= ================== @@ -28686,16 +29700,17 @@ version toolchain Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac -*homepage*: https://www3.cmbi.umcn.nl/molden +*homepage*: https://www.theochem.ru.nl/molden/ ======= ===================================== -version toolchain +version toolchain ======= ===================================== -``5.6`` ``foss/2016a`` -``5.7`` ``intel/2016b`` -``5.8`` ``foss/2018a`` -``6.1`` ``GCCcore/8.2.0`` +``5.6`` ``foss/2016a`` +``5.7`` ``intel/2016b`` +``5.8`` ``foss/2018a`` +``6.1`` ``GCCcore/8.2.0`` ``6.8`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``7.1`` ``GCCcore/11.3.0`` ======= ===================================== @@ -28709,7 +29724,7 @@ Molekel is an open-source multi-platform molecular visualization program. *homepage*: http://ugovaretto.github.io/molekel/wiki/pmwiki.php/Main/HomePage.html ========= ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ========== ``5.4.0`` ``-Linux_x86_64`` ``system`` ========= ================= ========== @@ -28725,18 +29740,18 @@ MolMod is a Python library with many compoments that are useful to write molecul *homepage*: https://molmod.github.io/molmod/ ========= ================== ============================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============================================== -``1.1`` ``-Python-2.7.11`` ``intel/2016a`` -``1.1`` ``-Python-2.7.12`` ``intel/2016b`` -``1.1`` ``-Python-2.7.13`` ``intel/2017a`` -``1.4.3`` ``-Python-2.7.14`` ``intel/2017b`` -``1.4.3`` ``-Python-3.6.3`` ``intel/2017b`` -``1.4.4`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``1.4.4`` ``-Python-2.7.15`` ``intel/2018b`` -``1.4.4`` ``-Python-3.7.2`` ``intel/2019a`` -``1.4.5`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.4.5`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.1`` ``-Python-2.7.11`` ``intel/2016a`` +``1.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.1`` ``-Python-2.7.13`` ``intel/2017a`` +``1.4.3`` ``-Python-2.7.14`` ``intel/2017b`` +``1.4.3`` ``-Python-3.6.3`` ``intel/2017b`` +``1.4.4`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``1.4.4`` ``-Python-2.7.15`` ``intel/2018b`` +``1.4.4`` ``-Python-3.7.2`` ``intel/2019a`` +``1.4.5`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.4.5`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``1.4.8`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` ========= ================== ============================================== @@ -28751,7 +29766,7 @@ Molpro is a complete system of ab initio programs for molecular electronic struc *homepage*: https://www.molpro.net ============= ======================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ============= ======================== ========== ``2010.1.23`` ``.Linux_x86_64`` ``system`` ``2015.1.0`` ``.linux_x86_64_intel`` ``system`` @@ -28770,12 +29785,31 @@ MONA is a tool that translates formulas to finite-state automata. The formulas m *homepage*: https://www.brics.dk/mona/index.html ========== ============== -version toolchain +version toolchain ========== ============== ``1.4-18`` ``GCC/11.2.0`` ========== ============== +.. _list_software_MONAI_372: + +*MONAI* ++++++++ + +MONAI is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of PyTorch Ecosystem. + +*homepage*: https://monai.io/ + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``0.8.0`` ``foss/2021a`` +``0.8.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``1.0.1`` ``foss/2022a`` +``1.0.1`` ``-CUDA-11.7.0`` ``foss/2022a`` +========= ================ ============== + + .. _list_software_mongolite_974: *mongolite* @@ -28786,7 +29820,7 @@ High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'. Inclu *homepage*: https://cran.r-project.org/web/packages/mongolite ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``2.3.0`` ``-R-4.0.0`` ``foss/2020a`` ``2.3.0`` ``-R-4.0.3`` ``foss/2020b`` @@ -28804,17 +29838,17 @@ An open source, cross-platform, implementation of C# and the CLR that is binary *homepage*: https://www.mono-project.com/ ============== =============================== -version toolchain +version toolchain ============== =============================== -``2.10.6`` ``intel/2016b`` -``4.6.2.7`` ``intel/2016b``, ``system`` -``4.8.0.495`` ``intel/2017a`` +``2.10.6`` ``intel/2016b`` +``4.6.2.7`` ``intel/2016b``, ``system`` +``4.8.0.495`` ``intel/2017a`` ``5.4.1.6`` ``foss/2017b``, ``intel/2017b`` -``5.10.0.160`` ``foss/2018a`` -``5.18.1.0`` ``foss/2018a`` -``6.4.0.198`` ``foss/2018b`` -``6.8.0.105`` ``GCCcore/8.3.0`` -``6.12.0.122`` ``GCCcore/11.2.0`` +``5.10.0.160`` ``foss/2018a`` +``5.18.1.0`` ``foss/2018a`` +``6.4.0.198`` ``foss/2018b`` +``6.8.0.105`` ``GCCcore/8.3.0`` +``6.12.0.122`` ``GCCcore/11.2.0`` ============== =============================== @@ -28828,7 +29862,7 @@ An analysis toolkit for single-cell RNA-seq. *homepage*: https://cole-trapnell-lab.github.io/monocle3/ ========= ========================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ========================= ============== ``0.2.0`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` ``0.2.3`` ``-R-4.0.3`` ``foss/2020b`` @@ -28845,12 +29879,28 @@ Moonjit is a Just-In-Time Compiler (JIT) for the Lua programming language. Lua *homepage*: https://github.com/moonjit/moonjit ========= ================= -version toolchain +version toolchain ========= ================= ``2.2.0`` ``GCCcore/9.3.0`` ========= ================= +.. _list_software_MOOSE_387: + +*MOOSE* ++++++++ + +The Multiphysics Object-Oriented Simulation Environment (MOOSE) is a finite-element, multiphysics framework primarily developed by Idaho National Laboratory + +*homepage*: https://mooseframework.inl.gov + +============== ================= ============== +version versionsuffix toolchain +============== ================= ============== +``2021-05-18`` ``-Python-3.7.4`` ``foss/2019b`` +============== ================= ============== + + .. _list_software_mordecai_836: *mordecai* @@ -28861,7 +29911,7 @@ mordecai is a full text geoparsing as a Python library. Extract the place names *homepage*: https://github.com/openeventdata/mordecai ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``2.0.1`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================= ============== @@ -28877,7 +29927,7 @@ MoreRONN is the spiritual successor of RONN and is useful for surveying disorde *homepage*: https://github.com/varun-ramraj/MoreRONN ======= ============= -version toolchain +version toolchain ======= ============= ``4.9`` ``GCC/8.3.0`` ======= ============= @@ -28893,12 +29943,12 @@ Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing *homepage*: https://github.com/brentp/mosdepth ========= =============== -version toolchain +version toolchain ========= =============== ``0.2.2`` ``intel/2018a`` ``0.2.3`` ``intel/2018a`` -``0.2.4`` ``foss/2018b`` -``0.3.3`` ``GCC/11.2.0`` +``0.2.4`` ``foss/2018b`` +``0.3.3`` ``GCC/11.2.0`` ========= =============== @@ -28912,11 +29962,11 @@ Mothur is a single piece of open-source, expandable software to fill the bioinf *homepage*: https://www.mothur.org/ ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``1.39.5`` ``-Python-2.7.13`` ``intel/2017a`` -``1.41.0`` ``-Python-2.7.15`` ``foss/2018b`` -``1.43.0`` ``-Python-3.7.2`` ``foss/2019a`` +``1.41.0`` ``-Python-2.7.15`` ``foss/2018b`` +``1.43.0`` ``-Python-3.7.2`` ``foss/2019a`` ========== ================== =============== @@ -28930,10 +29980,10 @@ Motif refers to both a graphical user interface (GUI) specification and the widg *homepage*: https://motif.ics.com/ ========= =============================================================================================================================================================================================== -version toolchain +version toolchain ========= =============================================================================================================================================================================================== -``2.3.5`` ``foss/2016a``, ``intel/2016a`` -``2.3.7`` ``intel/2017a`` +``2.3.5`` ``foss/2016a``, ``intel/2016a`` +``2.3.7`` ``intel/2017a`` ``2.3.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b``, ``intel/2018a``, ``intel/2019a`` ========= =============================================================================================================================================================================================== @@ -28948,13 +29998,14 @@ MotionCor2 correct anisotropic image motion at the single pixel level across the *homepage*: https://msg.ucsf.edu/ ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``1.2.6`` ``GCCcore/8.2.0`` -``1.3.1`` ``GCCcore/8.3.0`` -``1.3.2`` ``GCCcore/8.3.0`` -``1.4.2`` ``GCCcore/10.2.0`` +``1.2.6`` ``GCCcore/8.2.0`` +``1.3.1`` ``GCCcore/8.3.0`` +``1.3.2`` ``GCCcore/8.3.0`` +``1.4.2`` ``GCCcore/10.2.0`` ``1.4.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.5.0`` ``GCCcore/11.3.0`` ========= ====================================== @@ -28968,7 +30019,7 @@ Motion correction, explicit spatio-temporal regularization of motion tracking, r *homepage*: https://github.com/WeiXuanChan/motionSegmentation ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``2.7.9`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -28984,9 +30035,10 @@ MoviePy (full documentation) is a Python library for video editing: cutting, con *homepage*: https://zulko.github.io/moviepy/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.0.1`` ``-Python-3.7.2`` ``foss/2019a`` +``1.0.3`` ``foss/2021a`` ========= ================= ============== @@ -29000,7 +30052,7 @@ MPB is a free and open-source software package for computing the band structure *homepage*: https://mpb.readthedocs.io/en/latest/ ========= ================== =============================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================================== ``1.6.2`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2018a`` ========= ================== =============================================== @@ -29016,11 +30068,11 @@ Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily h *homepage*: http://www.multiprecision.org/ ========= =============== ============================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =============== ============================================================================== -``1.0.3`` ``intel/2017a`` -``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` -``1.1.0`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/9.3.0`` +``1.0.3`` ``intel/2017a`` +``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` +``1.1.0`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``GCCcore/9.3.0`` ``1.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= =============== ============================================================================== @@ -29035,14 +30087,14 @@ The MPFR library is a C library for multiple-precision floating-point computati *homepage*: https://www.mpfr.org ========= ============================================================================== -version toolchain +version toolchain ========= ============================================================================== -``2.4.2`` ``system`` -``3.1.4`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``3.1.5`` ``GCCcore/6.4.0``, ``intel/2017a`` -``3.1.6`` ``GCCcore/6.4.0`` -``4.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``4.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.4.2`` ``system`` +``3.1.4`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``3.1.5`` ``GCCcore/6.4.0``, ``intel/2017a`` +``3.1.6`` ``GCCcore/6.4.0`` +``4.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``4.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ============================================================================== @@ -29057,15 +30109,15 @@ MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) *homepage*: https://bitbucket.org/mpi4py/mpi4py ========= ================================= ================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================================= ================================ -``1.3.1`` ``-Python-2.7.11-timed-pingpong`` ``intel/2016a`` -``1.3.1`` ``-Python-2.7.12-timed-pingpong`` ``intel/2016b`` -``2.0.0`` ``-Python-2.7.12`` ``intel/2016b`` -``2.0.0`` ``-Python-2.7.13-timed-pingpong`` ``intel/2017a`` -``3.0.0`` ``-Python-2.7.14-timed-pingpong`` ``intel/2018a`` -``3.0.0`` ``-Python-3.6.3`` ``intel/2017b`` -``3.0.1`` ``-Python-3.6.6`` ``intel/2018b`` +``1.3.1`` ``-Python-2.7.11-timed-pingpong`` ``intel/2016a`` +``1.3.1`` ``-Python-2.7.12-timed-pingpong`` ``intel/2016b`` +``2.0.0`` ``-Python-2.7.12`` ``intel/2016b`` +``2.0.0`` ``-Python-2.7.13-timed-pingpong`` ``intel/2017a`` +``3.0.0`` ``-Python-2.7.14-timed-pingpong`` ``intel/2018a`` +``3.0.0`` ``-Python-3.6.3`` ``intel/2017b`` +``3.0.1`` ``-Python-3.6.6`` ``intel/2018b`` ``3.0.2`` ``-timed-pingpong`` ``gompi/2019a``, ``iimpi/2019a`` ========= ================================= ================================ @@ -29080,13 +30132,13 @@ MPICH is a high-performance and widely portable implementation of the Message P *homepage*: https://www.mpich.org/ ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``3.0.4`` ``GCC/4.8.1`` +``3.0.4`` ``GCC/4.8.1`` ``3.2`` ``GCC/4.9.3-2.25``, ``GCC/7.2.0-2.29`` -``3.2.1`` ``GCC/7.2.0-2.29`` -``3.3.2`` ``GCC/10.2.0``, ``GCC/9.3.0`` -``3.4.2`` ``GCC/10.3.0`` +``3.2.1`` ``GCC/7.2.0-2.29`` +``3.3.2`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``3.4.2`` ``GCC/10.3.0`` ========= ====================================== @@ -29100,7 +30152,7 @@ MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does no *homepage*: http://www.mpich.org/ ======= ============= -version toolchain +version toolchain ======= ============= ``1.1`` ``GCC/4.8.1`` ======= ============= @@ -29116,11 +30168,11 @@ MPI-Based File Utilities For Distributed Systems *homepage*: https://hpc.github.io/mpifileutils/ ========== ================================ -version toolchain +version toolchain ========== ================================ ``0.9.1`` ``gompi/2019a``, ``iimpi/2019a`` ``0.10`` ``gompi/2020a``, ``iimpi/2020a`` -``0.10.1`` ``gompi/2020a`` +``0.10.1`` ``gompi/2020a`` ========== ================================ @@ -29134,7 +30186,7 @@ mpiP is a lightweight profiling library for MPI applications. Because it only *homepage*: http://mpip.sourceforge.net/ ========= =================================================== -version toolchain +version toolchain ========= =================================================== ``3.4.1`` ``gompi/2019a``, ``iimpi/2019a``, ``iompi/2019.01`` ========= =================================================== @@ -29150,7 +30202,7 @@ MPJ Express is an open source Java message passing library that allows applicati *homepage*: http://mpj-express.org/ ======== ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================== ============== ``0.44`` ``-Java-1.8.0_92`` ``foss/2016a`` ======== ================== ============== @@ -29166,12 +30218,12 @@ mpmath can be used as an arbitrary-precision substitute for Python's float/compl *homepage*: https://mpmath.org/ ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== ``0.19`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``1.0.0`` ``-Python-2.7.14`` ``intel/2018a`` -``1.0.0`` ``-Python-2.7.15`` ``foss/2018b`` -``1.1.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``1.0.0`` ``-Python-2.7.14`` ``intel/2018a`` +``1.0.0`` ``-Python-2.7.15`` ``foss/2018b`` +``1.1.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ================== =============================== @@ -29185,11 +30237,11 @@ MrBayes is a program for Bayesian inference and model choice across a wide rang *homepage*: https://nbisweden.github.io/MrBayes/ ========== =============================================== -version toolchain +version toolchain ========== =============================================== ``3.2.6`` ``foss/2016a``, ``foss/2017a``, ``gompi/2020b`` -``3.2.7`` ``gompi/2020b``, ``gompic/2019b`` -``3.2.7a`` ``foss/2020a``, ``iimpi/2019a`` +``3.2.7`` ``gompi/2020b``, ``gompic/2019b`` +``3.2.7a`` ``foss/2020a``, ``iimpi/2019a`` ========== =============================================== @@ -29202,11 +30254,11 @@ mrcfile is a Python implementation of the MRC2014 file format, which is used in *homepage*: https://github.com/ccpem/mrcfile -========= ================================== -version toolchain -========= ================================== -``1.3.0`` ``foss/2020b``, ``fosscuda/2020b`` -========= ================================== +========= ================================================== +version toolchain +========= ================================================== +``1.3.0`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` +========= ================================================== .. _list_software_MRChem_540: @@ -29219,9 +30271,10 @@ MRChem is a numerical real-space code for molecular electronic structure calcula *homepage*: https://mrchem.readthedocs.io ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.0.0`` ``-Python-3.8.2`` ``foss/2020a`` +``1.1.1`` ``foss/2022a`` ========= ================= ============== @@ -29235,9 +30288,10 @@ MultiResolution Computation Program Package *homepage*: https://mrcpp.readthedocs.io ========= ============== -version toolchain +version toolchain ========= ============== ``1.3.6`` ``foss/2020a`` +``1.4.1`` ``foss/2022a`` ========= ============== @@ -29251,7 +30305,7 @@ MRIcron allows viewing of medical images. It includes tools to complement SPM a *homepage*: http://www.mccauslandcenter.sc.edu/mricro/mricron/ ================ ========== -version toolchain +version toolchain ================ ========== ``1.0.20180614`` ``system`` ``20150601`` ``system`` @@ -29268,15 +30322,15 @@ MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tra *homepage*: http://www.brain.org.au/software/index.html#mrtrix =================== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain =================== ================== =============== ``0.3.14`` ``-Python-2.7.11`` ``intel/2016a`` ``0.3.15`` ``-Python-2.7.12`` ``intel/2016b`` -``3.0-rc-20191217`` ``-Python-2.7.16`` ``foss/2019b`` -``3.0-rc-20191217`` ``-Python-3.7.4`` ``foss/2019b`` -``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` -``3.0.3`` ``foss/2021a`` -``3.0_RC2`` ``-Python-2.7.13`` ``foss/2017a`` +``3.0-rc-20191217`` ``-Python-2.7.16`` ``foss/2019b`` +``3.0-rc-20191217`` ``-Python-3.7.4`` ``foss/2019b`` +``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` +``3.0.3`` ``foss/2021a`` +``3.0_RC2`` ``-Python-2.7.13`` ``foss/2017a`` ``3.0_RC3`` ``-Python-2.7.14`` ``intel/2018a`` =================== ================== =============== @@ -29291,7 +30345,7 @@ MessagePack is an efficient binary serialization format, which lets you exchange *homepage*: http://msgpack.org/ ========= ================== -version toolchain +version toolchain ========= ================== ``3.3.0`` ``GCCcore/10.2.0`` ========= ================== @@ -29307,7 +30361,7 @@ Multimodal Surface Matching with Higher order Clique Reduction *homepage*: https://github.com/ecr05/MSM_HOCR ======= =============================== -version toolchain +version toolchain ======= =============================== ``1.0`` ``foss/2017b``, ``intel/2017b`` ======= =============================== @@ -29323,7 +30377,7 @@ Using combined evidence from replicates to evaluate ChIP-seq peaks *homepage*: https://genometric.github.io/MSPC/ ========= ========== -version toolchain +version toolchain ========= ========== ``3.3.1`` ``system`` ========= ========== @@ -29339,12 +30393,28 @@ msprime is a coalescent simulator and library for processing tree-based genetic *homepage*: https://msprime.readthedocs.io ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.7.0`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================= =============== +.. _list_software_mstore_666: + +*mstore* +++++++++ + +Molecular structure store for testing + +*homepage*: https://github.com/grimme-lab/mstore + +========= ============== +version toolchain +========= ============== +``0.2.0`` ``GCC/11.2.0`` +========= ============== + + .. _list_software_MTL4_289: *MTL4* @@ -29355,7 +30425,7 @@ The Matrix Template Library 4 incorporates the most modern programming technique *homepage*: http://www.simunova.com/mtl4 ============ ========== -version toolchain +version toolchain ============ ========== ``4.0.8878`` ``system`` ``4.0.9555`` ``system`` @@ -29372,7 +30442,7 @@ MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose phy *homepage*: https://mujoco.org/ ========= ================== -version toolchain +version toolchain ========= ================== ``2.1.1`` ``GCCcore/11.2.0`` ========= ================== @@ -29388,7 +30458,7 @@ MuJoCo is a physics engine for detailed, efficient rigid body simulations with c *homepage*: https://github.com/openai/mujoco-py ============ ============== -version toolchain +version toolchain ============ ============== ``2.1.2.14`` ``foss/2021b`` ============ ============== @@ -29404,12 +30474,28 @@ generate multiset combinations (n multichoose k). *homepage*: https://github.com/ekg/multichoose ========= ============================================================================= -version toolchain +version toolchain ========= ============================================================================= ``1.0.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ========= ============================================================================= +.. _list_software_MultilevelEstimators_2126: + +*MultilevelEstimators* +++++++++++++++++++++++ + +The Julia module for Multilevel Monte Carlo methods + +*homepage*: https://github.com/PieterjanRobbe/MultilevelEstimators.jl + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``0.1.0`` ``-Julia-1.7.2`` ``GCC/11.2.0`` +========= ================ ============== + + .. _list_software_MultiNest_933: *MultiNest* @@ -29420,7 +30506,7 @@ MultiNest is a Bayesian inference tool which calculates the evidence and explore *homepage*: https://ccpforge.cse.rl.ac.uk/gf/project/multinest/ ======== =============== -version toolchain +version toolchain ======== =============== ``3.10`` ``intel/2016a`` ======== =============== @@ -29436,22 +30522,22 @@ Aggregate results from bioinformatics analyses across many samples into a single *homepage*: https://multiqc.info ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== -``0.9`` ``-Python-2.7.12`` ``foss/2016b`` +``0.9`` ``-Python-2.7.12`` ``foss/2016b`` ``1.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.6`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.6`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.7`` ``-Python-2.7.15`` ``intel/2018b`` +``1.7`` ``-Python-2.7.15`` ``intel/2018b`` ``1.7`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.8`` ``-Python-2.7.16`` ``intel/2019b`` +``1.8`` ``-Python-2.7.16`` ``intel/2019b`` ``1.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.9`` ``-Python-3.7.4`` ``foss/2019b`` +``1.9`` ``-Python-3.7.4`` ``foss/2019b`` ``1.9`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.10.1`` ``foss/2020b`` -``1.11`` ``foss/2021a`` -``1.12`` ``foss/2021b`` +``1.10.1`` ``foss/2020b`` +``1.11`` ``foss/2021a`` +``1.12`` ``foss/2021b`` ========== ================== =============================== @@ -29465,9 +30551,9 @@ Multiwfn is an extremely powerful program for realizingi electronic wavefunctio *homepage*: http://sobereva.com/multiwfn/ ========= ================================ -version toolchain +version toolchain ========= ================================ -``3.4.1`` ``intel/2017b`` +``3.4.1`` ``intel/2017b`` ``3.6`` ``intel/2019a``, ``intel/2019b`` ========= ================================ @@ -29482,7 +30568,7 @@ muMerge is a tool for combining bed regions from multiple bed files that overlap *homepage*: https://github.com/Dowell-Lab/mumerge ========= ============== -version toolchain +version toolchain ========= ============== ``1.1.0`` ``foss/2022a`` ========= ============== @@ -29498,11 +30584,11 @@ MUMmer is a system for rapidly aligning entire genomes, whether in complete or *homepage*: http://mummer.sourceforge.net/ ============== ========================================================================= -version toolchain +version toolchain ============== ========================================================================= -``3.23`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``foss/2016b`` +``3.23`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``foss/2016b`` ``4.0.0beta2`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``foss/2018b`` -``4.0.0rc1`` ``GCCcore/11.2.0`` +``4.0.0rc1`` ``GCCcore/11.2.0`` ============== ========================================================================= @@ -29516,16 +30602,16 @@ A parallel sparse direct solver *homepage*: https://graal.ens-lyon.fr/MUMPS/ ========= ============== ================================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ============== ================================================================================================================= -``5.1.2`` ``-metis`` ``foss/2017b`` +``5.1.2`` ``-metis`` ``foss/2017b`` ``5.2.1`` ``-metis`` ``foss/2018b``, ``foss/2019a``, ``foss/2019b``, ``foss/2020a``, ``intel/2019a``, ``intel/2019b``, ``intel/2020a`` -``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` -``5.3.5`` ``-metis`` ``foss/2020b``, ``intel/2020b`` -``5.4.0`` ``-metis`` ``foss/2021a`` -``5.4.1`` ``-metis`` ``foss/2021b``, ``intel/2021b`` -``5.5.0`` ``-metis`` ``foss/2021a`` -``5.5.1`` ``-metis`` ``foss/2022a`` +``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` +``5.3.5`` ``-metis`` ``foss/2020b``, ``intel/2020b`` +``5.4.0`` ``-metis`` ``foss/2021a`` +``5.4.1`` ``-metis`` ``foss/2021b``, ``intel/2021b`` +``5.5.0`` ``-metis`` ``foss/2021a`` +``5.5.1`` ``-metis`` ``foss/2022a`` ========= ============== ================================================================================================================= @@ -29539,11 +30625,11 @@ muParser is an extensible high performance math expression parser library writt *homepage*: https://beltoforion.de/article.php?a=muparser ========= ===================================== -version toolchain +version toolchain ========= ===================================== -``2.2.5`` ``GCCcore/6.4.0`` +``2.2.5`` ``GCCcore/6.4.0`` ``2.3.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``2.3.3`` ``GCCcore/10.3.0`` +``2.3.3`` ``GCCcore/10.3.0`` ========= ===================================== @@ -29557,7 +30643,7 @@ A C++ Library for Parsing Expressions with Strings, Complex Numbers, Vectors, Ma *homepage*: https://beltoforion.de/en/muparserx/ ========= ====================================== -version toolchain +version toolchain ========= ====================================== ``4.0.8`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ====================================== @@ -29573,7 +30659,7 @@ MuPeXI: Mutant Peptide eXtractor and Informer. Given a list of somatic mutations *homepage*: https://github.com/ambj/MuPeXI ========= ============================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============================== ============== ``1.2.0`` ``-Perl-5.28.0-Python-2.7.15`` ``foss/2018b`` ========= ============================== ============== @@ -29589,13 +30675,13 @@ MUSCLE is one of the best-performing multiple alignment programs according to p *homepage*: https://drive5.com/muscle/ ============ =============== ===================================================================================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ============ =============== ===================================================================================================================================================================================================================== ``3.8.31`` ``GCC/7.3.0-2.30``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2017b``, ``foss/2018a``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``3.8.31`` ``-i86linux64`` ``system`` -``3.8.1551`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` -``5.0.1428`` ``GCCcore/10.3.0`` -``5.1`` ``GCCcore/11.2.0`` +``3.8.31`` ``-i86linux64`` ``system`` +``3.8.1551`` ``GCC/10.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` +``5.0.1428`` ``GCCcore/10.3.0`` +``5.1`` ``GCCcore/11.2.0`` ============ =============== ===================================================================================================================================================================================================================== @@ -29609,7 +30695,7 @@ Multi-subject Single Cell deconvolution (MuSiC) is a deconvolution method that u *homepage*: https://github.com/xuranw/MuSiC ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.6.2`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== @@ -29625,7 +30711,7 @@ MUST detects usage errors of the Message Passing Interface (MPI) and reports the *homepage*: https://hpc.rwth-aachen.de/must/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.6`` ``-Python-3.6.6`` ``foss/2018b`` ``1.6`` ``-Python-3.7.4`` ``foss/2019b`` @@ -29643,7 +30729,7 @@ MuTect is a method developed at the Broad Institute for the reliable and accura *homepage*: http://www.broadinstitute.org/cancer/cga/mutect ========= ================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ========== ``1.1.4`` ``-Java-1.7.0_76`` ``system`` ``1.1.4`` ``-Java-1.7.0_80`` ``system`` @@ -29661,7 +30747,7 @@ Mutil is a set of standard utilities that have been parallelized to maximize per *homepage*: http://people.nas.nasa.gov/~kolano/projects/mutil.html =========== =============== -version toolchain +version toolchain =========== =============== ``1.822.3`` ``intel/2016a`` =========== =============== @@ -29677,9 +30763,9 @@ This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH. *homepage*: http://mvapich.cse.ohio-state.edu/overview/mvapich2/ ========= ================== -version toolchain +version toolchain ========= ================== -``2.0.1`` ``GCC/4.8.4`` +``2.0.1`` ``GCC/4.8.4`` ``2.1`` ``GCC/4.9.3-2.25`` ``2.2b`` ``GCC/4.9.3-2.25`` ========= ================== @@ -29695,7 +30781,7 @@ Mini-XML is a tiny XML library that you can use to read and write XML and XML-l *homepage*: https://github.com/michaelrsweet/mxml ======= ================= -version toolchain +version toolchain ======= ================= ``3.2`` ``GCCcore/8.3.0`` ======= ================= @@ -29711,7 +30797,7 @@ Mxml is a pure C library (yet having an object oriented layout) that is meant to *homepage*: http://mxml.sourceforge.net ========= ============= -version toolchain +version toolchain ========= ============= ``0.9.2`` ``GCC/9.3.0`` ========= ============= @@ -29727,7 +30813,7 @@ Flexible and Efficient Library for Deep Learning *homepage*: http://mxnet.io/ ========= ========================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ========================== ============== ``0.9.3`` ``-Python-2.7.12-R-3.3.3`` ``foss/2016b`` ========= ========================== ============== @@ -29743,7 +30829,7 @@ MyCC is built and delivered as a tailored solution for metagenomics sequencescla *homepage*: https://sourceforge.net/projects/sb2nhri/files/MyCC/ ============== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================== =============== ``2017-03-01`` ``-Python-2.7.16`` ``intel/2019b`` ============== ================== =============== @@ -29759,7 +30845,7 @@ Python Client for MyGene.Info services. *homepage*: https://github.com/biothings/mygene.py ========= =============== -version toolchain +version toolchain ========= =============== ``3.1.0`` ``intel/2019a`` ========= =============== @@ -29775,7 +30861,7 @@ MyMediaLite is a lightweight, multi-purpose library of recommender system algori *homepage*: http://www.ismll.uni-hildesheim.de/mymedialite/ ======== =============== -version toolchain +version toolchain ======== =============== ``3.10`` ``intel/2016b`` ``3.11`` ``intel/2016b`` @@ -29793,12 +30879,12 @@ A mpi4py based random pair pingpong network stress test. *homepage*: https://github.com/hpcugent/mympingpong ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``0.7.0`` ``-Python-2.7.11`` ``intel/2016a`` -``0.7.1`` ``-Python-2.7.12`` ``intel/2016b`` -``0.8.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.8.0`` ``-Python-2.7.14`` ``intel/2018a`` +``0.7.0`` ``-Python-2.7.11`` ``intel/2016a`` +``0.7.1`` ``-Python-2.7.12`` ``intel/2016b`` +``0.8.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.8.0`` ``-Python-2.7.14`` ``intel/2018a`` ``0.8.0`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ========= ================== =============================== @@ -29813,7 +30899,7 @@ Myokit is an open-source Python-based toolkit that facilitates modeling and simu *homepage*: http://myokit.org ========== ================================== -version toolchain +version toolchain ========== ================================== ``1.32.0`` ``foss/2020b``, ``fosscuda/2020b`` ========== ================================== @@ -29829,7 +30915,7 @@ Optional static typing for Python *homepage*: http://www.mypy-lang.org/ ========= =============== -version toolchain +version toolchain ========= =============== ``0.4.5`` ``intel/2016b`` ========= =============== @@ -29845,10 +30931,10 @@ MySQL is one of the world's most widely used open-source relational database ma *homepage*: http://www.mysql.com/ ========== =============== ================== -version versionsuffix toolchain +version versionsuffix toolchain ========== =============== ================== ``5.6.26`` ``-clientonly`` ``GNU/4.9.3-2.25`` -``5.7.21`` ``-clientonly`` ``GCCcore/6.4.0`` +``5.7.21`` ``-clientonly`` ``GCCcore/6.4.0`` ========== =============== ================== @@ -29862,7 +30948,7 @@ MySQL database connector for Python *homepage*: https://github.com/farcepest/MySQLdb1 ========= ================================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================================== =============== ``1.2.5`` ``-Python-2.7.11`` ``intel/2016a`` ``1.2.5`` ``-Python-2.7.11-MariaDB-10.1.14`` ``intel/2016a`` @@ -29879,7 +30965,7 @@ Python interface to MySQL *homepage*: https://github.com/PyMySQL/mysqlclient-python ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== ``1.3.7`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ========= ================== =============================== @@ -29891,7 +30977,23 @@ version versionsuffix toolchain --- -:ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_namedlist_961` - :ref:`list_software_nano_428` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_NetPyNE_643` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_nghttp2_711` - :ref:`list_software_nghttp3_712` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_ngtcp2_590` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_num2words_945` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numdiff_745` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_NVSHMEM_542` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` +:ref:`list_software_n2v_278` - :ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_namedlist_961` - :ref:`list_software_nano_428` - :ref:`list_software_NanoComp_795` - :ref:`list_software_nanocompore_1185` - :ref:`list_software_NanoFilt_795` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanoget_748` - :ref:`list_software_NanoLyse_809` - :ref:`list_software_nanomath_854` - :ref:`list_software_nanomax-analysis-utils_2273` - :ref:`list_software_nanonet_755` - :ref:`list_software_NanoPlot_811` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NanopolishComp_1450` - :ref:`list_software_napari_635` - :ref:`list_software_NASM_303` - :ref:`list_software_nauty_561` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_NCCL-tests_896` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NECI_287` - :ref:`list_software_NEdit_468` - :ref:`list_software_Nek5000_483` - :ref:`list_software_Nektar++_699` - :ref:`list_software_neon_432` - :ref:`list_software_neptune-client_1451` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_NetPyNE_643` - :ref:`list_software_nettle_652` - :ref:`list_software_networkTools_1307` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_NewHybrids_1023` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_nf-core-mag_1036` - :ref:`list_software_NFFT_302` - :ref:`list_software_nghttp2_711` - :ref:`list_software_nghttp3_712` - :ref:`list_software_NGLess_556` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NGSpeciesID_1006` - :ref:`list_software_ngspice_745` - :ref:`list_software_ngtcp2_590` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_nifti2dicom_1112` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLMpy_464` - :ref:`list_software_nlohmann_json_1396` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_nnU-Net_645` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_Nsight-Compute_1399` - :ref:`list_software_Nsight-Systems_1426` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_nsync_555` - :ref:`list_software_ntCard_604` - :ref:`list_software_ntEdit_616` - :ref:`list_software_ntHits_634` - :ref:`list_software_NTL_238` - :ref:`list_software_NTPoly_582` - :ref:`list_software_num2words_945` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numdiff_745` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_NVHPC_383` - :ref:`list_software_nvofbf_641` - :ref:`list_software_nvompi_665` - :ref:`list_software_NVSHMEM_542` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` + + +.. _list_software_n2v_278: + +*n2v* ++++++ + +Noise2Void - Learning Denoising from Single Noisy Images The field of image denoising is currently dominated by discriminative deep learning methods that are trained on pairs of noisy input and clean target images. Recently it has been shown that such methods can also be trained without clean targets. Instead, independent pairs of noisy images can be used, in an approach known as NOISE2NOISE (N2N). Here, we introduce NOISE2VOID (N2V), a training scheme that takes this idea one step further. It does not require noisy image pairs, nor clean target images. Consequently, N2V allows us to train directly on the body of data to be denoised and can therefore be applied when other methods cannot. Especially interesting is the application to biomedical image data, where the acquisition of training targets, clean or noisy, is frequently not possible. We compare the performance of N2V to approaches that have either clean target images and/or noisy image pairs available. Intuitively, N2V cannot be expected to outperform methods that have more information available during training. Still, we observe that the denoising performance of NOISE2VOID drops in moderation and compares favorably to training-free denoising methods. + +*homepage*: https://github.com/juglab/n2v + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``0.3.2`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== .. _list_software_NAG_214: @@ -29904,9 +31006,9 @@ The worlds largest collection of robust, documented, tested and maintained numer *homepage*: http://www.nag.co.uk ======= ================================== -version toolchain +version toolchain ======= ================================== -``24`` ``PGI/17.4-GCC-6.4.0-2.28`` +``24`` ``PGI/17.4-GCC-6.4.0-2.28`` ``26`` ``GCCcore/6.4.0``, ``intel/2018a`` ======= ================================== @@ -29921,7 +31023,7 @@ The checking compiler for improved code portability and detailed error reporting *homepage*: http://www.nag.co.uk ========== ========== -version toolchain +version toolchain ========== ========== ``6.2.14`` ``system`` ========== ========== @@ -29937,15 +31039,16 @@ NAMD is a parallel molecular dynamics code designed for high-performance simulat *homepage*: https://www.ks.uiuc.edu/Research/namd/ ======== ================ ================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ======== ================ ================================================================ -``2.11`` ``-mpi`` ``intel/2016a`` -``2.12`` ``-CUDA-8.0.61`` ``foss/2016b`` +``2.11`` ``-mpi`` ``intel/2016a`` +``2.12`` ``-CUDA-8.0.61`` ``foss/2016b`` ``2.12`` ``-mpi`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``2.13`` ``fosscuda/2018b`` -``2.13`` ``-mpi`` ``foss/2018b``, ``foss/2019b``, ``intel/2018b`` -``2.14`` ``fosscuda/2019b`` -``2.14`` ``-mpi`` ``foss/2019b``, ``foss/2020a``, ``intel/2020a`` +``2.13`` ``fosscuda/2018b`` +``2.13`` ``-mpi`` ``foss/2018b``, ``foss/2019b``, ``intel/2018b`` +``2.14`` ``fosscuda/2019b`` +``2.14`` ``-CUDA-11.3.1`` ``foss/2021a`` +``2.14`` ``-mpi`` ``foss/2019b``, ``foss/2020a``, ``intel/2020a`` ======== ================ ================================================================ @@ -29959,7 +31062,7 @@ A Python object, similar to namedtuple, but for lists. *homepage*: https://gitlab.com/ericvsmith/namedlist ======= ================== -version toolchain +version toolchain ======= ================== ``1.8`` ``GCCcore/11.2.0`` ======= ================== @@ -29975,9 +31078,10 @@ a simple editor, inspired by Pico *homepage*: https://www.nano-editor.org/ ======= ================== -version toolchain +version toolchain ======= ================== ``6.4`` ``GCCcore/11.3.0`` +``7.0`` ``GCCcore/11.3.0`` ======= ================== @@ -29991,7 +31095,7 @@ Comparing runs of Oxford Nanopore sequencing data and alignments *homepage*: https://github.com/wdecoster/NanoComp ========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============== ``1.10.1`` ``-Python-3.7.4`` ``intel/2019b`` ``1.13.1`` ``intel/2020b`` @@ -30008,7 +31112,7 @@ Nanocompore identifies differences in ONT nanopore sequencing raw signal corresp *homepage*: https://nanocompore.rna.rocks/ ============== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================= =============== ``1.0.0rc3-2`` ``-Python-3.8.2`` ``intel/2020a`` ============== ================= =============== @@ -30019,14 +31123,15 @@ version versionsuffix toolchain *NanoFilt* ++++++++++ -Filtering and trimming of Oxford Nanopore Sequencing data +Filtering and trimming of long read sequencing data. *homepage*: https://github.com/wdecoster/nanofilt ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``2.6.0`` ``-Python-3.7.4`` ``intel/2019b`` +``2.8.0`` ``foss/2021b`` ========= ================= =============== @@ -30040,10 +31145,10 @@ Filtering and trimming of long read sequencing data. *homepage*: https://github.com/wdecoster/nanofilt ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== -``2.5.0`` ``-Python-3.6.6`` ``foss/2018b`` -``2.6.0`` ``-Python-3.7.4`` ``foss/2019b`` +``2.5.0`` ``-Python-3.6.6`` ``foss/2018b`` +``2.6.0`` ``-Python-3.7.4`` ``foss/2019b`` ``2.6.0`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================= =============== @@ -30058,13 +31163,30 @@ Functions to extract information from Oxford Nanopore sequencing data and alignm *homepage*: https://github.com/wdecoster/nanoget ========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============== ``1.12.1`` ``-Python-3.7.4`` ``intel/2019b`` ``1.15.0`` ``intel/2020b`` +``1.18.1`` ``foss/2021a`` ========== ================= =============== +.. _list_software_NanoLyse_809: + +*NanoLyse* +++++++++++ + +Remove reads mapping to the lambda phage genome from a fastq file. + +*homepage*: https://github.com/wdecoster/nanolyse + +========= ============== +version toolchain +========= ============== +``1.2.1`` ``foss/2021a`` +========= ============== + + .. _list_software_nanomath_854: *nanomath* @@ -30075,10 +31197,11 @@ A few simple math function for other Oxford Nanopore processing scripts *homepage*: https://github.com/wdecoster/nanomath ========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============== ``0.23.1`` ``-Python-3.7.4`` ``intel/2019b`` ``1.2.0`` ``intel/2020b`` +``1.2.1`` ``foss/2021a`` ========== ================= =============== @@ -30092,7 +31215,7 @@ A set of tools for handling and analysing data at the NanoMAX beamline. *homepage*: https://github.com/maxiv-science/nanomax-analysis-utils ========= ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================== ``0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``0.4.3`` ``foss/2020b``, ``fosscuda/2020b`` @@ -30109,7 +31232,7 @@ Nanonet provides recurrent neural network basecalling for Oxford Nanopore MinION *homepage*: https://github.com/nanoporetech/nanonet ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``2.0.0`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== @@ -30124,12 +31247,12 @@ Plotting suite for long read sequencing data and alignments *homepage*: https://github.com/wdecoster/NanoPlot -========== ================= =============== -version versionsuffix toolchain -========== ================= =============== +========== ================= =============================== +version versionsuffix toolchain +========== ================= =============================== ``1.28.4`` ``-Python-3.7.4`` ``intel/2019b`` -``1.33.0`` ``intel/2020b`` -========== ================= =============== +``1.33.0`` ``foss/2021a``, ``intel/2020b`` +========== ================= =============================== .. _list_software_nanopolish_1083: @@ -30142,13 +31265,13 @@ Software package for signal-level analysis of Oxford Nanopore sequencing data. *homepage*: https://github.com/jts/nanopolish ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== -``0.9.2`` ``intel/2018a`` +``0.9.2`` ``intel/2018a`` ``0.10.2`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``0.13.1`` ``-Python-3.6.6`` ``foss/2018b`` -``0.13.2`` ``-Python-3.8.2`` ``foss/2020a`` -``0.13.3`` ``foss/2020b`` +``0.13.1`` ``-Python-3.6.6`` ``foss/2018b`` +``0.13.2`` ``-Python-3.8.2`` ``foss/2020a`` +``0.13.3`` ``foss/2020b`` ========== ================== =============================== @@ -30162,12 +31285,28 @@ NanopolishComp is a Python3 package for downstream analyses of Nanopolish output *homepage*: https://adrienleger.com/NanopolishComp/ ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.6.11`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================= ============== +.. _list_software_napari_635: + +*napari* +++++++++ + +napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images. It's built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy). + +*homepage*: https://napari.org/ + +========== ============== +version toolchain +========== ============== +``0.4.15`` ``foss/2021b`` +========== ============== + + .. _list_software_NASM_303: *NASM* @@ -30177,17 +31316,17 @@ NASM: General-purpose x86 assembler *homepage*: https://www.nasm.us/ -=========== ==================================================================================== -version toolchain -=========== ==================================================================================== +=========== ================================================================================================== +version toolchain +=========== ================================================================================================== ``2.11.08`` ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a`` -``2.12.01`` ``foss/2016a``, ``intel/2016a`` -``2.12.02`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a``, ``system`` -``2.13.01`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``2.13.03`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.14.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.15.05`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -=========== ==================================================================================== +``2.12.01`` ``foss/2016a``, ``intel/2016a`` +``2.12.02`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a``, ``system`` +``2.13.01`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``2.13.03`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.14.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.15.05`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +=========== ================================================================================================== .. _list_software_nauty_561: @@ -30200,11 +31339,11 @@ nauty and Traces are programs for computing automorphism groups of graphs and di *homepage*: https://pallini.di.uniroma1.it/ ========== ==================== -version toolchain +version toolchain ========== ==================== ``2.6r12`` ``GCC/8.2.0-2.31.1`` ``2.7rc2`` ``GCC/8.2.0-2.31.1`` -``2.7rc5`` ``GCC/8.3.0`` +``2.7rc5`` ``GCC/8.3.0`` ========== ==================== @@ -30218,7 +31357,7 @@ The Natural Bond Orbital (NBO) program is a discovery tool for chemical insights *homepage*: http://nbo.chem.wisc.edu/ ======= =============== -version toolchain +version toolchain ======= =============== ``1.1`` ``intel/2016a`` ``7.0`` ``intel/2017b`` @@ -30235,7 +31374,7 @@ The NCBI Toolkit is a collection of utilities developed for the production and *homepage*: http://ncbi.github.io/cxx-toolkit/ ========== =============== -version toolchain +version toolchain ========== =============== ``18.0.0`` ``intel/2017a`` ========== =============== @@ -30251,17 +31390,18 @@ The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for us *homepage*: https://github.com/ncbi/ncbi-vdb =========== ================================================ -version toolchain +version toolchain =========== ================================================ -``2.5.8-1`` ``foss/2016b``, ``intel/2016a`` -``2.7.0`` ``foss/2016b`` +``2.5.8-1`` ``foss/2016b``, ``intel/2016a`` +``2.7.0`` ``foss/2016b`` ``2.8.2`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``2.9.1-1`` ``foss/2018a``, ``intel/2018a`` -``2.9.3`` ``foss/2018b`` -``2.10.4`` ``gompi/2019b`` -``2.10.7`` ``gompi/2020a`` -``2.10.9`` ``gompi/2020b`` -``2.11.2`` ``gompi/2021b`` +``2.9.1-1`` ``foss/2018a``, ``intel/2018a`` +``2.9.3`` ``foss/2018b`` +``2.10.4`` ``gompi/2019b`` +``2.10.7`` ``gompi/2020a`` +``2.10.9`` ``gompi/2020b``, ``gompi/2021a`` +``2.11.2`` ``gompi/2021b`` +``3.0.0`` ``gompi/2022a`` =========== ================================================ @@ -30275,20 +31415,21 @@ The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and mul *homepage*: https://developer.nvidia.com/nccl =========== =================== ============================== -version versionsuffix toolchain +version versionsuffix toolchain =========== =================== ============================== -``2.1.4`` ``-CUDA-9.0.176`` ``system`` -``2.2.13`` ``-CUDA-9.2.148.1`` ``system`` -``2.3.7`` ``fosscuda/2018b`` -``2.4.2`` ``gcccuda/2019a`` -``2.4.8`` ``gcccuda/2019b`` -``2.8.3`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0``, ``system`` +``2.1.4`` ``-CUDA-9.0.176`` ``system`` +``2.2.13`` ``-CUDA-9.2.148.1`` ``system`` +``2.3.7`` ``fosscuda/2018b`` +``2.4.2`` ``gcccuda/2019a`` +``2.4.8`` ``gcccuda/2019b`` +``2.8.3`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0``, ``system`` ``2.8.3`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0``, ``system`` -``2.9.9`` ``-CUDA-11.3.1`` ``system`` -``2.10.3`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` -``2.10.3`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` -``2.11.4`` ``gcccuda/2019b`` -``2.12.12`` ``-CUDA-11.7.0`` ``GCCcore/11.3.0`` +``2.9.9`` ``-CUDA-11.3.1`` ``system`` +``2.10.3`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` +``2.10.3`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` +``2.11.4`` ``gcccuda/2019b`` +``2.12.12`` ``-CUDA-11.7.0`` ``GCCcore/11.3.0`` +``2.16.2`` ``-CUDA-12.0.0`` ``GCCcore/12.2.0`` =========== =================== ============================== @@ -30301,11 +31442,12 @@ Tests check both the performance and the correctness of NCCL operations. *homepage*: https://github.com/NVIDIA/nccl-tests -========= ================ -version toolchain -========= ================ -``2.0.0`` ``gompic/2019b`` -========= ================ +========== ================ ================ +version versionsuffix toolchain +========== ================ ================ +``2.0.0`` ``gompic/2019b`` +``2.13.6`` ``-CUDA-11.7.0`` ``gompi/2022a`` +========== ================ ================ .. _list_software_ncdf4_463: @@ -30318,17 +31460,17 @@ ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files *homepage*: https://cran.r-project.org/web/packages/ncdf4 ========== ============= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= =============================== -``1.16`` ``-R-3.4.0`` ``intel/2017a`` -``1.16`` ``-R-3.4.3`` ``intel/2017b`` -``1.16`` ``-R-3.4.4`` ``intel/2018a`` +``1.16`` ``-R-3.4.0`` ``intel/2017a`` +``1.16`` ``-R-3.4.3`` ``intel/2017b`` +``1.16`` ``-R-3.4.4`` ``intel/2018a`` ``1.16.1`` ``-R-3.5.1`` ``foss/2018b``, ``intel/2018b`` -``1.16.1`` ``-R-3.6.0`` ``foss/2019a`` -``1.17`` ``foss/2019b`` -``1.17`` ``-R-4.0.0`` ``foss/2020a`` -``1.17`` ``-R-4.0.3`` ``foss/2020b`` -``1.17`` ``-R-4.1.0`` ``foss/2021a`` +``1.16.1`` ``-R-3.6.0`` ``foss/2019a`` +``1.17`` ``foss/2019b`` +``1.17`` ``-R-4.0.0`` ``foss/2020a`` +``1.17`` ``-R-4.0.3`` ``foss/2020b`` +``1.17`` ``-R-4.1.0`` ``foss/2021a`` ========== ============= =============================== @@ -30342,13 +31484,13 @@ Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find *homepage*: https://dev.yorhel.nl/ncdu ========== ============================== -version toolchain +version toolchain ========== ============================== -``1.13`` ``GCCcore/7.3.0`` -``1.14`` ``GCCcore/7.3.0`` -``1.15.1`` ``GCCcore/9.3.0`` +``1.13`` ``GCCcore/7.3.0`` +``1.14`` ``GCCcore/7.3.0`` +``1.15.1`` ``GCCcore/9.3.0`` ``1.16`` ``GCC/10.3.0``, ``GCC/11.2.0`` -``1.17`` ``GCC/11.3.0`` +``1.17`` ``GCC/11.3.0`` ========== ============================== @@ -30362,11 +31504,11 @@ NCIPLOT is a program for revealing non covalent interactions based on the reduc *homepage*: https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html ================ ======================= -version toolchain +version toolchain ================ ======================= ``4.0-20190718`` ``iccifort/2019.5.281`` ``4.0-20200106`` ``iccifort/2019.5.281`` -``4.0-20200624`` ``GCC/11.2.0`` +``4.0-20200624`` ``GCC/11.2.0`` ================ ======================= @@ -30380,10 +31522,10 @@ NCL is an interpreted language designed specifically for scientific data analysi *homepage*: https://www.ncl.ucar.edu ========= ================================================================================================================= -version toolchain +version toolchain ========= ================================================================================================================= -``6.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``6.5.0`` ``intel/2018a`` +``6.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` +``6.5.0`` ``intel/2018a`` ``6.6.2`` ``foss/2018b``, ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``intel/2018b``, ``intel/2019b``, ``intel/2020a`` ========= ================================================================================================================= @@ -30398,7 +31540,7 @@ The NEXUS Class Library is a C++ library for parsing NEXUS files. *homepage*: http://ncl.sourceforge.net/ ========== ==================== -version toolchain +version toolchain ========== ==================== ``2.1.18`` ``GCC/8.2.0-2.31.1`` ========== ==================== @@ -30414,20 +31556,22 @@ The NCO toolkit manipulates and analyzes data stored in netCDF-accessible format *homepage*: https://github.com/nco/nco ========= =============================== -version toolchain +version toolchain ========= =============================== -``4.6.0`` ``foss/2016a`` -``4.6.6`` ``intel/2017a`` -``4.7.0`` ``intel/2017b`` -``4.7.1`` ``intel/2017b`` -``4.7.4`` ``foss/2017b`` -``4.7.6`` ``intel/2018a`` +``4.6.0`` ``foss/2016a`` +``4.6.6`` ``intel/2017a`` +``4.7.0`` ``intel/2017b`` +``4.7.1`` ``intel/2017b`` +``4.7.4`` ``foss/2017b`` +``4.7.6`` ``intel/2018a`` ``4.7.9`` ``foss/2018b``, ``intel/2018b`` -``4.8.1`` ``foss/2019a`` -``4.9.3`` ``foss/2019b`` -``4.9.7`` ``foss/2020a``, ``foss/2020b`` -``5.0.1`` ``foss/2021a`` +``4.8.1`` ``foss/2019a`` +``4.9.3`` ``foss/2019b`` +``4.9.7`` ``foss/2020a``, ``foss/2020b`` +``5.0.1`` ``foss/2021a`` ``5.0.3`` ``foss/2021b``, ``intel/2021b`` +``5.1.0`` ``foss/2022a`` +``5.1.3`` ``foss/2021a`` ========= =============================== @@ -30441,7 +31585,7 @@ Compress is a fast, simple LZW file compressor. Compress does not have the high *homepage*: http://ncompress.sourceforge.net/ =========== ================= -version toolchain +version toolchain =========== ================= ``4.2.4.4`` ``GCCcore/6.4.0`` =========== ================= @@ -30457,13 +31601,13 @@ The Ncurses (new curses) library is a free software emulation of curses in Syst *homepage*: https://www.gnu.org/software/ncurses/ ======= ============================================================================================================================================================================================================================================================================================================================================================================= -version toolchain +version toolchain ======= ============================================================================================================================================================================================================================================================================================================================================================================= -``5.9`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25``, ``gimkl/2.11.5``, ``system`` +``5.9`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25``, ``gimkl/2.11.5``, ``system`` ``6.0`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``6.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` -``6.2`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``system`` -``6.3`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``system`` +``6.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` +``6.2`` ``FCC/4.5.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0``, ``system`` +``6.3`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``system`` ======= ============================================================================================================================================================================================================================================================================================================================================================================= @@ -30477,10 +31621,10 @@ Ncview is a visual browser for netCDF format files. Typically you would use ncv *homepage*: http://meteora.ucsd.edu/~pierce/ncview_home_page.html ========= ====================================================================================================================================================================================== -version toolchain +version toolchain ========= ====================================================================================================================================================================================== ``2.1.7`` ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``gompi/2019a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b``, ``iomkl/2018b`` -``2.1.8`` ``gompi/2020a``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a`` +``2.1.8`` ``gompi/2020a``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a`` ========= ====================================================================================================================================================================================== @@ -30494,7 +31638,7 @@ nd2reader is a pure-Python package that reads images produced by NIS Elements 4. *homepage*: https://www.lighthacking.nl/nd2reader/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``3.0.6`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== @@ -30510,12 +31654,28 @@ ne is a free (GPL'd) text editor based on the POSIX standard that runs (we hope) *homepage*: http://ne.di.unimi.it/ ========= =============== -version toolchain +version toolchain ========= =============== ``3.0.1`` ``gimkl/2017a`` ========= =============== +.. _list_software_NECI_287: + +*NECI* +++++++ + +Standalone NECI codebase designed for FCIQMC and other stochastic quantum chemistry methods. + +*homepage*: https://github.com/ghb24/NECI_STABLE + +============ ============== +version toolchain +============ ============== +``20220711`` ``foss/2022a`` +============ ============== + + .. _list_software_NEdit_468: *NEdit* @@ -30526,7 +31686,7 @@ NEdit is a multi-purpose text editor for the X Window System, which combines a *homepage*: http://www.nedit.org ======= ============== ========== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============== ========== ``5.5`` ``-Linux-x86`` ``system`` ======= ============== ========== @@ -30542,7 +31702,7 @@ a fast and scalable high-order solver for computational fluid dynamics *homepage*: https://nek5000.mcs.anl.gov/ ======== =============== -version toolchain +version toolchain ======== =============== ``17.0`` ``intel/2018a`` ======== =============== @@ -30558,7 +31718,7 @@ Nektar++ is a tensor product based finite element package designed to allow one *homepage*: https://www.nektar.info ========= ============== -version toolchain +version toolchain ========= ============== ``5.0.1`` ``foss/2020b`` ========= ============== @@ -30574,7 +31734,7 @@ neon is an HTTP/1.1 and WebDAV client library, with a C interface. *homepage*: https://github.com/notroj/neon ========== ================= -version toolchain +version toolchain ========== ================= ``0.31.2`` ``GCCcore/8.3.0`` ========== ================= @@ -30589,13 +31749,13 @@ Neptune is an experiment tracking hub that brings organization and collaboration *homepage*: https://docs.neptune.ai -=========== ================= ============== -version versionsuffix toolchain -=========== ================= ============== +=========== ================= ============================== +version versionsuffix toolchain +=========== ================= ============================== ``0.4.129`` ``-Python-3.8.2`` ``foss/2020a`` ``0.10.5`` ``foss/2020b`` -``0.16.2`` ``foss/2021a`` -=========== ================= ============== +``0.16.2`` ``foss/2021a``, ``foss/2022a`` +=========== ================= ============================== .. _list_software_Net-core_765: @@ -30608,7 +31768,7 @@ version versionsuffix toolchain *homepage*: https://dotnet.microsoft.com/ ========= ========== -version toolchain +version toolchain ========= ========== ``2.1.8`` ``system`` ``2.2.5`` ``system`` @@ -30626,24 +31786,24 @@ NetCDF (network Common Data Form) is a set of software libraries and machine-in *homepage*: https://www.unidata.ucar.edu/software/netcdf/ =========== ================ ========================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================ ========================================================================================================================== -``4.3.3.1`` ``foss/2016a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a`` -``4.4.0`` ``foss/2016a``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``4.4.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``4.3.3.1`` ``foss/2016a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a`` +``4.4.0`` ``foss/2016a``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` +``4.4.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``4.4.1.1`` ``foss/2016b``, ``foss/2017b``, ``fosscuda/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` -``4.4.1.1`` ``-HDF5-1.10.1`` ``foss/2017a``, ``intel/2017a`` -``4.4.1.1`` ``-HDF5-1.8.18`` ``intel/2017a`` -``4.4.1.1`` ``-HDF5-1.8.19`` ``foss/2017a``, ``foss/2017b``, ``intel/2017b`` -``4.5.0`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01`` -``4.6.0`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` -``4.6.1`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``4.6.2`` ``gompi/2019a``, ``iimpi/2019a`` -``4.7.1`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` -``4.7.4`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2020b`` -``4.8.0`` ``gompi/2021a``, ``iimpi/2021a`` -``4.8.1`` ``gompi/2021b``, ``iimpi/2021b`` -``4.9.0`` ``gompi/2022a`` +``4.4.1.1`` ``-HDF5-1.10.1`` ``foss/2017a``, ``intel/2017a`` +``4.4.1.1`` ``-HDF5-1.8.18`` ``intel/2017a`` +``4.4.1.1`` ``-HDF5-1.8.19`` ``foss/2017a``, ``foss/2017b``, ``intel/2017b`` +``4.5.0`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01`` +``4.6.0`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` +``4.6.1`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``4.6.2`` ``gompi/2019a``, ``iimpi/2019a`` +``4.7.1`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` +``4.7.4`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2020b`` +``4.8.0`` ``gompi/2021a``, ``iimpi/2021a`` +``4.8.1`` ``gompi/2021b``, ``iimpi/2021b`` +``4.9.0`` ``gompi/2022a``, ``iimpi/2022a`` =========== ================ ========================================================================================================================== @@ -30657,7 +31817,7 @@ NetCDF (network Common Data Form) is a set of software libraries and machine-i *homepage*: http://www.unidata.ucar.edu/software/netcdf/ ======= ============== -version toolchain +version toolchain ======= ============== ``4.2`` ``foss/2016a`` ======= ============== @@ -30672,14 +31832,14 @@ NetCDF (network Common Data Form) is a set of software libraries and machine-in *homepage*: https://www.unidata.ucar.edu/software/netcdf/ -========= ================ ========================================================================================================================================================================================= -version versionsuffix toolchain -========= ================ ========================================================================================================================================================================================= -``4.3.0`` ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``4.3.0`` ``-HDF5-1.8.18`` ``intel/2017a`` -``4.3.0`` ``-HDF5-1.8.19`` ``intel/2017b`` -``4.3.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b`` -========= ================ ========================================================================================================================================================================================= +========= ================ ========================================================================================================================================================================================================== +version versionsuffix toolchain +========= ================ ========================================================================================================================================================================================================== +``4.3.0`` ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` +``4.3.0`` ``-HDF5-1.8.18`` ``intel/2017a`` +``4.3.0`` ``-HDF5-1.8.19`` ``intel/2017b`` +``4.3.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b``, ``iimpi/2022a`` +========= ================ ========================================================================================================================================================================================================== .. _list_software_netCDF-Fortran_1309: @@ -30692,18 +31852,18 @@ NetCDF (network Common Data Form) is a set of software libraries and machine-in *homepage*: https://www.unidata.ucar.edu/software/netcdf/ ========= ================ ==================================================================================================================================================================================================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ==================================================================================================================================================================================================================================================================================================================================== -``4.4.1`` ``foss/2016b``, ``intel/2016b`` -``4.4.2`` ``intel/2016.02-GCC-4.9`` -``4.4.3`` ``foss/2016a``, ``intel/2016a`` +``4.4.1`` ``foss/2016b``, ``intel/2016b`` +``4.4.2`` ``intel/2016.02-GCC-4.9`` +``4.4.3`` ``foss/2016a``, ``intel/2016a`` ``4.4.4`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2018b`` -``4.4.4`` ``-HDF5-1.8.18`` ``intel/2017a`` -``4.4.4`` ``-HDF5-1.8.19`` ``foss/2017b``, ``intel/2017b`` -``4.4.5`` ``gompi/2019a``, ``iimpi/2019a`` -``4.5.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` -``4.5.3`` ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b`` -``4.6.0`` ``gompi/2022a`` +``4.4.4`` ``-HDF5-1.8.18`` ``intel/2017a`` +``4.4.4`` ``-HDF5-1.8.19`` ``foss/2017b``, ``intel/2017b`` +``4.4.5`` ``gompi/2019a``, ``iimpi/2019a`` +``4.5.2`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` +``4.5.3`` ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompic/2020b``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b`` +``4.6.0`` ``gompi/2022a``, ``iimpi/2022a`` ========= ================ ==================================================================================================================================================================================================================================================================================================================================== @@ -30717,24 +31877,24 @@ Python/numpy interface to netCDF. *homepage*: https://unidata.github.io/netcdf4-python/ =========== ============================= =================================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ============================= =================================================== -``1.2.9`` ``-Python-2.7.13`` ``intel/2017a`` -``1.3.1`` ``-Python-3.6.3`` ``intel/2017b`` -``1.3.1`` ``-Python-3.6.3-HDF5-1.8.19`` ``intel/2017b`` -``1.4.0`` ``-Python-3.6.2-HDF5-1.8.19`` ``foss/2017b`` -``1.4.0`` ``-Python-3.6.4`` ``intel/2018a`` -``1.4.1`` ``-Python-2.7.15`` ``intel/2018b`` -``1.4.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.4.2`` ``-Python-3.6.4`` ``foss/2018a`` -``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` -``1.5.2`` ``intel/2019a`` -``1.5.3`` ``-Python-2.7.16`` ``foss/2019b`` -``1.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.5.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.2.9`` ``-Python-2.7.13`` ``intel/2017a`` +``1.3.1`` ``-Python-3.6.3`` ``intel/2017b`` +``1.3.1`` ``-Python-3.6.3-HDF5-1.8.19`` ``intel/2017b`` +``1.4.0`` ``-Python-3.6.2-HDF5-1.8.19`` ``foss/2017b`` +``1.4.0`` ``-Python-3.6.4`` ``intel/2018a`` +``1.4.1`` ``-Python-2.7.15`` ``intel/2018b`` +``1.4.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.4.2`` ``-Python-3.6.4`` ``foss/2018a`` +``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` +``1.5.2`` ``intel/2019a`` +``1.5.3`` ``-Python-2.7.16`` ``foss/2019b`` +``1.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.5.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``1.5.5.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``1.5.7`` ``foss/2021a``, ``foss/2021b``, ``intel/2021b`` -``1.6.1`` ``foss/2022a`` +``1.5.7`` ``foss/2021a``, ``foss/2021b``, ``intel/2021b`` +``1.6.1`` ``foss/2022a``, ``intel/2022a`` =========== ============================= =================================================== @@ -30748,7 +31908,7 @@ The Portable Network Locality (netloc) software package provides network topolo *homepage*: http://www.open-mpi.org/software/netloc ======= ============= -version toolchain +version toolchain ======= ============= ``0.5`` ``GCC/4.8.3`` ======= ============= @@ -30764,7 +31924,7 @@ NetLogo is a multi-agent programmable modeling environment. It is used by tens o *homepage*: https://ccl.northwestern.edu/netlogo/ ========= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========== ``5.3.1`` ``-64`` ``system`` ``6.0.4`` ``-64`` ``system`` @@ -30782,7 +31942,7 @@ NetMHC 4.0 software predicts binding of peptides to a number of different HLA *homepage*: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHC ======== ========== -version toolchain +version toolchain ======== ========== ``4.0a`` ``system`` ======== ========== @@ -30798,7 +31958,7 @@ NetMHCIIpan 3.2 server predicts binding of peptides to MHC class II molecules. *homepage*: https://www.cbs.dtu.dk/services/NetMHCIIpan/ ======= ==================================== -version toolchain +version toolchain ======= ==================================== ``3.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ======= ==================================== @@ -30814,7 +31974,7 @@ The NetMHCpan software predicts binding of peptides to any known MHC molecule *homepage*: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCpan ======== ========== -version toolchain +version toolchain ======== ========== ``4.0a`` ``system`` ======== ========== @@ -30830,9 +31990,9 @@ NetPIPE is a protocol independent communication performance benchmark that visua *homepage*: https://netpipe.cs.ksu.edu/ ========= ================================ -version toolchain +version toolchain ========= ================================ -``5.1`` ``intel/2018a`` +``5.1`` ``intel/2018a`` ``5.1.4`` ``gompi/2020b``, ``iimpi/2020b`` ========= ================================ @@ -30847,7 +32007,7 @@ NetPyNE is an open-source Python package to facilitate the development, parallel *homepage*: http://www.netpyne.org =========== ============== -version toolchain +version toolchain =========== ============== ``1.0.2.1`` ``foss/2021b`` =========== ============== @@ -30863,18 +32023,18 @@ Nettle is a cryptographic library that is designed to fit easily in more or les *homepage*: https://www.lysator.liu.se/~nisse/nettle/ ========= =========================================================================================================================================== -version toolchain +version toolchain ========= =========================================================================================================================================== -``3.1.1`` ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` -``3.2`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` -``3.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017a`` +``3.1.1`` ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` +``3.2`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` +``3.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017a`` ``3.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018a`` -``3.4.1`` ``GCCcore/8.2.0`` -``3.5.1`` ``GCCcore/8.3.0`` -``3.6`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.7.2`` ``GCCcore/10.3.0`` -``3.7.3`` ``GCCcore/11.2.0`` -``3.8`` ``GCCcore/11.3.0`` +``3.4.1`` ``GCCcore/8.2.0`` +``3.5.1`` ``GCCcore/8.3.0`` +``3.6`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.7.2`` ``GCCcore/10.3.0`` +``3.7.3`` ``GCCcore/11.2.0`` +``3.8`` ``GCCcore/11.3.0`` ========= =========================================================================================================================================== @@ -30888,7 +32048,7 @@ Dynamical Network Analysis is a method of characterizing allosteric signalling t *homepage*: http://faculty.scs.illinois.edu/schulten/software/networkTools/ ======= ============= -version toolchain +version toolchain ======= ============= ``2`` ``GCC/9.3.0`` ======= ============= @@ -30904,26 +32064,26 @@ NetworkX is a Python package for the creation, manipulation, and study of the st *homepage*: https://pypi.python.org/pypi/networkx ========= ================== ======================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ======================================================================== -``1.1`` ``-Python-2.7.12`` ``intel/2016b`` -``1.11`` ``-Python-2.7.11`` ``foss/2016a`` -``1.11`` ``-Python-2.7.14`` ``intel/2017b`` -``1.11`` ``-Python-3.5.1`` ``foss/2016a`` -``2.0`` ``-Python-2.7.14`` ``intel/2017b`` -``2.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b`` -``2.2`` ``-Python-2.7.16`` ``foss/2019b`` -``2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``1.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.11`` ``-Python-2.7.11`` ``foss/2016a`` +``1.11`` ``-Python-2.7.14`` ``intel/2017b`` +``1.11`` ``-Python-3.5.1`` ``foss/2016a`` +``2.0`` ``-Python-2.7.14`` ``intel/2017b`` +``2.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b`` +``2.2`` ``-Python-2.7.16`` ``foss/2019b`` +``2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``2.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` -``2.4`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` +``2.4`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` ``2.5`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -``2.5.1`` ``foss/2021a`` -``2.6.2`` ``foss/2020b`` -``2.6.3`` ``foss/2021a``, ``foss/2021b``, ``intel/2021b`` -``2.8.4`` ``foss/2022a`` +``2.5.1`` ``foss/2021a`` +``2.6.2`` ``foss/2020b`` +``2.6.3`` ``foss/2021a``, ``foss/2021b``, ``intel/2021b`` +``2.8.4`` ``foss/2022a`` ========= ================== ======================================================================== @@ -30937,7 +32097,7 @@ NeuroKit is a Python module that provides high-level integrative functions with *homepage*: https://neurokit.readthedocs.io ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.2.7`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== @@ -30953,11 +32113,11 @@ Empirically-based simulations of neurons and networks of neurons. *homepage*: https://www.neuron.yale.edu/neuron ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``7.4`` ``intel/2016b`` ``7.6.5`` ``-Python-2.7.15`` ``intel/2018b`` -``7.8.2`` ``foss/2021b`` +``7.8.2`` ``foss/2021b`` ========= ================== =============== @@ -30971,7 +32131,7 @@ This implements a Gibbs sampler to estimate the posterior probability that genet *homepage*: https://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm#NewHybs ============= ============== -version toolchain +version toolchain ============= ============== ``1.1_Beta3`` ``GCC/10.2.0`` ============= ============== @@ -30984,10 +32144,10 @@ version toolchain Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data -*homepage*: https://www.nextflow.io +*homepage*: https://www.nextflow.io/ =========== ========== -version toolchain +version toolchain =========== ========== ``19.04.0`` ``system`` ``19.07.0`` ``system`` @@ -31000,6 +32160,7 @@ version toolchain ``21.10.6`` ``system`` ``22.04.0`` ``system`` ``22.10.0`` ``system`` +``22.10.1`` ``system`` =========== ========== @@ -31013,12 +32174,28 @@ NextGenMap is a flexible highly sensitive short read mapping tool that handles *homepage*: http://cibiv.github.io/NextGenMap/ ========= ============================== -version toolchain +version toolchain ========= ============================== ``0.5.5`` ``GCC/11.2.0``, ``foss/2016b`` ========= ============================== +.. _list_software_nf-core-mag_1036: + +*nf-core-mag* ++++++++++++++ + +The Nextflow pipeline 'mag' ported to EasyBuild/EESSI. + +*homepage*: https://nf-co.re/mag + +============ ============== +version toolchain +============ ============== +``20221110`` ``foss/2021a`` +============ ============== + + .. _list_software_NFFT_302: *NFFT* @@ -31029,12 +32206,12 @@ The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transf *homepage*: https://www-user.tu-chemnitz.de/~potts/nfft/ ========= ============================================== -version toolchain +version toolchain ========= ============================================== -``3.1.3`` ``foss/2020b``, ``fosscuda/2020b`` -``3.5.1`` ``foss/2018b``, ``foss/2019a`` +``3.1.3`` ``foss/2020b``, ``fosscuda/2020b`` +``3.5.1`` ``foss/2018b``, ``foss/2019a`` ``3.5.2`` ``foss/2020a``, ``foss/2021a``, ``foss/2021b`` -``3.5.3`` ``foss/2022a`` +``3.5.3`` ``foss/2022a`` ========= ============================================== @@ -31047,11 +32224,11 @@ This is an implementation of the Hypertext Transfer Protocol version 2 in C. Th *homepage*: https://github.com/nghttp2/nghttp2 -========== ============== -version toolchain -========== ============== -``1.48.0`` ``GCC/11.2.0`` -========== ============== +========== ============================== +version toolchain +========== ============================== +``1.48.0`` ``GCC/11.2.0``, ``GCC/11.3.0`` +========== ============================== .. _list_software_nghttp3_712: @@ -31063,11 +32240,11 @@ nghttp3 is an implementation of RFC 9114 HTTP/3 mapping over QUIC and RFC 9204 *homepage*: https://github.com/ngtcp2/nghttp3 -========= ================== -version toolchain -========= ================== -``0.6.0`` ``GCCcore/11.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``0.6.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ====================================== .. _list_software_NGLess_556: @@ -31080,7 +32257,7 @@ NGLess is a domain-specific language for NGS (next-generation sequencing data) p *homepage*: https://ngless.embl.de/ ========= =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= =================== ========== ``1.1.1`` ``-static-Linux64`` ``system`` ========= =================== ========== @@ -31096,10 +32273,11 @@ IPython widget to interactively view molecular structures and trajectories. *homepage*: https://github.com/arose/nglview ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``2.7.0`` ``-Python-3.7.2`` ``intel/2019a`` ``2.7.7`` ``-Python-3.8.2`` ``intel/2020a`` +``3.0.3`` ``foss/2021a`` ========= ================= =============== @@ -31113,19 +32291,19 @@ NGS is a new, domain-specific API for accessing reads, alignments and pileups pr *homepage*: https://github.com/ncbi/ngs ========== =================== ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== =================== ====================================== -``1.2.3`` ``foss/2016b``, ``intel/2016a`` -``1.2.5`` ``foss/2016b`` -``1.3.0`` ``GCCcore/6.4.0``, ``intel/2017a`` -``2.9.1`` ``-Java-1.8.0_162`` ``foss/2018a``, ``intel/2018a`` -``2.9.3`` ``-Java-1.8`` ``foss/2018b`` -``2.10.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` -``2.10.0`` ``-Java-11`` ``GCCcore/8.2.0`` -``2.10.4`` ``-Java-11`` ``GCCcore/8.3.0`` -``2.10.5`` ``GCCcore/9.3.0`` +``1.2.3`` ``foss/2016b``, ``intel/2016a`` +``1.2.5`` ``foss/2016b`` +``1.3.0`` ``GCCcore/6.4.0``, ``intel/2017a`` +``2.9.1`` ``-Java-1.8.0_162`` ``foss/2018a``, ``intel/2018a`` +``2.9.3`` ``-Java-1.8`` ``foss/2018b`` +``2.10.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` +``2.10.0`` ``-Java-11`` ``GCCcore/8.2.0`` +``2.10.4`` ``-Java-11`` ``GCCcore/8.3.0`` +``2.10.5`` ``GCCcore/9.3.0`` ``2.10.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.11.2`` ``GCCcore/11.2.0`` +``2.11.2`` ``GCCcore/11.2.0`` ========== =================== ====================================== @@ -31139,7 +32317,7 @@ NGS is a new, domain-specific API for accessing reads, alignments and pileups pr *homepage*: https://github.com/ncbi/ngs ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``1.2.3`` ``-Python-2.7.11`` ``intel/2016a`` ``2.9.3`` ``-Python-3.6.6`` ``intel/2018b`` @@ -31157,7 +32335,7 @@ NGSadmix is a tool for finding admixture proportions from NGS data, based on ge *homepage*: http://www.popgen.dk/software/index.php/NgsAdmix ======= ================== -version toolchain +version toolchain ======= ================== ``32`` ``GCC/7.3.0-2.30`` ======= ================== @@ -31173,7 +32351,7 @@ NGSpeciesID is a tool for clustering and consensus forming of targeted ONT reads *homepage*: https://github.com/ksahlin/NGSpeciesID =========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================= ============== ``0.1.1.1`` ``-Python-3.7.4`` ``foss/2019b`` ``0.1.2.1`` ``foss/2021b`` @@ -31190,7 +32368,7 @@ Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on t *homepage*: https://ngspice.sourceforge.net ======= ============== -version toolchain +version toolchain ======= ============== ``31`` ``foss/2019b`` ======= ============== @@ -31205,11 +32383,11 @@ version toolchain *homepage*: https://github.com/ngtcp2/ngtcp2 -========= ============== -version toolchain -========= ============== -``0.7.0`` ``GCC/11.2.0`` -========= ============== +========= ============================== +version toolchain +========= ============================== +``0.7.0`` ``GCC/11.2.0``, ``GCC/11.3.0`` +========= ============================== .. _list_software_NiBabel_653: @@ -31222,21 +32400,22 @@ NiBabel provides read/write access to some common medical and neuroimaging file *homepage*: https://nipy.github.io/nibabel ========= ================================= ================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================================= ================================================== -``2.0.2`` ``-Python-2.7.11`` ``intel/2016a`` -``2.0.2`` ``-Python-2.7.11-freetype-2.6.3`` ``intel/2016a`` -``2.1.0`` ``-Python-2.7.13`` ``intel/2017a`` -``2.2.1`` ``-Python-3.6.4`` ``intel/2018a`` -``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``2.3.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.3.0`` ``-Python-3.6.6`` ``foss/2018b`` -``2.4.0`` ``foss/2019a``, ``intel/2019a`` -``2.5.1`` ``-Python-3.6.6`` ``foss/2018b`` -``3.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``3.2.0`` ``-Python-3.8.2`` ``foss/2020a`` +``2.0.2`` ``-Python-2.7.11`` ``intel/2016a`` +``2.0.2`` ``-Python-2.7.11-freetype-2.6.3`` ``intel/2016a`` +``2.1.0`` ``-Python-2.7.13`` ``intel/2017a`` +``2.2.1`` ``-Python-3.6.4`` ``intel/2018a`` +``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``2.3.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``2.3.0`` ``-Python-3.6.6`` ``foss/2018b`` +``2.4.0`` ``foss/2019a``, ``intel/2019a`` +``2.5.1`` ``-Python-3.6.6`` ``foss/2018b`` +``3.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.2.0`` ``-Python-3.8.2`` ``foss/2020a`` ``3.2.1`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` -``3.2.2`` ``foss/2021b`` +``3.2.2`` ``foss/2021b`` +``4.0.2`` ``foss/2022a`` ========= ================================= ================================================== @@ -31250,7 +32429,7 @@ Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 *homepage*: http://niftilib.sourceforge.net/ ========= ================= -version toolchain +version toolchain ========= ================= ``2.0.0`` ``GCCcore/6.4.0`` ========= ================= @@ -31266,7 +32445,7 @@ Nifti2Dicom is a conversion tool that converts 3D NIfTI files (and other formats *homepage*: https://github.com/biolab-unige/nifti2dicom ========== ============== -version toolchain +version toolchain ========== ============== ``0.4.11`` ``foss/2019b`` ========== ============== @@ -31282,13 +32461,13 @@ Nilearn is a Python module for fast and easy statistical learning on NeuroImagin *homepage*: https://nilearn.github.io/ ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== ``0.5.2`` ``foss/2019a``, ``intel/2019a`` ``0.5.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``0.5.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``0.7.0`` ``-Python-3.8.2`` ``foss/2020a`` -``0.7.1`` ``foss/2020b`` +``0.7.0`` ``-Python-3.8.2`` ``foss/2020a`` +``0.7.1`` ``foss/2020b`` ========= ================== =============================== @@ -31302,11 +32481,11 @@ Nim is a systems and applications programming language. *homepage*: https://nim-lang.org/ ========== ================== -version toolchain +version toolchain ========== ================== -``0.18.0`` ``GCCcore/6.4.0`` -``0.19.2`` ``GCCcore/7.3.0`` -``1.0.0`` ``GCCcore/8.3.0`` +``0.18.0`` ``GCCcore/6.4.0`` +``0.19.2`` ``GCCcore/7.3.0`` +``1.0.0`` ``GCCcore/8.3.0`` ``1.4.6`` ``GCCcore/10.2.0`` ``1.4.8`` ``GCCcore/10.3.0`` ``1.6.6`` ``GCCcore/11.2.0`` @@ -31323,7 +32502,7 @@ NIMBLE is a system for building and sharing analysis methods for statistical mod *homepage*: https://r-nimble.org ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``0.7.0`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== @@ -31339,13 +32518,14 @@ Ninja is a small build system with a focus on speed. *homepage*: https://ninja-build.org/ ========== ==================================================================================== -version toolchain +version toolchain ========== ==================================================================================== ``1.8.2`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017b``, ``intel/2018a`` -``1.9.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` -``1.10.0`` ``GCCcore/9.3.0`` -``1.10.1`` ``GCCcore/10.2.0`` -``1.10.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.9.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` +``1.10.0`` ``GCCcore/9.3.0`` +``1.10.1`` ``GCCcore/10.2.0`` +``1.10.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.11.1`` ``GCCcore/12.2.0`` ========== ==================================================================================== @@ -31359,12 +32539,12 @@ Nipype is a Python project that provides a uniform interface to existing neuroim *homepage*: https://nipype.readthedocs.io ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``1.0.2`` ``-Python-3.6.4`` ``intel/2018a`` -``1.1.3`` ``-Python-3.6.6`` ``foss/2018b`` +``1.1.3`` ``-Python-3.6.6`` ``foss/2018b`` ``1.4.2`` ``-Python-3.7.4`` ``intel/2019b`` -``1.8.5`` ``foss/2021a`` +``1.8.5`` ``foss/2021a`` ========= ================= =============== @@ -31378,7 +32558,7 @@ NLMpy is a Python package for the creation of neutral landscape models that are *homepage*: https://pypi.org/project/nlmpy ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.1.5`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================= =============== @@ -31394,7 +32574,7 @@ JSON for Modern C++ *homepage*: https://github.com/nlohmann/json ========== ================== -version toolchain +version toolchain ========== ================== ``3.10.0`` ``GCCcore/10.3.0`` ``3.10.4`` ``GCCcore/11.2.0`` @@ -31412,13 +32592,13 @@ NLopt is a free/open-source library for nonlinear optimization, providing a com *homepage*: http://ab-initio.mit.edu/wiki/index.php/NLopt ========= =================================================================================================================================================================================================================================================== -version toolchain +version toolchain ========= =================================================================================================================================================================================================================================================== ``2.4.2`` ``GCC/5.4.0-2.26``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``iomkl/2018a`` -``2.6.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.6.2`` ``GCCcore/10.2.0`` -``2.7.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``2.7.1`` ``GCCcore/11.3.0`` +``2.6.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.6.2`` ``GCCcore/10.2.0`` +``2.7.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.7.1`` ``GCCcore/11.3.0`` ========= =================================================================================================================================================================================================================================================== @@ -31432,14 +32612,14 @@ NLTK is a leading platform for building Python programs to work with human langu *homepage*: https://www.nltk.org/ ========= ================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================================== -``3.2.2`` ``-Python-2.7.13`` ``intel/2017a`` -``3.2.4`` ``-Python-2.7.13`` ``intel/2017a`` -``3.5`` ``-Python-3.7.4`` ``foss/2019b`` +``3.2.2`` ``-Python-2.7.13`` ``intel/2017a`` +``3.2.4`` ``-Python-2.7.13`` ``intel/2017a`` +``3.5`` ``-Python-3.7.4`` ``foss/2019b`` ``3.5`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` -``3.6.7`` ``foss/2021a`` -``3.7`` ``foss/2021b`` +``3.6.7`` ``foss/2021a`` +``3.7`` ``foss/2021b`` ========= ================== ================================== @@ -31453,7 +32633,7 @@ nnU-Net is the first segmentation method that is designed to deal with the datas *homepage*: https://github.com/MIC-DKFZ/nnUNet ========= ============== -version toolchain +version toolchain ========= ============== ``1.7.0`` ``foss/2020b`` ========= ============== @@ -31469,7 +32649,7 @@ Node-RED is a programming tool for wiring together hardware devices, APIs and on *homepage*: http://nodered.org ========== ============== -version toolchain +version toolchain ========== ============== ``0.16.2`` ``foss/2017a`` ========== ============== @@ -31485,19 +32665,20 @@ Node.js is a platform built on Chrome's JavaScript runtime for easily building *homepage*: http://nodejs.org =========== ======================================================= -version toolchain +version toolchain =========== ======================================================= -``4.4.7`` ``foss/2016a`` -``6.10.3`` ``foss/2017a`` -``8.9.4`` ``foss/2017a`` -``10.15.1`` ``foss/2018b`` -``10.15.3`` ``GCCcore/8.2.0`` +``4.4.7`` ``foss/2016a`` +``6.10.3`` ``foss/2017a`` +``8.9.4`` ``foss/2017a`` +``10.15.1`` ``foss/2018b`` +``10.15.3`` ``GCCcore/8.2.0`` ``12.16.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``12.19.0`` ``GCCcore/10.2.0`` -``14.17.0`` ``GCCcore/10.3.0`` -``14.17.2`` ``GCCcore/10.3.0`` -``14.17.6`` ``GCCcore/11.2.0`` -``16.15.1`` ``GCCcore/11.3.0`` +``12.19.0`` ``GCCcore/10.2.0`` +``14.17.0`` ``GCCcore/10.3.0`` +``14.17.2`` ``GCCcore/10.3.0`` +``14.17.6`` ``GCCcore/11.2.0`` +``16.15.1`` ``GCCcore/11.3.0`` +``18.12.1`` ``GCCcore/12.2.0`` =========== ======================================================= @@ -31511,11 +32692,11 @@ Normaliz is a open source tool for computations in affine monoids, vector config *homepage*: https://www.normaliz.uni-osnabrueck.de/ ========= =============== -version toolchain +version toolchain ========= =============== ``3.6.3`` ``intel/2018b`` ``3.7.4`` ``gompi/2019a`` -``3.8.4`` ``GCC/8.3.0`` +``3.8.4`` ``GCC/8.3.0`` ========= =============== @@ -31529,10 +32710,10 @@ Parameterized testing with any Python test framework. *homepage*: hmat://github.com/wolever/nose-parameterized ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== -``0.5.0`` ``-Python-2.7.11`` ``foss/2016a`` -``0.5.0`` ``-Python-3.5.1`` ``foss/2016a`` +``0.5.0`` ``-Python-2.7.11`` ``foss/2016a`` +``0.5.0`` ``-Python-3.5.1`` ``foss/2016a`` ``0.5.0`` ``-Python-3.5.2`` ``intel/2016b`` ``0.6.0`` ``-Python-3.6.1`` ``intel/2017a`` ========= ================== =============== @@ -31548,9 +32729,9 @@ NovoCraft is a software bundle. NovoAlign: Market’s leading aligner with ful *homepage*: http://www.novocraft.com/ =========== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ============= ============== -``3.09.00`` ``system`` +``3.09.00`` ``system`` ``3.09.01`` ``-R-3.5.1`` ``foss/2018b`` =========== ============= ============== @@ -31565,7 +32746,7 @@ NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short cir *homepage*: https://github.com/ndierckx/NOVOPlasty ======= ================= -version toolchain +version toolchain ======= ================= ``3.7`` ``GCCcore/8.3.0`` ======= ================= @@ -31581,7 +32762,7 @@ npstat implements some population genetics tests and estimators that can be appl *homepage*: https://code.google.com/archive/p/npstat/ ======== =============================== -version toolchain +version toolchain ======== =============================== ``0.99`` ``foss/2016a``, ``intel/2016a`` ======== =============================== @@ -31597,7 +32778,7 @@ NRG Ljubljana is an efficient implementation of the numerical renormalization gr *homepage*: http://nrgljubljana.ijs.si/ ============ ============== -version toolchain +version toolchain ============ ============== ``2.4.3.23`` ``foss/2016b`` ============ ============== @@ -31613,7 +32794,7 @@ NVIDIA® Nsight™ Compute is an interactive kernel profiler for CUDA applicatio *homepage*: https://developer.nvidia.com/nsight-compute ============ ========== -version toolchain +version toolchain ============ ========== ``2020.3.0`` ``system`` ``2021.2.0`` ``system`` @@ -31630,7 +32811,7 @@ NVIDIA® Nsight™ Systems is a system-wide performance analysis tool designed t *homepage*: https://developer.nvidia.com/nsight-compute ============ ========== -version toolchain +version toolchain ============ ========== ``2020.5.1`` ``system`` ============ ========== @@ -31646,15 +32827,16 @@ Netscape Portable Runtime (NSPR) provides a platform-neutral API for system leve *homepage*: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR ======== ==================================== -version toolchain +version toolchain ======== ==================================== ``4.20`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``4.21`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``4.25`` ``GCCcore/9.3.0`` -``4.29`` ``GCCcore/10.2.0`` -``4.30`` ``GCCcore/10.3.0`` -``4.32`` ``GCCcore/11.2.0`` -``4.34`` ``GCCcore/11.3.0`` +``4.25`` ``GCCcore/9.3.0`` +``4.29`` ``GCCcore/10.2.0`` +``4.30`` ``GCCcore/10.3.0`` +``4.32`` ``GCCcore/11.2.0`` +``4.34`` ``GCCcore/11.3.0`` +``4.35`` ``GCCcore/12.2.0`` ======== ==================================== @@ -31668,16 +32850,17 @@ Network Security Services (NSS) is a set of libraries designed to support cross- *homepage*: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS ========== ==================================== -version toolchain +version toolchain ========== ==================================== ``3.39`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``3.42.1`` ``GCCcore/8.2.0`` -``3.45`` ``GCCcore/8.3.0`` -``3.51`` ``GCCcore/9.3.0`` -``3.57`` ``GCCcore/10.2.0`` -``3.65`` ``GCCcore/10.3.0`` -``3.69`` ``GCCcore/11.2.0`` -``3.79`` ``GCCcore/11.3.0`` +``3.42.1`` ``GCCcore/8.2.0`` +``3.45`` ``GCCcore/8.3.0`` +``3.51`` ``GCCcore/9.3.0`` +``3.57`` ``GCCcore/10.2.0`` +``3.65`` ``GCCcore/10.3.0`` +``3.69`` ``GCCcore/11.2.0`` +``3.79`` ``GCCcore/11.3.0`` +``3.85`` ``GCCcore/12.2.0`` ========== ==================================== @@ -31691,10 +32874,10 @@ nsync is a C library that exports various synchronization primitives, such as mu *homepage*: https://github.com/google/nsync ========== ================================================================================================ -version toolchain +version toolchain ========== ================================================================================================ ``1.24.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.25.0`` ``GCCcore/11.3.0`` +``1.25.0`` ``GCCcore/11.3.0`` ========== ================================================================================================ @@ -31708,7 +32891,7 @@ ntCard is a streaming algorithm for estimating the frequencies of k-mers in geno *homepage*: https://www.bcgsc.ca/resources/software/ntcard ========= ============================= -version toolchain +version toolchain ========= ============================= ``1.2.1`` ``GCC/11.2.0``, ``GCC/8.3.0`` ========= ============================= @@ -31724,7 +32907,7 @@ ntEdit is a fast and scalable genomics application for polishing genome assembly *homepage*: https://github.com/bcgsc/ntEdit ========= ====================================== -version toolchain +version toolchain ========= ====================================== ``1.3.1`` ``iccifort/2018.3.222-GCC-7.3.0-2.30`` ========= ====================================== @@ -31740,7 +32923,7 @@ ntHits is a method for identifying repeats in high-throughput DNA sequencing dat *homepage*: https://github.com/bcgsc/ntHits ========= ====================================== -version toolchain +version toolchain ========= ====================================== ``0.0.1`` ``iccifort/2018.3.222-GCC-7.3.0-2.30`` ========= ====================================== @@ -31756,7 +32939,7 @@ NTL is a high-performance, portable C++ library providing data structures and al *homepage*: https://shoup.net/ntl/ ========== ==================== -version toolchain +version toolchain ========== ==================== ``11.3.4`` ``GCC/8.2.0-2.31.1`` ========== ==================== @@ -31772,11 +32955,11 @@ is a massively parallel library for computing the functions of sparse, symmetric *homepage*: https://github.com/william-dawson/NTPoly ========= =============================== -version toolchain +version toolchain ========= =============================== ``2.5.1`` ``foss/2020b``, ``intel/2020b`` ``2.7.0`` ``foss/2021a``, ``intel/2021a`` -``2.7.1`` ``intel/2020b`` +``2.7.1`` ``intel/2020b`` ========= =============================== @@ -31790,7 +32973,7 @@ Modules to convert numbers to words. 42 --> forty-two *homepage*: https://github.com/savoirfairelinux/num2words ========== ================== -version toolchain +version toolchain ========== ================== ``0.5.10`` ``GCCcore/10.3.0`` ========== ================== @@ -31806,15 +32989,15 @@ The numactl program allows you to run your application program on specific cpu's *homepage*: http://oss.sgi.com/projects/libnuma/ ========== ============================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain +version toolchain ========== ============================================================================================================================================================================================================================================================================================================================================================================================================================================== -``2.0.9`` ``GCC/4.8.3`` -``2.0.10`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25`` +``2.0.9`` ``GCC/4.8.3`` +``2.0.10`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25`` ``2.0.11`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.3.0-2.26``, ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``GCC/6.2.0-2.27``, ``GCC/6.3.0-2.27``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` -``2.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2.0.13`` ``GCCcore/10.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -``2.0.14`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` -``2.0.16`` ``GCCcore/12.2.0`` +``2.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.0.13`` ``GCCcore/10.2.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` +``2.0.14`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.0.16`` ``GCCcore/12.2.0`` ========== ============================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -31828,25 +33011,25 @@ Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by *homepage*: https://numba.pydata.org/ ========== ================== =================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =================================================== -``0.24.0`` ``-Python-2.7.11`` ``intel/2016a`` -``0.24.0`` ``-Python-3.5.1`` ``intel/2016a`` -``0.26.0`` ``-Python-2.7.11`` ``intel/2016a`` -``0.32.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.37.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` -``0.37.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``0.39.0`` ``-Python-3.6.6`` ``foss/2018b`` -``0.43.1`` ``intel/2019a`` -``0.46.0`` ``foss/2019a`` -``0.47.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``0.50.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``0.50.1`` ``-Python-3.8.2`` ``foss/2020a`` +``0.24.0`` ``-Python-2.7.11`` ``intel/2016a`` +``0.24.0`` ``-Python-3.5.1`` ``intel/2016a`` +``0.26.0`` ``-Python-2.7.11`` ``intel/2016a`` +``0.32.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.37.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` +``0.37.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.39.0`` ``-Python-3.6.6`` ``foss/2018b`` +``0.43.1`` ``intel/2019a`` +``0.46.0`` ``foss/2019a`` +``0.47.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``0.50.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.50.1`` ``-Python-3.8.2`` ``foss/2020a`` ``0.52.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``0.52.0`` ``-Python-3.8.2`` ``foss/2020a`` -``0.53.1`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` -``0.54.1`` ``foss/2021b``, ``intel/2021b`` -``0.54.1`` ``-CUDA-11.4.1`` ``foss/2021b`` +``0.52.0`` ``-Python-3.8.2`` ``foss/2020a`` +``0.53.1`` ``foss/2020b``, ``foss/2021a``, ``fosscuda/2020b`` +``0.54.1`` ``foss/2021b``, ``intel/2021b`` +``0.54.1`` ``-CUDA-11.4.1`` ``foss/2021b`` ========== ================== =================================================== @@ -31860,7 +33043,7 @@ Numdiff (which I will also write numdiff) is a little program that can be used t *homepage*: https://www.nongnu.org/numdiff/ ========= ================== -version toolchain +version toolchain ========= ================== ``5.9.0`` ``GCCcore/10.2.0`` ========= ================== @@ -31876,24 +33059,24 @@ The numexpr package evaluates multiple-operator array expressions many times fas *homepage*: https://numexpr.readthedocs.io/en/latest/ ========= ================== =================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =================================================== -``2.5.2`` ``-Python-2.7.11`` ``intel/2016a`` -``2.6.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.6.1`` ``-Python-3.5.2`` ``intel/2016b`` -``2.6.4`` ``-Python-2.7.13`` ``foss/2017a`` -``2.6.4`` ``-Python-2.7.14`` ``intel/2018a`` -``2.6.4`` ``-Python-3.5.1`` ``foss/2016a`` -``2.6.4`` ``-Python-3.6.1`` ``intel/2017a`` -``2.6.4`` ``-Python-3.6.3`` ``intel/2017b`` -``2.6.4`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``2.6.5`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``2.5.2`` ``-Python-2.7.11`` ``intel/2016a`` +``2.6.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``2.6.1`` ``-Python-3.5.2`` ``intel/2016b`` +``2.6.4`` ``-Python-2.7.13`` ``foss/2017a`` +``2.6.4`` ``-Python-2.7.14`` ``intel/2018a`` +``2.6.4`` ``-Python-3.5.1`` ``foss/2016a`` +``2.6.4`` ``-Python-3.6.1`` ``intel/2017a`` +``2.6.4`` ``-Python-3.6.3`` ``intel/2017b`` +``2.6.4`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``2.6.5`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.6.5`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``2.7.0`` ``intel/2019a`` -``2.7.1`` ``-Python-2.7.16`` ``intel/2019b`` -``2.7.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``2.7.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``2.8.1`` ``foss/2021a``, ``intel/2021a`` +``2.7.0`` ``intel/2019a`` +``2.7.1`` ``-Python-2.7.16`` ``intel/2019b`` +``2.7.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.7.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``2.8.1`` ``foss/2021a``, ``intel/2021a`` ========= ================== =================================================== @@ -31907,15 +33090,15 @@ NumPy is the fundamental package for scientific computing with Python. It contai *homepage*: http://www.numpy.org ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== ``1.8.2`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``1.9.2`` ``-Python-2.7.12`` ``intel/2016b`` -``1.10.4`` ``-Python-2.7.11`` ``intel/2016a`` -``1.11.0`` ``-Python-2.7.11`` ``intel/2016a`` -``1.12.1`` ``-Python-3.5.2`` ``intel/2016b`` -``1.13.0`` ``-Python-2.7.13`` ``intel/2017a`` -``1.13.1`` ``-Python-3.6.1`` ``intel/2017a`` +``1.9.2`` ``-Python-2.7.12`` ``intel/2016b`` +``1.10.4`` ``-Python-2.7.11`` ``intel/2016a`` +``1.11.0`` ``-Python-2.7.11`` ``intel/2016a`` +``1.12.1`` ``-Python-3.5.2`` ``intel/2016b`` +``1.13.0`` ``-Python-2.7.13`` ``intel/2017a`` +``1.13.1`` ``-Python-3.6.1`` ``intel/2017a`` ========== ================== =============================== @@ -31928,19 +33111,52 @@ C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) *homepage*: https://developer.nvidia.com/hpc-sdk/ -========= ========== -version toolchain -========= ========== -``20.7`` ``system`` -``20.9`` ``system`` -``20.11`` ``system`` -``21.2`` ``system`` -``21.3`` ``system`` -``21.5`` ``system`` -``21.7`` ``system`` -``21.9`` ``system`` -``21.11`` ``system`` -========= ========== +========= ================ ========== +version versionsuffix toolchain +========= ================ ========== +``20.7`` ``system`` +``20.9`` ``system`` +``20.11`` ``system`` +``21.2`` ``system`` +``21.3`` ``system`` +``21.5`` ``system`` +``21.7`` ``system`` +``21.9`` ``system`` +``21.11`` ``system`` +``22.7`` ``-CUDA-11.7.0`` ``system`` +========= ================ ========== + + +.. _list_software_nvofbf_641: + +*nvofbf* +++++++++ + +NVHPC based toolchain, including OpenMPI for MPI support, OpenBLAS (via FlexiBLAS for BLAS and LAPACK support), FFTW and ScaLAPACK. + +*homepage*: (none) + +=========== ========== +version toolchain +=========== ========== +``2022.07`` ``system`` +=========== ========== + + +.. _list_software_nvompi_665: + +*nvompi* +++++++++ + +NVHPC based compiler toolchain, including OpenMPI for MPI support. + +*homepage*: (none) + +=========== ========== +version toolchain +=========== ========== +``2022.07`` ``system`` +=========== ========== .. _list_software_NVSHMEM_542: @@ -31953,9 +33169,11 @@ NVSHMEM is a parallel programming interface based on OpenSHMEM that provides ef *homepage*: https://developer.nvidia.com/nvshmem ========= ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =============== +``2.4.1`` ``-CUDA-11.4.1`` ``gompi/2021b`` ``2.5.0`` ``-CUDA-11.7.0`` ``gompi/2022a`` +``2.7.0`` ``-CUDA-11.7.0`` ``gompi/2022a`` ========= ================ =============== @@ -31969,13 +33187,13 @@ htop-like GPU usage monitor *homepage*: https://github.com/Syllo/nvtop ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``1.0.0`` ``fosscuda/2018b`` -``1.1.0`` ``fosscuda/2019b`` +``1.0.0`` ``fosscuda/2018b`` +``1.1.0`` ``fosscuda/2019b`` ``1.2.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``1.2.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.0.2`` ``GCCcore/11.3.0`` +``2.0.2`` ``GCCcore/11.3.0`` ========= ====================================== @@ -31989,14 +33207,14 @@ NWChem aims to provide its users with computational chemistry tools that are sca *homepage*: https://www.nwchem-sw.org ===================== ============================================== ================================ -version versionsuffix toolchain +version versionsuffix toolchain ===================== ============================================== ================================ -``6.6.revision27746`` ``-2015-10-20-Python-2.7.12`` ``iomkl/2017a`` -``6.6.revision27746`` ``-2015-10-20-patches-20170814-Python-2.7.13`` ``intel/2017a`` +``6.6.revision27746`` ``-2015-10-20-Python-2.7.12`` ``iomkl/2017a`` +``6.6.revision27746`` ``-2015-10-20-patches-20170814-Python-2.7.13`` ``intel/2017a`` ``6.8.revision47`` ``-2017-12-14-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` -``7.0.0`` ``-Python-3.7.4`` ``intel/2019b`` -``7.0.2`` ``intel/2021a`` -``7.0.2`` ``-Python-3.7.4`` ``intel/2019b`` +``7.0.0`` ``-Python-3.7.4`` ``intel/2019b`` +``7.0.2`` ``intel/2021a``, ``intel/2022a`` +``7.0.2`` ``-Python-3.7.4`` ``intel/2019b`` ===================== ============================================== ================================ @@ -32010,7 +33228,7 @@ NxTrim is a software to remove Nextera Mate Pair junction adapters and categoris *homepage*: https://github.com/sequencing/NxTrim ========= ============== -version toolchain +version toolchain ========= ============== ``0.4.3`` ``foss/2018a`` ========= ============== @@ -32022,7 +33240,7 @@ version toolchain --- -:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OGDF_288` - :ref:`list_software_olaFlow_724` - :ref:`list_software_OMA_221` - :ref:`list_software_onedrive_860` - :ref:`list_software_ONNX_323` - :ref:`list_software_ONNX-Runtime_1108` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_ont-remora_1028` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCensus-python_1746` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFace_769` - :ref:`list_software_OpenFAST_704` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenFold_791` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSceneGraph_1394` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_Optuna_631` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` +:ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OBITools3_798` - :ref:`list_software_OCaml_460` - :ref:`list_software_occt_425` - :ref:`list_software_oceanspy_866` - :ref:`list_software_OCNet_441` - :ref:`list_software_Octave_610` - :ref:`list_software_Octopus-vcf_1113` - :ref:`list_software_OGDF_288` - :ref:`list_software_olaFlow_724` - :ref:`list_software_olego_534` - :ref:`list_software_OMA_221` - :ref:`list_software_OmegaFold_878` - :ref:`list_software_onedrive_860` - :ref:`list_software_ONNX_323` - :ref:`list_software_ONNX-Runtime_1108` - :ref:`list_software_ont-fast5-api_1224` - :ref:`list_software_ont-remora_1028` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_Open-Data-Cube-Core_1691` - :ref:`list_software_OpenAI-Gym_886` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_openCARP_728` - :ref:`list_software_OpenCensus-python_1746` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFace_769` - :ref:`list_software_OpenFAST_704` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenFold_791` - :ref:`list_software_OpenForceField_1381` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMM-PLUMED_1056` - :ref:`list_software_OpenMMTools_1085` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenMS_562` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_OpenPIV_641` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSceneGraph_1394` - :ref:`list_software_OpenSees_802` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OpenStackClient_1511` - :ref:`list_software_OPERA_375` - :ref:`list_software_OPERA-MS_580` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_Optuna_631` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_ORFfinder_863` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_Osi_299` - :ref:`list_software_OSPRay_542` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_OVITO_401` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: @@ -32035,9 +33253,9 @@ Oases is a de novo transcriptome assembler designed to produce transcripts from *homepage*: http://www.ebi.ac.uk/~zerbino/oases/ ========== ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= =============== -``0.2.08`` ``foss/2016b`` +``0.2.08`` ``foss/2016b`` ``0.2.08`` ``-kmer_101`` ``intel/2017b`` ========== ============= =============== @@ -32052,7 +33270,7 @@ The OBITools programs aims to help you to manipulate various data and sequence f *homepage*: http://www.grenoble.prabi.fr/trac/OBITools ========== ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ============== ``1.2.9`` ``-Python-2.7.11`` ``foss/2016a`` ``1.2.13`` ``-Python-2.7.15`` ``foss/2019a`` @@ -32069,7 +33287,7 @@ A package for the management of analyses and data in DNA metabarcoding. *homepage*: https://metabarcoding.org/obitools3 =========== ================== -version toolchain +version toolchain =========== ================== ``3.0.1b8`` ``GCCcore/10.2.0`` =========== ================== @@ -32085,7 +33303,7 @@ OCaml is a general purpose industrial-strength programming language with an emp *homepage*: http://ocaml.org/ ========== ============== -version toolchain +version toolchain ========== ============== ``4.02.3`` ``foss/2016a`` ``4.07.1`` ``foss/2018b`` @@ -32102,13 +33320,29 @@ Open CASCADE Technology (OCCT) is an object-oriented C++ class library designed *homepage*: https://www.opencascade.com/ =========== ============== -version toolchain +version toolchain =========== ============== ``7.3.0p4`` ``foss/2019b`` ``7.5.0p1`` ``foss/2021a`` =========== ============== +.. _list_software_oceanspy_866: + +*oceanspy* +++++++++++ + +OceanSpy - A Python package to facilitate ocean model data analysis and visualization. + +*homepage*: https://github.com/hainegroup/oceanspy + +========= ============== +version toolchain +========= ============== +``0.2.0`` ``foss/2022a`` +========= ============== + + .. _list_software_OCNet_441: *OCNet* @@ -32119,7 +33353,7 @@ Generate and analyze Optimal Channel Networks (OCNs): oriented spanning trees re *homepage*: https://cran.r-project.org/web/packages/OCNet ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``0.2.0`` ``-R-3.6.0`` ``foss/2019a`` ========= ============= ============== @@ -32135,16 +33369,17 @@ GNU Octave is a high-level interpreted language, primarily intended for numerica *homepage*: https://www.gnu.org/software/octave/ ========= ============= ================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ================================================ -``4.0.0`` ``foss/2016a`` -``4.0.3`` ``intel/2016b`` +``4.0.0`` ``foss/2016a`` +``4.0.3`` ``intel/2016b`` ``4.2.1`` ``foss/2018a``, ``intel/2016b``, ``intel/2017a`` -``4.2.1`` ``-mt`` ``intel/2017a`` -``4.2.2`` ``foss/2018a`` -``4.4.1`` ``foss/2018b`` -``5.1.0`` ``foss/2019a``, ``foss/2019b`` -``6.2.0`` ``foss/2020b`` +``4.2.1`` ``-mt`` ``intel/2017a`` +``4.2.2`` ``foss/2018a`` +``4.4.1`` ``foss/2018b`` +``5.1.0`` ``foss/2019a``, ``foss/2019b`` +``6.2.0`` ``foss/2020b`` +``7.1.0`` ``foss/2021b`` ========= ============= ================================================ @@ -32158,7 +33393,7 @@ Octopus is a mapping-based variant caller that implements several calling models *homepage*: https://github.com/luntergroup/octopus ========= ============== -version toolchain +version toolchain ========= ============== ``0.7.1`` ``foss/2020b`` ``0.7.2`` ``foss/2020b`` @@ -32175,7 +33410,7 @@ OGDF is a self-contained C++ library for graph algorithms, in particular for (bu *homepage*: https://ogdf.uos.de/ ================== ============== -version toolchain +version toolchain ================== ============== ``dogwood-202202`` ``GCC/11.2.0`` ================== ============== @@ -32191,12 +33426,28 @@ olaFlow CFD Suite is a free and open source project committed to bringing the la *homepage*: https://olaflow.github.io/ ============ ============== -version toolchain +version toolchain ============ ============== ``20210820`` ``foss/2021b`` ============ ============== +.. _list_software_olego_534: + +*olego* ++++++++ + +OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seed-and-extend scheme, and does not rely on a separate external mapper. + +*homepage*: https://github.com/chaolinzhanglab/olego + +========= ============== +version toolchain +========= ============== +``1.1.9`` ``GCC/11.2.0`` +========= ============== + + .. _list_software_OMA_221: *OMA* @@ -32207,12 +33458,28 @@ The OMA ('Orthologous MAtrix') project is a method and database for the inferenc *homepage*: https://omabrowser.org/standalone/ ========= ========== -version toolchain +version toolchain ========= ========== ``2.1.1`` ``system`` ========= ========== +.. _list_software_OmegaFold_878: + +*OmegaFold* ++++++++++++ + +OmegaFold: High-resolution de novo Structure Prediction from Primary Sequence + +*homepage*: https://github.com/HeliXonProtein/OmegaFold + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``1.1.0`` ``-CUDA-11.7.0`` ``foss/2022a`` +========= ================ ============== + + .. _list_software_onedrive_860: *onedrive* @@ -32223,7 +33490,7 @@ A free Microsoft OneDrive Client which supports OneDrive Personal, OneDrive for *homepage*: https://abraunegg.github.io/ ========== ================== -version toolchain +version toolchain ========== ================== ``2.4.11`` ``GCCcore/10.2.0`` ``2.4.21`` ``GCCcore/11.3.0`` @@ -32240,7 +33507,7 @@ Open Neural Network Exchange (ONNX) is an open ecosystem that empowers AI develo *homepage*: https://onnx.ai/ ========== ============== -version toolchain +version toolchain ========== ============== ``1.11.0`` ``foss/2021a`` ========== ============== @@ -32256,7 +33523,7 @@ ONNX Runtime inference can enable faster customer experiences and lower costs, s *homepage*: https://onnxruntime.ai/ ========== ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================ ============== ``1.10.0`` ``foss/2021a`` ``1.10.0`` ``-CUDA-11.3.1`` ``foss/2021a`` @@ -32273,12 +33540,12 @@ ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 *homepage*: https://github.com/nanoporetech/ont_fast5_api ========= ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================== ``3.3.0`` ``foss/2020b``, ``fosscuda/2020b`` -``3.3.0`` ``-Python-3.7.4`` ``foss/2019b`` -``4.0.0`` ``foss/2021a`` -``4.0.2`` ``foss/2021a``, ``foss/2021b`` +``3.3.0`` ``-Python-3.7.4`` ``foss/2019b`` +``4.0.0`` ``foss/2021a`` +``4.0.2`` ``foss/2021a``, ``foss/2021b`` ========= ================= ================================== @@ -32292,7 +33559,7 @@ Methylation/modified base calling separated from basecalling. Remora primarily p *homepage*: https://github.com/nanoporetech/remora ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``0.1.2`` ``foss/2021a`` ``0.1.2`` ``-CUDA-11.3.1`` ``foss/2021a`` @@ -32311,7 +33578,7 @@ OOMPA is a suite of R packages for the analysis of gene expression (RNA), proteo *homepage*: https://r-forge.r-project.org/projects/oompa ========= ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= =============== ``3.1.2`` ``-R-3.3.1`` ``intel/2016b`` ========= ============= =============== @@ -32327,11 +33594,12 @@ OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-sour *homepage*: https://www.score-p.org ========= ======================================================= -version toolchain +version toolchain ========= ======================================================= -``2.0`` ``foss/2016a`` +``2.0`` ``foss/2016a`` ``2.0.5`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.0.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.0.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.0.7`` ``GCCcore/11.3.0`` ========= ======================================================= @@ -32345,7 +33613,7 @@ The Open Data Cube Core provides an integrated gridded data analysis environment *homepage*: https://github.com/opendatacube/datacube-core ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.8.3`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -32361,7 +33629,7 @@ A toolkit for developing and comparing reinforcement learning algorithms. *homepage*: https://gym.openai.com ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.17.1`` ``-Python-3.7.4`` ``foss/2019b`` ``0.21.0`` ``foss/2021b`` @@ -32378,17 +33646,17 @@ Open Babel is a chemical toolbox designed to speak the many languages of chemic *homepage*: https://openbabel.org ========= ================== ================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================================ -``2.3.2`` ``-Python-2.7.11`` ``foss/2016a`` -``2.4.1`` ``-Python-2.7.14`` ``intel/2017b`` -``2.4.1`` ``-Python-2.7.15`` ``intel/2018b`` -``2.4.1`` ``-Python-3.6.6`` ``intel/2018b`` -``2.4.1`` ``-Python-3.7.2`` ``intel/2019a`` -``3.0.0`` ``-Python-3.7.4`` ``gompi/2019b`` +``2.3.2`` ``-Python-2.7.11`` ``foss/2016a`` +``2.4.1`` ``-Python-2.7.14`` ``intel/2017b`` +``2.4.1`` ``-Python-2.7.15`` ``intel/2018b`` +``2.4.1`` ``-Python-3.6.6`` ``intel/2018b`` +``2.4.1`` ``-Python-3.7.2`` ``intel/2019a`` +``3.0.0`` ``-Python-3.7.4`` ``gompi/2019b`` ``3.1.1`` ``gompi/2021a``, ``gompi/2022a`` -``3.1.1`` ``-Python-3.7.4`` ``gompi/2019b`` -``3.1.1`` ``-Python-3.8.2`` ``iimpi/2020a`` +``3.1.1`` ``-Python-3.7.4`` ``gompi/2019b`` +``3.1.1`` ``-Python-3.8.2`` ``iimpi/2020a`` ========= ================== ================================ @@ -32402,32 +33670,33 @@ OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. *homepage*: https://xianyi.github.com/OpenBLAS/ ========== ================= ========================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ========================================================== -``0.2.9`` ``-LAPACK-3.5.0`` ``GCC/4.8.3`` -``0.2.12`` ``-LAPACK-3.5.0`` ``GCC/4.9.2`` -``0.2.13`` ``-LAPACK-3.5.0`` ``GCC/4.8.4``, ``GCC/4.9.2`` -``0.2.14`` ``-LAPACK-3.5.0`` ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25`` -``0.2.15`` ``-LAPACK-3.6.0`` ``GCC/4.9.3-2.25`` +``0.2.9`` ``-LAPACK-3.5.0`` ``GCC/4.8.3`` +``0.2.12`` ``-LAPACK-3.5.0`` ``GCC/4.9.2`` +``0.2.13`` ``-LAPACK-3.5.0`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``0.2.14`` ``-LAPACK-3.5.0`` ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25`` +``0.2.15`` ``-LAPACK-3.6.0`` ``GCC/4.9.3-2.25`` ``0.2.18`` ``-LAPACK-3.6.0`` ``GCC/4.9.4-2.25``, ``GCC/5.3.0-2.26``, ``GCC/5.4.0-2.26`` -``0.2.18`` ``-LAPACK-3.6.1`` ``GCC/5.4.0-2.26``, ``gompi/2016.07`` -``0.2.19`` ``-LAPACK-3.6.1`` ``gompi/2016.09`` -``0.2.19`` ``-LAPACK-3.7.0`` ``GCC/5.4.0-2.26``, ``GCC/6.3.0-2.27`` +``0.2.18`` ``-LAPACK-3.6.1`` ``GCC/5.4.0-2.26``, ``gompi/2016.07`` +``0.2.19`` ``-LAPACK-3.6.1`` ``gompi/2016.09`` +``0.2.19`` ``-LAPACK-3.7.0`` ``GCC/5.4.0-2.26``, ``GCC/6.3.0-2.27`` ``0.2.20`` ``GCC/5.4.0-2.26``, ``GCC/6.4.0-2.28``, ``GCC/7.2.0-2.29`` -``0.3.0`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30`` -``0.3.1`` ``GCC/7.3.0-2.30`` -``0.3.3`` ``GCC/8.2.0-2.31.1`` -``0.3.4`` ``GCC/8.2.0-2.31.1`` -``0.3.5`` ``GCC/8.2.0-2.31.1`` -``0.3.6`` ``GCC/8.3.0-2.32`` -``0.3.7`` ``GCC/8.3.0`` -``0.3.8`` ``GCC/9.2.0`` -``0.3.9`` ``GCC/9.3.0`` -``0.3.12`` ``GCC/10.2.0`` -``0.3.15`` ``GCC/10.3.0`` -``0.3.17`` ``GCC/10.3.0``, ``GCC/11.2.0`` -``0.3.18`` ``GCC/11.2.0`` -``0.3.20`` ``GCC/11.2.0``, ``GCC/11.3.0`` +``0.3.0`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30`` +``0.3.1`` ``GCC/7.3.0-2.30`` +``0.3.3`` ``GCC/8.2.0-2.31.1`` +``0.3.4`` ``GCC/8.2.0-2.31.1`` +``0.3.5`` ``GCC/8.2.0-2.31.1`` +``0.3.6`` ``GCC/8.3.0-2.32`` +``0.3.7`` ``GCC/8.3.0`` +``0.3.8`` ``GCC/9.2.0`` +``0.3.9`` ``GCC/9.3.0`` +``0.3.12`` ``GCC/10.2.0`` +``0.3.15`` ``GCC/10.3.0`` +``0.3.17`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``0.3.18`` ``GCC/11.2.0`` +``0.3.20`` ``GCC/11.2.0``, ``GCC/11.3.0``, ``NVHPC/22.7-CUDA-11.7.0`` +``0.3.21`` ``GCC/12.2.0`` ========== ================= ========================================================== @@ -32441,7 +33710,7 @@ openCARP is an open cardiac electrophysiology simulator for in-silico experiment *homepage*: https://opencarp.org ======= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= ============== ``3.2`` ``-Python-3.8.2`` ``foss/2020a`` ``6.0`` ``foss/2020b`` @@ -32459,7 +33728,7 @@ OpenCensus for Python. OpenCensus provides a framework to measure a server's res *homepage*: https://opencensus.io/ ========= ================== -version toolchain +version toolchain ========= ================== ``0.8.0`` ``GCCcore/11.2.0`` ========= ================== @@ -32475,7 +33744,7 @@ OpenCoarrays is an open-source software project that supports the coarray Fortra *homepage*: https://github.com/sourceryinstitute/opencoarrays ========= =============== -version toolchain +version toolchain ========= =============== ``1.9.0`` ``gompi/2017a`` ``2.2.0`` ``gompi/2018b`` @@ -32494,7 +33763,7 @@ OpenColorIO (OCIO) is a complete color management solution geared towards motion *homepage*: http://opencolorio.org/ ========= ============== -version toolchain +version toolchain ========= ============== ``1.1.0`` ``foss/2018b`` ========= ============== @@ -32510,31 +33779,32 @@ OpenCV (Open Source Computer Vision Library) is an open source computer vision *homepage*: https://opencv.org/ ========== ========================= ================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========== ========================= ================================================================ -``2.4.12`` ``intel/2016a`` +``2.4.12`` ``intel/2016a`` ``3.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``3.3.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``3.3.0`` ``-Python-3.6.1`` ``intel/2017a`` -``3.3.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``3.4.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``3.4.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``3.4.1`` ``-Python-3.6.4-contrib`` ``foss/2018a`` -``3.4.5`` ``-Python-2.7.15`` ``foss/2018b`` -``3.4.7`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a`` -``3.4.7`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` -``4.0.1`` ``-Python-2.7.15`` ``foss/2018b`` -``4.0.1`` ``-Python-3.6.6`` ``foss/2018b`` -``4.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``4.2.0`` ``-Python-3.8.2`` ``foss/2020a`` -``4.2.0`` ``-Python-3.8.2-contrib`` ``foss/2020a`` -``4.5.1`` ``-contrib`` ``foss/2020b``, ``fosscuda/2020b`` -``4.5.3`` ``-CUDA-11.3.1-contrib`` ``foss/2021a`` -``4.5.3`` ``-contrib`` ``foss/2021a`` -``4.5.5`` ``-CUDA-11.4.1-contrib`` ``foss/2021b`` -``4.5.5`` ``-contrib`` ``foss/2021b`` -``4.6.0`` ``-contrib`` ``foss/2022a`` +``3.3.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``3.3.0`` ``-Python-3.6.1`` ``intel/2017a`` +``3.3.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``3.4.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``3.4.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``3.4.1`` ``-Python-3.6.4-contrib`` ``foss/2018a`` +``3.4.5`` ``-Python-2.7.15`` ``foss/2018b`` +``3.4.7`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a`` +``3.4.7`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` +``4.0.1`` ``-Python-2.7.15`` ``foss/2018b`` +``4.0.1`` ``-Python-3.6.6`` ``foss/2018b`` +``4.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``4.2.0`` ``-Python-3.8.2`` ``foss/2020a`` +``4.2.0`` ``-Python-3.8.2-contrib`` ``foss/2020a`` +``4.5.1`` ``-contrib`` ``foss/2020b``, ``fosscuda/2020b`` +``4.5.3`` ``-CUDA-11.3.1-contrib`` ``foss/2021a`` +``4.5.3`` ``-contrib`` ``foss/2021a`` +``4.5.5`` ``-CUDA-11.4.1-contrib`` ``foss/2021b`` +``4.5.5`` ``-contrib`` ``foss/2021b`` +``4.6.0`` ``-CUDA-11.7.0-contrib`` ``foss/2022a`` +``4.6.0`` ``-contrib`` ``foss/2022a`` ========== ========================= ================================================================ @@ -32548,16 +33818,16 @@ OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial *homepage*: https://www.openexr.com/ ========= ================================ -version toolchain +version toolchain ========= ================================ ``2.2.0`` ``intel/2016b``, ``intel/2017a`` -``2.3.0`` ``foss/2018b``, ``intel/2018b`` -``2.4.0`` ``GCCcore/8.3.0`` -``2.4.1`` ``GCCcore/9.3.0`` -``2.5.5`` ``GCCcore/10.2.0`` -``3.0.1`` ``GCCcore/10.3.0`` -``3.1.1`` ``GCCcore/11.2.0`` -``3.1.5`` ``GCCcore/11.3.0`` +``2.3.0`` ``foss/2018b``, ``intel/2018b`` +``2.4.0`` ``GCCcore/8.3.0`` +``2.4.1`` ``GCCcore/9.3.0`` +``2.5.5`` ``GCCcore/10.2.0`` +``3.0.1`` ``GCCcore/10.3.0`` +``3.1.1`` ``GCCcore/11.2.0`` +``3.1.5`` ``GCCcore/11.3.0`` ========= ================================ @@ -32571,7 +33841,7 @@ OpenFace – a state-of-the art tool intended for facial landmark detection, hea *homepage*: https://github.com/TadasBaltrusaitis/OpenFace ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``2.2.0`` ``foss/2021a`` ``2.2.0`` ``-CUDA-11.3.1`` ``foss/2021a`` @@ -32588,7 +33858,7 @@ OpenFAST is a wind turbine simulation tool which builds on FAST v8. FAST.Farm ex *homepage*: http://openfast.readthedocs.io/ ========= ============== -version toolchain +version toolchain ========= ============== ``3.0.0`` ``foss/2021b`` ========= ============== @@ -32604,37 +33874,38 @@ OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive *homepage*: https://www.openfoam.com/ ================ ============= ================================================= -version versionsuffix toolchain +version versionsuffix toolchain ================ ============= ================================================= ``2.2.2`` ``intel/2016a``, ``intel/2017a``, ``intel/2018a`` -``2.2.x`` ``intel/2019a`` -``2.3.1`` ``intel/2017a``, ``intel/2019b`` -``2.4.0`` ``intel/2017a``, ``intel/2019a`` -``3.0.0`` ``foss/2016a`` -``3.0.1`` ``intel/2016b``, ``intel/2018a`` -``4.0`` ``foss/2016b``, ``intel/2016b`` -``4.1`` ``foss/2016b``, ``intel/2017a`` -``4.x-20170904`` ``intel/2016b`` -``5.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``5.0-20180108`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``6`` ``foss/2018b``, ``foss/2019b``, ``intel/2018a`` -``7`` ``foss/2019b`` -``7`` ``-20200508`` ``foss/2019b`` -``8`` ``foss/2020a``, ``foss/2020b`` -``8`` ``-20210316`` ``foss/2020b`` -``9`` ``foss/2021a`` -``v1606+`` ``foss/2018b`` -``v1612+`` ``foss/2018b`` -``v1712`` ``foss/2017b``, ``intel/2017b`` -``v1806`` ``foss/2018b`` -``v1812`` ``foss/2018b`` -``v1906`` ``foss/2019b`` -``v1912`` ``foss/2019b``, ``intel/2019b`` -``v2006`` ``foss/2020a``, ``intel/2020a`` -``v2012`` ``foss/2020a`` -``v2106`` ``foss/2021a`` -``v2112`` ``foss/2021b`` -``v2206`` ``foss/2022a`` +``2.2.x`` ``intel/2019a`` +``2.3.1`` ``intel/2017a``, ``intel/2019b`` +``2.4.0`` ``intel/2017a``, ``intel/2019a`` +``3.0.0`` ``foss/2016a`` +``3.0.1`` ``intel/2016b``, ``intel/2018a`` +``4.0`` ``foss/2016b``, ``intel/2016b`` +``4.1`` ``foss/2016b``, ``intel/2017a`` +``4.x-20170904`` ``intel/2016b`` +``5.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``5.0-20180108`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``6`` ``foss/2018b``, ``foss/2019b``, ``intel/2018a`` +``7`` ``foss/2019b`` +``7`` ``-20200508`` ``foss/2019b`` +``8`` ``foss/2020a``, ``foss/2020b`` +``8`` ``-20210316`` ``foss/2020b`` +``9`` ``foss/2021a``, ``intel/2021a`` +``10`` ``foss/2022a`` +``v1606+`` ``foss/2018b`` +``v1612+`` ``foss/2018b`` +``v1712`` ``foss/2017b``, ``intel/2017b`` +``v1806`` ``foss/2018b`` +``v1812`` ``foss/2018b`` +``v1906`` ``foss/2019b`` +``v1912`` ``foss/2019b``, ``intel/2019b`` +``v2006`` ``foss/2020a``, ``intel/2020a`` +``v2012`` ``foss/2020a`` +``v2106`` ``foss/2021a`` +``v2112`` ``foss/2021b`` +``v2206`` ``foss/2022a`` ================ ============= ================================================= @@ -32648,14 +33919,14 @@ OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive *homepage*: http://www.extend-project.de/ ================ ================== ================================= -version versionsuffix toolchain +version versionsuffix toolchain ================ ================== ================================= -``3.1`` ``gimkl/2.11.5`` +``3.1`` ``gimkl/2.11.5`` ``3.2`` ``gimkl/2.11.5``, ``intel/2016a`` -``4.0`` ``intel/2017a`` -``4.0`` ``-Python-2.7.16`` ``intel/2019b`` -``4.1-20191120`` ``-Python-2.7.16`` ``intel/2019b`` -``4.1-20200408`` ``-Python-2.7.16`` ``foss/2019b`` +``4.0`` ``intel/2017a`` +``4.0`` ``-Python-2.7.16`` ``intel/2019b`` +``4.1-20191120`` ``-Python-2.7.16`` ``intel/2019b`` +``4.1-20200408`` ``-Python-2.7.16`` ``foss/2019b`` ================ ================== ================================= @@ -32669,9 +33940,10 @@ A faithful PyTorch reproduction of DeepMind's AlphaFold 2 *homepage*: https://github.com/aqlaboratory/openfold ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``1.0.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``1.0.1`` ``-CUDA-11.3.1`` ``foss/2021a`` ========= ================ ============== @@ -32685,7 +33957,7 @@ Simulation and Parameter Estimation in Geophysics - A python package for simula *homepage*: https://github.com/openforcefield/openforcefield/releases ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.7.0`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================= =============== @@ -32701,13 +33973,14 @@ OpenImageIO is a library for reading and writing images, and a bunch of related *homepage*: https://openimageio.org/ ============ ================================ -version toolchain +version toolchain ============ ================================ -``1.6.17`` ``intel/2016b`` -``1.7.17`` ``intel/2017a`` -``1.8.16`` ``foss/2018b``, ``intel/2018b`` +``1.6.17`` ``intel/2016b`` +``1.7.17`` ``intel/2017a`` +``1.8.16`` ``foss/2018b``, ``intel/2018b`` ``2.0.12`` ``gompi/2019b``, ``iimpi/2019b`` ``2.1.12.0`` ``gompi/2020a``, ``iimpi/2020a`` +``2.3.17.0`` ``GCC/11.3.0`` ============ ================================ @@ -32721,13 +33994,13 @@ OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been d *homepage*: https://www.openjpeg.org/ ========= ============================================================================= -version toolchain +version toolchain ========= ============================================================================= -``2.1`` ``GCCcore/6.4.0`` -``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.1`` ``GCCcore/6.4.0`` +``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.4.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``2.5.0`` ``GCCcore/11.3.0`` +``2.5.0`` ``GCCcore/11.3.0`` ========= ============================================================================= @@ -32741,9 +34014,9 @@ Open Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of *homepage*: https://openkim.org/ ========= ================================================ -version toolchain +version toolchain ========= ================================================ -``1.9.2`` ``foss/2016b``, ``foss/2017b`` +``1.9.2`` ``foss/2016b``, ``foss/2017b`` ``1.9.7`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` ========= ================================================ @@ -32758,10 +34031,10 @@ Open Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of *homepage*: https://openkim.org/ ============ ==================================================================================== -version toolchain +version toolchain ============ ==================================================================================== ``20190725`` ``GCCcore/10.2.0``, ``foss/2019a``, ``foss/2019b``, ``intel/2019a``, ``intel/2019b`` -``20210128`` ``GCCcore/10.2.0`` +``20210128`` ``GCCcore/10.2.0`` ============ ==================================================================================== @@ -32775,17 +34048,17 @@ OpenMM is a toolkit for molecular simulation. *homepage*: https://openmm.org ========= =================== =================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =================== =================================================== -``7.1.1`` ``-Python-3.6.3`` ``intel/2017b`` -``7.4.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``7.4.2`` ``-Python-3.8.2`` ``intel/2020a`` +``7.1.1`` ``-Python-3.6.3`` ``intel/2017b`` +``7.4.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``7.4.2`` ``-Python-3.8.2`` ``intel/2020a`` ``7.5.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``7.5.0`` ``-Python-3.8.2`` ``fosscuda/2020a``, ``intel/2020a`` -``7.5.1`` ``foss/2020b``, ``fosscuda/2020b`` -``7.5.1`` ``-DeepMind-patch`` ``foss/2021a`` -``7.7.0`` ``foss/2021a``, ``foss/2022a`` -``7.7.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``7.5.0`` ``-Python-3.8.2`` ``fosscuda/2020a``, ``intel/2020a`` +``7.5.1`` ``foss/2020b``, ``fosscuda/2020b`` +``7.5.1`` ``-DeepMind-patch`` ``foss/2021a`` +``7.7.0`` ``foss/2021a``, ``foss/2022a`` +``7.7.0`` ``-CUDA-11.3.1`` ``foss/2021a`` ========= =================== =================================================== @@ -32799,7 +34072,7 @@ This project provides a connection between OpenMM and PLUMED. It allows you to b *homepage*: https://github.com/openmm/openmm-plumed/ ======= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= =============== ``1.0`` ``-Python-3.8.2`` ``intel/2020a`` ======= ================= =============== @@ -32815,7 +34088,7 @@ A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation *homepage*: https://github.com/choderalab/openmmtools ========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============== ``0.20.0`` ``-Python-3.8.2`` ``intel/2020a`` ========== ================= =============== @@ -32826,17 +34099,20 @@ version versionsuffix toolchain *OpenMolcas* ++++++++++++ -OpenMolcas is a quantum chemistry software package +OpenMolcas is a quantum chemistry software package. *homepage*: https://gitlab.com/Molcas/OpenMolcas ========= ====================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ====================== =============== ``18.09`` ``-Python-3.6.6`` ``intel/2018b`` ``20.10`` ``-Python-3.8.2`` ``intel/2020a`` ``20.10`` ``-Python-3.8.2-noGA`` ``intel/2020a`` ``21.06`` ``intel/2021a`` +``22.06`` ``intel/2022a`` +``22.10`` ``intel/2022a`` +``22.10`` ``-noGA`` ``intel/2022a`` ========= ====================== =============== @@ -32850,49 +34126,49 @@ The Open MPI Project is an open source MPI implementation. *homepage*: http://www.open-mpi.org/ ========== ================ ==================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================ ==================================================================================================================== -``1.6.5`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.3`` -``1.6.5`` ``-no-OFED`` ``GCC/4.8.1``, ``GCC/4.8.2`` -``1.7.3`` ``GCC/4.8.2`` -``1.8.1`` ``GCC/4.8.3`` -``1.8.3`` ``GCC/4.9.2`` -``1.8.4`` ``GCC/4.8.4``, ``GCC/4.9.2`` -``1.8.5`` ``GNU/4.9.2-2.25`` -``1.8.6`` ``GNU/4.9.3-2.25`` -``1.8.8`` ``GNU/4.9.3-2.25`` -``1.10.1`` ``GCC/4.9.3-2.25`` +``1.6.5`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.3`` +``1.6.5`` ``-no-OFED`` ``GCC/4.8.1``, ``GCC/4.8.2`` +``1.7.3`` ``GCC/4.8.2`` +``1.8.1`` ``GCC/4.8.3`` +``1.8.3`` ``GCC/4.9.2`` +``1.8.4`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``1.8.5`` ``GNU/4.9.2-2.25`` +``1.8.6`` ``GNU/4.9.3-2.25`` +``1.8.8`` ``GNU/4.9.3-2.25`` +``1.10.1`` ``GCC/4.9.3-2.25`` ``1.10.2`` ``GCC/4.9.3-2.25``, ``GCC/5.3.0-2.26``, ``GCC/6.1.0-2.27``, ``PGI/16.3-GCC-4.9.3-2.25``, ``PGI/16.4-GCC-5.3.0-2.26`` -``1.10.3`` ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` -``1.10.4`` ``PGI/16.7-GCC-5.4.0-2.26``, ``iccifort/2016.3.210-GCC-4.9.3-2.25`` -``2.0.0`` ``GCC/5.2.0`` -``2.0.1`` ``GCC/6.2.0-2.27``, ``iccifort/2017.1.132-GCC-5.4.0-2.26`` -``2.0.2`` ``GCC/6.3.0-2.27``, ``iccifort/2017.1.132-GCC-6.3.0-2.27`` -``2.0.2`` ``-opa`` ``GCC/6.3.0-2.27`` -``2.1.0`` ``GCC/6.3.0-2.28`` -``2.1.1`` ``GCC/6.4.0-2.28``, ``gcccuda/2017b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` -``2.1.2`` ``GCC/6.4.0-2.28``, ``gcccuda/2018a``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` -``2.1.3`` ``iccifort/2018.2.199-GCC-6.4.0-2.28`` -``3.0.0`` ``GCC/7.2.0-2.29`` -``3.1.0`` ``GCC/7.3.0-2.30`` -``3.1.1`` ``GCC/7.3.0-2.30``, ``gcccuda/2018b``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` -``3.1.2`` ``GCC/8.2.0-2.31.1`` -``3.1.3`` ``GCC/8.2.0-2.31.1``, ``gcccuda/2019a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``3.1.4`` ``GCC/8.3.0``, ``GCC/8.3.0-2.32``, ``gcccuda/2019b``, ``iccifort/2019.5.281`` -``4.0.0`` ``GCC/8.2.0-2.31.1`` -``4.0.0`` ``-hpcx`` ``GCC/8.2.0-2.31.1`` -``4.0.1`` ``GCC/8.3.0-2.32`` -``4.0.2`` ``GCC/9.2.0-2.32`` -``4.0.3`` ``GCC/9.3.0``, ``gcccuda/2020a``, ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` -``4.0.5`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` -``4.0.5`` ``-CUDA-11.2.1`` ``NVHPC/21.2`` -``4.0.6`` ``GCC/10.3.0`` -``4.0.7`` ``GCC/10.3.0`` -``4.1.0`` ``GCC/10.2.0`` -``4.1.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0`` -``4.1.2`` ``GCC/10.2.0``, ``GCC/11.2.0`` -``4.1.4`` ``GCC/11.3.0`` -``system`` ``GCC/system-2.29`` +``1.10.3`` ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` +``1.10.4`` ``PGI/16.7-GCC-5.4.0-2.26``, ``iccifort/2016.3.210-GCC-4.9.3-2.25`` +``2.0.0`` ``GCC/5.2.0`` +``2.0.1`` ``GCC/6.2.0-2.27``, ``iccifort/2017.1.132-GCC-5.4.0-2.26`` +``2.0.2`` ``GCC/6.3.0-2.27``, ``iccifort/2017.1.132-GCC-6.3.0-2.27`` +``2.0.2`` ``-opa`` ``GCC/6.3.0-2.27`` +``2.1.0`` ``GCC/6.3.0-2.28`` +``2.1.1`` ``GCC/6.4.0-2.28``, ``gcccuda/2017b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +``2.1.2`` ``GCC/6.4.0-2.28``, ``gcccuda/2018a``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` +``2.1.3`` ``iccifort/2018.2.199-GCC-6.4.0-2.28`` +``3.0.0`` ``GCC/7.2.0-2.29`` +``3.1.0`` ``GCC/7.3.0-2.30`` +``3.1.1`` ``GCC/7.3.0-2.30``, ``gcccuda/2018b``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` +``3.1.2`` ``GCC/8.2.0-2.31.1`` +``3.1.3`` ``GCC/8.2.0-2.31.1``, ``gcccuda/2019a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``3.1.4`` ``GCC/8.3.0``, ``GCC/8.3.0-2.32``, ``gcccuda/2019b``, ``iccifort/2019.5.281`` +``4.0.0`` ``GCC/8.2.0-2.31.1`` +``4.0.0`` ``-hpcx`` ``GCC/8.2.0-2.31.1`` +``4.0.1`` ``GCC/8.3.0-2.32`` +``4.0.2`` ``GCC/9.2.0-2.32`` +``4.0.3`` ``GCC/9.3.0``, ``gcccuda/2020a``, ``iccifort/2020.1.217``, ``iccifortcuda/2020a`` +``4.0.5`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` +``4.0.5`` ``-CUDA-11.2.1`` ``NVHPC/21.2`` +``4.0.6`` ``GCC/10.3.0`` +``4.0.7`` ``GCC/10.3.0`` +``4.1.0`` ``GCC/10.2.0`` +``4.1.1`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel-compilers/2021.2.0`` +``4.1.2`` ``GCC/10.2.0``, ``GCC/11.2.0`` +``4.1.4`` ``GCC/11.3.0``, ``GCC/12.2.0``, ``NVHPC/22.7-CUDA-11.7.0`` +``system`` ``GCC/system-2.29`` ========== ================ ==================================================================================================================== @@ -32906,7 +34182,7 @@ As part of the deNBI Center for integrative Bioinformatics, OpenMS offers an ope *homepage*: https://www.openms.de/ ========= ============== -version toolchain +version toolchain ========= ============== ``2.4.0`` ``foss/2018b`` ========= ============== @@ -32922,7 +34198,7 @@ The Apache OpenNLP library is a machine learning based toolkit for the processin *homepage*: https://opennlp.apache.org/ ========= ========== -version toolchain +version toolchain ========= ========== ``1.8.1`` ``system`` ========= ========== @@ -32938,7 +34214,7 @@ OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM *homepage*: http://code.google.com/p/openpgm/ =========== ================================================================================================================================================================================================================================================================================ -version toolchain +version toolchain =========== ================================================================================================================================================================================================================================================================================ ``5.2.122`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` =========== ================================================================================================================================================================================================================================================================================ @@ -32954,7 +34230,7 @@ OpenPIV is an open source Particle Image Velocimetry analysis software *homepage*: http://www.openpiv.net ========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============== ``0.21.8`` ``-Python-3.7.4`` ``intel/2019b`` ========== ================= =============== @@ -32969,15 +34245,16 @@ A Python library to read/write Excel 2010 xlsx/xlsm files *homepage*: https://openpyxl.readthedocs.io -========= ================== ====================================== -version versionsuffix toolchain -========= ================== ====================================== -``2.6.2`` ``GCCcore/8.2.0`` -``2.6.4`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` -``3.0.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``3.0.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``3.0.9`` ``GCCcore/11.2.0`` -========= ================== ====================================== +========== ================== ====================================== +version versionsuffix toolchain +========== ================== ====================================== +``2.6.2`` ``GCCcore/8.2.0`` +``2.6.4`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +``3.0.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``3.0.7`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``3.0.9`` ``GCCcore/11.2.0`` +``3.0.10`` ``GCCcore/11.3.0`` +========== ================== ====================================== .. _list_software_OpenRefine_1003: @@ -32990,7 +34267,7 @@ OpenRefine is a power tool that allows you to load data, understand it, clean it *homepage*: https://github.com/OpenRefine/OpenRefine ========= =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= =================== ========== ``2.7`` ``-Java-1.8.0_144`` ``system`` ``3.4.1`` ``-Java-11`` ``system`` @@ -33006,11 +34283,11 @@ The OpenSceneGraph is an open source high performance 3D graphics toolkit, used *homepage*: http://www.openscenegraph.org/ -========= ============================== -version toolchain -========= ============================== -``3.6.5`` ``foss/2021a``, ``foss/2021b`` -========= ============================== +========= ============================================== +version toolchain +========= ============================================== +``3.6.5`` ``foss/2021a``, ``foss/2021b``, ``foss/2022a`` +========= ============================================== .. _list_software_OpenSees_802: @@ -33023,7 +34300,7 @@ Open System for Earthquake Engineering Simulation *homepage*: https://opensees.berkeley.edu/index.php ========= ========================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ========================== =============== ``3.2.0`` ``-Python-3.8.2`` ``intel/2020a`` ``3.2.0`` ``-Python-3.8.2-parallel`` ``intel/2020a`` @@ -33039,12 +34316,12 @@ OpenSlide is a C library that provides a simple interface to read whole-slide im *homepage*: https://openslide.org/ -========= =============== ===================================== -version versionsuffix toolchain -========= =============== ===================================== +========= =============== ========================================================= +version versionsuffix toolchain +========= =============== ========================================================= ``3.4.1`` ``GCCcore/11.2.0``, ``GCCcore/8.2.0`` -``3.4.1`` ``-largefiles`` ``GCCcore/10.3.0``, ``GCCcore/8.2.0`` -========= =============== ===================================== +``3.4.1`` ``-largefiles`` ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0`` +========= =============== ========================================================= .. _list_software_openslide-python_1682: @@ -33057,10 +34334,11 @@ OpenSlide Python is a Python interface to the OpenSlide library. *homepage*: https://github.com/openslide/openslide-python ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``1.1.1`` ``GCCcore/8.2.0`` +``1.1.1`` ``GCCcore/8.2.0`` ``1.1.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.2.0`` ``GCCcore/11.3.0`` ========= ====================================== @@ -33074,25 +34352,25 @@ The OpenSSL Project is a collaborative effort to develop a robust, commercial-gr *homepage*: https://www.openssl.org/ ========== ===================================================================== -version toolchain +version toolchain ========== ===================================================================== -``1.0`` ``system`` -``1.0.1f`` ``GCC/4.8.2`` -``1.0.1k`` ``GCC/4.9.2`` -``1.0.1s`` ``foss/2016a``, ``intel/2016a`` -``1.0.2g`` ``GCCcore/4.9.3`` +``1.0`` ``system`` +``1.0.1f`` ``GCC/4.8.2`` +``1.0.1k`` ``GCC/4.9.2`` +``1.0.1s`` ``foss/2016a``, ``intel/2016a`` +``1.0.2g`` ``GCCcore/4.9.3`` ``1.0.2h`` ``foss/2016.04``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``1.1`` ``system`` -``1.1.0c`` ``GCC/5.4.0-2.26`` -``1.1.0e`` ``intel/2016b`` -``1.1.0h`` ``GCCcore/7.3.0`` -``1.1.1b`` ``GCCcore/8.2.0`` -``1.1.1d`` ``GCCcore/8.3.0`` -``1.1.1e`` ``GCCcore/9.3.0`` -``1.1.1h`` ``GCCcore/10.2.0`` -``1.1.1k`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.1.1n`` ``GCCcore/11.3.0`` -``1.1.1q`` ``GCCcore/10.3.0`` +``1.1`` ``system`` +``1.1.0c`` ``GCC/5.4.0-2.26`` +``1.1.0e`` ``intel/2016b`` +``1.1.0h`` ``GCCcore/7.3.0`` +``1.1.1b`` ``GCCcore/8.2.0`` +``1.1.1d`` ``GCCcore/8.3.0`` +``1.1.1e`` ``GCCcore/9.3.0`` +``1.1.1h`` ``GCCcore/10.2.0`` +``1.1.1k`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``1.1.1n`` ``GCCcore/11.3.0`` +``1.1.1q`` ``GCCcore/10.3.0`` ========== ===================================================================== @@ -33106,10 +34384,11 @@ OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the *homepage*: https://docs.openstack.org/python-openstackclient/latest/ ========= ================== -version toolchain +version toolchain ========= ================== ``5.5.0`` ``GCCcore/10.2.0`` ``5.8.0`` ``GCCcore/11.2.0`` +``6.0.0`` ``GCCcore/12.2.0`` ========= ================== @@ -33123,7 +34402,7 @@ An optimal genome scaffolding program *homepage*: https://sourceforge.net/projects/operasf ========= ================ =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =============================== ``2.0.6`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` ========= ================ =============================== @@ -33139,7 +34418,7 @@ OPERA-MS is a hybrid metagenomic assembler which combines the advantages of sho *homepage*: https://github.com/CSB5/OPERA-MS ================== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ================= ============== ``0.9.0-20200802`` ``-Python-3.8.2`` ``foss/2020a`` ================== ================= ============== @@ -33155,7 +34434,7 @@ OptiType is a novel HLA genotyping algorithm based on integer linear programming *homepage*: https://github.com/FRED-2/OptiType ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``1.3.2`` ``-Python-2.7.15`` ``foss/2018b`` ``1.3.2`` ``-Python-3.6.6`` ``foss/2018b`` @@ -33172,12 +34451,12 @@ OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple fram *homepage*: https://developer.nvidia.com/optix ========= ================== -version toolchain +version toolchain ========= ================== ``3.8.0`` ``GNU/4.9.3-2.25`` ``3.9.0`` ``GNU/4.9.3-2.25`` -``6.5.0`` ``system`` -``7.2.0`` ``system`` +``6.5.0`` ``system`` +``7.2.0`` ``system`` ========= ================== @@ -33191,7 +34470,7 @@ Optuna is an automatic hyperparameter optimization software framework, particula *homepage*: https://optuna.org/ ========== ============== -version toolchain +version toolchain ========== ============== ``2.9.1`` ``foss/2021a`` ``2.10.0`` ``foss/2021b`` @@ -33208,7 +34487,7 @@ Google Optimization Tools (a.k.a., OR-Tools) is an open-source, fast and portabl *homepage*: https://developers.google.com/optimization/ ======= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= ============== ``7.1`` ``-Python-3.7.2`` ``foss/2019a`` ======= ================= ============== @@ -33224,21 +34503,21 @@ ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum c *homepage*: https://orcaforum.kofo.mpg.de ====================== ================== ================================ -version versionsuffix toolchain +version versionsuffix toolchain ====================== ================== ================================ -``3_0_2-linux_x86-64`` ``-OpenMPI-1.8.1`` ``system`` -``4.0.0.2`` ``-OpenMPI-2.0.2`` ``system`` -``4.0.1`` ``-OpenMPI-2.0.2`` ``system`` -``4.1.0`` ``-OpenMPI-3.1.3`` ``system`` -``4.2.0`` ``gompi/2019b`` -``4.2.1`` ``gompi/2019b`` -``5.0.0`` ``gompi/2021a`` -``5.0.0`` ``-static`` ``gompi/2021a`` -``5.0.1`` ``gompi/2021a`` -``5.0.1`` ``-static`` ``gompi/2021a`` +``3_0_2-linux_x86-64`` ``-OpenMPI-1.8.1`` ``system`` +``4.0.0.2`` ``-OpenMPI-2.0.2`` ``system`` +``4.0.1`` ``-OpenMPI-2.0.2`` ``system`` +``4.1.0`` ``-OpenMPI-3.1.3`` ``system`` +``4.2.0`` ``gompi/2019b`` +``4.2.1`` ``gompi/2019b`` +``5.0.0`` ``gompi/2021a`` +``5.0.0`` ``-static`` ``gompi/2021a`` +``5.0.1`` ``gompi/2021a`` +``5.0.1`` ``-static`` ``gompi/2021a`` ``5.0.2`` ``gompi/2021a``, ``gompi/2021b`` ``5.0.2`` ``-static`` ``gompi/2021a``, ``gompi/2021b`` -``5.0.3`` ``gompi/2021b`` +``5.0.3`` ``gompi/2021b`` ====================== ================== ================================ @@ -33252,7 +34531,7 @@ ORF finder searches for open reading frames (ORFs) in the DNA sequence you ente *homepage*: https://www.ncbi.nlm.nih.gov/orffinder/ ========= ========== -version toolchain +version toolchain ========= ========== ``0.4.3`` ``system`` ========= ========== @@ -33268,9 +34547,9 @@ A simple and not slow open reading frame (ORF) caller. *homepage*: https://github.com/wwood/OrfM ========= ======================================== -version toolchain +version toolchain ========= ======================================== -``0.6.1`` ``foss/2016b`` +``0.6.1`` ``foss/2016b`` ``0.7.1`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ========= ======================================== @@ -33285,14 +34564,14 @@ OrthoFinder is a fast, accurate and comprehensive platform for comparative genom *homepage*: https://github.com/davidemms/OrthoFinder ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``2.2.7`` ``-Python-2.7.14`` ``intel/2018a`` ``2.3.3`` ``-Python-2.7.15`` ``intel/2018b`` -``2.3.8`` ``-Python-2.7.16`` ``foss/2019b`` +``2.3.8`` ``-Python-2.7.16`` ``foss/2019b`` ``2.3.11`` ``-Python-3.7.4`` ``intel/2019b`` -``2.5.2`` ``foss/2020b`` -``2.5.4`` ``foss/2020b`` +``2.5.2`` ``foss/2020b`` +``2.5.4`` ``foss/2020b`` ========== ================== =============== @@ -33306,7 +34585,7 @@ OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. *homepage*: http://orthomcl.org/ ========= ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =============== ``1.4`` ``-Perl-5.24.0`` ``intel/2016b`` ``2.0.9`` ``-Perl-5.24.0`` ``intel/2016b`` @@ -33323,11 +34602,11 @@ Osi (Open Solver Interface) provides an abstract base class to a generic linear *homepage*: https://github.com/coin-or/Osi =========== ================================== -version toolchain +version toolchain =========== ================================== -``0.108.5`` ``GCCcore/7.3.0``, ``foss/2018b`` +``0.108.5`` ``GCCcore/7.3.0``, ``foss/2018b`` ``0.108.6`` ``GCC/10.3.0``, ``GCCcore/10.2.0`` -``0.108.7`` ``GCC/11.2.0`` +``0.108.7`` ``GCC/11.2.0`` =========== ================================== @@ -33341,7 +34620,7 @@ Open, Scalable, and Portable Ray Tracing Engine *homepage*: https://www.ospray.org ========= ========== -version toolchain +version toolchain ========= ========== ``2.5.0`` ``system`` ========= ========== @@ -33357,19 +34636,21 @@ OSU Micro-Benchmarks *homepage*: https://mvapich.cse.ohio-state.edu/benchmarks/ ========= ================ ============================================================================================================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============================================================================================================================================================================================= -``5.3.2`` ``foss/2016a``, ``foss/2017a`` -``5.6.2`` ``gompi/2019a`` +``5.3.2`` ``foss/2016a``, ``foss/2017a`` +``5.6.2`` ``gompi/2019a`` ``5.6.3`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpic/2019b``, ``iimpic/2020a`` -``5.7`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b`` -``5.7.1`` ``ffmpi/4.5.0``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021a``, ``iompi/2021a`` -``5.7.1`` ``-CUDA-11.3.1`` ``gompi/2021a`` -``5.8`` ``iimpi/2021b`` -``5.9`` ``gompi/2022.05``, ``gompi/2022a`` -``5.9`` ``-CUDA-11.3.1`` ``gompi/2021a`` -``5.9`` ``-CUDA-11.4.1`` ``gompi/2021b`` -``5.9`` ``-CUDA-11.7.0`` ``gompi/2022a`` +``5.7`` ``gompi/2020b``, ``gompic/2020b``, ``iimpi/2020b`` +``5.7.1`` ``ffmpi/4.5.0``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2021a``, ``iompi/2021a`` +``5.7.1`` ``-CUDA-11.3.1`` ``gompi/2021a`` +``5.8`` ``iimpi/2021b`` +``5.9`` ``gompi/2022.05``, ``gompi/2022a`` +``5.9`` ``-CUDA-11.3.1`` ``gompi/2021a`` +``5.9`` ``-CUDA-11.4.1`` ``gompi/2021b`` +``5.9`` ``-CUDA-11.7.0`` ``gompi/2022a`` +``5.9`` ``-ROCm-4.5.0`` ``gompi/2021b`` +``6.2`` ``gompi/2022.10``, ``gompi/2022b`` ========= ================ ============================================================================================================================================================================================= @@ -33382,14 +34663,31 @@ The Open Trace Format 2 is a highly scalable, memory efficient event trace data *homepage*: https://www.score-p.org -======= ======================================================= -version toolchain -======= ======================================================= -``2.0`` ``foss/2016a``, ``foss/2017a`` -``2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``3.0`` ``GCCcore/11.3.0`` -======= ======================================================= +========= ======================================================= +version toolchain +========= ======================================================= +``2.0`` ``foss/2016a``, ``foss/2017a`` +``2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``3.0`` ``GCCcore/11.3.0`` +``3.0.2`` ``GCCcore/11.3.0`` +========= ======================================================= + + +.. _list_software_OVITO_401: + +*OVITO* ++++++++ + +OVITO is a scientific visualization and data analysis solution for atomistic and other particle-based models. It helps scientists gain meaningful and quick insights from numerical simulation results. + +*homepage*: https://www.ovito.org + +========== ============= =============== +version versionsuffix toolchain +========== ============= =============== +``3.7.11`` ``-basic`` ``gompi/2022a`` +========== ============= =============== .. _list_software_ownCloud_843: @@ -33402,9 +34700,9 @@ The ownCloud Desktop Client is a tool to synchronize files from ownCloud Server *homepage*: https://github.com/owncloud/client ========= ================= -version toolchain +version toolchain ========= ================= -``2.4.3`` ``foss/2018b`` +``2.4.3`` ``foss/2018b`` ``2.5.4`` ``GCCcore/8.2.0`` ========= ================= @@ -33419,7 +34717,7 @@ A command line tool for quantification of perfusion from ASL data *homepage*: https://github.com/ibme-qubic/oxford_asl ========= ========================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ========================== =============== ``3.9.6`` ``-centos7-Python-2.7.13`` ``intel/2017a`` ========= ========================== =============== @@ -33431,7 +34729,7 @@ version versionsuffix toolchain --- -:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_pairsnp_765` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_paladin_729` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_panito_651` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parameterized_1389` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patch_528` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pfind_529` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_Phantompeakqualtools_2140` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_porefoam_857` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_presto_669` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_purge_dups_1086` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyEVTK_515` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_PyFrag_585` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGenomeTracks_1452` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyMOL_433` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_pyradiomics_1188` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-irodsclient_1903` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch-Lightning_1690` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` +:ref:`list_software_p11-kit_583` - :ref:`list_software_p4-phylogenetics_1615` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_pagmo_532` - :ref:`list_software_pairsnp_765` - :ref:`list_software_PAL2NAL_490` - :ref:`list_software_paladin_729` - :ref:`list_software_PAML_298` - :ref:`list_software_panaroo_752` - :ref:`list_software_pandapower_1073` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Panedr_602` - :ref:`list_software_Pango_501` - :ref:`list_software_pangolin_856` - :ref:`list_software_panito_651` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parameterized_1389` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_Parcels_714` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_PartitionFinder_1554` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patch_528` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_PAUP_310` - :ref:`list_software_pauvre_659` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_PennCNV_632` - :ref:`list_software_PEPT_313` - :ref:`list_software_Percolator_1051` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PEST++_402` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pfind_529` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHANOTATE_676` - :ref:`list_software_Phantompeakqualtools_2140` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phonemizer_1089` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_photontorch_1208` - :ref:`list_software_phototonic_1095` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyloPhlAn_991` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_Pingouin_841` - :ref:`list_software_Pint_411` - :ref:`list_software_pip_329` - :ref:`list_software_PIPITS_473` - :ref:`list_software_pIRS_350` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconf_744` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_plantcv_760` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PlasmaPy_807` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_plinkQC_690` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly-orca_1142` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_pmx_341` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_poetry_675` - :ref:`list_software_polars_657` - :ref:`list_software_polymake_866` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popscle_758` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_porefoam_857` - :ref:`list_software_poretools_999` - :ref:`list_software_Portcullis_1073` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPanGGOLiN_847` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preCICE_603` - :ref:`list_software_PREQUAL_538` - :ref:`list_software_preseq_656` - :ref:`list_software_presto_669` - :ref:`list_software_pretty-yaml_1160` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_ProFit_596` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_ProtHint_824` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_protozero_1012` - :ref:`list_software_PRSice_550` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_PsiCLASS_674` - :ref:`list_software_PSIPRED_535` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pugixml_774` - :ref:`list_software_pullseq_774` - :ref:`list_software_PuLP_353` - :ref:`list_software_purge_dups_1086` - :ref:`list_software_py_233` - :ref:`list_software_py-aiger_798` - :ref:`list_software_py-aiger-bdd_1141` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_pyABC_431` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_PyBerny_713` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCalib_676` - :ref:`list_software_pyccel_640` - :ref:`list_software_PyCharm_692` - :ref:`list_software_PyCheMPS2_763` - :ref:`list_software_PyCifRW_644` - :ref:`list_software_PyClone_698` - :ref:`list_software_pycma_538` - :ref:`list_software_pycocotools_1214` - :ref:`list_software_pycodestyle_1205` - :ref:`list_software_PyCogent_809` - :ref:`list_software_pycoQC_591` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PycURL_543` - :ref:`list_software_PyDamage_776` - :ref:`list_software_pydantic_860` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pydot_560` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyEVTK_515` - :ref:`list_software_pyFAI_441` - :ref:`list_software_pyfaidx_757` - :ref:`list_software_pyfasta_760` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFoam_588` - :ref:`list_software_PyFR_353` - :ref:`list_software_PyFrag_585` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGenomeTracks_1452` - :ref:`list_software_PyGEOS_503` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_pygmo_556` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygraphviz_1108` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_PyImageJ_758` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_pylift_664` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_PyMC3_396` - :ref:`list_software_pymca_538` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyMOL_433` - :ref:`list_software_PyNAST_511` - :ref:`list_software_pyobjcryst_1113` - :ref:`list_software_PyOD_348` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenCL_746` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyparsing_989` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_PYPOWER_566` - :ref:`list_software_pyproj_676` - :ref:`list_software_PyPSA_429` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_pyradiomics_1188` - :ref:`list_software_PyRe_384` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_pyro-api_817` - :ref:`list_software_pyro-ppl_835` - :ref:`list_software_Pyro4_478` - :ref:`list_software_PyRosetta_939` - :ref:`list_software_Pysam_522` - :ref:`list_software_pysamstats_1113` - :ref:`list_software_PySAT_433` - :ref:`list_software_pyScaf_614` - :ref:`list_software_pySCENIC_670` - :ref:`list_software_PySCF_421` - :ref:`list_software_pysheds_768` - :ref:`list_software_pyshp_564` - :ref:`list_software_PySide2_640` - :ref:`list_software_pysndfx_780` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pyspoa_668` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pysteps_792` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_pytest-benchmark_1665` - :ref:`list_software_pytest-xdist_1282` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-docx_1149` - :ref:`list_software_python-hl7_986` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-irodsclient_1903` - :ref:`list_software_python-isal_1144` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-libsbml_1460` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_python-telegram-bot_1938` - :ref:`list_software_python-weka-wrapper3_2008` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyTorch-Geometric_1685` - :ref:`list_software_PyTorch-Lightning_1690` - :ref:`list_software_PyTorch3D_832` - :ref:`list_software_PyVCF_424` - :ref:`list_software_pyWannier90_1062` - :ref:`list_software_PyWavelets_1044` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: @@ -33444,11 +34742,11 @@ Provides a way to load and enumerate PKCS#11 modules. Provides a standard confi *homepage*: https://p11-glue.freedesktop.org/p11-kit.html ========== ====================================================================== -version toolchain +version toolchain ========== ====================================================================== ``0.23.2`` ``GCCcore/5.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` -``0.24.0`` ``GCCcore/10.3.0`` -``0.24.1`` ``GCCcore/11.2.0`` +``0.24.0`` ``GCCcore/10.3.0`` +``0.24.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ====================================================================== @@ -33462,7 +34760,7 @@ A Python phyloinformatic toolkit, and an implementation of tree-heterogeneous mo *homepage*: http://p4.nhm.ac.uk/ ================ ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ================ ================= ============== ``1.4-20210322`` ``-Python-3.7.4`` ``foss/2019b`` ================ ================= ============== @@ -33478,10 +34776,10 @@ p4est is a C library to manage a collection (a forest) of multiple connected ada *homepage*: https://www.p4est.org ======= =============================== -version toolchain +version toolchain ======= =============================== ``2.2`` ``foss/2019a``, ``intel/2019a`` -``2.8`` ``foss/2021a`` +``2.8`` ``foss/2021a`` ======= =============================== @@ -33495,11 +34793,11 @@ Visualization suite for VASP *homepage*: http://www.p4vasp.at/ ========== ================== ================================ -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================================ -``0.3.29`` ``-Python-2.7.11`` ``intel/2016a`` +``0.3.29`` ``-Python-2.7.11`` ``intel/2016a`` ``0.3.30`` ``-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` -``0.3.30`` ``-Python-2.7.15`` ``foss/2018b`` +``0.3.30`` ``-Python-2.7.15`` ``foss/2018b`` ========== ================== ================================ @@ -33513,12 +34811,12 @@ p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for U *homepage*: http://p7zip.sourceforge.net/ ========== =========================================================================== -version toolchain +version toolchain ========== =========================================================================== -``9.38.1`` ``GCC/4.9.2``, ``system`` +``9.38.1`` ``GCC/4.9.2``, ``system`` ``16.02`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2018a`` -``17.03`` ``GCCcore/10.2.0`` -``17.04`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``17.03`` ``GCCcore/10.2.0`` +``17.04`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== =========================================================================== @@ -33532,12 +34830,12 @@ Packing Optimization for Molecular Dynamics Simulations *homepage*: http://m3g.iqm.unicamp.br/packmol =========== =============================== -version toolchain +version toolchain =========== =============================== -``16.103`` ``intel/2016a`` +``16.103`` ``intel/2016a`` ``18.013`` ``foss/2018a``, ``intel/2018a`` -``20.2.2`` ``GCC/10.2.0`` -``v20.2.2`` ``iccifort/2020.1.217`` +``20.2.2`` ``GCC/10.2.0`` +``v20.2.2`` ``iccifort/2020.1.217`` =========== =============================== @@ -33551,9 +34849,9 @@ pagmo is a C++ scientific library for massively parallel optimization. *homepage*: https://esa.github.io/pagmo2 ========== ============================== -version toolchain +version toolchain ========== ============================== -``2.17.0`` ``foss/2020b`` +``2.17.0`` ``foss/2020b`` ``2.18.0`` ``foss/2021a``, ``foss/2021b`` ========== ============================== @@ -33568,7 +34866,7 @@ A set of scripts for very quickly obtaining pairwise SNP distance matrices from *homepage*: https://github.com/gtonkinhill/pairsnp ========= ============== -version toolchain +version toolchain ========= ============== ``0.0.7`` ``foss/2021a`` ========= ============== @@ -33584,7 +34882,7 @@ PAL2NAL is a program that converts a multiple sequence alignment of proteins and *homepage*: http://www.bork.embl.de/pal2nal/ ======= ====================================== -version toolchain +version toolchain ======= ====================================== ``14`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ======= ====================================== @@ -33600,7 +34898,7 @@ Protein ALignment And Detection INterface PALADIN is a protein sequence alignme *homepage*: https://github.com/ToniWestbrook/paladin ========= ====================================== -version toolchain +version toolchain ========= ====================================== ``1.4.6`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ====================================== @@ -33616,9 +34914,9 @@ PAML is a package of programs for phylogenetic analyses of DNA or protein sequ *homepage*: http://abacus.gene.ucl.ac.uk/software/paml.html ======== ============================================================================= -version toolchain +version toolchain ======== ============================================================================= -``4.9i`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +``4.9i`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ``4.9j`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ======== ============================================================================= @@ -33633,7 +34931,7 @@ A pangenome analysis pipeline. *homepage*: https://gtonkinhill.github.io/panaroo/ ========= ============== -version toolchain +version toolchain ========= ============== ``1.2.8`` ``foss/2020b`` ``1.2.9`` ``foss/2021a`` @@ -33650,7 +34948,7 @@ An easy to use open source tool for power system modeling, analysis and optimiza *homepage*: http://www.pandapower.org/ ========= ============== -version toolchain +version toolchain ========= ============== ``2.7.0`` ``foss/2020b`` ========= ============== @@ -33666,20 +34964,20 @@ pandas is an open source, BSD-licensed library providing high-performance, easy- *homepage*: https://pypi.python.org/pypi/pandas/ ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== ``0.18.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``0.18.0`` ``-Python-3.5.1`` ``foss/2016a``, ``intel/2016a`` -``0.18.1`` ``-Python-2.7.12`` ``intel/2016b`` -``0.18.1`` ``-Python-3.5.2`` ``intel/2016b`` +``0.18.1`` ``-Python-2.7.12`` ``intel/2016b`` +``0.18.1`` ``-Python-3.5.2`` ``intel/2016b`` ``0.19.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``0.19.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``0.19.1`` ``-Python-2.7.12`` ``intel/2016b`` -``0.19.1`` ``-Python-3.5.2`` ``intel/2016b`` -``0.20.1`` ``-Python-3.6.1`` ``intel/2017a`` -``0.21.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.21.0`` ``-Python-3.6.3`` ``intel/2017b`` -``1.1.2`` ``-Python-3.8.2`` ``foss/2020a`` +``0.19.1`` ``-Python-2.7.12`` ``intel/2016b`` +``0.19.1`` ``-Python-3.5.2`` ``intel/2016b`` +``0.20.1`` ``-Python-3.6.1`` ``intel/2017a`` +``0.21.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.21.0`` ``-Python-3.6.3`` ``intel/2017b`` +``1.1.2`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================== =============================== @@ -33693,7 +34991,7 @@ Up to date remote data access for pandas, works for multiple versions of pandas. *homepage*: https://pypi.org/project/pandas-datareader ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.7.0`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== @@ -33709,10 +35007,10 @@ PANDASEQ is a program to align Illumina reads, optionally with PCR primers embed *homepage*: https://github.com/neufeld/pandaseq ======== ========================================================== -version toolchain +version toolchain ======== ========================================================== ``2.10`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` -``2.11`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``2.11`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ======== ========================================================== @@ -33726,7 +35024,7 @@ If you need to convert files from one markup format into another, pandoc is your *homepage*: http://pandoc.org ========= ========== -version toolchain +version toolchain ========= ========== ``2.1.3`` ``system`` ``2.5`` ``system`` @@ -33735,6 +35033,22 @@ version toolchain ========= ========== +.. _list_software_Panedr_602: + +*Panedr* +++++++++ + +Panedr uses the Pyedr library to read a Gromacs EDR binary energy XDR file and returns its contents as a pandas dataframe. + +*homepage*: https://github.com/MDAnalysis/panedr + +========= ============== +version toolchain +========= ============== +``0.7.0`` ``foss/2021a`` +========= ============== + + .. _list_software_Pango_501: *Pango* @@ -33745,23 +35059,24 @@ Pango is a library for laying out and rendering of text, with an emphasis on int *homepage*: https://www.pango.org/ =========== ==================================== -version toolchain +version toolchain =========== ==================================== -``1.39.0`` ``foss/2016a``, ``intel/2016a`` -``1.40.1`` ``foss/2016a``, ``intel/2016a`` -``1.40.3`` ``foss/2016b``, ``intel/2016b`` -``1.40.5`` ``intel/2017a`` -``1.40.12`` ``intel/2017a`` -``1.40.14`` ``foss/2017b``, ``intel/2017b`` -``1.41.0`` ``foss/2017b``, ``intel/2017b`` -``1.41.1`` ``foss/2018a``, ``intel/2018a`` -``1.42.4`` ``foss/2018b``, ``fosscuda/2018b`` -``1.43.0`` ``GCCcore/8.2.0`` +``1.39.0`` ``foss/2016a``, ``intel/2016a`` +``1.40.1`` ``foss/2016a``, ``intel/2016a`` +``1.40.3`` ``foss/2016b``, ``intel/2016b`` +``1.40.5`` ``intel/2017a`` +``1.40.12`` ``intel/2017a`` +``1.40.14`` ``foss/2017b``, ``intel/2017b`` +``1.41.0`` ``foss/2017b``, ``intel/2017b`` +``1.41.1`` ``foss/2018a``, ``intel/2018a`` +``1.42.4`` ``foss/2018b``, ``fosscuda/2018b`` +``1.43.0`` ``GCCcore/8.2.0`` ``1.44.7`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.47.0`` ``GCCcore/10.2.0`` -``1.48.5`` ``GCCcore/10.3.0`` -``1.48.8`` ``GCCcore/11.2.0`` -``1.50.7`` ``GCCcore/11.3.0`` +``1.47.0`` ``GCCcore/10.2.0`` +``1.48.5`` ``GCCcore/10.3.0`` +``1.48.8`` ``GCCcore/11.2.0`` +``1.50.7`` ``GCCcore/11.3.0`` +``1.50.12`` ``GCCcore/12.2.0`` =========== ==================================== @@ -33775,7 +35090,7 @@ Software package for assigning SARS-CoV-2 genome sequences to global lineages. T *homepage*: https://cov-lineages.org/pangolin.html ========== ========================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ========================== ============== ``3.1.11`` ``foss/2020b`` ``3.1.16`` ``-pangoLEARN-2021-10-18`` ``foss/2021b`` @@ -33793,7 +35108,7 @@ Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA align *homepage*: https://github.com/sanger-pathogens/panito ========= ============== -version toolchain +version toolchain ========= ============== ``0.0.1`` ``GCC/10.3.0`` ========= ============== @@ -33809,14 +35124,15 @@ PAPI provides the tool designer and application engineer with a consistent inte *homepage*: https://icl.cs.utk.edu/projects/papi/ =========== ======================================================== -version toolchain +version toolchain =========== ======================================================== -``5.4.3`` ``foss/2016a`` -``5.5.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` -``5.6.0`` ``GCCcore/6.4.0`` -``5.7.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``5.4.3`` ``foss/2016a`` +``5.5.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``5.6.0`` ``GCCcore/6.4.0`` +``5.7.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``6.0.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``6.0.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``6.0.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``7.0.0`` ``GCCcore/11.3.0`` =========== ======================================================== @@ -33830,27 +35146,27 @@ parallel: Build and execute shell commands in parallel *homepage*: https://savannah.gnu.org/projects/parallel/ ============ =============================== -version toolchain +version toolchain ============ =============================== -``20141122`` ``GCC/4.9.2`` -``20150322`` ``GCC/4.9.2`` -``20150822`` ``GCC/4.9.2`` -``20160622`` ``foss/2016a`` -``20170822`` ``intel/2017a`` -``20171022`` ``intel/2017b`` +``20141122`` ``GCC/4.9.2`` +``20150322`` ``GCC/4.9.2`` +``20150822`` ``GCC/4.9.2`` +``20160622`` ``foss/2016a`` +``20170822`` ``intel/2017a`` +``20171022`` ``intel/2017b`` ``20171122`` ``foss/2017b``, ``intel/2017b`` -``20180422`` ``intel/2018a`` -``20180822`` ``foss/2018b`` -``20181222`` ``intel/2018b`` -``20190222`` ``GCCcore/7.3.0`` -``20190622`` ``GCCcore/8.2.0`` -``20190922`` ``GCCcore/8.3.0`` -``20200422`` ``GCCcore/9.3.0`` -``20200522`` ``GCCcore/9.3.0`` -``20210322`` ``GCCcore/10.2.0`` -``20210622`` ``GCCcore/10.3.0`` -``20210722`` ``GCCcore/11.2.0`` -``20220722`` ``GCCcore/11.3.0`` +``20180422`` ``intel/2018a`` +``20180822`` ``foss/2018b`` +``20181222`` ``intel/2018b`` +``20190222`` ``GCCcore/7.3.0`` +``20190622`` ``GCCcore/8.2.0`` +``20190922`` ``GCCcore/8.3.0`` +``20200422`` ``GCCcore/9.3.0`` +``20200522`` ``GCCcore/9.3.0`` +``20210322`` ``GCCcore/10.2.0`` +``20210622`` ``GCCcore/10.3.0`` +``20210722`` ``GCCcore/11.2.0`` +``20220722`` ``GCCcore/11.3.0`` ============ =============================== @@ -33864,11 +35180,11 @@ parallel fastq-dump wrapper *homepage*: https://github.com/rvalieris/parallel-fastq-dump ========= ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================= ``0.6.5`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``0.6.6`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``0.6.7`` ``gompi/2020b`` +``0.6.7`` ``gompi/2020b`` ========= ================= ================= @@ -33882,7 +35198,7 @@ A high-level Parallel I/O Library for structured grid applications *homepage*: https://github.com/NCAR/ParallelIO ========== =============== -version toolchain +version toolchain ========== =============== ``2.2.2a`` ``intel/2017a`` ========== =============== @@ -33898,7 +35214,7 @@ Parameterized testing with any Python test framework *homepage*: https://github.com/wolever/parameterized ========= ================== -version toolchain +version toolchain ========= ================== ``0.8.1`` ``GCCcore/10.3.0`` ========= ================== @@ -33914,14 +35230,14 @@ parasail is a SIMD C (C99) library containing implementations of the Smith-Wate *homepage*: https://github.com/jeffdaily/parasail ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``2.2`` ``intel/2018a`` -``2.4`` ``foss/2018b`` -``2.4.1`` ``GCC/8.3.0``, ``intel/2019b`` +``2.2`` ``intel/2018a`` +``2.4`` ``foss/2018b`` +``2.4.1`` ``GCC/8.3.0``, ``intel/2019b`` ``2.4.2`` ``GCC/9.3.0``, ``iccifort/2020.1.217`` -``2.4.3`` ``GCC/10.2.0``, ``GCC/10.3.0`` -``2.5`` ``GCC/11.2.0`` +``2.4.3`` ``GCC/10.2.0``, ``GCC/10.3.0`` +``2.5`` ``GCC/11.2.0`` ========= ====================================== @@ -33935,7 +35251,7 @@ A very powerful performance visualization and analysis tool based on traces tha *homepage*: https://tools.bsc.es/paraver ========= ============== -version toolchain +version toolchain ========= ============== ``4.8.1`` ``foss/2019a`` ``4.9.2`` ``foss/2021a`` @@ -33952,23 +35268,39 @@ ParaView is a scientific parallel visualizer. *homepage*: https://www.paraview.org ========== ====================== ================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ====================== ================================================================================================= -``4.4.0`` ``foss/2016a``, ``intel/2016a`` -``4.4.0`` ``-mpi`` ``gimkl/2.11.5`` -``5.1.2`` ``-mpi`` ``foss/2016b``, ``intel/2016b`` -``5.2.0`` ``-mpi`` ``foss/2016b``, ``intel/2017a`` -``5.3.0`` ``-mpi`` ``foss/2016b`` +``4.4.0`` ``foss/2016a``, ``intel/2016a`` +``4.4.0`` ``-mpi`` ``gimkl/2.11.5`` +``5.1.2`` ``-mpi`` ``foss/2016b``, ``intel/2016b`` +``5.2.0`` ``-mpi`` ``foss/2016b``, ``intel/2017a`` +``5.3.0`` ``-mpi`` ``foss/2016b`` ``5.4.1`` ``-mpi`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``5.5.2`` ``-Python-2.7.15-mpi`` ``foss/2018b`` -``5.6.2`` ``-Python-3.7.4-mpi`` ``foss/2019b``, ``intel/2019b`` -``5.8.0`` ``-Python-3.8.2-mpi`` ``foss/2020a``, ``intel/2020a`` -``5.8.1`` ``-mpi`` ``foss/2020b`` -``5.9.1`` ``-mpi`` ``foss/2021a``, ``foss/2021b`` -``5.10.1`` ``-mpi`` ``foss/2022a`` +``5.5.2`` ``-Python-2.7.15-mpi`` ``foss/2018b`` +``5.6.2`` ``-Python-3.7.4-mpi`` ``foss/2019b``, ``intel/2019b`` +``5.8.0`` ``-Python-3.8.2-mpi`` ``foss/2020a``, ``intel/2020a`` +``5.8.1`` ``-mpi`` ``foss/2020b`` +``5.9.1`` ``-mpi`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` +``5.10.1`` ``-mpi`` ``foss/2022a`` ========== ====================== ================================================================================================= +.. _list_software_Parcels_714: + +*Parcels* ++++++++++ + +Parcels (Probably A Really Computationally Efficient Lagrangian Simulator) is a set of Python classes and methods to create customisable particle tracking simulations using output from Ocean Circulation models. Parcels can be used to track passive and active particulates such as water, plankton, plastic and fish. + +*homepage*: http://www.oceanparcels.org/ + +========= ============== +version toolchain +========= ============== +``2.4.0`` ``foss/2022a`` +========= ============== + + .. _list_software_PARI-GP_496: *PARI-GP* @@ -33979,7 +35311,7 @@ PARI/GP is a widely used computer algebra system designed for fast computations *homepage*: http://pari.math.u-bordeaux.fr ========= ============== -version toolchain +version toolchain ========= ============== ``2.7.6`` ``foss/2016a`` ========= ============== @@ -33995,7 +35327,7 @@ ParmEd is a general tool for aiding in investigations of biomolecular systems us *homepage*: https://parmed.github.io/ParmEd ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``2.7.3`` ``-Python-3.6.3`` ``intel/2017b`` ``3.2.0`` ``-Python-3.7.4`` ``intel/2019b`` @@ -34012,11 +35344,11 @@ ParMETIS is an MPI-based parallel library that implements a variety of algorithm *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview -========= ================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain -========= ================================================================================================================================================================================================================================================================================================================================================================================================================================== -``4.0.3`` ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -========= ================================================================================================================================================================================================================================================================================================================================================================================================================================== +========= =================================================================================================================================================================================================================================================================================================================================================================================================================================================== +version toolchain +========= =================================================================================================================================================================================================================================================================================================================================================================================================================================================== +``4.0.3`` ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``gompi/2022a``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpi/2020b``, ``iimpi/2021a``, ``iimpi/2021b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` +========= =================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_ParMGridGen_1040: @@ -34029,7 +35361,7 @@ ParMGridGen is an MPI-based parallel library that is based on the serial package *homepage*: http://www-users.cs.umn.edu/~moulitsa/software.html ======= ====================================================================================================================== -version toolchain +version toolchain ======= ====================================================================================================================== ``1.0`` ``gimkl/2.11.5``, ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``intel/2016a``, ``intel/2017a`` ======= ====================================================================================================================== @@ -34045,7 +35377,7 @@ PartitionFinder 2 is a Python program for simultaneously choosing partitioning s *homepage*: https://www.robertlanfear.com/partitionfinder ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``2.1.1`` ``-Python-2.7.16`` ``intel/2019b`` ========= ================== =============== @@ -34061,7 +35393,7 @@ PASTA (Practical Alignment using SATe and Transitivity) *homepage*: https://github.com/smirarab/pasta ========= ================= ==================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ==================== ``1.8.5`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` ========= ================= ==================== @@ -34077,7 +35409,7 @@ PaStiX (Parallel Sparse matriX package) is a scientific library that provides a *homepage*: http://pastix.gforge.inria.fr/ ========= ============== -version toolchain +version toolchain ========= ============== ``5.2.3`` ``foss/2017b`` ========= ============== @@ -34093,7 +35425,7 @@ Patch takes a patch file containing a difference listing produced by the diff pr *homepage*: https://savannah.gnu.org/projects/patch ========= ========== -version toolchain +version toolchain ========= ========== ``2.7.6`` ``system`` ========= ========== @@ -34109,14 +35441,14 @@ PatchELF is a small utility to modify the dynamic linker and RPATH of ELF execut *homepage*: http://nixos.org/patchelf.html ========== ========================================================= -version toolchain +version toolchain ========== ========================================================= -``0.8`` ``GNU/4.9.3-2.25`` -``0.9`` ``GCCcore/6.4.0``, ``foss/2016a`` -``0.10`` ``GCCcore/7.2.0``, ``GCCcore/8.3.0`` +``0.8`` ``GNU/4.9.3-2.25`` +``0.9`` ``GCCcore/6.4.0``, ``foss/2016a`` +``0.10`` ``GCCcore/7.2.0``, ``GCCcore/8.3.0`` ``0.12`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``0.13`` ``GCCcore/11.2.0`` -``0.15.0`` ``GCCcore/11.3.0`` +``0.13`` ``GCCcore/11.2.0`` +``0.15.0`` ``GCCcore/11.3.0`` ========== ========================================================= @@ -34130,13 +35462,13 @@ path.py is a Python library implementing path objects as first-class entities, *homepage*: https://github.com/jaraco/path.py ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``8.2.1`` ``-Python-2.7.11`` ``foss/2016a`` +``8.2.1`` ``-Python-2.7.11`` ``foss/2016a`` ``8.2.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``8.2.1`` ``-Python-3.5.1`` ``foss/2016a`` -``8.2.1`` ``-Python-3.5.2`` ``intel/2016b`` -``10.1`` ``-Python-2.7.12`` ``intel/2016b`` +``8.2.1`` ``-Python-3.5.1`` ``foss/2016a`` +``8.2.1`` ``-Python-3.5.2`` ``intel/2016b`` +``10.1`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============================== @@ -34150,7 +35482,7 @@ PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computatio *homepage*: https://paup.phylosolutions.com/ =========== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain =========== ============= ========== ``4.0a166`` ``-centos64`` ``system`` ``4.0a168`` ``-centos64`` ``system`` @@ -34167,8 +35499,9 @@ Tools for plotting Oxford Nanopore and other long-read data *homepage*: https://github.com/conchoecia/pauvre ========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============== +``0.2.3`` ``foss/2021a`` ``0.1923`` ``-Python-3.7.4`` ``intel/2019b`` ``0.1924`` ``intel/2020b`` ========== ================= =============== @@ -34184,7 +35517,7 @@ The pbbam software package provides components to create, query, & edit PacBio B *homepage*: http://pbbam.readthedocs.io/ ============ =============== -version toolchain +version toolchain ============ =============== ``1.0.6`` ``gompi/2019a`` ``20170508`` ``intel/2017a`` @@ -34201,7 +35534,7 @@ The pbcopper library provides a suite of data structures, algorithms, and utili *homepage*: https://github.com/PacificBiosciences/pbcopper ========= =============== -version toolchain +version toolchain ========= =============== ``1.3.0`` ``gompi/2019a`` ========= =============== @@ -34217,7 +35550,7 @@ pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) whi *homepage*: https://github.com/PacificBiosciences/pbdagcon ============ =============== -version toolchain +version toolchain ============ =============== ``20170330`` ``intel/2017a`` ============ =============== @@ -34233,7 +35566,7 @@ A minimap2 frontend for PacBio native data formats *homepage*: https://github.com/PacificBiosciences/pbmm2 ========= =============== -version toolchain +version toolchain ========= =============== ``1.1.0`` ``gompi/2019a`` ========= =============== @@ -34249,9 +35582,9 @@ The pbs_python package is a wrapper class for the Torque C library. With this pa *homepage*: https://oss.trac.surfsara.nl/pbs_python ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== -``4.6.0`` ``system`` +``4.6.0`` ``system`` ``4.6.0`` ``-Python-2.7.11`` ``intel/2016a`` ``4.6.0`` ``-Python-2.7.12`` ``intel/2016b`` ``4.6.0`` ``-Python-2.7.13`` ``intel/2017a`` @@ -34268,7 +35601,7 @@ PBJelly is a highly automated pipeline that aligns long sequencing reads (such a *homepage*: https://sourceforge.net/p/pb-jelly/wiki/Home/ =========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== =============== ``15.8.24`` ``-Python-2.7.12`` ``intel/2016b`` =========== ================== =============== @@ -34284,7 +35617,7 @@ PCAngsd, which estimates the covariance matrix for low depth NGS data in an ite *homepage*: http://www.popgen.dk/software/index.php/PCAngsd ======== ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================== ============== ``0.97`` ``-Python-2.7.14`` ``foss/2018a`` ======== ================== ============== @@ -34300,7 +35633,7 @@ The compiler is based on the original Portable C Compiler by S. C. Johnson, wri *homepage*: http://pcc.ludd.ltu.se/ ============ ========== -version toolchain +version toolchain ============ ========== ``20131024`` ``system`` ============ ========== @@ -34316,7 +35649,7 @@ The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/ *homepage*: http://pointclouds.org/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.7.2`` ``-Python-2.7.11`` ``intel/2016a`` ``1.8.1`` ``-Python-2.7.14`` ``intel/2017b`` @@ -34333,10 +35666,10 @@ An API for the Polarizable Continuum Model. *homepage*: https://pcmsolver.readthedocs.org ============ ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============== ``1.1.4`` ``-Python-2.7.11`` ``intel/2016a`` -``1.2.3`` ``-Python-3.6.6`` ``foss/2018b`` +``1.2.3`` ``-Python-3.6.6`` ``foss/2018b`` ``1.2.3`` ``-Python-3.7.2`` ``gompi/2019a`` ``1.2.3`` ``-Python-3.7.4`` ``iimpi/2019b`` ``20160205`` ``-Python-2.7.11`` ``intel/2016a`` @@ -34353,7 +35686,7 @@ PCRaster Is a collection of software targeted at the development and deployment *homepage*: http://pcraster.geo.uu.nl/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``4.1.0`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== @@ -34369,16 +35702,16 @@ The PCRE library is a set of functions that implement regular expression patter *homepage*: https://www.pcre.org/ ======== ================================================================================== -version toolchain +version toolchain ======== ================================================================================== ``8.38`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` -``8.39`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` -``8.40`` ``GCCcore/6.3.0``, ``gimkl/2017a``, ``intel/2016b``, ``intel/2017a`` -``8.41`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``8.42`` ``GCCcore/6.4.0`` -``8.43`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``8.44`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``8.45`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``8.39`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` +``8.40`` ``GCCcore/6.3.0``, ``gimkl/2017a``, ``intel/2016b``, ``intel/2017a`` +``8.41`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``8.42`` ``GCCcore/6.4.0`` +``8.43`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``8.44`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``8.45`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ======== ================================================================================== @@ -34391,18 +35724,18 @@ The PCRE library is a set of functions that implement regular expression pattern *homepage*: https://www.pcre.org/ -========= ==================================== -version toolchain -========= ==================================== -``10.21`` ``foss/2016a`` -``10.31`` ``foss/2018b`` +========= ====================================== +version toolchain +========= ====================================== +``10.21`` ``foss/2016a`` +``10.31`` ``foss/2018b`` ``10.33`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``10.34`` ``GCCcore/9.3.0`` -``10.35`` ``GCCcore/10.2.0`` -``10.36`` ``GCCcore/10.3.0`` -``10.37`` ``GCCcore/11.2.0`` -``10.40`` ``GCCcore/11.3.0`` -========= ==================================== +``10.34`` ``GCCcore/9.3.0`` +``10.35`` ``GCCcore/10.2.0`` +``10.36`` ``GCCcore/10.3.0`` +``10.37`` ``GCCcore/11.2.0`` +``10.40`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` +========= ====================================== .. _list_software_PDT_232: @@ -34414,13 +35747,13 @@ Program Database Toolkit (PDT) is a framework for analyzing source code written *homepage*: https://www.cs.uoregon.edu/research/pdt/ -========== ======================================================== -version toolchain -========== ======================================================== -``3.22`` ``foss/2016a`` +========== ========================================================= +version toolchain +========== ========================================================= +``3.22`` ``foss/2016a`` ``3.25`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.25.1`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -========== ======================================================== +``3.25.1`` ``GCCcore/10.3.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +========== ========================================================= .. _list_software_PEAR_296: @@ -34433,10 +35766,10 @@ PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. *homepage*: http://sco.h-its.org/exelixis/web/software/pear/ ========== ==================================================================================== -version toolchain +version toolchain ========== ==================================================================================== -``0.9.8`` ``foss/2016b``, ``intel/2016b`` -``0.9.10`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` +``0.9.8`` ``foss/2016b``, ``intel/2016b`` +``0.9.10`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ``0.9.11`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` ========== ==================================================================================== @@ -34451,7 +35784,7 @@ A free software tool for Copy Number Variation (CNV) detection from SNP genotypi *homepage*: https://penncnv.openbioinformatics.org/ ========= ================= -version toolchain +version toolchain ========= ================= ``1.0.5`` ``GCCcore/8.3.0`` ========= ================= @@ -34467,7 +35800,7 @@ A Python library that integrates all the tools necessary to perform research usi *homepage*: https://pept.readthedocs.io/en/latest/ ========= ============== -version toolchain +version toolchain ========= ============== ``0.4.1`` ``foss/2021a`` ========= ============== @@ -34483,7 +35816,7 @@ Semi-supervised learning for peptide identification from shotgun proteomics data *homepage*: https://github.com/percolator/percolator ======= =============== -version toolchain +version toolchain ======= =============== ``3.4`` ``gompi/2019a`` ======= =============== @@ -34499,36 +35832,36 @@ Larry Wall's Practical Extraction and Report Language *homepage*: https://www.perl.org/ ========== ============= ========================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ========================================================================================= -``5.20.1`` ``-bare`` ``GCC/4.8.2``, ``GCC/4.9.2`` -``5.20.2`` ``-bare`` ``GCC/4.9.2`` -``5.20.3`` ``foss/2016a``, ``intel/2016a`` -``5.22.0`` ``-bare`` ``GCC/4.9.2`` -``5.22.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` -``5.22.1`` ``-bare`` ``foss/2016a``, ``intel/2016a`` -``5.22.2`` ``intel/2016a`` +``5.20.1`` ``-bare`` ``GCC/4.8.2``, ``GCC/4.9.2`` +``5.20.2`` ``-bare`` ``GCC/4.9.2`` +``5.20.3`` ``foss/2016a``, ``intel/2016a`` +``5.22.0`` ``-bare`` ``GCC/4.9.2`` +``5.22.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` +``5.22.1`` ``-bare`` ``foss/2016a``, ``intel/2016a`` +``5.22.2`` ``intel/2016a`` ``5.24.0`` ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` -``5.24.0`` ``-bare`` ``foss/2016b`` -``5.24.1`` ``GCCcore/6.3.0``, ``foss/2017a``, ``intel/2017a`` -``5.26.0`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01`` -``5.26.1`` ``GCCcore/6.4.0``, ``foss/2018a`` -``5.26.1`` ``-bare`` ``foss/2018a`` -``5.28.0`` ``GCCcore/7.3.0`` -``5.28.1`` ``GCCcore/8.2.0`` -``5.30.0`` ``GCCcore/8.3.0`` -``5.30.0`` ``-minimal`` ``GCCcore/8.3.0`` -``5.30.2`` ``GCCcore/9.3.0`` -``5.30.2`` ``-minimal`` ``GCCcore/9.3.0`` -``5.32.0`` ``GCCcore/10.2.0`` -``5.32.0`` ``-minimal`` ``GCCcore/10.2.0`` -``5.32.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` -``5.32.1`` ``-minimal`` ``GCCcore/10.3.0`` -``5.34.0`` ``GCCcore/11.2.0`` -``5.34.0`` ``-minimal`` ``GCCcore/11.2.0`` -``5.34.1`` ``GCCcore/11.3.0`` -``5.34.1`` ``-minimal`` ``GCCcore/11.3.0`` -``5.36.0`` ``GCCcore/12.1.0``, ``GCCcore/12.2.0`` +``5.24.0`` ``-bare`` ``foss/2016b`` +``5.24.1`` ``GCCcore/6.3.0``, ``foss/2017a``, ``intel/2017a`` +``5.26.0`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01`` +``5.26.1`` ``GCCcore/6.4.0``, ``foss/2018a`` +``5.26.1`` ``-bare`` ``foss/2018a`` +``5.28.0`` ``GCCcore/7.3.0`` +``5.28.1`` ``GCCcore/8.2.0`` +``5.30.0`` ``GCCcore/8.3.0`` +``5.30.0`` ``-minimal`` ``GCCcore/8.3.0`` +``5.30.2`` ``GCCcore/9.3.0`` +``5.30.2`` ``-minimal`` ``GCCcore/9.3.0`` +``5.32.0`` ``GCCcore/10.2.0`` +``5.32.0`` ``-minimal`` ``GCCcore/10.2.0`` +``5.32.1`` ``FCC/4.5.0``, ``GCCcore/10.3.0`` +``5.32.1`` ``-minimal`` ``GCCcore/10.3.0`` +``5.34.0`` ``GCCcore/11.2.0`` +``5.34.0`` ``-minimal`` ``GCCcore/11.2.0`` +``5.34.1`` ``GCCcore/11.3.0`` +``5.34.1`` ``-minimal`` ``GCCcore/11.3.0`` +``5.36.0`` ``GCCcore/12.1.0``, ``GCCcore/12.2.0`` ========== ============= ========================================================================================= @@ -34542,7 +35875,7 @@ cpanm - get, unpack build and install modules from CPAN *homepage*: https://github.com/miyagawa/cpanminus ========== ========== -version toolchain +version toolchain ========== ========== ``1.7039`` ``system`` ========== ========== @@ -34558,7 +35891,7 @@ Libraries historically supplied with Perl 4 *homepage*: https://metacpan.org/pod/Perl4::CoreLibs ========= ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =============== ``0.003`` ``-Perl-5.24.1`` ``intel/2017a`` ========= ================ =============== @@ -34574,7 +35907,7 @@ PEST++ is a software suite aimed at supporting complex numerical models in the *homepage*: https://github.com/usgs/pestpp ========= ============== -version toolchain +version toolchain ========= ============== ``5.0.5`` ``foss/2020a`` ========= ============== @@ -34590,21 +35923,22 @@ PETSc, pronounced PET-see (the S is silent), is a suite of data structures and r *homepage*: http://www.mcs.anl.gov/petsc ========== ==================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ==================== =============================== -``3.7.2`` ``-Python-2.7.11`` ``intel/2016a`` -``3.7.3`` ``-Python-2.7.11`` ``foss/2016a`` -``3.7.5`` ``-downloaded-deps`` ``intel/2016b`` -``3.8.3`` ``-downloaded-deps`` ``foss/2017b`` -``3.9.1`` ``-downloaded-deps`` ``foss/2018a`` +``3.7.2`` ``-Python-2.7.11`` ``intel/2016a`` +``3.7.3`` ``-Python-2.7.11`` ``foss/2016a`` +``3.7.5`` ``-downloaded-deps`` ``intel/2016b`` +``3.8.3`` ``-downloaded-deps`` ``foss/2017b`` +``3.9.1`` ``-downloaded-deps`` ``foss/2018a`` ``3.9.3`` ``foss/2018a``, ``intel/2018a`` -``3.11.0`` ``-downloaded-deps`` ``foss/2018b`` +``3.11.0`` ``-downloaded-deps`` ``foss/2018b`` ``3.11.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``3.12.4`` ``-Python-2.7.16`` ``intel/2019b`` +``3.12.4`` ``-Python-2.7.16`` ``intel/2019b`` ``3.12.4`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.12.4`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``3.14.4`` ``foss/2020b``, ``intel/2020b`` -``3.15.1`` ``foss/2021a`` +``3.15.1`` ``foss/2021a`` +``3.17.4`` ``foss/2022a`` ========== ==================== =============================== @@ -34618,7 +35952,7 @@ petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for S *homepage*: https://bitbucket.org/petsc/petsc4py ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``3.9.1`` ``-Python-3.6.4`` ``foss/2018a`` ``3.12.0`` ``-Python-3.7.4`` ``foss/2019b`` @@ -34636,7 +35970,7 @@ Drop-in replacement for find, implemented for using parallel access and MPI. *homepage*: https://github.com/VI4IO/pfind ============ =============== -version toolchain +version toolchain ============ =============== ``20220613`` ``gompi/2021b`` ============ =============== @@ -34652,11 +35986,11 @@ A suite of tools to build and search generalized profiles (protein and DNA). *homepage*: https://github.com/sib-swiss/pftools3 ============ ================================== -version toolchain +version toolchain ============ ================================== ``3.2.11`` ``GCCcore/10.3.0``, ``foss/2021a`` -``3.2.12`` ``GCCcore/11.2.0`` -``20160324`` ``foss/2016a`` +``3.2.12`` ``GCCcore/11.2.0`` +``20160324`` ``foss/2016a`` ============ ================================== @@ -34670,7 +36004,7 @@ pFUnit is a unit testing framework enabling JUnit-like testing of serial and MP *homepage*: https://github.com/Goddard-Fortran-Ecosystem/pFUnit ========= =============== -version toolchain +version toolchain ========= =============== ``3.2.9`` ``gompi/2018b`` ``4.2.0`` ``gompi/2020b`` @@ -34687,7 +36021,7 @@ An automated data conversion tool for connecting population genetics and genomic *homepage*: http://cmpg.unibe.ch/software/PGDSpider/ =========== ================== ========== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ========== ``2.1.0.3`` ``-Java-1.7.0_80`` ``system`` =========== ================== ========== @@ -34703,7 +36037,7 @@ C, C++ and Fortran compilers from The Portland Group - PGI *homepage*: https://www.pgroup.com/ ========= ======================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ======================= ========== ``15.7`` ``-GNU-4.9.2-2.25`` ``system`` ``15.7`` ``-GNU-4.9.3-2.25`` ``system`` @@ -34738,7 +36072,7 @@ PHANOTATE: a tool to annotate phage genomes *homepage*: https://github.com/deprekate/PHANOTATE ============ ============== -version toolchain +version toolchain ============ ============== ``20190724`` ``foss/2018b`` ============ ============== @@ -34754,7 +36088,7 @@ It computes informative enrichment and quality measures for ChIP-seq/DNase-seq/F *homepage*: https://github.com/kundajelab/phantompeakqualtools ========= ============== -version toolchain +version toolchain ========= ============== ``1.2.2`` ``foss/2021b`` ========= ============== @@ -34770,7 +36104,7 @@ The program PHASE implements a Bayesian statistical method for reconstructing h *homepage*: http://stephenslab.uchicago.edu/phase/download.html ========= ========== -version toolchain +version toolchain ========= ========== ``2.1.1`` ``system`` ========= ========== @@ -34786,9 +36120,9 @@ PHAST is a freely available software package for comparative and evolutionary ge *homepage*: http://compgen.cshl.edu/phast/ ======= ========================================================== -version toolchain +version toolchain ======= ========================================================== -``1.4`` ``intel/2017a`` +``1.4`` ``intel/2017a`` ``1.5`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ======= ========================================================== @@ -34803,7 +36137,7 @@ Provides an accessible R interface to the phenome wide association study. *homepage*: https://www.vumc.org/cpm/center-precision-medicine-blog/phewas-r-package ============ ============= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= =============================== ``0.12`` ``-R-3.3.3`` ``foss/2016b``, ``intel/2016b`` ``0.99.5-2`` ``-R-3.6.0`` ``foss/2019a``, ``intel/2019a`` @@ -34820,7 +36154,7 @@ The PhiPack software package implements (in C) a few tests for recombination and *homepage*: http://www.maths.otago.ac.nz/~dbryant/software.html ============== ======================================== -version toolchain +version toolchain ============== ======================================== ``2016.06.14`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ============== ======================================== @@ -34836,7 +36170,7 @@ PHLAT is a bioinformatics algorithm that offers HLA typing at four-digit resolut *homepage*: https://sites.google.com/site/phlatfortype/ ======= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== ============== ``1.1`` ``-Python-2.7.15`` ``foss/2018b`` ======= ================== ============== @@ -34852,7 +36186,7 @@ The phonemizer allows simple phonemization of words and texts in many languages. *homepage*: https://github.com/bootphon/phonemizer ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``2.2.1`` ``-Python-3.8.2`` ``gompi/2020a`` ========= ================= =============== @@ -34868,9 +36202,9 @@ phono3py calculates phonon-phonon interaction and related properties using the s *homepage*: https://atztogo.github.io/phono3py/ ============= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ============= ================== =============================== -``1.12.5.35`` ``-Python-2.7.14`` ``intel/2017b`` +``1.12.5.35`` ``-Python-2.7.14`` ``intel/2017b`` ``1.12.7.55`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ============= ================== =============================== @@ -34885,18 +36219,19 @@ Phonopy is an open source package of phonon calculations based on the supercell *homepage*: https://atztogo.github.io/phonopy/ ============= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ============= ================== =============================== -``1.10.1`` ``-Python-2.7.11`` ``intel/2016a`` -``1.12.2.20`` ``-Python-2.7.14`` ``intel/2017b`` +``1.10.1`` ``-Python-2.7.11`` ``intel/2016a`` +``1.12.2.20`` ``-Python-2.7.14`` ``intel/2017b`` ``1.12.6.66`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``1.13.0.64`` ``-Python-2.7.14`` ``intel/2018a`` -``1.14.2`` ``-Python-2.7.15`` ``intel/2018b`` -``2.0.0`` ``-Python-2.7.14`` ``intel/2018a`` -``2.2.0`` ``-Python-3.7.2`` ``intel/2019a`` -``2.7.1`` ``-Python-3.7.4`` ``intel/2019b`` -``2.7.1`` ``-Python-3.8.2`` ``intel/2020a`` -``2.12.0`` ``foss/2020b`` +``1.13.0.64`` ``-Python-2.7.14`` ``intel/2018a`` +``1.14.2`` ``-Python-2.7.15`` ``intel/2018b`` +``2.0.0`` ``-Python-2.7.14`` ``intel/2018a`` +``2.2.0`` ``-Python-3.7.2`` ``intel/2019a`` +``2.7.1`` ``-Python-3.7.4`` ``intel/2019b`` +``2.7.1`` ``-Python-3.8.2`` ``intel/2020a`` +``2.12.0`` ``foss/2020b`` +``2.16.3`` ``foss/2022a`` ============= ================== =============================== @@ -34910,7 +36245,7 @@ Photontorch is a photonic simulator for highly parallel simulation and optimizat *homepage*: https://docs.photontorch.com/ ========= ================================== -version toolchain +version toolchain ========= ================================== ``0.4.1`` ``foss/2020b``, ``fosscuda/2020b`` ========= ================================== @@ -34926,7 +36261,7 @@ Phototonic is an image viewer and organizer *homepage*: https://github.com/oferkv/phototonic ======= ================== -version toolchain +version toolchain ======= ================== ``2.1`` ``GCCcore/10.3.0`` ======= ================== @@ -34942,9 +36277,9 @@ PHYLIP is a free package of programs for inferring phylogenies. *homepage*: http://evolution.genetics.washington.edu/phylip ========= ========================================================================= -version toolchain +version toolchain ========= ========================================================================= -``3.696`` ``foss/2016a``, ``intel/2016a`` +``3.696`` ``foss/2016a``, ``intel/2016a`` ``3.697`` ``GCC/6.4.0-2.28``, ``GCC/9.3.0``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ========= ========================================================================= @@ -34959,7 +36294,7 @@ A Bayesian software for phylogenetic reconstruction using mixture models *homepage*: https://github.com/bayesiancook/pbmpi ============ =============== -version toolchain +version toolchain ============ =============== ``20161021`` ``intel/2016b`` ============ =============== @@ -34975,7 +36310,7 @@ C++ library for high performance phylogenetics *homepage*: https://github.com/pranjalv123/phylokit ======= ==================== -version toolchain +version toolchain ======= ==================== ``1.0`` ``GCC/8.2.0-2.31.1`` ======= ==================== @@ -34991,7 +36326,7 @@ Dynamic programming for phylogenetics applications *homepage*: https://github.com/pranjalv123/phylonaut ============ =============== -version toolchain +version toolchain ============ =============== ``20190626`` ``gompi/2019a`` ============ =============== @@ -35007,7 +36342,7 @@ PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of g *homepage*: https://github.com/biobakery/phylophlan ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``3.0`` ``-Python-3.8.2`` ``foss/2020a`` ``3.0.2`` ``foss/2021a`` @@ -35024,7 +36359,7 @@ Phylogenetic estimation using (Maximum) Likelihood *homepage*: https://github.com/stephaneguindon/phyml ================ ============== -version toolchain +version toolchain ================ ============== ``3.3.20190321`` ``foss/2018b`` ``3.3.20200621`` ``foss/2020b`` @@ -35041,7 +36376,7 @@ phyx performs phylogenetics analyses on trees and sequences. *homepage*: https://github.com/FePhyFoFum/phyx ======== ============== -version toolchain +version toolchain ======== ============== ``1.01`` ``foss/2019a`` ======== ============== @@ -35057,7 +36392,7 @@ A set of tools (in Java) for working with next generation sequencing data in the *homepage*: https://sourceforge.net/projects/picard =========== =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain =========== =================== ========== ``1.39`` ``system`` ``1.100`` ``system`` @@ -35100,12 +36435,13 @@ pigz, which stands for parallel implementation of gzip, is a fully functional r *homepage*: https://zlib.net/pigz/ ========= ================================================================================================================================= -version toolchain +version toolchain ========= ================================================================================================================================= -``2.3.3`` ``foss/2016b`` -``2.3.4`` ``GCCcore/6.4.0`` +``2.3.3`` ``foss/2016b`` +``2.3.4`` ``GCCcore/6.4.0`` ``2.4`` ``GCCcore/10.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a`` -``2.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.7`` ``GCCcore/11.3.0`` ========= ================================================================================================================================= @@ -35119,13 +36455,13 @@ The Python Imaging Library (PIL) adds image processing capabilities to your Pyth *homepage*: http://www.pythonware.com/products/pil ========= ================================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================================= =============================== -``1.1.7`` ``-Python-2.7.11`` ``intel/2016a`` -``1.1.7`` ``-Python-2.7.11-freetype-2.6.3`` ``intel/2016a`` +``1.1.7`` ``-Python-2.7.11`` ``intel/2016a`` +``1.1.7`` ``-Python-2.7.11-freetype-2.6.3`` ``intel/2016a`` ``1.1.7`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.1.7`` ``-Python-2.7.13`` ``intel/2017a`` -``1.1.7`` ``-Python-2.7.15`` ``foss/2019a`` +``1.1.7`` ``-Python-2.7.13`` ``intel/2017a`` +``1.1.7`` ``-Python-2.7.15`` ``foss/2019a`` ========= ================================= =============================== @@ -35139,7 +36475,7 @@ PileOMeth processes a coordinate-sorted and indexed BAM or CRAM file containing *homepage*: https://github.com/dpryan79/PileOMeth ========== ============== -version toolchain +version toolchain ========== ============== ``0.1.11`` ``foss/2016b`` ========== ============== @@ -35155,34 +36491,35 @@ Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Py *homepage*: https://pillow.readthedocs.org/ ========= ================================= =================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================================= =================================================== -``3.2.0`` ``-Python-2.7.11`` ``intel/2016a`` -``3.2.0`` ``-Python-2.7.11-freetype-2.6.3`` ``foss/2016a``, ``intel/2016a`` -``3.4.2`` ``-Python-2.7.12`` ``intel/2016b`` -``3.4.2`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``3.4.2`` ``-Python-3.5.2-freetype-2.6.5`` ``intel/2016b`` -``4.1.0`` ``-Python-2.7.13`` ``intel/2017a`` -``4.1.1`` ``-Python-3.6.1`` ``intel/2017a`` -``4.2.1`` ``-Python-3.6.1`` ``intel/2017a`` -``4.3.0`` ``-Python-2.7.13`` ``intel/2017a`` -``4.3.0`` ``-Python-2.7.14`` ``intel/2017b`` -``4.3.0`` ``-Python-3.6.3`` ``foss/2017b`` -``5.0.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``5.0.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``5.0.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``5.3.0`` ``-Python-2.7.15`` ``foss/2018b`` +``3.2.0`` ``-Python-2.7.11`` ``intel/2016a`` +``3.2.0`` ``-Python-2.7.11-freetype-2.6.3`` ``foss/2016a``, ``intel/2016a`` +``3.4.2`` ``-Python-2.7.12`` ``intel/2016b`` +``3.4.2`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``3.4.2`` ``-Python-3.5.2-freetype-2.6.5`` ``intel/2016b`` +``4.1.0`` ``-Python-2.7.13`` ``intel/2017a`` +``4.1.1`` ``-Python-3.6.1`` ``intel/2017a`` +``4.2.1`` ``-Python-3.6.1`` ``intel/2017a`` +``4.3.0`` ``-Python-2.7.13`` ``intel/2017a`` +``4.3.0`` ``-Python-2.7.14`` ``intel/2017b`` +``4.3.0`` ``-Python-3.6.3`` ``foss/2017b`` +``5.0.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``5.0.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``5.0.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``5.3.0`` ``-Python-2.7.15`` ``foss/2018b`` ``5.3.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``6.0.0`` ``GCCcore/8.2.0`` -``6.2.1`` ``GCCcore/8.3.0`` -``6.2.2`` ``-Python-2.7.18`` ``foss/2020b`` -``7.0.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``8.0.1`` ``GCCcore/10.2.0`` -``8.2.0`` ``GCCcore/10.3.0`` -``8.3.1`` ``GCCcore/11.2.0`` -``8.3.2`` ``GCCcore/11.2.0`` -``9.1.0`` ``GCCcore/10.3.0`` -``9.1.1`` ``GCCcore/11.3.0`` +``6.0.0`` ``GCCcore/8.2.0`` +``6.2.1`` ``GCCcore/8.3.0`` +``6.2.2`` ``-Python-2.7.18`` ``foss/2020b`` +``7.0.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``8.0.1`` ``GCCcore/10.2.0`` +``8.2.0`` ``GCCcore/10.3.0`` +``8.3.1`` ``GCCcore/11.2.0`` +``8.3.2`` ``GCCcore/11.2.0`` +``9.1.0`` ``GCCcore/10.3.0`` +``9.1.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``9.2.0`` ``GCCcore/10.2.0`` ========= ================================= =================================================== @@ -35196,17 +36533,17 @@ Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Py *homepage*: https://github.com/uploadcare/pillow-simd =============== ================= =================================================== -version versionsuffix toolchain +version versionsuffix toolchain =============== ================= =================================================== -``5.0.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``5.0.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``5.3.0.post0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``6.0.x.post0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``7.1.2`` ``GCCcore/10.2.0`` -``7.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``8.2.0`` ``GCCcore/10.3.0`` -``8.3.1`` ``GCCcore/11.2.0`` -``8.3.2`` ``GCCcore/11.2.0`` -``9.2.0`` ``GCCcore/11.3.0`` +``6.0.x.post0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``7.1.2`` ``GCCcore/10.2.0`` +``7.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``8.2.0`` ``GCCcore/10.3.0`` +``8.3.1`` ``GCCcore/11.2.0`` +``8.3.2`` ``GCCcore/11.2.0`` +``9.2.0`` ``GCCcore/11.3.0`` =============== ================= =================================================== @@ -35220,7 +36557,7 @@ Pilon is an automated genome assembly improvement and variant detection tool *homepage*: https://github.com/broadinstitute/pilon ======== =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ======== =================== ========== ``1.22`` ``-Java-1.8`` ``system`` ``1.22`` ``-Java-1.8.0_162`` ``system`` @@ -35239,7 +36576,7 @@ PIMS is a lazy-loading interface to sequential data with numpy-like slicing. *homepage*: https://soft-matter.github.io/pims ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.4.1`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== @@ -35254,12 +36591,12 @@ Pindel can detect breakpoints of large deletions, medium sized insertions, inve *homepage*: http://gmt.genome.wustl.edu/packages/pindel/ -==================== ================================== -version toolchain -==================== ================================== -``0.2.5b8`` ``foss/2016b`` -``0.2.5b9-20170508`` ``GCC/11.2.0``, ``GCC/6.4.0-2.28`` -==================== ================================== +==================== ================================================== +version toolchain +==================== ================================================== +``0.2.5b8`` ``foss/2016b`` +``0.2.5b9-20170508`` ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/6.4.0-2.28`` +==================== ================================================== .. _list_software_Pingouin_841: @@ -35272,7 +36609,7 @@ Pingouin is an open-source statistical package written in Python 3 and based mos *homepage*: https://pingouin-stats.org/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.3.8`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -35287,11 +36624,12 @@ Pint is a Python package to define, operate and manipulate physical quantities: *homepage*: https://github.com/hgrecco/pint -======== ================= ================= -version versionsuffix toolchain -======== ================= ================= -``0.14`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -======== ================= ================= +========== ================= ================== +version versionsuffix toolchain +========== ================= ================== +``0.14`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.19.2`` ``GCCcore/11.2.0`` +========== ================= ================== .. _list_software_pip_329: @@ -35304,10 +36642,10 @@ The PyPA recommended tool for installing Python packages. *homepage*: https://pip.pypa.io ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``8.0.2`` ``-Python-2.7.11`` ``intel/2016a`` -``8.1.2`` ``-Python-2.7.11`` ``foss/2016a`` +``8.0.2`` ``-Python-2.7.11`` ``intel/2016a`` +``8.1.2`` ``-Python-2.7.11`` ``foss/2016a`` ``8.1.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ========= ================== =============================== @@ -35322,7 +36660,7 @@ An automated pipeline for analyses of fungal internal transcribed spacer (ITS) s *homepage*: https://github.com/hsgweon/pipits ======= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= ============== ``2.7`` ``-Python-3.8.2`` ``foss/2020a`` ``2.8`` ``foss/2021a`` @@ -35339,7 +36677,7 @@ pIRS (profile based Illumina pair-end Reads Simulator) is a program for simulati *homepage*: https://github.com/galaxy001/pirs ========= =============== -version toolchain +version toolchain ========= =============== ``2.0.2`` ``gompi/2019b`` ========= =============== @@ -35355,7 +36693,7 @@ Somatic and germline variant caller for amplicon data. Recommended caller for tu *homepage*: https://github.com/Illumina/Pisces ============ ================= -version toolchain +version toolchain ============ ================= ``5.2.7.47`` ``GCCcore/6.4.0`` ============ ================= @@ -35371,7 +36709,7 @@ piSvM is a parallel implementation of the Support Vector Machine (SVM) algorithm *homepage*: http://pisvm.sourceforge.net/ ======= =============== -version toolchain +version toolchain ======= =============== ``1.3`` ``intel/2017b`` ======= =============== @@ -35387,7 +36725,7 @@ piSvM is a parallel implementation of the Support Vector Machine (SVM) algorithm *homepage*: https://github.com/mricherzhagen/pisvm ================ =============== -version toolchain +version toolchain ================ =============== ``1.2-20150622`` ``intel/2017b`` ================ =============== @@ -35403,12 +36741,13 @@ Pixman is a low-level software library for pixel manipulation, providing featur *homepage*: http://www.pixman.org/ ========== ============================================================================================================================================ -version toolchain +version toolchain ========== ============================================================================================================================================ ``0.34.0`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``0.38.0`` ``GCCcore/8.2.0`` -``0.38.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``0.40.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``0.38.0`` ``GCCcore/8.2.0`` +``0.38.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``0.40.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``0.42.2`` ``GCCcore/12.2.0`` ========== ============================================================================================================================================ @@ -35422,7 +36761,7 @@ Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer sampl *homepage*: https://github.com/pmelsted/pizzly ========== ============== -version toolchain +version toolchain ========== ============== ``0.37.3`` ``foss/2018b`` ========== ============== @@ -35438,11 +36777,11 @@ pkg-config is a helper tool used when compiling applications and libraries. It *homepage*: http://www.freedesktop.org/wiki/Software/pkg-config/ ========== ================================================================================================================================================================================================================================================ -version toolchain +version toolchain ========== ================================================================================================================================================================================================================================================ -``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` -``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` +``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``0.29.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``intel/2017a``, ``system`` ========== ================================================================================================================================================================================================================================================ @@ -35457,10 +36796,10 @@ pkgconf is a program which helps to configure compiler and linker flags for deve *homepage*: https://github.com/pkgconf/pkgconf ========= ================================================== -version toolchain +version toolchain ========= ================================================== ``1.8.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``system`` -``1.9.3`` ``GCCcore/12.2.0`` +``1.9.3`` ``GCCcore/12.2.0`` ========= ================================================== @@ -35474,25 +36813,25 @@ pkgconfig is a Python module to interface with the pkg-config command line tool *homepage*: https://github.com/matze/pkgconfig ========= ================== =================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =================================================== -``1.1.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``1.1.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.1.0`` ``-Python-3.5.1`` ``foss/2016a`` -``1.1.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``1.2.2`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``1.1.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``1.1.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``1.1.0`` ``-Python-3.5.1`` ``foss/2016a`` +``1.1.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``1.2.2`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` ``1.2.2`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b`` -``1.2.2`` ``-Python-3.6.1`` ``foss/2017a``, ``intel/2017a`` +``1.2.2`` ``-Python-3.6.1`` ``foss/2017a``, ``intel/2017a`` ``1.2.2`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b`` -``1.3.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``1.3.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``1.3.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``1.3.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.3.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.3.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``1.5.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``1.5.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``1.5.1`` ``-python`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0`` -``1.5.4`` ``-python`` ``GCCcore/10.3.0`` -``1.5.5`` ``-python`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.5.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``1.5.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``1.5.1`` ``-python`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0`` +``1.5.4`` ``-python`` ``GCCcore/10.3.0`` +``1.5.5`` ``-python`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ================== =================================================== @@ -35506,7 +36845,7 @@ PlantCV: Plant phenotyping using computer vision. *homepage*: https://pypi.org/project/plantcv/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``3.8.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -35522,7 +36861,7 @@ Plasmid exploration of bacterial genomes *homepage*: https://github.com/GuilhemRoyer/PlaScope ========= ============== -version toolchain +version toolchain ========= ============== ``1.3.1`` ``foss/2018b`` ========= ============== @@ -35538,7 +36877,7 @@ Open source Python ecosystem for plasma research and education *homepage*: https://www.plasmapy.org ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.3.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -35554,7 +36893,7 @@ PLAST is a parallel alignment search tool for comparing large protein banks *homepage*: http://www.irisa.fr/symbiose/projects/plast/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.3.1`` ``-Java-1.8.0_92`` ``foss/2016a`` ========= ================== ============== @@ -35570,9 +36909,9 @@ PLATform for Assembling NUcleotide Sequences *homepage*: http://platanus.bio.titech.ac.jp/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== -``1.2.1`` ``-linux-x86_64`` ``system`` +``1.2.1`` ``-linux-x86_64`` ``system`` ``1.2.4`` ``foss/2017a`` ========= ================= ============== @@ -35587,7 +36926,7 @@ Platypus is a tool designed for efficient and accurate variant-detection in hig *homepage*: http://www.well.ox.ac.uk/platypus ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.8.1`` ``-Python-2.7.11`` ``intel/2016a`` ========= ================== =============== @@ -35603,10 +36942,10 @@ plc is the public Planck Likelihood Code. It provides C and Fortran libraries t *homepage*: http://pla.esac.esa.int/pla/#home ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== ``3.0.1`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2018b`` -``3.0.1`` ``-Python-3.7.4`` ``foss/2019b`` +``3.0.1`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== =============================== @@ -35620,21 +36959,21 @@ Whole-genome association analysis toolset *homepage*: https://www.cog-genomics.org/plink/2.0/ =========================== ============================== -version toolchain +version toolchain =========================== ============================== ``1.07`` ``foss/2016a``, ``foss/2016b`` -``1.07-x86_64`` ``system`` -``1.9b5`` ``golf/2020a`` -``1.9b_4.1-x86_64`` ``system`` -``1.9b_6.17-x86_64`` ``system`` -``1.9b_6.21-x86_64`` ``system`` -``2.00-alpha1-x86_64`` ``system`` -``2.00-alpha2-x86_64`` ``system`` -``2.00-alpha2-x86_64_avx2`` ``system`` +``1.07-x86_64`` ``system`` +``1.9b5`` ``golf/2020a`` +``1.9b_4.1-x86_64`` ``system`` +``1.9b_6.17-x86_64`` ``system`` +``1.9b_6.21-x86_64`` ``system`` +``2.00-alpha1-x86_64`` ``system`` +``2.00-alpha2-x86_64`` ``system`` +``2.00-alpha2-x86_64_avx2`` ``system`` ``2.00a2.3`` ``GCC/10.3.0``, ``GCC/11.2.0`` -``2.00a2.3_x86_64`` ``system`` -``2.00a3.1`` ``GCC/11.2.0`` -``2.00a3.6`` ``GCC/11.3.0`` +``2.00a2.3_x86_64`` ``system`` +``2.00a3.1`` ``GCC/11.2.0`` +``2.00a3.6`` ``GCC/11.3.0`` =========================== ============================== @@ -35648,7 +36987,7 @@ plinkQC is a R/CRAN package for genotype quality control in genetic association *homepage*: https://meyer-lab-cshl.github.io/plinkQC/ ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``0.3.3`` ``-R-4.0.0`` ``foss/2020a`` ========= ============= ============== @@ -35664,7 +37003,7 @@ PLINK/SEQ is an open-source C/C++ library for working with human genetic varia *homepage*: https://atgu.mgh.harvard.edu/plinkseq/ ======== ========================================================== -version toolchain +version toolchain ======== ========================================================== ``0.10`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ======== ========================================================== @@ -35680,7 +37019,7 @@ Ploticus is a free GPL software utility that can produce various types of plots *homepage*: http://ploticus.sourceforge.net/doc/welcome.html ======== ================= -version toolchain +version toolchain ======== ================= ``2.42`` ``GCCcore/7.3.0`` ======== ================= @@ -35696,7 +37035,7 @@ Easily translate 'ggplot2' graphs to an interactive web-based version and/or cr *homepage*: https://cran.r-project.org/web/packages/plotly ========= ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= =============== ``4.7.1`` ``-R-3.4.0`` ``intel/2017a`` ``4.8.0`` ``-R-3.4.4`` ``intel/2018a`` @@ -35713,9 +37052,9 @@ Orca is an Electron app that generates images and reports of Plotly things like *homepage*: https://github.com/plotly/orca ========= ===================================== -version toolchain +version toolchain ========= ===================================== -``1.3.0`` ``GCCcore/8.3.0`` +``1.3.0`` ``GCCcore/8.3.0`` ``1.3.1`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= ===================================== @@ -35730,14 +37069,14 @@ An open-source, interactive graphing library for Python *homepage*: https://plot.ly/python ========== ====================================== -version toolchain +version toolchain ========== ====================================== -``4.1.0`` ``intel/2019a`` -``4.4.1`` ``intel/2019b`` -``4.8.1`` ``GCCcore/9.3.0`` +``4.1.0`` ``intel/2019a`` +``4.4.1`` ``intel/2019b`` +``4.8.1`` ``GCCcore/9.3.0`` ``4.14.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``5.1.0`` ``GCCcore/10.3.0`` -``5.4.0`` ``GCCcore/11.2.0`` +``5.1.0`` ``GCCcore/10.3.0`` +``5.4.0`` ``GCCcore/11.2.0`` ========== ====================================== @@ -35751,9 +37090,9 @@ PLplot is a cross-platform software package for creating scientific plots whose *homepage*: http://plplot.sourceforge.net ========== ================================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================================ =============== -``5.11.1`` ``-Java-1.7.0_80-Python-2.7.11`` ``foss/2016a`` +``5.11.1`` ``-Java-1.7.0_80-Python-2.7.11`` ``foss/2016a`` ``5.11.1`` ``-Java-1.7.0_80-Python-2.7.12`` ``intel/2016b`` ========== ================================ =============== @@ -35768,29 +37107,29 @@ PLUMED is an open source library for free energy calculations in molecular syste *homepage*: https://www.plumed.org ========= ================== ================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================================================ -``2.2.2`` ``intel/2016a`` -``2.2.3`` ``foss/2016b``, ``intel/2016b`` -``2.3.0`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b`` -``2.3.4`` ``intel/2017b`` +``2.2.2`` ``intel/2016a`` +``2.2.3`` ``foss/2016b``, ``intel/2016b`` +``2.3.0`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b`` +``2.3.4`` ``intel/2017b`` ``2.4.0`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``2.4.0`` ``-PathCV`` ``intel/2018a`` -``2.4.1`` ``iomkl/2018a`` -``2.4.2`` ``foss/2018b``, ``intel/2018b`` -``2.5.0`` ``intel/2018b`` -``2.5.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` -``2.5.1`` ``foss/2019a``, ``intel/2018b`` -``2.5.1`` ``-PathCV`` ``intel/2018b`` -``2.5.2`` ``-Python-3.7.2`` ``intel/2019a`` -``2.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``2.5b`` ``-Python-2.7.14`` ``intel/2018a`` -``2.6.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``2.6.2`` ``foss/2020b``, ``intel/2020b`` -``2.7.0`` ``foss/2020b`` -``2.7.2`` ``foss/2021a``, ``intel/2021a`` -``2.7.3`` ``foss/2021b`` -``2.8.0`` ``foss/2021b`` +``2.4.0`` ``-PathCV`` ``intel/2018a`` +``2.4.1`` ``iomkl/2018a`` +``2.4.2`` ``foss/2018b``, ``intel/2018b`` +``2.5.0`` ``intel/2018b`` +``2.5.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` +``2.5.1`` ``foss/2019a``, ``intel/2018b`` +``2.5.1`` ``-PathCV`` ``intel/2018b`` +``2.5.2`` ``-Python-3.7.2`` ``intel/2019a`` +``2.5.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``2.5b`` ``-Python-2.7.14`` ``intel/2018a`` +``2.6.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``2.6.2`` ``foss/2020b``, ``intel/2020b`` +``2.7.0`` ``foss/2020b`` +``2.7.2`` ``foss/2021a``, ``intel/2021a`` +``2.7.3`` ``foss/2021b`` +``2.8.0`` ``foss/2021b`` ========= ================== ================================================ @@ -35804,9 +37143,9 @@ PLY is yet another implementation of lex and yacc for Python. *homepage*: http://www.dabeaz.com/ply/ ======== ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ======== ================= ================= -``3.11`` ``-Python-3.6.4`` ``foss/2018a`` +``3.11`` ``-Python-3.6.4`` ``foss/2018a`` ``3.11`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ======== ================= ================= @@ -35821,20 +37160,21 @@ Process Management for Exascale Environments PMI Exascale (PMIx) represents an a *homepage*: https://pmix.org/ ========= ======================================================= -version toolchain +version toolchain ========= ======================================================= -``1.2.5`` ``GCCcore/6.4.0`` -``2.1.3`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``1.2.5`` ``GCCcore/6.4.0`` +``2.1.3`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``2.2.1`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``2.2.3`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``3.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``3.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2.2.3`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``3.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``3.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``3.1.4`` ``GCCcore/8.3.0`` -``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.2.3`` ``GCCcore/10.3.0`` -``4.1.0`` ``GCCcore/11.2.0`` -``4.1.2`` ``GCCcore/11.3.0`` +``3.1.4`` ``GCCcore/8.3.0`` +``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.2.3`` ``GCCcore/10.3.0`` +``4.1.0`` ``GCCcore/11.2.0`` +``4.1.2`` ``GCCcore/11.3.0`` +``4.2.2`` ``GCCcore/12.2.0`` ========= ======================================================= @@ -35848,7 +37188,7 @@ pmx (formerly pymacs) is a small bunch of classes to read structure files such a *homepage*: https://github.com/deGrootLab/pmx ======= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== ============== ``2.0`` ``-Python-2.7.18`` ``foss/2020b`` ======= ================== ============== @@ -35864,14 +37204,14 @@ Parallel netCDF: A Parallel I/O Library for NetCDF File Access *homepage*: https://trac.mcs.anl.gov/projects/parallel-netcdf ========== ===================================================================================== -version toolchain +version toolchain ========== ===================================================================================== -``1.8.1`` ``intel/2017a`` -``1.9.0`` ``intel/2018a`` -``1.10.0`` ``foss/2018b``, ``intel/2018b`` +``1.8.1`` ``intel/2017a`` +``1.9.0`` ``intel/2018a`` +``1.10.0`` ``foss/2018b``, ``intel/2018b`` ``1.12.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompic/2019b``, ``gompic/2020a``, ``iimpi/2020a`` -``1.12.2`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2021a`` -``1.12.3`` ``gompi/2021b``, ``gompi/2022a`` +``1.12.2`` ``gompi/2020b``, ``gompi/2021a``, ``gompic/2020b``, ``iimpi/2021a`` +``1.12.3`` ``gompi/2021b``, ``gompi/2022a`` ========== ===================================================================================== @@ -35882,17 +37222,17 @@ version toolchain Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard -*homepage*: https://portablecl.org +*homepage*: http://portablecl.org ======= ========================================================== -version toolchain +version toolchain ======= ========================================================== -``1.2`` ``GCC/7.3.0-2.30`` -``1.3`` ``GCC/8.2.0-2.31.1``, ``gcccuda/2019a`` -``1.4`` ``GCC/8.3.0``, ``gcccuda/2019b`` -``1.5`` ``GCC/9.3.0`` +``1.2`` ``GCC/7.3.0-2.30`` +``1.3`` ``GCC/8.2.0-2.31.1``, ``gcccuda/2019a`` +``1.4`` ``GCC/8.3.0``, ``gcccuda/2019b`` +``1.5`` ``GCC/9.3.0`` ``1.6`` ``GCC/10.2.0``, ``gcccuda/2020b``, ``iccifort/2020.4.304`` -``1.8`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` +``1.8`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0`` ======= ========================================================== @@ -35906,12 +37246,28 @@ Python packaging and dependency management made easy *homepage*: https://python-poetry.org/ ========= ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================= ``1.0.9`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ================= ================= +.. _list_software_polars_657: + +*polars* +++++++++ + +Lightning-fast DataFrame library for Rust and Python. + +*homepage*: https://pola.rs/ + +========== ============== +version toolchain +========== ============== +``0.15.6`` ``foss/2022a`` +========== ============== + + .. _list_software_polymake_866: *polymake* @@ -35922,7 +37278,7 @@ polymake is open source software for research in polyhedral geometry. It deals w *homepage*: https://polymake.org ========= ============== -version toolchain +version toolchain ========= ============== ``4.0r1`` ``foss/2019b`` ========= ============== @@ -35938,7 +37294,7 @@ Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI. *homepage*: http://www.pgroup.com/index.htm =========== ========== -version toolchain +version toolchain =========== ========== ``2016.03`` ``system`` ``2016.04`` ``system`` @@ -35956,7 +37312,7 @@ Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI. *homepage*: http://www.pgroup.com/index.htm =========== ========== -version toolchain +version toolchain =========== ========== ``2016.03`` ``system`` ``2016.04`` ``system`` @@ -35974,12 +37330,13 @@ Poppler is a PDF rendering library *homepage*: https://poppler.freedesktop.org =========== ============================== -version toolchain +version toolchain =========== ============================== -``0.70.1`` ``foss/2018b`` -``0.90.1`` ``GCCcore/8.3.0`` +``0.70.1`` ``foss/2018b`` +``0.90.1`` ``GCCcore/8.3.0`` ``21.06.1`` ``GCC/10.2.0``, ``GCC/10.3.0`` -``22.01.0`` ``GCC/11.2.0`` +``22.01.0`` ``GCC/11.2.0`` +``22.12.0`` ``GCC/11.3.0`` =========== ============================== @@ -35993,7 +37350,7 @@ A suite of population scale analysis tools for single-cell genomics data includi *homepage*: https://github.com/statgen/popscle ============ ============== -version toolchain +version toolchain ============ ============== ``0.1-beta`` ``foss/2019b`` ============ ============== @@ -36009,9 +37366,9 @@ Popt is a C library for parsing command line parameters. *homepage*: http://freecode.com/projects/popt ======== ========================= -version toolchain +version toolchain ======== ========================= -``1.14`` ``GCC/4.8.2`` +``1.14`` ``GCC/4.8.2`` ``1.16`` ``GCC/4.9.2``, ``system`` ======== ========================= @@ -36025,14 +37382,14 @@ Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. *homepage*: https://github.com/rrwick/Porechop -========= ================= ================== -version versionsuffix toolchain -========= ================= ================== -``0.2.3`` ``-Python-3.5.2`` ``foss/2016b`` -``0.2.4`` ``GCCcore/11.2.0`` -``0.2.4`` ``-Python-3.6.6`` ``foss/2018b`` -``0.2.4`` ``-Python-3.7.4`` ``intel/2019b`` -========= ================= ================== +========= ================= ====================================== +version versionsuffix toolchain +========= ================= ====================================== +``0.2.3`` ``-Python-3.5.2`` ``foss/2016b`` +``0.2.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``0.2.4`` ``-Python-3.6.6`` ``foss/2018b`` +``0.2.4`` ``-Python-3.7.4`` ``intel/2019b`` +========= ================= ====================================== .. _list_software_porefoam_857: @@ -36045,7 +37402,7 @@ Direct pore-scale simulation of single- and two-phase flow through confined medi *homepage*: https://github.com/ImperialCollegeLondon/porefoam ============== ============== -version toolchain +version toolchain ============== ============== ``2021-09-21`` ``foss/2020a`` ============== ============== @@ -36061,7 +37418,7 @@ A toolkit for working with nanopore sequencing data from Oxford Nanopore. *homepage*: https://poretools.readthedocs.io/en/latest/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.6.0`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============== @@ -36077,7 +37434,7 @@ Portcullis stands for PORTable CULLing of Invalid Splice junctions from pre-alig *homepage*: https://github.com/maplesond/portcullis ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.2.2`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -36093,7 +37450,7 @@ Postgres-XL is a horizontally scalable open source SQL database cluster, flexibl *homepage*: http://www.postgres-xl.org ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``9.5r1`` ``-Python-2.7.11`` ``intel/2016a`` ========= ================== =============== @@ -36109,22 +37466,22 @@ PostgreSQL is a powerful, open source object-relational database system. It is *homepage*: https://www.postgresql.org/ ========= ================== ================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================================================================ -``9.4.7`` ``-Python-2.7.11`` ``intel/2016a`` -``9.5.2`` ``-Python-2.7.11`` ``intel/2016a`` -``9.6.0`` ``-Python-2.7.12`` ``intel/2016b`` -``9.6.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``10.2`` ``-Python-2.7.14`` ``intel/2018a`` -``10.3`` ``foss/2018b`` +``9.4.7`` ``-Python-2.7.11`` ``intel/2016a`` +``9.5.2`` ``-Python-2.7.11`` ``intel/2016a`` +``9.6.0`` ``-Python-2.7.12`` ``intel/2016b`` +``9.6.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``10.2`` ``-Python-2.7.14`` ``intel/2018a`` +``10.3`` ``foss/2018b`` ``10.3`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``11.3`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` -``11.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``12.4`` ``GCCcore/9.3.0`` -``13.2`` ``GCCcore/10.2.0`` -``13.3`` ``GCCcore/10.3.0`` -``13.4`` ``GCCcore/11.2.0`` -``14.4`` ``GCCcore/11.3.0`` +``11.3`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``11.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``12.4`` ``GCCcore/9.3.0`` +``13.2`` ``GCCcore/10.2.0`` +``13.3`` ``GCCcore/10.3.0`` +``13.4`` ``GCCcore/11.2.0`` +``14.4`` ``GCCcore/11.3.0`` ========= ================== ================================================================ @@ -36138,7 +37495,7 @@ POT (Python Optimal Transport) is a Python library provide several solvers for o *homepage*: https://github.com/rflamary/POT ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.5.1`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================= =============== @@ -36154,12 +37511,12 @@ The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which *homepage*: https://www.povray.org/ ============ ================================================================================= -version toolchain +version toolchain ============ ================================================================================= -``3.7.0.0`` ``intel/2016b`` +``3.7.0.0`` ``intel/2016b`` ``3.7.0.7`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``3.7.0.8`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` -``3.7.0.10`` ``GCC/11.3.0`` +``3.7.0.8`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``3.7.0.10`` ``GCC/11.3.0`` ============ ================================================================================= @@ -36173,7 +37530,7 @@ PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangeno *homepage*: https://github.com/labgem/PPanGGOLiN =========== ============== -version toolchain +version toolchain =========== ============== ``1.1.136`` ``foss/2021b`` =========== ============== @@ -36189,7 +37546,7 @@ PPfold is a new implementation of pfold, written in Java 6.0. It can predict the *homepage*: ihttp://www.daimi.au.dk/~compbio/pfold/downloads.html ========= ================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ========== ``3.1.1`` ``-Java-1.8.0_66`` ``system`` ========= ================== ========== @@ -36205,7 +37562,7 @@ The Parma Polyhedra Library (PPL) provides numerical abstractions especially ta *homepage*: https://www.bugseng.com/parma-polyhedra-library ======= ================= -version toolchain +version toolchain ======= ================= ``1.2`` ``GCCcore/6.4.0`` ======= ================= @@ -36221,7 +37578,7 @@ Pplacer places query sequences on a fixed reference phylogenetic tree to maximiz *homepage*: http://matsen.fhcrc.org/pplacer/ =============== ========== -version toolchain +version toolchain =============== ========== ``1.1.alpha19`` ``system`` =============== ========== @@ -36237,7 +37594,7 @@ This Python package provides a wrapper to the C++ Parma Polyhedra Library (PPL). *homepage*: https://pypi.org/project/pplpy/ ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== ``0.8.4`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``0.8.4`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` @@ -36254,7 +37611,7 @@ PRANK is a probabilistic multiple alignment program for DNA, codon and amino-a *homepage*: http://wasabiapp.org/software/prank/ ========== ============================================================================== -version toolchain +version toolchain ========== ============================================================================== ``170427`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0``, ``intel/2018a`` ========== ============================================================================== @@ -36270,7 +37627,7 @@ PRC is a stand-alone program for aligning and scoring two profile hidden Markov *homepage*: http//supfam.org/PRC/ ========= =============== -version toolchain +version toolchain ========= =============== ``1.5.6`` ``intel/2018a`` ========= =============== @@ -36286,9 +37643,9 @@ preCICE (Precise Code Interaction Coupling Environment) is a coupling library fo *homepage*: https://www.precice.org/ ========= ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============================== -``2.1.1`` ``-Python-3.8.2`` ``foss/2020a`` +``2.1.1`` ``-Python-3.8.2`` ``foss/2020a`` ``2.2.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========= ================= =============================== @@ -36303,7 +37660,7 @@ A program to identify and mask regions with non-homologous adjacent characters i *homepage*: https://github.com/simonwhelan/prequal ======== ================== -version toolchain +version toolchain ======== ================== ``1.02`` ``GCCcore/11.2.0`` ======== ================== @@ -36319,11 +37676,11 @@ Software for predicting library complexity and genome coverage in high-throughpu *homepage*: https://smithlabresearch.org/software/preseq ========= =============================== -version toolchain +version toolchain ========= =============================== -``2.0.2`` ``foss/2016b`` +``2.0.2`` ``foss/2016b`` ``2.0.3`` ``foss/2018b``, ``intel/2018a`` -``3.1.2`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``3.1.2`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========= =============================== @@ -36337,7 +37694,7 @@ Presto performs a fast Wilcoxon rank sum test and auROC analysis. *homepage*: https://github.com/immunogenomics/presto ================== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ============= ============== ``1.0.0-20200718`` ``-R-4.1.2`` ``foss/2021b`` ================== ============= ============== @@ -36353,10 +37710,10 @@ PyYAML-based python module to produce pretty and readable YAML-serialized data. *homepage*: https://github.com/mk-fg/pretty-yaml =========== ================== -version toolchain +version toolchain =========== ================== -``19.12.0`` ``GCCcore/8.3.0`` -``20.4.0`` ``GCCcore/9.3.0`` +``19.12.0`` ``GCCcore/8.3.0`` +``20.4.0`` ``GCCcore/9.3.0`` ``21.10.1`` ``GCCcore/10.3.0`` =========== ================== @@ -36371,11 +37728,11 @@ Primer3 is a widely used program for designing PCR primers (PCR = 'Polymerase Ch *homepage*: https://primer3.org/ ========= ========================================================= -version toolchain +version toolchain ========= ========================================================= -``2.3.7`` ``intel/2017b`` +``2.3.7`` ``intel/2017b`` ``2.4.0`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``2.5.0`` ``GCC/9.3.0`` +``2.5.0`` ``GCC/9.3.0`` ========= ========================================================= @@ -36389,7 +37746,7 @@ A bioinformatics tool to PRe-process and show INformation of SEQuence data. *homepage*: http://prinseq.sourceforge.net ========== ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================ ============== ``0.20.4`` ``-Perl-5.28.0`` ``foss/2018b`` ``0.20.4`` ``-Perl-5.32.0`` ``foss/2020b`` @@ -36407,7 +37764,7 @@ X.org PrintProto protocol headers. *homepage*: http://xorg.freedesktop.org/ ========= =============== -version toolchain +version toolchain ========= =============== ``1.0.5`` ``intel/2016a`` ========= =============== @@ -36423,10 +37780,10 @@ PRISMS-PF is a powerful, massively parallel finite element code for conducting p *homepage*: https://prisms-center.github.io/phaseField ========= =============================== -version toolchain +version toolchain ========= =============================== ``2.1.1`` ``foss/2019a``, ``intel/2019a`` -``2.2`` ``foss/2021a`` +``2.2`` ``foss/2021a`` ========= =============================== @@ -36440,7 +37797,7 @@ Tool for genome-wide association analysis of imputed genetic data. *homepage*: http://www.genabel.org/packages/ProbABEL ========= ============================= -version toolchain +version toolchain ========= ============================= ``0.5.0`` ``GCCcore/9.3.0``, ``system`` ========= ============================= @@ -36456,9 +37813,9 @@ Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbi *homepage*: https://github.com/hyattpd/Prodigal/ ========= ========================================================================================================================================================= -version toolchain +version toolchain ========= ========================================================================================================================================================= -``2.6.2`` ``GCC/4.9.3-binutils-2.25`` +``2.6.2`` ``GCC/4.9.3-binutils-2.25`` ``2.6.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ========================================================================================================================================================= @@ -36473,7 +37830,7 @@ ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate program *homepage*: http://www.bioinf.org.uk/software/profit ======= ============== -version toolchain +version toolchain ======= ============== ``3.3`` ``GCC/10.3.0`` ======= ============== @@ -36489,18 +37846,18 @@ Program proj is a standard Unix filter function which converts geographic longit *homepage*: https://proj.org ========= ================================================================================= -version toolchain +version toolchain ========= ================================================================================= -``4.9.2`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``4.9.2`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``4.9.3`` ``foss/2016b``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``5.0.0`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018a`` -``6.0.0`` ``GCCcore/8.2.0`` -``6.2.1`` ``GCCcore/8.3.0`` -``7.0.0`` ``GCCcore/9.3.0`` -``7.2.1`` ``GCCcore/10.2.0`` -``8.0.1`` ``GCCcore/10.3.0`` -``8.1.0`` ``GCCcore/11.2.0`` -``9.0.0`` ``GCCcore/11.3.0`` +``6.0.0`` ``GCCcore/8.2.0`` +``6.2.1`` ``GCCcore/8.3.0`` +``7.0.0`` ``GCCcore/9.3.0`` +``7.2.1`` ``GCCcore/10.2.0`` +``8.0.1`` ``GCCcore/10.3.0`` +``8.1.0`` ``GCCcore/11.2.0`` +``9.0.0`` ``GCCcore/11.3.0`` ========= ================================================================================= @@ -36514,7 +37871,7 @@ An open source software framework for quantum computing *homepage*: https://projectq.ch ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.4.2`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================= =============== @@ -36530,12 +37887,12 @@ Prokka is a software tool for the rapid annotation of prokaryotic genomes. *homepage*: https://www.vicbioinformatics.com/software.prokka.shtml ========== ================== ================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================================================================== -``1.11`` ``-BioPerl-1.7.0`` ``foss/2016b`` -``1.13`` ``-BioPerl-1.7.2`` ``intel/2018a`` -``1.13.4`` ``foss/2018b`` -``1.13.7`` ``gompi/2019a`` +``1.11`` ``-BioPerl-1.7.0`` ``foss/2016b`` +``1.13`` ``-BioPerl-1.7.2`` ``intel/2018a`` +``1.13.4`` ``foss/2018b`` +``1.13.7`` ``gompi/2019a`` ``1.14.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompi/2020b``, ``gompi/2021a`` ========== ================== ================================================================== @@ -36550,13 +37907,13 @@ prompt_toolkit is a Python library for building powerful interactive command lin *homepage*: https://github.com/jonathanslenders/python-prompt-toolkit ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== -``1.0.3`` ``-Python-2.7.11`` ``foss/2016a`` -``1.0.3`` ``-Python-3.5.1`` ``foss/2016a`` +``1.0.3`` ``-Python-2.7.11`` ``foss/2016a`` +``1.0.3`` ``-Python-3.5.1`` ``foss/2016a`` ``1.0.6`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.0.6`` ``-Python-3.5.2`` ``intel/2016b`` -``1.0.13`` ``-Python-2.7.12`` ``intel/2016b`` +``1.0.6`` ``-Python-3.5.2`` ``intel/2016b`` +``1.0.13`` ``-Python-2.7.12`` ``intel/2016b`` ========== ================== =============================== @@ -36570,7 +37927,7 @@ PacBio hybrid error correction through iterative short read consensus *homepage*: https://github.com/BioInf-Wuerzburg/proovread ========== =============== -version toolchain +version toolchain ========== =============== ``2.14.1`` ``intel/2017b`` ========== =============== @@ -36586,7 +37943,7 @@ Propy is a protein description software. It allows analyzing sequence-derived st *homepage*: https://code.google.com/archive/p/protpy ======= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== ============== ``1.0`` ``-Python-2.7.13`` ``foss/2017a`` ======= ================== ============== @@ -36602,7 +37959,7 @@ Proteinortho is a tool to detect orthologous genes within different species. *homepage*: http://www.bioinf.uni-leipzig.de/Software/proteinortho/ ========= ============================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============================= ============== ``5.16b`` ``-Python-3.6.4-Perl-5.26.1`` ``foss/2018a`` ========= ============================= ============== @@ -36618,10 +37975,10 @@ ProtHint is a pipeline for predicting and scoring hints (in the form of introns, *homepage*: https://github.com/gatech-genemark/ProtHint ========= ================= ======================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ======================================== ``2.4.0`` ``-Python-3.7.2`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2.4.0`` ``-Python-3.7.4`` ``iccifort/2019.5.281`` +``2.4.0`` ``-Python-3.7.4`` ``iccifort/2019.5.281`` ========= ================= ======================================== @@ -36635,24 +37992,24 @@ Google Protocol Buffers *homepage*: https://github.com/google/protobuf/ =========== ==================================================================== -version toolchain +version toolchain =========== ==================================================================== ``2.5.0`` ``GCCcore/10.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``system`` -``2.6.1`` ``system`` -``3.0.2`` ``foss/2016a`` -``3.2.0`` ``foss/2016b``, ``intel/2016b`` -``3.3.0`` ``foss/2016b``, ``intel/2017a`` -``3.4.0`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` -``3.5.1`` ``intel/2017b`` -``3.6.0`` ``GCCcore/7.3.0`` -``3.6.1`` ``GCCcore/7.3.0`` -``3.6.1.2`` ``GCCcore/8.2.0`` -``3.7.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.10.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``3.13.0`` ``GCCcore/9.3.0`` -``3.14.0`` ``GCCcore/10.2.0`` -``3.17.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``3.19.4`` ``GCCcore/11.3.0`` +``2.6.1`` ``system`` +``3.0.2`` ``foss/2016a`` +``3.2.0`` ``foss/2016b``, ``intel/2016b`` +``3.3.0`` ``foss/2016b``, ``intel/2017a`` +``3.4.0`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` +``3.5.1`` ``intel/2017b`` +``3.6.0`` ``GCCcore/7.3.0`` +``3.6.1`` ``GCCcore/7.3.0`` +``3.6.1.2`` ``GCCcore/8.2.0`` +``3.7.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.10.0`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``3.13.0`` ``GCCcore/9.3.0`` +``3.14.0`` ``GCCcore/10.2.0`` +``3.17.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``3.19.4`` ``GCCcore/11.3.0`` =========== ==================================================================== @@ -36666,26 +38023,26 @@ Python Protocol Buffers runtime library. *homepage*: https://github.com/google/protobuf/ ========== ================== ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ====================================== -``3.0.2`` ``-Python-2.7.11`` ``foss/2016a`` -``3.0.2`` ``-Python-3.5.1`` ``foss/2016a`` -``3.2.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.2.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``3.3.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.3.0`` ``-Python-3.5.2`` ``foss/2016b`` -``3.3.0`` ``-Python-3.6.1`` ``intel/2017a`` -``3.4.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.4.0`` ``-Python-2.7.14`` ``intel/2017b`` -``3.4.0`` ``-Python-3.6.1`` ``intel/2017a`` -``3.4.0`` ``-Python-3.6.3`` ``intel/2017b`` -``3.6.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``3.6.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``3.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``3.13.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` -``3.14.0`` ``GCCcore/10.2.0`` +``3.0.2`` ``-Python-2.7.11`` ``foss/2016a`` +``3.0.2`` ``-Python-3.5.1`` ``foss/2016a`` +``3.2.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.2.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``3.3.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.3.0`` ``-Python-3.5.2`` ``foss/2016b`` +``3.3.0`` ``-Python-3.6.1`` ``intel/2017a`` +``3.4.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.4.0`` ``-Python-2.7.14`` ``intel/2017b`` +``3.4.0`` ``-Python-3.6.1`` ``intel/2017a`` +``3.4.0`` ``-Python-3.6.3`` ``intel/2017b`` +``3.6.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``3.6.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``3.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``3.13.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``3.14.0`` ``GCCcore/10.2.0`` ``3.17.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``3.19.4`` ``GCCcore/11.3.0`` +``3.19.4`` ``GCCcore/11.3.0`` ========== ================== ====================================== @@ -36699,7 +38056,7 @@ Minimalistic protocol buffer decoder and encoder in C++. *homepage*: https://github.com/mapbox/protozero ========= ================= -version toolchain +version toolchain ========= ================= ``1.6.8`` ``GCCcore/7.3.0`` ``1.7.0`` ``GCCcore/8.3.0`` @@ -36716,12 +38073,12 @@ PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculatin *homepage*: https://www.prsice.info/ ========== ===================================== -version toolchain +version toolchain ========== ===================================== -``2.2.12`` ``GCCcore/8.3.0`` -``2.3.1`` ``GCCcore/9.3.0`` +``2.2.12`` ``GCCcore/8.3.0`` +``2.3.1`` ``GCCcore/9.3.0`` ``2.3.3`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``2.3.5`` ``GCCcore/11.3.0`` +``2.3.5`` ``GCCcore/11.3.0`` ========== ===================================== @@ -36735,11 +38092,11 @@ ParaStation is a robust and efficient cluster middleware, consisting of a high- *homepage*: http://www.par-tec.com ============ ============= -version toolchain +version toolchain ============ ============= ``5.0.43`` ``GCC/4.8.2`` ``5.0.44-1`` ``GCC/4.9.2`` -``5.0.48-1`` ``system`` +``5.0.48-1`` ``system`` ============ ============= @@ -36753,7 +38110,7 @@ PSI4 is an open-source suite of ab initio quantum chemistry programs designed fo *homepage*: http://www.psicode.org/ ================== ===================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ===================== =============== ``4.0b6-20160201`` ``-mt-Python-2.7.11`` ``intel/2016a`` ================== ===================== =============== @@ -36769,17 +38126,33 @@ PSI4 is an open-source suite of ab initio quantum chemistry programs designed fo *homepage*: http://www.psicode.org/ ========= ========================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ========================= =============== ``1.0`` ``-Python-2.7.11`` ``intel/2016a`` ``1.0`` ``-mt-Python-2.7.11`` ``intel/2016a`` ``1.2.1`` ``-Python-2.7.15`` ``intel/2018b`` ``1.2.1`` ``-Python-2.7.15-maxam8`` ``intel/2018b`` -``1.3.1`` ``-Python-3.7.2`` ``foss/2019a`` +``1.3.1`` ``-Python-3.7.2`` ``foss/2019a`` ``1.3.2`` ``-Python-3.7.4`` ``intel/2019b`` ========= ========================= =============== +.. _list_software_PsiCLASS_674: + +*PsiCLASS* +++++++++++ + +PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. + +*homepage*: https://github.com/splicebox/PsiCLASS + +========= ============== +version toolchain +========= ============== +``1.0.3`` ``GCC/11.2.0`` +========= ============== + + .. _list_software_PSIPRED_535: *PSIPRED* @@ -36790,7 +38163,7 @@ Accurate protein secondary structure prediction *homepage*: http://bioinf.cs.ucl.ac.uk ======== ============= -version toolchain +version toolchain ======== ============= ``4.02`` ``GCC/8.3.0`` ======== ============= @@ -36806,7 +38179,7 @@ This software package infers population size history from a diploid sequence usi *homepage*: https://github.com/lh3/psmc ========= ============================== -version toolchain +version toolchain ========= ============================== ``0.6.5`` ``foss/2016a``, ``foss/2018a`` ========= ============================== @@ -36822,7 +38195,7 @@ ParaStation MPI is an open source high-performance MPI 3.0 implementation, based *homepage*: https://github.com/ParaStation/psmpi2 =========== ============= ============= -version versionsuffix toolchain +version versionsuffix toolchain =========== ============= ============= ``5.1.0-1`` ``GCC/4.9.2`` ``5.1.5-1`` ``GCC/4.9.3`` @@ -36840,7 +38213,7 @@ ParaStation is a robust and efficient cluster middleware, consisting of a high- *homepage*: http://www.par-tec.com ========== ============= ============= -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ============= ``5.0.29`` ``GCC/4.8.2`` ``5.0.29`` ``-mt`` ``GCC/4.8.2`` @@ -36857,7 +38230,7 @@ Interpolating scaling function Poisson Solver Library *homepage*: http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html ========= ================================================================================================= -version toolchain +version toolchain ========= ================================================================================================= ``1.7.6`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ``1.8.3`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b`` @@ -36874,7 +38247,7 @@ PSORTb v3.0.4 is the most precise bacterial localization prediction tool availab *homepage*: http://psort.org/psortb/index.html ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``3.0.4`` ``-Perl-5.22.1`` ``foss/2016a`` ========= ================ ============== @@ -36890,7 +38263,7 @@ psrecord is a small utility that uses the psutil library to record the CPU and *homepage*: https://github.com/astrofrog/psrecord ======= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== =============== ``1.1`` ``-Python-2.7.14`` ``intel/2018a`` ``1.1`` ``-Python-2.7.15`` ``intel/2018b`` @@ -36909,7 +38282,7 @@ pstoedit translates PostScript and PDF graphics into other vector formats *homepage*: http://pstoedit.net/ ======== ==================================== -version toolchain +version toolchain ======== ==================================== ``3.70`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ======== ==================================== @@ -36924,17 +38297,18 @@ A cross-platform process and system utilities module for Python *homepage*: https://github.com/giampaolo/psutil -========= ================== =============================== -version versionsuffix toolchain -========= ================== =============================== -``4.2.0`` ``-Python-2.7.11`` ``intel/2016a`` +========= ================== ====================================== +version versionsuffix toolchain +========= ================== ====================================== +``4.2.0`` ``-Python-2.7.11`` ``intel/2016a`` ``4.3.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``5.4.3`` ``-Python-2.7.14`` ``intel/2017b`` -``5.4.7`` ``-Python-2.7.15`` ``foss/2018b`` -``5.4.7`` ``-Python-3.6.6`` ``foss/2018b`` -``5.6.1`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``5.6.3`` ``GCCcore/8.2.0`` -========= ================== =============================== +``5.4.3`` ``-Python-2.7.14`` ``intel/2017b`` +``5.4.7`` ``-Python-2.7.15`` ``foss/2018b`` +``5.4.7`` ``-Python-3.6.6`` ``foss/2018b`` +``5.6.1`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``5.6.3`` ``GCCcore/8.2.0`` +``5.9.3`` ``GCCcore/10.2.0``, ``GCCcore/11.3.0`` +========= ================== ====================================== .. _list_software_psycopg2_823: @@ -36947,11 +38321,11 @@ Psycopg is the most popular PostgreSQL adapter for the Python programming langua *homepage*: http://initd.org/psycopg/ ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== ``2.7`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.8.3`` ``-Python-3.7.2`` ``foss/2019a`` -``2.8.6`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``2.8.3`` ``-Python-3.7.2`` ``foss/2019a`` +``2.8.6`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ========= ================== =============================== @@ -36965,7 +38339,7 @@ ptemcee, pronounced "tem-cee", is fork of Daniel Foreman-Mackey's wonderful emce *homepage*: https://github.com/willvousden/ptemcee ========= ============== -version toolchain +version toolchain ========= ============== ``1.0.0`` ``foss/2019a`` ========= ============== @@ -36981,7 +38355,7 @@ Post-Transcriptional Exon Shuffling (PTES) Identification Pipeline *homepage*: https://sourceforge.net/projects/ptesfinder-v1/ ======= =============== -version toolchain +version toolchain ======= =============== ``1`` ``intel/2017b`` ======= =============== @@ -36997,7 +38371,7 @@ This repository contains C++ source code for the TCR clustering and correlation *homepage*: https://github.com/phbradley/pubtcrs ============ =============== -version toolchain +version toolchain ============ =============== ``20180622`` ``intel/2019a`` ============ =============== @@ -37012,12 +38386,12 @@ pugixml is a light-weight C++ XML processing library *homepage*: https://pugixml.org/ -========== ================== -version toolchain -========== ================== +========== ====================================== +version toolchain +========== ====================================== ``1.11.4`` ``GCCcore/10.3.0`` -``1.12.1`` ``GCCcore/11.2.0`` -========== ================== +``1.12.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========== ====================================== .. _list_software_pullseq_774: @@ -37029,11 +38403,11 @@ Utility program for extracting sequences from a fasta/fastq file *homepage*: https://github.com/bcthomas/pullseq -========= ===================================== -version toolchain -========= ===================================== -``1.0.2`` ``GCCcore/11.2.0``, ``GCCcore/7.3.0`` -========= ===================================== +========= ========================================================= +version toolchain +========= ========================================================= +``1.0.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/7.3.0`` +========= ========================================================= .. _list_software_PuLP_353: @@ -37046,7 +38420,7 @@ PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and c *homepage*: https://github.com/coin-or/pulp ========= ============== -version toolchain +version toolchain ========= ============== ``2.5.1`` ``foss/2021a`` ========= ============== @@ -37062,7 +38436,7 @@ purge haplotigs and overlaps in an assembly based on read depth *homepage*: https://github.com/dfguan/purge_dups ========= ============== -version toolchain +version toolchain ========= ============== ``1.2.5`` ``foss/2021b`` ========= ============== @@ -37078,7 +38452,7 @@ library with cross-python path, ini-parsing, io, code, log facilities *homepage*: https://pylib.readthedocs.org/ ========== ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ============== ``1.4.31`` ``-Python-2.7.11`` ``foss/2016a`` ``1.4.31`` ``-Python-3.5.1`` ``foss/2016a`` @@ -37095,9 +38469,9 @@ A python library for manipulating sequential and combinatorial circuits. This mo *homepage*: https://github.com/mvcisback/py-aiger ========== ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================== -``6.1.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``6.1.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``6.1.14`` ``GCCcore/10.2.0`` ========== ================= ================== @@ -37112,7 +38486,7 @@ Aiger to BDD bridge. *homepage*: https://github.com/mvcisback/py-aiger-bdd ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -37128,7 +38502,7 @@ py-cpuinfo gets CPU info with pure Python. *homepage*: https://github.com/workhorsy/py-cpuinfo ========= ========== -version toolchain +version toolchain ========= ========== ``5.0.0`` ``system`` ========= ========== @@ -37144,7 +38518,7 @@ Massively parallel, distributed and scalable ABC-SMC (Approximate Bayesian Compu *homepage*: https://github.com/icb-dcm/pyabc ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.10.4`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================= ============== @@ -37160,11 +38534,11 @@ PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python *homepage*: https://pyamg.github.io ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``3.0.1`` ``-Python-2.7.11`` ``intel/2016a`` +``3.0.1`` ``-Python-2.7.11`` ``intel/2016a`` ``4.0.0`` ``foss/2020b``, ``intel/2020b`` -``4.2.3`` ``foss/2021a`` +``4.2.3`` ``foss/2021a`` ========= ================== =============================== @@ -37178,7 +38552,7 @@ Python 3 Atmospheric Phase Screen *homepage*: https://github.com/AngeliqueBenoit/pyaps3 ============ ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ============== ``20190407`` ``-Python-3.7.2`` ``foss/2019a`` ============ ================= ============== @@ -37194,14 +38568,15 @@ pybedtools wraps and extends BEDTools and offers feature-level manipulations fro *homepage*: https://daler.github.io/pybedtools ========== ================== ======================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ======================================================= -``0.7.10`` ``-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` -``0.7.10`` ``-Python-3.6.6`` ``foss/2018b`` -``0.8.0`` ``foss/2019a``, ``intel/2019a`` -``0.8.1`` ``foss/2019b`` +``0.7.10`` ``-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` +``0.7.10`` ``-Python-3.6.6`` ``foss/2018b`` +``0.8.0`` ``foss/2019a``, ``intel/2019a`` +``0.8.1`` ``foss/2019b`` ``0.8.2`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``iccifort/2020.4.304`` -``0.8.2`` ``-Python-2.7.18`` ``GCC/10.2.0`` +``0.8.2`` ``-Python-2.7.18`` ``GCC/10.2.0`` +``0.9.0`` ``GCC/11.3.0`` ========== ================== ======================================================= @@ -37215,9 +38590,10 @@ PyBerny is an optimizer of molecular geometries with respect to the total energy *homepage*: https://github.com/jhrmnn/pyberny ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.6.2`` ``-Python-3.8.2`` ``intel/2020a`` +``0.6.3`` ``foss/2022a`` ========= ================= =============== @@ -37231,10 +38607,10 @@ A python extension, written in C, for quick access to bigBed files and access t *homepage*: https://github.com/deeptools/pyBigWig ========== ================= ================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================================== -``0.3.13`` ``-Python-3.6.6`` ``foss/2018b`` -``0.3.17`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` +``0.3.13`` ``-Python-3.6.6`` ``foss/2018b`` +``0.3.17`` ``GCCcore/8.2.0``, ``GCCcore/9.3.0`` ``0.3.18`` ``GCCcore/10.2.0``, ``foss/2021a``, ``foss/2021b`` ========== ================= ================================================== @@ -37249,12 +38625,12 @@ pybind11 is a lightweight header-only library that exposes C++ types in Python a *homepage*: https://pybind11.readthedocs.io ========= ================== ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================== -``2.2.4`` ``-Python-3.6.4`` ``foss/2018a`` -``2.2.4`` ``-Python-3.6.6`` ``intel/2018b`` -``2.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``2.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``2.2.4`` ``-Python-3.6.4`` ``foss/2018a`` +``2.2.4`` ``-Python-3.6.6`` ``intel/2018b`` +``2.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``2.6.0`` ``GCCcore/10.2.0`` ``2.6.2`` ``GCCcore/10.3.0`` ``2.7.1`` ``GCCcore/11.2.0`` @@ -37273,19 +38649,19 @@ Python bindings for the cairo library *homepage*: https://pycairo.readthedocs.io/ ========== ================== ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ====================================== -``1.10.0`` ``-Python-2.7.11`` ``intel/2016a`` -``1.16.1`` ``-Python-3.6.3`` ``foss/2017b`` -``1.16.2`` ``-Python-2.7.14`` ``intel/2017b`` -``1.18.0`` ``-Python-2.7.14`` ``intel/2018a`` -``1.18.0`` ``-Python-2.7.15`` ``foss/2018b`` -``1.18.0`` ``-Python-3.6.6`` ``foss/2018b`` -``1.18.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``1.18.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.20.0`` ``GCCcore/10.2.0`` +``1.10.0`` ``-Python-2.7.11`` ``intel/2016a`` +``1.16.1`` ``-Python-3.6.3`` ``foss/2017b`` +``1.16.2`` ``-Python-2.7.14`` ``intel/2017b`` +``1.18.0`` ``-Python-2.7.14`` ``intel/2018a`` +``1.18.0`` ``-Python-2.7.15`` ``foss/2018b`` +``1.18.0`` ``-Python-3.6.6`` ``foss/2018b`` +``1.18.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``1.18.2`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.20.0`` ``GCCcore/10.2.0`` ``1.20.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``1.21.0`` ``GCCcore/11.3.0`` +``1.21.0`` ``GCCcore/11.3.0`` ========== ================== ====================================== @@ -37299,12 +38675,28 @@ Python library for classifier calibration *homepage*: https://github.com/classifier-calibration/PyCalib ============== ============== -version toolchain +version toolchain ============== ============== ``0.1.0.dev0`` ``foss/2021b`` ============== ============== +.. _list_software_pyccel_640: + +*pyccel* +++++++++ + +Python extension language using accelerators + +*homepage*: https://github.com/pyccel/pyccel + +========= ============== +version toolchain +========= ============== +``1.7.0`` ``foss/2022a`` +========= ============== + + .. _list_software_PyCharm_692: *PyCharm* @@ -37315,7 +38707,7 @@ PyCharm Community Edition: Python IDE for Professional Developers *homepage*: https://www.jetbrains.com/pycharm/ ============ ========== -version toolchain +version toolchain ============ ========== ``2017.2.3`` ``system`` ``2019.3.1`` ``system`` @@ -37324,6 +38716,22 @@ version toolchain ============ ========== +.. _list_software_PyCheMPS2_763: + +*PyCheMPS2* ++++++++++++ + +PyCheMPS2 is a python interface to CheMPS2, for compilation without MPI. CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. + +*homepage*: https://sebwouters.github.io/CheMPS2 + +========== ============== +version toolchain +========== ============== +``1.8.12`` ``foss/2022a`` +========== ============== + + .. _list_software_PyCifRW_644: *PyCifRW* @@ -37334,7 +38742,7 @@ PyCIFRW provides support for reading and writing CIF (Crystallographic Informati *homepage*: https://bitbucket.org/jamesrhester/pycifrw/src/development ========= ================= -version toolchain +version toolchain ========= ================= ``4.4.2`` ``GCCcore/8.3.0`` ========= ================= @@ -37350,7 +38758,7 @@ PyClone is a Python package that wraps rclone and provides a threaded interface *homepage*: https://gitlab.com/ltgiv/pyclone ============ ================== -version toolchain +version toolchain ============ ================== ``2020.9b2`` ``GCCcore/10.2.0`` ============ ================== @@ -37366,7 +38774,7 @@ A stochastic numerical optimization algorithm for difficult (non-convex, ill-con *homepage*: https://github.com/CMA-ES/pycma ========= =============== -version toolchain +version toolchain ========= =============== ``2.7.0`` ``intel/2019a`` ========= =============== @@ -37382,12 +38790,12 @@ Official APIs for the MS-COCO dataset *homepage*: https://pypi.org/project/pycocotools ========= ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================== ``2.0.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.0.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.0.2`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` -``2.0.4`` ``foss/2021a`` +``2.0.4`` ``foss/2021a`` ========= ================= ================================== @@ -37401,7 +38809,7 @@ pycodestyle is a tool to check your Python code against some of the style conven *homepage*: https://pycodestyle.readthedocs.io ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``2.5.0`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== @@ -37417,11 +38825,11 @@ PyCogent is a software library for genomic biology. It is a fully integrated an *homepage*: http://pycogent.org ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``1.5.3`` ``-Python-2.7.12`` ``intel/2016b`` +``1.5.3`` ``-Python-2.7.12`` ``intel/2016b`` ``1.9`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.9`` ``-Python-2.7.15`` ``foss/2018b`` +``1.9`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== =============================== @@ -37435,7 +38843,7 @@ PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore *homepage*: https://tleonardi.github.io/pycoQC ========= ============== -version toolchain +version toolchain ========= ============== ``2.5.2`` ``foss/2021a`` ========= ============== @@ -37451,14 +38859,14 @@ PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python. *homepage*: https://mathema.tician.de/software/pycuda ============ =============================== ======================================= -version versionsuffix toolchain +version versionsuffix toolchain ============ =============================== ======================================= -``2016.1.2`` ``-Python-2.7.12`` ``intel/2016b`` -``2017.1.1`` ``-CUDA-9.0.176-Python-2.7.14`` ``foss/2017b`` -``2017.1.1`` ``-Python-2.7.14`` ``intel/2018a`` -``2018.1`` ``-Python-3.6.4-CUDA-9.1.85`` ``intel/2018a`` +``2016.1.2`` ``-Python-2.7.12`` ``intel/2016b`` +``2017.1.1`` ``-CUDA-9.0.176-Python-2.7.14`` ``foss/2017b`` +``2017.1.1`` ``-Python-2.7.14`` ``intel/2018a`` +``2018.1`` ``-Python-3.6.4-CUDA-9.1.85`` ``intel/2018a`` ``2019.1.2`` ``-Python-3.7.4`` ``fosscuda/2019b``, ``intelcuda/2019b`` -``2020.1`` ``fosscuda/2020b`` +``2020.1`` ``fosscuda/2020b`` ============ =============================== ======================================= @@ -37472,12 +38880,28 @@ PycURL is a Python interface to libcurl. PycURL can be used to fetch objects ide *homepage*: http://pycurl.io/ ============ ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ================= ``7.43.0.5`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ============ ================= ================= +.. _list_software_PyDamage_776: + +*PyDamage* +++++++++++ + +Pydamage, is a Python software to automate the process of contig damage identification and estimation. After modelling the ancient DNA damage using the C to T transitions, Pydamage uses a likelihood ratio test to discriminate between truly ancient, and modern contigs originating from sample contamination. + +*homepage*: https://github.com/maxibor/pydamage + +======== ============== +version toolchain +======== ============== +``0.70`` ``foss/2021a`` +======== ============== + + .. _list_software_pydantic_860: *pydantic* @@ -37487,11 +38911,12 @@ Data validation and settings management using Python type hinting. *homepage*: https://github.com/samuelcolvin/pydantic -========= ================= ================= -version versionsuffix toolchain -========= ================= ================= -``1.6.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -========= ================= ================= +========== ================= ================== +version versionsuffix toolchain +========== ================= ================== +``1.6.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``1.10.2`` ``GCCcore/11.2.0`` +========== ================= ================== .. _list_software_PyDatastream_1231: @@ -37504,7 +38929,7 @@ Lightweight SOAP client *homepage*: https://pypi.python.org/pypi/suds-py3 ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.5.1`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== @@ -37520,14 +38945,15 @@ Pure python package for DICOM medical file reading and writing. *homepage*: https://pydicom.github.io/ ========= ================== ====================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ====================================== -``0.9.9`` ``-Python-2.7.11`` ``intel/2016a`` -``1.2.2`` ``GCCcore/8.2.0`` -``1.4.2`` ``GCCcore/8.3.0`` -``2.1.2`` ``GCCcore/10.2.0`` -``2.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``0.9.9`` ``-Python-2.7.11`` ``intel/2016a`` +``1.2.2`` ``GCCcore/8.2.0`` +``1.4.2`` ``GCCcore/8.3.0`` +``2.1.2`` ``GCCcore/10.2.0`` +``2.1.2`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``2.2.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.3.0`` ``GCCcore/11.3.0`` ========= ================== ====================================== @@ -37541,7 +38967,7 @@ Pydlpoly is a molecular dynamics simulation package which is a modified version *homepage*: http://cmc.aci.ruhr-uni-bochum.de/cmc/ ============ ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============== ``20150225`` ``-Python-2.7.12`` ``intel/2016b`` ``20150225`` ``-Python-2.7.13`` ``intel/2017a`` @@ -37558,9 +38984,9 @@ Python interface to Graphviz's Dot language. *homepage*: https://github.com/pydot/pydot ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``1.4.1`` ``GCCcore/9.3.0``, ``foss/2019b`` +``1.4.1`` ``GCCcore/9.3.0``, ``foss/2019b`` ``1.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ========= ====================================== @@ -37575,11 +39001,11 @@ A basic Python-based EGA download client *homepage*: https://github.com/EGA-archive/ega-download-client ========== ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================== -``3.0.33`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``3.4.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``3.4.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``3.0.33`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``3.4.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``3.4.0`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``4.0.0`` ``GCCcore/11.2.0`` ========== ================= ================== @@ -37594,7 +39020,7 @@ PyEnchant is a spellchecking library for Python, based on the excellent Enchant *homepage*: https://pythonhosted.org/pyenchant/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.6.8`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== @@ -37610,7 +39036,7 @@ EVTK (Export VTK) package allows exporting data to binary VTK files for visualiz *homepage*: https://github.com/paulo-herrera/PyEVTK ========= ============== -version toolchain +version toolchain ========= ============== ``1.4.1`` ``foss/2021b`` ``2.0.0`` ``foss/2021b`` @@ -37627,7 +39053,7 @@ Python implementation of fast azimuthal integration. *homepage*: https://github.com/silx-kit/pyFAI ========== ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================== ``0.19.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``0.20.0`` ``foss/2020b``, ``fosscuda/2020b`` @@ -37644,10 +39070,10 @@ pyfaidx: efficient pythonic random access to fasta subsequences *homepage*: https://pypi.python.org/pypi/pyfaidx =========== ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================= ================== ``0.5.9.5`` ``GCCcore/10.2.0`` -``0.5.9.5`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.5.9.5`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``0.6.3.1`` ``GCCcore/10.3.0`` ``0.7.0`` ``GCCcore/11.2.0`` =========== ================= ================== @@ -37663,7 +39089,7 @@ fast, memory-efficient, pythonic (and command-line) access to fasta sequence fil *homepage*: https://pypi.org/project/pyfasta/ ========= ============== -version toolchain +version toolchain ========= ============== ``0.5.2`` ``foss/2020b`` ========= ============== @@ -37679,10 +39105,10 @@ Python FFmpeg wrapper *homepage*: https://github.com/mhaller/pyffmpeg =========== ================== ================ -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ================ ``2.1beta`` ``-Python-2.7.10`` ``gimkl/2.11.5`` -``2.1beta`` ``-Python-2.7.11`` ``intel/2016a`` +``2.1beta`` ``-Python-2.7.11`` ``intel/2016a`` =========== ================== ================ @@ -37696,10 +39122,10 @@ A pythonic wrapper around FFTW, the FFT library, presenting a unified interface *homepage*: https://github.com/pyFFTW/pyFFTW ========== ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================== -``0.11.1`` ``intel/2019a`` -``0.11.1`` ``-Python-3.6.6`` ``foss/2018b`` +``0.11.1`` ``intel/2019a`` +``0.11.1`` ``-Python-3.6.6`` ``foss/2018b`` ``0.12.0`` ``foss/2020b``, ``fosscuda/2020b`` ========== ================= ================================== @@ -37714,7 +39140,7 @@ The PyFITS module is a Python library providing access to FITS (Flexible Image T *homepage*: https://pythonhosted.org/pyfits/ ======= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== =============== ``3.5`` ``-Python-2.7.15`` ``intel/2018b`` ======= ================== =============== @@ -37730,7 +39156,7 @@ PyFMI is a package for loading and interacting with Functional Mock-Up Units (FM *homepage*: https://pypi.org/project/PyFMI/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``2.4.0`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============== @@ -37746,7 +39172,7 @@ A Python library to control OpenFOAM-runs and manipulate OpenFOAM-data. *homepage*: http://openfoamwiki.net/index.php/Contrib/PyFoam ========== ============== -version toolchain +version toolchain ========== ============== ``2020.5`` ``foss/2020b`` ========== ============== @@ -37762,9 +39188,9 @@ PyFR is an open-source Python based framework for solving advection-diffusion ty *homepage*: http://www.pyfr.org ========= ============================= =================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============================= =================== -``1.7.6`` ``-Python-3.6.4-CUDA-9.1.85`` ``intel/2018a`` +``1.7.6`` ``-Python-3.6.4-CUDA-9.1.85`` ``intel/2018a`` ``1.9.0`` ``-Python-3.7.4`` ``intelcuda/2019b`` ========= ============================= =================== @@ -37779,7 +39205,7 @@ PyFrag 2019 resolves three main challenges associated with the automatized compu *homepage*: https://pyfragdocument.readthedocs.io/en/latest/includeme.html ================= ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ================= ============= =============== ``2019-20220216`` ``-ASA`` ``intel/2020b`` ================= ============= =============== @@ -37795,7 +39221,7 @@ Python package for easy C++ declarations navigation. *homepage*: https://pypi.python.org/pypi/pygccxml ============ ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ============== ``20160706`` ``-Python-2.7.11`` ``foss/2016a`` ``20160706`` ``-Python-3.5.1`` ``foss/2016a`` @@ -37812,7 +39238,7 @@ pyGenomeTracks aims to produce high-quality genome browser tracks that are highl *homepage*: https://pygenometracks.readthedocs.io ======= ============== -version toolchain +version toolchain ======= ============== ``3.7`` ``foss/2021b`` ======= ============== @@ -37828,10 +39254,10 @@ PyGEOS is a C/Python library with vectorized geometry functions. The geometry op *homepage*: https://pygeos.readthedocs.io ========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============== -``0.7.1`` ``-Python-3.7.4`` ``foss/2019b`` -``0.8`` ``-Python-3.8.2`` ``foss/2020a`` +``0.7.1`` ``-Python-3.7.4`` ``foss/2019b`` +``0.8`` ``-Python-3.8.2`` ``foss/2020a`` ``0.10.2`` ``intel/2020b`` ========== ================= =============== @@ -37846,7 +39272,7 @@ pyGIMLi is an open-source multi-method library for solving inverse and forward *homepage*: http://www.pygimli.org/ ============ ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ============== ``20160803`` ``-Python-2.7.11`` ``foss/2016a`` ``20160803`` ``-Python-3.5.1`` ``foss/2016a`` @@ -37863,7 +39289,7 @@ Generic syntax highlighter suitable for use in code hosting, forums, wikis or ot *homepage*: https://pygments.org/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.1.3`` ``-Python-2.7.11`` ``foss/2016a`` ``2.1.3`` ``-Python-3.5.1`` ``foss/2016a`` @@ -37880,9 +39306,9 @@ pygmo is a scientific Python library for massively parallel optimization. *homepage*: https://esa.github.io/pygmo2 ========== ============================== -version toolchain +version toolchain ========== ============================== -``2.16.1`` ``foss/2020b`` +``2.16.1`` ``foss/2020b`` ``2.18.0`` ``foss/2021a``, ``foss/2021b`` ========== ============================== @@ -37897,15 +39323,15 @@ PyGObject is a Python package which provides bindings for GObject based librarie *homepage*: https://pygobject.readthedocs.io/ ========== ================== ================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================== -``2.28.6`` ``-Python-2.7.11`` ``intel/2016a`` -``2.28.6`` ``-Python-2.7.14`` ``intel/2017b`` -``2.28.7`` ``-Python-2.7.14`` ``intel/2018a`` -``2.28.7`` ``-Python-2.7.15`` ``foss/2018b`` -``3.34.0`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` -``3.34.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``3.34.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.28.6`` ``-Python-2.7.11`` ``intel/2016a`` +``2.28.6`` ``-Python-2.7.14`` ``intel/2017b`` +``2.28.7`` ``-Python-2.7.14`` ``intel/2018a`` +``2.28.7`` ``-Python-2.7.15`` ``foss/2018b`` +``3.34.0`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +``3.34.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``3.34.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``3.42.1`` ``GCCcore/11.3.0`` ========== ================== ================== @@ -37920,9 +39346,9 @@ PyGraphviz is a Python interface to the Graphviz graph layout and visualization *homepage*: https://pygraphviz.github.io/ ======= ============================== -version toolchain +version toolchain ======= ============================== -``1.5`` ``foss/2019b`` +``1.5`` ``foss/2019b`` ``1.7`` ``foss/2020b``, ``foss/2021a`` ======= ============================== @@ -37937,7 +39363,7 @@ Python interface for reading and writing GRIB data *homepage*: https://jswhit.github.io/pygrib ========= ============== -version toolchain +version toolchain ========= ============== ``2.0.4`` ``foss/2019a`` ========= ============== @@ -37953,11 +39379,11 @@ PyGTK lets you to easily create programs with a graphical user interface using *homepage*: http://www.pygtk.org/ ========== ================== ================================ -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================================ -``2.24.0`` ``-Python-2.7.11`` ``intel/2016a`` +``2.24.0`` ``-Python-2.7.11`` ``intel/2016a`` ``2.24.0`` ``-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` -``2.24.0`` ``-Python-2.7.15`` ``foss/2018b`` +``2.24.0`` ``-Python-2.7.15`` ``foss/2018b`` ========== ================== ================================ @@ -37971,11 +39397,11 @@ PyGTS is a python package used to construct, manipulate, and perform computati *homepage*: https://sourceforge.net/projects/pygts/ ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== ``0.3.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``0.3.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``0.3.1`` ``-Python-2.7.14`` ``intel/2018a`` +``0.3.1`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============================== @@ -37989,14 +39415,14 @@ PyGWAS is a library for running Genome Wide Association studies. *homepage*: https://github.com/timeu/pygwas ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``1.2.0`` ``-Python-2.7.11`` ``foss/2016a`` -``1.3.1`` ``-Python-2.7.11`` ``foss/2016a`` -``1.4.0`` ``-Python-2.7.11`` ``foss/2016a`` -``1.5.0`` ``-Python-2.7.11`` ``foss/2016a`` +``1.2.0`` ``-Python-2.7.11`` ``foss/2016a`` +``1.3.1`` ``-Python-2.7.11`` ``foss/2016a`` +``1.4.0`` ``-Python-2.7.11`` ``foss/2016a`` +``1.5.0`` ``-Python-2.7.11`` ``foss/2016a`` ``1.6.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``1.7.1`` ``-Python-2.7.13`` ``foss/2017a`` +``1.7.1`` ``-Python-2.7.13`` ``foss/2017a`` ========= ================== =============================== @@ -38010,12 +39436,28 @@ Python wrapper around the NCSA HDF version 4 library *homepage*: https://github.com/fhs/pyhdf ========== ============== -version toolchain +version toolchain ========== ============== ``0.10.1`` ``foss/2019a`` ========== ============== +.. _list_software_PyImageJ_758: + +*PyImageJ* +++++++++++ + +PyImageJ provides a set of wrapper functions for integration between ImageJ2 and Python. It also supports the original ImageJ API and data structures. A major advantage of this approach is the ability to combine ImageJ and ImageJ2 with other tools available from the Python software ecosystem, including NumPy, SciPy, scikit-image, CellProfiler, OpenCV, ITK and many more. + +*homepage*: https://pyimagej.readthedocs.io/ + +========= ============== +version toolchain +========= ============== +``1.3.1`` ``foss/2021a`` +========= ============== + + .. _list_software_pyiron_673: *pyiron* @@ -38026,7 +39468,7 @@ An integrated development environment (IDE) for computational materials science. *homepage*: https://github.com/pyiron/pyiron ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.2.5`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================= =============== @@ -38042,7 +39484,7 @@ Pyke introduces a form of Logic Programming (inspired by Prolog) to the Python *homepage*: http://sourceforge.net/projects/pyke/ ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``1.1.1`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================= =============== @@ -38058,7 +39500,7 @@ pylift is an uplift library that provides, primarily: (1) Fast uplift modeling *homepage*: https://github.com/df-foundation/pylift ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.1.5`` ``-Python-3.7.4`` ``foss/2019b`` ``0.1.5`` ``-Python-3.8.2`` ``foss/2020a`` @@ -38075,12 +39517,12 @@ Pylint is a tool that checks for errors in Python code, tries to enforce a codi *homepage*: https://www.pylint.org/ ========= ================== ================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================================================ ``1.9.3`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``1.9.5`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` -``1.9.5`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` -``2.7.4`` ``GCCcore/10.2.0`` +``1.9.5`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``1.9.5`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` +``2.7.4`` ``GCCcore/10.2.0`` ========= ================== ================================================ @@ -38094,15 +39536,15 @@ Python Materials Genomics is a robust materials analysis code that defines core *homepage*: https://pypi.python.org/pypi/pymatgen ============== ================== ========================= -version versionsuffix toolchain +version versionsuffix toolchain ============== ================== ========================= ``3.5.0`` ``-Python-2.7.11`` ``intel/2016.02-GCC-4.9`` -``4.1.1`` ``-Python-2.7.12`` ``intel/2016b`` -``4.3.2`` ``-Python-2.7.12`` ``intel/2016b`` -``4.7.3`` ``-Python-2.7.13`` ``intel/2017a`` -``2017.10.16`` ``-Python-2.7.14`` ``intel/2017b`` -``2017.10.16`` ``-Python-3.6.3`` ``intel/2017b`` -``2022.0.4`` ``foss/2020b`` +``4.1.1`` ``-Python-2.7.12`` ``intel/2016b`` +``4.3.2`` ``-Python-2.7.12`` ``intel/2016b`` +``4.7.3`` ``-Python-2.7.13`` ``intel/2017a`` +``2017.10.16`` ``-Python-2.7.14`` ``intel/2017b`` +``2017.10.16`` ``-Python-3.6.3`` ``intel/2017b`` +``2022.0.4`` ``foss/2020b`` ============== ================== ========================= @@ -38116,7 +39558,7 @@ Pymatgen-db is a database add-on for the Python Materials Genomics (pymatgen) m *homepage*: https://pypi.python.org/pypi/pymatgen-db ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.6.5`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== @@ -38132,7 +39574,7 @@ The pymbar package contains the pymbar suite of tools for the analysis of simula *homepage*: http://pymbar.readthedocs.io/en/master/ ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``3.0.3`` ``-Python-3.6.3`` ``intel/2017b`` ``3.0.3`` ``-Python-3.8.2`` ``intel/2020a`` @@ -38149,9 +39591,9 @@ Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machin *homepage*: https://docs.pymc.io/ ========== ================= ==================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ==================================================================== -``3.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``3.8`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.11.1`` ``foss/2021b``, ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021b`` ========== ================= ==================================================================== @@ -38166,7 +39608,7 @@ The PyMca X-Ray Fluorescence Toolkit, including PyMca5 and fisx. *homepage*: https://github.com/vasole/pymca ========= ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================== ``5.6.3`` ``foss/2020b``, ``fosscuda/2020b`` ``5.6.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` @@ -38183,7 +39625,7 @@ A comprehensive, fast, pure-Python memcached client. *homepage*: https://github.com/pinterest/pymemcache ========= ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============================== ``2.1.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ========= ================= =============================== @@ -38199,7 +39641,7 @@ PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D *homepage*: https://github.com/schrodinger/pymol-open-source ========= ============== -version toolchain +version toolchain ========= ============== ``2.5.0`` ``foss/2020b`` ========= ============== @@ -38215,10 +39657,10 @@ PyNAST is a reimplementation of the NAST sequence aligner, which has become a p *homepage*: https://biocore.github.io/pynast ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== ``1.2.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``1.2.2`` ``-Python-2.7.15`` ``foss/2018b`` +``1.2.2`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== =============================== @@ -38232,10 +39674,10 @@ Python bindings to ObjCryst++, the Object-Oriented Crystallographic Library. *homepage*: https://github.com/diffpy/pyobjcryst =============== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain =============== ================= =============== ``2.1.0.post2`` ``-Python-3.8.2`` ``intel/2020a`` -``2.2.1`` ``foss/2021b`` +``2.2.1`` ``foss/2021b`` =============== ================= =============== @@ -38249,7 +39691,7 @@ PyOD is a comprehensive and scalable Python toolkit for detecting outlying objec *homepage*: https://pyod.readthedocs.io ========= =============================== -version toolchain +version toolchain ========= =============================== ``0.8.7`` ``foss/2020b``, ``intel/2020b`` ========= =============================== @@ -38265,12 +39707,12 @@ Pyomo is a Python-based open-source software package that supports a diverse set *homepage*: https://www.pyomo.org/ ========= ================== ============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============================== -``5.5.0`` ``-Python-2.7.15`` ``foss/2018b`` -``5.5.0`` ``-Python-3.6.6`` ``foss/2018b`` +``5.5.0`` ``-Python-2.7.15`` ``foss/2018b`` +``5.5.0`` ``-Python-3.6.6`` ``foss/2018b`` ``6.0.1`` ``foss/2020b``, ``foss/2021a`` -``6.4.2`` ``foss/2022a`` +``6.4.2`` ``foss/2022a`` ========= ================== ============================== @@ -38284,11 +39726,11 @@ PyOpenCL lets you access GPUs and other massively parallel compute devices from *homepage*: https://mathema.tician.de/software/pyopencl/ ============= ================= =================================================== -version versionsuffix toolchain +version versionsuffix toolchain ============= ================= =================================================== -``2020.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2020.2.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``2021.1.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``2021.2.13`` ``foss/2021b`` +``2021.2.13`` ``foss/2021b`` ============= ================= =================================================== @@ -38302,16 +39744,16 @@ PyOpenGL is the most common cross platform Python binding to OpenGL and related *homepage*: http://pyopengl.sourceforge.net =========== ================== ========================================================= -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ========================================================= -``3.1.1a1`` ``GCCcore/8.2.0`` -``3.1.1a1`` ``-Python-2.7.11`` ``intel/2016a`` -``3.1.1a1`` ``-Python-2.7.12`` ``foss/2016b`` -``3.1.1a1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` -``3.1.3b2`` ``-Python-2.7.14`` ``intel/2018a`` -``3.1.3b2`` ``-Python-2.7.15`` ``foss/2018b`` +``3.1.1a1`` ``GCCcore/8.2.0`` +``3.1.1a1`` ``-Python-2.7.11`` ``intel/2016a`` +``3.1.1a1`` ``-Python-2.7.12`` ``foss/2016b`` +``3.1.1a1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` +``3.1.3b2`` ``-Python-2.7.14`` ``intel/2018a`` +``3.1.3b2`` ``-Python-2.7.15`` ``foss/2018b`` ``3.1.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0`` -``3.1.6`` ``GCCcore/11.2.0`` +``3.1.6`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` =========== ================== ========================================================= @@ -38325,7 +39767,7 @@ The pyparsing module is an alternative approach to creating and executing simple *homepage*: https://github.com/pyparsing/pyparsing ========= ================== ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================= ``2.4.6`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` ========= ================== ================= @@ -38341,7 +39783,7 @@ Py++ is a code generator for Boost.Python that simplifies writing Python bindin *homepage*: https://bitbucket.org/ompl/pyplusplus ============ ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ============== ``20160707`` ``-Python-2.7.11`` ``foss/2016a`` ``20160707`` ``-Python-3.5.1`` ``foss/2016a`` @@ -38358,7 +39800,7 @@ PYPOWER is a power flow and Optimal Power Flow (OPF) solver. It is a port of MAT *homepage*: https://github.com/rwl/PYPOWER ========== ============== -version toolchain +version toolchain ========== ============== ``5.1.15`` ``foss/2020b`` ========== ============== @@ -38373,16 +39815,17 @@ Python interface to PROJ4 library for cartographic transformations *homepage*: https://pyproj4.github.io/pyproj -=============== ================= ================== -version versionsuffix toolchain -=============== ================= ================== -``2.1.3`` ``GCCcore/8.2.0`` -``2.4.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``2.6.1.post1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +=============== ================= ====================================== +version versionsuffix toolchain +=============== ================= ====================================== +``2.1.3`` ``GCCcore/8.2.0`` +``2.4.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.6.1.post1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``3.0.1`` ``GCCcore/10.2.0`` ``3.1.0`` ``GCCcore/10.3.0`` -``3.3.1`` ``GCCcore/11.2.0`` -=============== ================= ================== +``3.3.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``3.4.0`` ``GCCcore/11.3.0`` +=============== ================= ====================================== .. _list_software_PyPSA_429: @@ -38395,7 +39838,7 @@ PyPSA is an open source toolbox for simulating and optimising modern power syste *homepage*: https://pypsa.readthedocs.io/ ========== ============== -version toolchain +version toolchain ========== ============== ``0.17.1`` ``foss/2020b`` ========== ============== @@ -38411,10 +39854,10 @@ QSTEM is a program for quantitative image simulation in electron microscopy, inc *homepage*: https://github.com/jacobjma/PyQSTEM ========= ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================== ``1.0.3`` ``-ASE-3.22.0`` ``foss/2020b``, ``fosscuda/2020b`` -``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ========= ================= ================================== @@ -38428,14 +39871,14 @@ PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework. *homepage*: http://www.riverbankcomputing.co.uk/software/pyqt ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== -``4.11.4`` ``-Python-2.7.11`` ``intel/2016a`` -``4.11.4`` ``-Python-2.7.12`` ``intel/2016b`` +``4.11.4`` ``-Python-2.7.11`` ``intel/2016a`` +``4.11.4`` ``-Python-2.7.12`` ``intel/2016b`` ``4.12`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``4.12`` ``-Python-2.7.13`` ``intel/2017a`` -``4.12.1`` ``-Python-2.7.14`` ``foss/2018a`` -``4.12.3`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``4.12`` ``-Python-2.7.13`` ``intel/2017a`` +``4.12.1`` ``-Python-2.7.14`` ``foss/2018a`` +``4.12.3`` ``-Python-2.7.15`` ``fosscuda/2018b`` ========== ================== =============================== @@ -38449,20 +39892,21 @@ PyQt5 is a set of Python bindings for v5 of the Qt application framework from Th *homepage*: http://www.riverbankcomputing.co.uk/software/pyqt ========== ================== ========================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ========================================================== -``5.7`` ``-Python-2.7.11`` ``foss/2016a`` -``5.7.1`` ``-Python-2.7.12`` ``intel/2016b`` -``5.8.2`` ``-Python-2.7.13`` ``intel/2017a`` -``5.9.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``5.9.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``5.11.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` -``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``5.13.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``5.15.1`` ``GCCcore/10.2.0`` -``5.15.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``5.7`` ``-Python-2.7.11`` ``foss/2016a`` +``5.7.1`` ``-Python-2.7.12`` ``intel/2016b`` +``5.8.2`` ``-Python-2.7.13`` ``intel/2017a`` +``5.9.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``5.9.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``5.11.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``5.13.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``5.15.1`` ``GCCcore/10.2.0`` +``5.15.1`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``5.15.4`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``5.15.5`` ``GCCcore/11.3.0`` ========== ================== ========================================================== @@ -38476,14 +39920,14 @@ PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and n *homepage*: http://www.pyqtgraph.org/ ========== ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================== -``0.10.0`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.10.0`` ``-Python-3.7.2`` ``intel/2019a`` -``0.11.0`` ``-Python-3.7.4`` ``foss/2019b`` +``0.10.0`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.10.0`` ``-Python-3.7.2`` ``intel/2019a`` +``0.11.0`` ``-Python-3.7.4`` ``foss/2019b`` ``0.11.1`` ``foss/2020b``, ``fosscuda/2020b`` -``0.12.3`` ``foss/2021a`` +``0.12.3`` ``foss/2021a`` ========== ================= ================================== @@ -38497,7 +39941,7 @@ Open-source python package for the extraction of Radiomics features from 2D and *homepage*: https://pyradiomics.readthedocs.io/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``3.0.1`` ``foss/2021a`` ``3.0.1`` ``-Python-3.7.4`` ``foss/2019b`` @@ -38514,7 +39958,7 @@ PyRe (Python Reliability) is a Python module for structural reliability analysis *homepage*: https://hackl.science/pyre ================== ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ================== ================= =============================== ``5.0.3-20190221`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ================== ================= =============================== @@ -38530,9 +39974,9 @@ PyRETIS is a Python library for rare event molecular simulations with emphasis o *homepage*: http://www.pyretis.org ========= ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============================== -``2.1.0`` ``-Python-3.6.6`` ``intel/2018b`` +``2.1.0`` ``-Python-3.6.6`` ``intel/2018b`` ``2.5.0`` ``foss/2020b``, ``intel/2020b`` ``2.5.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========= ================= =============================== @@ -38548,7 +39992,7 @@ Debugger capable of attaching to and injecting code into python processes. *homepage*: https://github.com/google/pyringe ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.0.2`` ``-Python-2.7.11`` ``intel/2016a`` ========= ================== =============== @@ -38564,7 +40008,7 @@ Pyro is a flexible, scalable deep probabilistic programming library built on PyT *homepage*: https://github.com/pyro-ppl/pyro-api ========= ================== -version toolchain +version toolchain ========= ================== ``0.1.2`` ``fosscuda/2020b`` ========= ================== @@ -38580,7 +40024,7 @@ Pyro is a flexible, scalable deep probabilistic programming library built on PyT *homepage*: https://github.com/pyro-ppl/pyro ========= ================== -version toolchain +version toolchain ========= ================== ``1.5.2`` ``fosscuda/2020b`` ========= ================== @@ -38596,7 +40040,7 @@ Pyro means PYthon Remote Objects. It is a library that enables you to build appl *homepage*: https://pypi.python.org/pypi/Pyro4 ======== ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================== ============== ``4.47`` ``-Python-2.7.11`` ``foss/2016a`` ======== ================== ============== @@ -38612,7 +40056,7 @@ PyRosetta is an interactive Python-based interface to the powerful Rosetta molec *homepage*: https://www.pyrosetta.org/ ================= ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ================= ================= ================= ``4.release-292`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ================= ================= ================= @@ -38628,30 +40072,30 @@ Pysam is a python module for reading and manipulating Samfiles. It's a lightwe *homepage*: https://github.com/pysam-developers/pysam ============ ================== ============================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ============================================================================================================== -``0.8.4`` ``-Python-2.7.12`` ``intel/2016b`` -``0.9.1.4`` ``-Python-2.7.12`` ``foss/2016b`` -``0.10.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``0.12.0.1`` ``-Python-2.7.13`` ``intel/2017a`` -``0.12.0.1`` ``-Python-2.7.14`` ``intel/2017b`` -``0.12.0.1`` ``-Python-3.6.3`` ``intel/2017b`` -``0.13`` ``-Python-2.7.14`` ``intel/2017b`` -``0.13.0`` ``-Python-3.6.3`` ``intel/2017b`` -``0.14`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``0.14`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``0.14`` ``-Python-3.6.4`` ``intel/2018a`` -``0.14.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``0.14.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``0.15.1`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``0.15.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.15.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``0.15.3`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``0.8.4`` ``-Python-2.7.12`` ``intel/2016b`` +``0.9.1.4`` ``-Python-2.7.12`` ``foss/2016b`` +``0.10.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``0.12.0.1`` ``-Python-2.7.13`` ``intel/2017a`` +``0.12.0.1`` ``-Python-2.7.14`` ``intel/2017b`` +``0.12.0.1`` ``-Python-3.6.3`` ``intel/2017b`` +``0.13`` ``-Python-2.7.14`` ``intel/2017b`` +``0.13.0`` ``-Python-3.6.3`` ``intel/2017b`` +``0.14`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``0.14`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``0.14`` ``-Python-3.6.4`` ``intel/2018a`` +``0.14.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``0.14.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.15.1`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.15.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.15.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` +``0.15.3`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ``0.16.0.1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``iccifort/2020.4.304`` -``0.16.0.1`` ``-Python-2.7.18`` ``GCC/10.2.0`` -``0.17.0`` ``GCC/11.2.0`` -``0.18.0`` ``GCC/11.2.0`` -``0.19.1`` ``GCC/11.3.0`` +``0.16.0.1`` ``-Python-2.7.18`` ``GCC/10.2.0`` +``0.17.0`` ``GCC/11.2.0`` +``0.18.0`` ``GCC/11.2.0`` +``0.19.1`` ``GCC/11.3.0`` ============ ================== ============================================================================================================== @@ -38665,7 +40109,7 @@ A Python utility for calculating statistics against genome positions based on se *homepage*: https://github.com/alimanfoo/pysamstats ========= ============== -version toolchain +version toolchain ========= ============== ``1.1.2`` ``foss/2020b`` ========= ============== @@ -38681,9 +40125,9 @@ PySAT is a Python toolkit, which aims at providing a simple and unified interfac *homepage*: https://pysathq.github.io/ =============== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain =============== ================= ============== -``0.1.6.dev11`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``0.1.6.dev11`` ``-Python-3.8.2`` ``GCC/9.3.0`` ``0.1.7.dev1`` ``GCC/10.2.0`` =============== ================= ============== @@ -38698,7 +40142,7 @@ pyScaf orders contigs from genome assemblies utilising several types of informat *homepage*: https://github.com/lpryszcz/pyScaf ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``0.12a4`` ``-Python-2.7.14`` ``intel/2017b`` ========== ================== =============== @@ -38714,7 +40158,7 @@ pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Singl *homepage*: https://github.com/aertslab/pySCENIC ========== ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============================== ``0.10.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ========== ================= =============================== @@ -38729,12 +40173,12 @@ PySCF is an open-source collection of electronic structure modules powered by Py *homepage*: http://www.pyscf.org -========= ================= ============================== -version versionsuffix toolchain -========= ================= ============================== -``1.6.3`` ``-Python-3.7.2`` ``foss/2019a`` -``1.7.6`` ``foss/2020b``, ``foss/2021a`` -========= ================= ============================== +========= ================= =============================================== +version versionsuffix toolchain +========= ================= =============================================== +``1.6.3`` ``-Python-3.7.2`` ``foss/2019a`` +``1.7.6`` ``foss/2020b``, ``foss/2021a``, ``gomkl/2021a`` +========= ================= =============================================== .. _list_software_pysheds_768: @@ -38747,7 +40191,7 @@ Simple and fast watershed delineation in python. *homepage*: https://mattbartos.com/pysheds/ =========== ============== -version toolchain +version toolchain =========== ============== ``0.2.7.1`` ``foss/2020b`` =========== ============== @@ -38763,9 +40207,9 @@ Pure Python read/write support for ESRI Shapefile format *homepage*: https://github.com/GeospatialPython/pyshp ========== ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================== -``1.2.12`` ``-Python-3.6.2`` ``foss/2017b`` +``1.2.12`` ``-Python-3.6.2`` ``foss/2017b`` ``2.1.3`` ``GCCcore/10.2.0`` ========== ================= ================== @@ -38780,7 +40224,7 @@ PySide2 is the official Python module from the Qt for Python project, which *homepage*: https://pypi.python.org/pypi/PySide2 ============ ================== -version toolchain +version toolchain ============ ================== ``5.14.2.3`` ``GCCcore/10.2.0`` ============ ================== @@ -38796,7 +40240,7 @@ A lightweight Python wrapper for SoX - Sound eXchange. Supported effects range *homepage*: https://github.com/carlthome/python-audio-effects ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.3.6`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -38812,11 +40256,11 @@ Pysolar is a collection of Python libraries for simulating the irradiation of a *homepage*: https://pysolar.org/ ======= ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= ================= -``0.7`` ``-Python-3.6.3`` ``intel/2017b`` -``0.7`` ``-Python-3.6.4`` ``intel/2018a`` -``0.8`` ``-Python-3.6.6`` ``intel/2018b`` +``0.7`` ``-Python-3.6.3`` ``intel/2017b`` +``0.7`` ``-Python-3.6.4`` ``intel/2018a`` +``0.8`` ``-Python-3.6.6`` ``intel/2018b`` ``0.8`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ======= ================= ================= @@ -38831,9 +40275,9 @@ Python bindings to spoa. *homepage*: https://github.com/nanoporetech/pyspoa ========= ================= ============================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============================================== -``0.0.4`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``0.0.4`` ``-Python-3.7.4`` ``GCC/8.3.0`` ``0.0.8`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0`` ========= ================= ============================================== @@ -38848,7 +40292,7 @@ pysqlite is an interface to the SQLite 3.x embedded relational database engine. *homepage*: https://pypi.python.org/pypi/pysqlite ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.8.2`` ``-Python-2.7.11`` ``foss/2016a`` ========= ================== ============== @@ -38864,14 +40308,30 @@ Python interface to Stan, a package for Bayesian inference using the No-U-Turn *homepage*: https://github.com/stan-dev/pystan ============ ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= =============================== -``2.19.0.0`` ``-Python-3.6.4`` ``intel/2018a`` +``2.19.0.0`` ``-Python-3.6.4`` ``intel/2018a`` ``2.19.1.1`` ``foss/2020b``, ``intel/2020b`` -``3.5.0`` ``foss/2021b`` +``3.5.0`` ``foss/2021b`` ============ ================= =============================== +.. _list_software_pysteps_792: + +*pysteps* ++++++++++ + +Pysteps is an open-source and community-driven Python library for probabilistic precipitation nowcasting, i.e. short-term ensemble prediction systems. + +*homepage*: https://pysteps.github.io/ + +========= ============== +version toolchain +========= ============== +``1.7.1`` ``foss/2022a`` +========= ============== + + .. _list_software_pystran_785: *pystran* @@ -38882,7 +40342,7 @@ Toolset of dynamical model STRucture ANalysis algorithms *homepage*: https://stijnvanhoey.github.io/pystran/ ============== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================== =============== ``2017.04.20`` ``-Python-2.7.14`` ``intel/2017b`` ============== ================== =============== @@ -38898,26 +40358,26 @@ PyTables is a package for managing hierarchical datasets and designed to efficie *homepage*: https://www.pytables.org =========== ================== =================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== =================================================================================== -``3.2.2`` ``-Python-2.7.12`` ``foss/2016b`` -``3.2.3.1`` ``-Python-2.7.12`` ``intel/2016b`` -``3.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.3.0`` ``-Python-3.5.2`` ``intel/2016b`` -``3.4.2`` ``-Python-2.7.13`` ``foss/2017a`` -``3.4.2`` ``-Python-3.6.1`` ``intel/2017a`` -``3.4.2`` ``-Python-3.6.3`` ``intel/2017b`` -``3.4.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``3.4.4`` ``-Python-2.7.15`` ``foss/2018b`` -``3.4.4`` ``-Python-3.5.1`` ``foss/2016a`` -``3.4.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``3.5.2`` ``intel/2019a`` -``3.5.2`` ``-Python-2.7.14`` ``intel/2018a`` -``3.5.2`` ``-Python-2.7.16`` ``intel/2019b`` -``3.5.2`` ``-Python-2.7.18`` ``foss/2020b`` +``3.2.2`` ``-Python-2.7.12`` ``foss/2016b`` +``3.2.3.1`` ``-Python-2.7.12`` ``intel/2016b`` +``3.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.3.0`` ``-Python-3.5.2`` ``intel/2016b`` +``3.4.2`` ``-Python-2.7.13`` ``foss/2017a`` +``3.4.2`` ``-Python-3.6.1`` ``intel/2017a`` +``3.4.2`` ``-Python-3.6.3`` ``intel/2017b`` +``3.4.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``3.4.4`` ``-Python-2.7.15`` ``foss/2018b`` +``3.4.4`` ``-Python-3.5.1`` ``foss/2016a`` +``3.4.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``3.5.2`` ``intel/2019a`` +``3.5.2`` ``-Python-2.7.14`` ``intel/2018a`` +``3.5.2`` ``-Python-2.7.16`` ``intel/2019b`` +``3.5.2`` ``-Python-2.7.18`` ``foss/2020b`` ``3.6.1`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2020b``, ``intel/2020b`` -``3.6.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``3.6.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``3.6.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``3.6.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` =========== ================== =================================================================================== @@ -38931,19 +40391,20 @@ pytest: simple powerful testing with Python *homepage*: https://pytest.org ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``3.0.1`` ``-Python-2.7.11`` ``foss/2016a`` -``3.0.1`` ``-Python-3.5.1`` ``foss/2016a`` +``3.0.1`` ``-Python-2.7.11`` ``foss/2016a`` +``3.0.1`` ``-Python-3.5.1`` ``foss/2016a`` ``3.8.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``3.8.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``3.8.2`` ``-Python-2.7.15`` ``intel/2018b`` +``3.8.2`` ``-Python-2.7.15`` ``intel/2018b`` ``3.8.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``3.8.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``4.3.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``4.4.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``4.4.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``6.0.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``6.0.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``7.1.3`` ``GCCcore/11.2.0`` ========= ================== =============================== @@ -38957,7 +40418,7 @@ A pytest fixture for benchmarking code. *homepage*: https://github.com/ionelmc/pytest-benchmark ========= ================== -version toolchain +version toolchain ========= ================== ``3.4.1`` ``GCCcore/10.2.0`` ========= ================== @@ -38973,9 +40434,9 @@ xdist: pytest distributed testing plugin The pytest-xdist plugin extends pytest *homepage*: https://github.com/pytest-dev/pytest-xdist ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``2.1.0`` ``GCCcore/10.2.0`` +``2.1.0`` ``GCCcore/10.2.0`` ``2.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` ``2.5.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ====================================== @@ -38991,7 +40452,7 @@ PYTHIA is a standard tool for the generation of events in high-energy collisions *homepage*: http://home.thep.lu.se/~torbjorn/Pythia.html ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``8.226`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== @@ -39007,45 +40468,47 @@ Python is a programming language that lets you work more quickly and integrate y *homepage*: https://python.org/ ========== ================= ================================================================================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================================================================================================================================================= -``2.7.9`` ``-bare`` ``GCC/4.8.4``, ``GCC/4.9.2`` -``2.7.10`` ``gimkl/2.11.5`` -``2.7.10`` ``-bare`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25`` -``2.7.11`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``2.7.11`` ``-bare`` ``GCC/4.9.3-2.25`` -``2.7.11`` ``-libX11-1.6.3`` ``intel/2016a`` -``2.7.12`` ``foss/2016b``, ``intel/2016b``, ``iomkl/2017a`` -``2.7.12`` ``-bare`` ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` -``2.7.13`` ``foss/2017a``, ``intel/2017a`` -``2.7.13`` ``-bare`` ``GCCcore/6.3.0`` +``2.7.9`` ``-bare`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``2.7.10`` ``gimkl/2.11.5`` +``2.7.10`` ``-bare`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25`` +``2.7.11`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` +``2.7.11`` ``-bare`` ``GCC/4.9.3-2.25`` +``2.7.11`` ``-libX11-1.6.3`` ``intel/2016a`` +``2.7.12`` ``foss/2016b``, ``intel/2016b``, ``iomkl/2017a`` +``2.7.12`` ``-bare`` ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` +``2.7.13`` ``foss/2017a``, ``intel/2017a`` +``2.7.13`` ``-bare`` ``GCCcore/6.3.0`` ``2.7.14`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2018a`` -``2.7.14`` ``-bare`` ``GCCcore/6.4.0`` -``2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``2.7.15`` ``-bare`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``2.7.16`` ``GCCcore/8.3.0`` -``2.7.16`` ``-bare`` ``GCCcore/8.3.0`` -``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``2.7.18`` ``-bare`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` -``3.5.1`` ``foss/2016a``, ``intel/2016a`` -``3.5.2`` ``foss/2016.04``, ``foss/2016b``, ``intel/2016b`` -``3.5.2`` ``-bare`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` -``3.6.1`` ``foss/2017a``, ``intel/2017a`` -``3.6.2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.00`` -``3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018.01``, ``intelcuda/2017b`` -``3.6.4`` ``foss/2017a``, ``foss/2018a``, ``fosscuda/2018a``, ``golf/2018a``, ``iimkl/2018a``, ``intel/2018a``, ``iomkl/2018.02``, ``iomkl/2018a`` -``3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.7.0`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.7.2`` ``GCCcore/8.2.0`` -``3.7.4`` ``GCCcore/8.3.0`` -``3.8.2`` ``GCCcore/9.3.0`` -``3.8.6`` ``GCCcore/10.2.0`` -``3.9.5`` ``GCCcore/10.3.0`` -``3.9.5`` ``-bare`` ``GCCcore/10.3.0`` -``3.9.6`` ``GCCcore/11.2.0`` -``3.9.6`` ``-bare`` ``GCCcore/11.2.0`` -``3.10.4`` ``GCCcore/11.3.0`` -``3.10.4`` ``-bare`` ``GCCcore/11.3.0`` +``2.7.14`` ``-bare`` ``GCCcore/6.4.0`` +``2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``2.7.15`` ``-bare`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` +``2.7.16`` ``GCCcore/8.3.0`` +``2.7.16`` ``-bare`` ``GCCcore/8.3.0`` +``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``2.7.18`` ``-bare`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/9.3.0`` +``3.5.1`` ``foss/2016a``, ``intel/2016a`` +``3.5.2`` ``foss/2016.04``, ``foss/2016b``, ``intel/2016b`` +``3.5.2`` ``-bare`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` +``3.6.1`` ``foss/2017a``, ``intel/2017a`` +``3.6.2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.00`` +``3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018.01``, ``intelcuda/2017b`` +``3.6.4`` ``foss/2017a``, ``foss/2018a``, ``fosscuda/2018a``, ``golf/2018a``, ``iimkl/2018a``, ``intel/2018a``, ``iomkl/2018.02``, ``iomkl/2018a`` +``3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``3.7.0`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``3.7.2`` ``GCCcore/8.2.0`` +``3.7.4`` ``GCCcore/8.3.0`` +``3.8.2`` ``GCCcore/9.3.0`` +``3.8.6`` ``GCCcore/10.2.0`` +``3.9.5`` ``GCCcore/10.3.0`` +``3.9.5`` ``-bare`` ``GCCcore/10.3.0`` +``3.9.6`` ``GCCcore/11.2.0`` +``3.9.6`` ``-bare`` ``GCCcore/11.2.0`` +``3.10.4`` ``GCCcore/11.3.0`` +``3.10.4`` ``-bare`` ``GCCcore/11.3.0`` +``3.10.8`` ``GCCcore/12.2.0`` +``3.10.8`` ``-bare`` ``GCCcore/12.2.0`` ========== ================= ================================================================================================================================================================= @@ -39059,7 +40522,7 @@ python-docx is a Python library for creating and updating Microsoft Word (.docx) *homepage*: https://python-docx.readthedocs.io/en/latest/ ========== ================== -version toolchain +version toolchain ========== ================== ``0.8.11`` ``GCCcore/10.2.0`` ========== ================== @@ -39075,7 +40538,7 @@ A simple library for parsing messages of Health Level 7 (HL7) version 2.x into P *homepage*: https://github.com/johnpaulett/python-hl7 ========= ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================= ``0.3.4`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========= ================= ================= @@ -39091,14 +40554,14 @@ Python interface to the igraph high performance graph library, primarily aimed a *homepage*: https://igraph.org/python =============== ================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain =============== ================== ================================== -``0.7.1.post6`` ``-Python-2.7.14`` ``intel/2017b`` -``0.7.1.post6`` ``-Python-3.6.6`` ``foss/2018b`` -``0.8.0`` ``foss/2019b``, ``foss/2020a`` +``0.7.1.post6`` ``-Python-2.7.14`` ``intel/2017b`` +``0.7.1.post6`` ``-Python-3.6.6`` ``foss/2018b`` +``0.8.0`` ``foss/2019b``, ``foss/2020a`` ``0.9.0`` ``foss/2020b``, ``fosscuda/2020b`` -``0.9.6`` ``foss/2021a`` -``0.9.8`` ``foss/2021b`` +``0.9.6`` ``foss/2021a`` +``0.9.8`` ``foss/2021b`` =============== ================== ================================== @@ -39112,7 +40575,7 @@ A python API for iRODS *homepage*: https://github.com/irods/python-irodsclient ========= ====================================== -version toolchain +version toolchain ========= ====================================== ``1.1.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ====================================== @@ -39128,10 +40591,11 @@ Faster zlib and gzip compatible compression and decompression by providing pyth *homepage*: https://github.com/pycompression/python-isal ========== ====================================== -version toolchain +version toolchain ========== ====================================== -``0.11.0`` ``GCCcore/10.3.0`` +``0.11.0`` ``GCCcore/10.3.0`` ``0.11.1`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` +``1.1.0`` ``GCCcore/11.3.0`` ========== ====================================== @@ -39145,7 +40609,7 @@ Python extension for computing string edit distances and similarities. *homepage*: https://pypi.org/project/python-Levenshtein/ ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.12.0`` ``-Python-3.6.6`` ``foss/2018b`` ``0.12.0`` ``-Python-3.7.4`` ``foss/2019b`` @@ -39153,6 +40617,22 @@ version versionsuffix toolchain ========== ================= ============== +.. _list_software_python-libsbml_1460: + +*python-libsbml* +++++++++++++++++ + +LibSBML Python API. + +*homepage*: https://sbml.org/ + +========== ============== +version toolchain +========== ============== +``5.19.7`` ``foss/2021a`` +========== ============== + + .. _list_software_python-parasail_1564: *python-parasail* @@ -39163,17 +40643,33 @@ Python Bindings for the Parasail C Library *homepage*: https://github.com/jeffdaily/parasail-python ========== ================== ================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================================================================== -``1.1.12`` ``-Python-2.7.14`` ``intel/2018a`` -``1.1.16`` ``-Python-3.6.6`` ``foss/2018b`` -``1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``1.2.2`` ``-Python-3.8.2`` ``intel/2020a`` -``1.2.3`` ``-Python-3.8.2`` ``foss/2020a`` +``1.1.12`` ``-Python-2.7.14`` ``intel/2018a`` +``1.1.16`` ``-Python-3.6.6`` ``foss/2018b`` +``1.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``1.2.2`` ``-Python-3.8.2`` ``intel/2020a`` +``1.2.3`` ``-Python-3.8.2`` ``foss/2020a`` ``1.2.4`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``fosscuda/2020b`` ========== ================== ================================================================== +.. _list_software_python-telegram-bot_1938: + +*python-telegram-bot* ++++++++++++++++++++++ + +This library provides a pure Python, asynchronous interface for the Telegram Bot API. It's compatible with Python versions 3.7+. + +*homepage*: https://python-telegram-bot.org/ + +========== ================== +version toolchain +========== ================== +``20.0a0`` ``GCCcore/10.2.0`` +========== ================== + + .. _list_software_python-weka-wrapper3_2008: *python-weka-wrapper3* @@ -39184,7 +40680,7 @@ Python3 wrapper for the Weka Machine Learning Workbench *homepage*: https://github.com/fracpete/python-weka-wrapper3 ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.1.11`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================= ============== @@ -39200,7 +40696,7 @@ Pythran is an ahead of time compiler for a subset of the Python language, with a *homepage*: https://pythran.readthedocs.io =============== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain =============== ================= ============== ``0.9.4.post1`` ``-Python-3.7.4`` ``foss/2019b`` =============== ================= ============== @@ -39216,33 +40712,36 @@ Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTo *homepage*: https://pytorch.org/ ========== ============================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============================= ================================== -``0.3.1`` ``-Python-2.7.14`` ``fosscuda/2017b`` -``0.3.1`` ``-Python-3.6.3`` ``fosscuda/2017b`` -``0.3.1`` ``-Python-3.6.4`` ``intel/2018a`` -``0.3.1`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` -``0.4.1`` ``-Python-3.6.4`` ``intel/2018a`` +``0.3.1`` ``-Python-2.7.14`` ``fosscuda/2017b`` +``0.3.1`` ``-Python-3.6.3`` ``fosscuda/2017b`` +``0.3.1`` ``-Python-3.6.4`` ``intel/2018a`` +``0.3.1`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` +``0.4.1`` ``-Python-3.6.4`` ``intel/2018a`` ``1.0.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``1.1.0`` ``-Python-3.7.2`` ``foss/2019a`` +``1.1.0`` ``-Python-3.7.2`` ``foss/2019a`` ``1.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` -``1.3.1`` ``fosscuda/2020b`` +``1.3.1`` ``fosscuda/2020b`` ``1.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``1.4.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``1.6.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``1.6.0`` ``-Python-3.7.4-imkl`` ``fosscuda/2019b`` +``1.6.0`` ``-Python-3.7.4-imkl`` ``fosscuda/2019b`` ``1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` -``1.7.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``1.7.1`` ``-Python-3.8.2`` ``fosscuda/2020a`` +``1.7.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.7.1`` ``-Python-3.8.2`` ``fosscuda/2020a`` ``1.8.1`` ``foss/2020b``, ``fosscuda/2020b`` -``1.8.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.8.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``1.9.0`` ``foss/2020b``, ``fosscuda/2020b`` -``1.9.0`` ``-imkl`` ``fosscuda/2020b`` +``1.9.0`` ``-imkl`` ``fosscuda/2020b`` ``1.10.0`` ``foss/2021a``, ``fosscuda/2020b`` -``1.10.0`` ``-CUDA-11.3.1`` ``foss/2021a`` -``1.11.0`` ``-CUDA-11.3.1`` ``foss/2021a`` -``1.12.0`` ``foss/2022a`` -``1.12.0`` ``-CUDA-11.7.0`` ``foss/2022a`` +``1.10.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``1.11.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``1.12.0`` ``foss/2022a`` +``1.12.0`` ``-CUDA-11.7.0`` ``foss/2022a`` +``1.12.1`` ``foss/2021a``, ``foss/2022a`` +``1.12.1`` ``-CUDA-11.3.1`` ``foss/2021a`` +``1.12.1`` ``-CUDA-11.7.0`` ``foss/2022a`` ========== ============================= ================================== @@ -39256,13 +40755,14 @@ PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTor *homepage*: https://github.com/rusty1s/pytorch_geometric ========= =============================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =============================== ================================== -``1.3.2`` ``-Python-3.7.4`` ``foss/2019b`` -``1.4.2`` ``-Python-3.7.4-PyTorch-1.4.0`` ``foss/2019b`` +``1.3.2`` ``-Python-3.7.4`` ``foss/2019b`` +``1.4.2`` ``-Python-3.7.4-PyTorch-1.4.0`` ``foss/2019b`` ``1.6.3`` ``foss/2020b``, ``fosscuda/2020b`` -``1.6.3`` ``-Python-3.7.4-PyTorch-1.8.1`` ``fosscuda/2019b`` -``2.0.1`` ``-PyTorch-1.9.0`` ``fosscuda/2020b`` +``1.6.3`` ``-Python-3.7.4-PyTorch-1.8.1`` ``fosscuda/2019b`` +``2.0.1`` ``-PyTorch-1.9.0`` ``fosscuda/2020b`` +``2.1.0`` ``-PyTorch-1.12.1-CUDA-11.3.1`` ``foss/2021a`` ========= =============================== ================================== @@ -39276,12 +40776,14 @@ PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers. *homepage*: https://pytorchlightning.ai ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``1.5.9`` ``foss/2021a`` ``1.5.9`` ``-CUDA-11.3.1`` ``foss/2021a`` ``1.7.7`` ``foss/2022a`` ``1.7.7`` ``-CUDA-11.7.0`` ``foss/2022a`` +``1.8.4`` ``foss/2022a`` +``1.8.4`` ``-CUDA-11.7.0`` ``foss/2022a`` ========= ================ ============== @@ -39295,7 +40797,7 @@ PyTorch3D is FAIR's library of reusable components for deep learning with 3D dat *homepage*: https://pytorch3d.org/ ========= ================== ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================== ``0.4.0`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` ========= ================== ================== @@ -39311,12 +40813,28 @@ A Variant Call Format reader for Python. *homepage*: https://github.com/jamescasbon/PyVCF ========= ================== ============= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============= ``0.6.8`` ``-Python-2.7.16`` ``GCC/8.3.0`` ========= ================== ============= +.. _list_software_pyWannier90_1062: + +*pyWannier90* ++++++++++++++ + +A Wannier90 Python interface for VASP and PySCF + +*homepage*: https://github.com/hungpham2017/pyWannier90 + +============== =============================== +version toolchain +============== =============================== +``2021-12-07`` ``foss/2021a``, ``gomkl/2021a`` +============== =============================== + + .. _list_software_PyWavelets_1044: *PyWavelets* @@ -39327,10 +40845,10 @@ PyWavelets is open source wavelet transform software for Python. *homepage*: https://pywavelets.readthedocs.io ========= ================= =================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =================== ``1.1.1`` ``intelcuda/2020b`` -``1.1.1`` ``-Python-3.7.4`` ``intel/2019b`` +``1.1.1`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================= =================== @@ -39344,26 +40862,26 @@ PyYAML is a YAML parser and emitter for the Python programming language. *homepage*: https://github.com/yaml/pyyaml ========= ================== ==================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ==================================================================================== -``3.11`` ``-Python-2.7.11`` ``intel/2016a`` -``3.12`` ``system`` -``3.12`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.12`` ``-Python-2.7.13`` ``intel/2017a`` +``3.11`` ``-Python-2.7.11`` ``intel/2016a`` +``3.12`` ``system`` +``3.12`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.12`` ``-Python-2.7.13`` ``intel/2017a`` ``3.12`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a`` -``3.12`` ``-Python-3.5.2`` ``intel/2016b`` -``3.12`` ``-Python-3.6.1`` ``intel/2017a`` -``3.12`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b`` -``3.12`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``3.13`` ``system`` -``3.13`` ``-Python-2.7.15`` ``fosscuda/2018b``, ``intel/2018b`` -``3.13`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``5.1`` ``GCCcore/8.2.0`` -``5.1.2`` ``GCCcore/8.3.0`` -``5.3`` ``GCCcore/9.3.0`` -``5.3.1`` ``GCCcore/10.2.0`` -``5.4.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``6.0`` ``GCCcore/11.3.0`` +``3.12`` ``-Python-3.5.2`` ``intel/2016b`` +``3.12`` ``-Python-3.6.1`` ``intel/2017a`` +``3.12`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b`` +``3.12`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``3.13`` ``system`` +``3.13`` ``-Python-2.7.15`` ``fosscuda/2018b``, ``intel/2018b`` +``3.13`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``5.1`` ``GCCcore/8.2.0`` +``5.1.2`` ``GCCcore/8.3.0`` +``5.3`` ``GCCcore/9.3.0`` +``5.3.1`` ``GCCcore/10.2.0`` +``5.4.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``6.0`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========= ================== ==================================================================================== @@ -39377,22 +40895,22 @@ Python bindings for ZeroMQ *homepage*: https://www.zeromq.org/bindings:python ========== ======================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ======================= =============================== ``15.2.0`` ``-Python-2.7.11-zmq4`` ``foss/2016a``, ``intel/2016a`` -``15.2.0`` ``-Python-3.5.1-zmq4`` ``intel/2016a`` -``15.3.0`` ``-Python-2.7.11-zmq4`` ``foss/2016a`` -``15.3.0`` ``-Python-3.5.1-zmq4`` ``foss/2016a`` -``15.4.0`` ``-Python-2.7.12-zmq4`` ``intel/2016b`` -``15.4.0`` ``-Python-3.5.2-zmq4`` ``intel/2016b`` +``15.2.0`` ``-Python-3.5.1-zmq4`` ``intel/2016a`` +``15.3.0`` ``-Python-2.7.11-zmq4`` ``foss/2016a`` +``15.3.0`` ``-Python-3.5.1-zmq4`` ``foss/2016a`` +``15.4.0`` ``-Python-2.7.12-zmq4`` ``intel/2016b`` +``15.4.0`` ``-Python-3.5.2-zmq4`` ``intel/2016b`` ``16.0.2`` ``-Python-2.7.12-zmq4`` ``foss/2016b``, ``intel/2016b`` ``16.0.2`` ``-Python-2.7.13-zmq4`` ``foss/2017a``, ``intel/2017a`` ``16.0.2`` ``-Python-3.5.2-zmq4`` ``foss/2016b``, ``intel/2016b`` -``16.0.3`` ``-Python-2.7.14-zmq4`` ``intel/2017b`` -``17.0.0`` ``-Python-2.7.14-zmq4`` ``foss/2018a`` -``17.0.0`` ``-Python-3.6.4-zmq4`` ``foss/2018a`` -``18.1.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``22.3.0`` ``GCCcore/10.3.0`` +``16.0.3`` ``-Python-2.7.14-zmq4`` ``intel/2017b`` +``17.0.0`` ``-Python-2.7.14-zmq4`` ``foss/2018a`` +``17.0.0`` ``-Python-3.6.4-zmq4`` ``foss/2018a`` +``18.1.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``22.3.0`` ``GCCcore/10.3.0`` ========== ======================= =============================== @@ -39415,7 +40933,7 @@ EVB, FEP and LIE simulator. *homepage*: https://github.com/qusers/Q6 ============ =============== -version toolchain +version toolchain ============ =============== ``20180205`` ``gompi/2019a`` ============ =============== @@ -39426,15 +40944,16 @@ version toolchain *QCA* +++++ -Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX. +Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX. -*homepage*: http://delta.affinix.com/qca/ +*homepage*: https://userbase.kde.org/QCA ========= ================================================== -version toolchain +version toolchain ========= ================================================== -``2.1.0`` ``foss/2016a``, ``intel/2016b`` +``2.1.0`` ``foss/2016a``, ``intel/2016b`` ``2.1.3`` ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b`` +``2.3.5`` ``GCCcore/11.2.0`` ========= ================================================== @@ -39448,10 +40967,10 @@ qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from *homepage*: https://github.com/nanoporetech/qcat/releases ========= ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============================== ``1.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.1.0`` ``-Python-3.8.2`` ``intel/2020a`` +``1.1.0`` ``-Python-3.8.2`` ``intel/2020a`` ========= ================= =============================== @@ -39465,7 +40984,7 @@ A python service for easy execution of many tasks inside a single allocation. *homepage*: https://qcg-pilotjob.readthedocs.org ========== ============== -version toolchain +version toolchain ========== ============== ``0.12.3`` ``foss/2021a`` ========== ============== @@ -39481,7 +41000,7 @@ libcint is an open source library for analytical Gaussian integrals. qcint is an *homepage*: http://wiki.sunqm.net/libcint ========== ============== -version toolchain +version toolchain ========== ============== ``3.0.18`` ``foss/2019a`` ========== ============== @@ -39497,7 +41016,7 @@ QCxMS is a quantum chemical based program to calculate electron ionization (EI) *homepage*: https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms.html ========= ========== -version toolchain +version toolchain ========= ========== ``5.0.3`` ``system`` ========= ========== @@ -39513,7 +41032,7 @@ Quad Double computation package *homepage*: https://github.com/scibuilder/QD ========== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ============== ``0.8.9`` ``foss/2021a`` ``2.3.17`` ``-20160110`` ``NVHPC/21.2`` @@ -39530,7 +41049,7 @@ A user-friendly program to select microsatellite markers and design primers fro *homepage*: http://net.imbe.fr/~emeglecz/qdd.html ========= ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =============== ``3.1.2`` ``-Perl-5.28.0`` ``intel/2018b`` ========= ================ =============== @@ -39546,7 +41065,7 @@ QEMU is a generic and open source machine emulator and virtualizer. *homepage*: https://www.qemu.org/ ========== =============== -version toolchain +version toolchain ========== =============== ``2.10.1`` ``intel/2017b`` ========== =============== @@ -39562,11 +41081,12 @@ QGIS is a user friendly Open Source Geographic Information System (GIS) *homepage*: http://www.qgis.org/ =========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== =============== ``2.14.12`` ``-Python-2.7.12`` ``intel/2016b`` -``2.18.4`` ``-Python-2.7.12`` ``foss/2016b`` -``3.4.12`` ``-Python-3.7.2`` ``foss/2019a`` +``2.18.4`` ``-Python-2.7.12`` ``foss/2016b`` +``3.4.12`` ``-Python-3.7.2`` ``foss/2019a`` +``3.28.1`` ``foss/2021b`` =========== ================== =============== @@ -39580,11 +41100,11 @@ Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfsp *homepage*: http://www.qhull.org ========== ============================================================================================================================================================================= -version toolchain +version toolchain ========== ============================================================================================================================================================================= ``2015.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``2019.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``2020.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2019.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``2020.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ============================================================================================================================================================================= @@ -39598,7 +41118,7 @@ QIIME is an open-source bioinformatics pipeline for performing microbiome analys *homepage*: http://qiime.org/ ========= ========== -version toolchain +version toolchain ========= ========== ``1.9.1`` ``system`` ========= ========== @@ -39614,7 +41134,7 @@ QIIME is an open-source bioinformatics pipeline for performing microbiome analys *homepage*: http://qiime2.org/ =========== ========== -version toolchain +version toolchain =========== ========== ``2017.10`` ``system`` ``2018.2`` ``system`` @@ -39623,6 +41143,7 @@ version toolchain ``2020.8`` ``system`` ``2020.11`` ``system`` ``2021.8`` ``system`` +``2022.8`` ``system`` =========== ========== @@ -39636,7 +41157,7 @@ Qiskit is an open-source framework for working with noisy quantum computers at *homepage*: https://qiskit.org ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.11.1`` ``-Python-3.7.2`` ``foss/2019a`` ``0.12.0`` ``-Python-3.7.2`` ``foss/2019a`` @@ -39654,7 +41175,7 @@ QJson is a Qt-based library that maps JSON data to QVariant objects and vice ver *homepage*: http://qjson.sourceforge.net/ ========= ====================================================================== -version toolchain +version toolchain ========= ====================================================================== ``0.9.0`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b`` ========= ====================================================================== @@ -39670,7 +41191,7 @@ QML is a Python2/3-compatible toolkit for representation learning of properties *homepage*: https://www.qmlcode.org ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``0.2.10`` ``-Python-2.7.13`` ``intel/2017a`` ========== ================== =============== @@ -39686,7 +41207,7 @@ A fast and differentiable QP solver for PyTorch. *homepage*: https://locuslab.github.io/qpth/ =================== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain =================== ================= ============== ``0.0.13-20190626`` ``-Python-3.7.2`` ``foss/2019a`` =================== ================= ============== @@ -39701,11 +41222,11 @@ qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions *homepage*: https://sourceforge.net/projects/qrupdate/ -========= ========================================================================================================================================================================================================================= -version toolchain -========= ========================================================================================================================================================================================================================= -``1.1.2`` ``GCC/5.4.0-2.26``, ``GCC/8.2.0-2.31.1``, ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -========= ========================================================================================================================================================================================================================= +========= ============================================================================================================================================================================================================================================= +version toolchain +========= ============================================================================================================================================================================================================================================= +``1.1.2`` ``GCC/5.4.0-2.26``, ``GCC/8.2.0-2.31.1``, ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` +========= ============================================================================================================================================================================================================================================= .. _list_software_QScintilla_1012: @@ -39718,11 +41239,12 @@ QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control *homepage*: https://www.riverbankcomputing.com/software/qscintilla ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== ``2.9.4`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2.10`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.11.2`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``2.11.2`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``2.11.6`` ``GCCcore/11.2.0`` ========== ================== =============================== @@ -39736,12 +41258,12 @@ Qt is a comprehensive cross-platform C++ application framework. *homepage*: http://qt.io/ ========= ================ ============================================================================================================================================================================================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============================================================================================================================================================================================================================================ -``3.3.8`` ``intel/2016a`` -``4.8.6`` ``system`` +``3.3.8`` ``intel/2016a`` +``4.8.6`` ``system`` ``4.8.7`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``4.8.7`` ``-GLib-2.48.0`` ``foss/2016a``, ``intel/2016a`` +``4.8.7`` ``-GLib-2.48.0`` ``foss/2016a``, ``intel/2016a`` ========= ================ ============================================================================================================================================================================================================================================ @@ -39755,22 +41277,23 @@ Qt is a comprehensive cross-platform C++ application framework. *homepage*: https://qt.io/ ========== ==================================================================================== -version toolchain +version toolchain ========== ==================================================================================== -``5.6.0`` ``foss/2016a``, ``intel/2016a`` -``5.7.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``5.7.1`` ``intel/2016b`` -``5.8.0`` ``foss/2017a``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` -``5.9.3`` ``foss/2017b`` -``5.9.8`` ``fosscuda/2018b`` +``5.6.0`` ``foss/2016a``, ``intel/2016a`` +``5.7.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``5.7.1`` ``intel/2016b`` +``5.8.0`` ``foss/2017a``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` +``5.9.3`` ``foss/2017b`` +``5.9.8`` ``fosscuda/2018b`` ``5.10.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` -``5.11.2`` ``foss/2018b`` -``5.12.3`` ``GCCcore/8.2.0`` -``5.13.1`` ``GCCcore/8.3.0`` -``5.14.1`` ``GCCcore/9.3.0`` -``5.14.2`` ``GCCcore/10.2.0`` -``5.15.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``5.15.5`` ``GCCcore/11.3.0`` +``5.11.2`` ``foss/2018b`` +``5.12.3`` ``GCCcore/8.2.0`` +``5.13.1`` ``GCCcore/8.3.0`` +``5.14.1`` ``GCCcore/9.3.0`` +``5.14.2`` ``GCCcore/10.2.0`` +``5.15.2`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``5.15.5`` ``GCCcore/11.3.0`` +``5.15.7`` ``GCCcore/12.2.0`` ========== ==================================================================================== @@ -39783,12 +41306,12 @@ Qt Port of WebKit. WebKit is an open source web browser engine. *homepage*: https://github.com/qt/qtwebkit -================== ================== -version toolchain -================== ================== -``5.212.0-alpha3`` ``GCCcore/8.2.0`` -``5.212.0-alpha4`` ``GCCcore/10.2.0`` -================== ================== +================== ====================================== +version toolchain +================== ====================================== +``5.212.0-alpha3`` ``GCCcore/8.2.0`` +``5.212.0-alpha4`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` +================== ====================================== .. _list_software_Qtconsole_952: @@ -39796,15 +41319,16 @@ version toolchain *Qtconsole* +++++++++++ -A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. The Qtconsole is a very lightweight application that largely feels like a terminal, but provides a number of enhancements only possible in a GUI, such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and more. +A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. The Qtconsole is a very lightweight application that largely feels like a terminal, but provides a number of enhancements only possible in a GUI, such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and more. *homepage*: https://jupyter.org/ ========= ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================== ``4.7.7`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``5.0.2`` ``GCCcore/10.2.0`` +``5.0.2`` ``GCCcore/10.2.0`` +``5.3.2`` ``GCCcore/11.2.0`` ========= ================= ================================== @@ -39817,11 +41341,12 @@ Platform-independent Qt API for storing passwords securely. *homepage*: https://github.com/frankosterfeld/qtkeychain -========= ================================= -version toolchain -========= ================================= -``0.9.1`` ``GCCcore/8.2.0``, ``foss/2018b`` -========= ================================= +========== ================================= +version toolchain +========== ================================= +``0.9.1`` ``GCCcore/8.2.0``, ``foss/2018b`` +``0.13.2`` ``GCCcore/11.2.0`` +========== ================================= .. _list_software_QTLtools_802: @@ -39834,10 +41359,10 @@ QTLtools is a tool set for molecular QTL discovery and analysis. It allows to go *homepage*: https://qtltools.github.io/qtltools/ ========= =============== -version toolchain +version toolchain ========= =============== ``1.1`` ``intel/2016b`` -``1.3.1`` ``foss/2020b`` +``1.3.1`` ``foss/2020b`` ========= =============== @@ -39851,7 +41376,7 @@ qtop is a nifty command-line tool for monitoring queueing systems, esp. PBS/torq *homepage*: http://cern.ch/fotis/QTOP/ ======= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= ========== ``53`` ``-1`` ``system`` ======= ============= ========== @@ -39862,15 +41387,16 @@ version versionsuffix toolchain *QtPy* ++++++ -QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide. +QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide. *homepage*: https://github.com/spyder-ide/qtpy ========= ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================== ``1.9.0`` ``GCCcore/10.2.0`` -``1.9.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``1.9.0`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``2.2.1`` ``GCCcore/11.2.0`` ========= ================= ================== @@ -39884,7 +41410,7 @@ Qualimap 2 is a platform-independent application written in Java and R that prov *homepage*: http://qualimap.bioinfo.cipf.es/ ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``2.2.1`` ``-R-3.6.0`` ``foss/2019a`` ``2.2.1`` ``-R-4.0.3`` ``foss/2020b`` @@ -39902,10 +41428,10 @@ A Python library for Quandl’s RESTful API. *homepage*: https://pypi.python.org/pypi/Quandl ========= ================= ============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============================== -``3.4.2`` ``-Python-3.6.4`` ``intel/2018a`` -``3.4.8`` ``foss/2019a`` +``3.4.2`` ``-Python-3.6.4`` ``intel/2018a`` +``3.4.8`` ``foss/2019a`` ``3.6.1`` ``foss/2020b``, ``foss/2021a`` ========= ================= ============================== @@ -39920,23 +41446,23 @@ Quantum ESPRESSO is an integrated suite of computer codes for electronic-struct *homepage*: https://www.quantum-espresso.org ========= ============= ================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ================================================================================================= -``5.3.0`` ``intel/2016.02-GCC-4.9`` -``5.4.0`` ``intel/2016.02-GCC-4.9`` -``5.4.0`` ``-hybrid`` ``foss/2016b`` -``6.0`` ``intel/2016b`` -``6.1`` ``intel/2017a`` -``6.2`` ``intel/2017b`` -``6.2.1`` ``iomkl/2017b`` -``6.3`` ``foss/2018b``, ``intel/2018b`` -``6.4.1`` ``intel/2019a`` -``6.5`` ``intel/2019a``, ``intel/2019b`` -``6.6`` ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2019b`` +``5.3.0`` ``intel/2016.02-GCC-4.9`` +``5.4.0`` ``intel/2016.02-GCC-4.9`` +``5.4.0`` ``-hybrid`` ``foss/2016b`` +``6.0`` ``intel/2016b`` +``6.1`` ``intel/2017a`` +``6.2`` ``intel/2017b`` +``6.2.1`` ``iomkl/2017b`` +``6.3`` ``foss/2018b``, ``intel/2018b`` +``6.4.1`` ``intel/2019a`` +``6.5`` ``intel/2019a``, ``intel/2019b`` +``6.6`` ``foss/2019b``, ``foss/2020a``, ``foss/2020b``, ``intel/2019b`` ``6.7`` ``foss/2019b``, ``foss/2020b``, ``foss/2021a``, ``intel/2019b``, ``intel/2021a``, ``iomkl/2019b`` -``6.8`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` -``7.0`` ``foss/2021b``, ``intel/2021b`` -``7.1`` ``foss/2022a``, ``intel/2022a`` +``6.8`` ``foss/2021a``, ``foss/2021b``, ``intel/2021a`` +``7.0`` ``foss/2021b``, ``intel/2021b`` +``7.1`` ``foss/2022a``, ``intel/2022a`` ========= ============= ================================================================================================= @@ -39950,15 +41476,15 @@ QUAST evaluates genome assemblies by computing various metrics. It works both wi *homepage*: https://github.com/ablab/quast ========= ================== ============================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============================================== -``4.6.0`` ``-Python-3.5.2`` ``foss/2016b`` -``4.6.3`` ``-Python-3.6.4`` ``foss/2018a`` +``4.6.0`` ``-Python-3.5.2`` ``foss/2016b`` +``4.6.3`` ``-Python-3.6.4`` ``foss/2018a`` ``5.0.2`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b`` -``5.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` -``5.0.2`` ``-Python-2.7.18`` ``foss/2020b`` -``5.0.2`` ``-Python-3.7.2`` ``foss/2019a`` -``5.0.2`` ``-Python-3.8.2`` ``foss/2020a`` +``5.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` +``5.0.2`` ``-Python-2.7.18`` ``foss/2020b`` +``5.0.2`` ``-Python-3.7.2`` ``foss/2019a`` +``5.0.2`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== ============================================== @@ -39972,7 +41498,7 @@ QuaZIP is the C++ wrapper for Gilles Vollant's ZIP/UNZIP package (AKA Minizip) *homepage*: https://stachenov.github.io/quazip ========= ================= -version toolchain +version toolchain ========= ================= ``0.8.1`` ``GCCcore/8.2.0`` ========= ================= @@ -39988,7 +41514,7 @@ QuickFF is a Python package developed at the Center for Molecular Modeling (CMM) *homepage*: https://molmod.github.io/QuickFF/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``2.1.4`` ``-Python-2.7.12`` ``intel/2016b`` ``2.2.0`` ``-Python-2.7.14`` ``intel/2017b`` @@ -40008,7 +41534,7 @@ QuickPIC is a 3D parallel (MPI & OpenMP Hybrid) Quasi-Static PIC code, which is *homepage*: https://github.com/UCLA-Plasma-Simulation-Group/QuickPIC-OpenSource ============ =============== -version toolchain +version toolchain ============ =============== ``20210224`` ``gompi/2021b`` ============ =============== @@ -40024,7 +41550,7 @@ Quip compresses next-generation sequencing data with extreme prejudice. It supp *homepage*: http://homes.cs.washington.edu/~dcjones/quip ========= ============= -version toolchain +version toolchain ========= ============= ``1.1.8`` ``GCC/4.8.2`` ========= ============= @@ -40040,7 +41566,7 @@ QuorUM is an error corrector for Illumina reads *homepage*: http://www.genome.umd.edu/quorum.html ========= =============== -version toolchain +version toolchain ========= =============== ``1.1.1`` ``intel/2017a`` ========= =============== @@ -40056,9 +41582,9 @@ QuTiP is open-source software for simulating the dynamics of open quantum system *homepage*: http://qutip.org ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``4.1.0`` ``-Python-2.7.12`` ``intel/2016b`` +``4.1.0`` ``-Python-2.7.12`` ``intel/2016b`` ``4.3.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ========= ================== =============================== @@ -40073,13 +41599,13 @@ The Qwt library contains GUI Components and utility classes which are primarily *homepage*: https://qwt.sourceforge.io/ ========= ==================================================== -version toolchain +version toolchain ========= ==================================================== -``6.1.2`` ``intel/2016a`` -``6.1.3`` ``foss/2016b``, ``intel/2016b`` +``6.1.2`` ``intel/2016a`` +``6.1.3`` ``foss/2016b``, ``intel/2016b`` ``6.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` -``6.1.5`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``6.2.0`` ``GCCcore/10.3.0`` +``6.1.5`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``6.2.0`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ==================================================== @@ -40093,7 +41619,7 @@ The QwtPolar library contains classes for displaying values on a polar coordinat *homepage*: http://qwtpolar.sourceforge.net/ ========= ====================================================================== -version toolchain +version toolchain ========= ====================================================================== ``1.1.1`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b`` ========= ====================================================================== @@ -40105,7 +41631,7 @@ version toolchain --- -:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_RaGOO_408` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_RAPSearch2_875` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redis_503` - :ref:`list_software_redis-py_813` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_regionmask_1072` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_RheoTool_812` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rising_652` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_ruamel.yaml_1127` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_ruffus_667` - :ref:`list_software_Rust_430` +:ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-INLA_419` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-opencv_778` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_radeontop_972` - :ref:`list_software_RaGOO_408` - :ref:`list_software_Ragout_626` - :ref:`list_software_RagTag_566` - :ref:`list_software_rampart_759` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_RAPSearch2_875` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_rasterio_873` - :ref:`list_software_rasterstats_1216` - :ref:`list_software_Ratatosk_841` - :ref:`list_software_RAxML_420` - :ref:`list_software_RAxML-NG_614` - :ref:`list_software_Ray-assembler_1303` - :ref:`list_software_Ray-project_1104` - :ref:`list_software_Raysect_731` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_rclone_643` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_RcppGSL_635` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_RE2_201` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Reapr_506` - :ref:`list_software_RECON_375` - :ref:`list_software_Red_283` - :ref:`list_software_Redis_503` - :ref:`list_software_redis-py_813` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_regionmask_1072` - :ref:`list_software_RegTools_815` - :ref:`list_software_Relate_605` - :ref:`list_software_RELION_457` - :ref:`list_software_ReMatCh_644` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_RepeatModeler_1321` - :ref:`list_software_RepeatScout_1135` - :ref:`list_software_request_777` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_resolos_775` - :ref:`list_software_retworkx_902` - :ref:`list_software_RevBayes_801` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_Rgurobi_730` - :ref:`list_software_rhdf5_473` - :ref:`list_software_RheoTool_812` - :ref:`list_software_rickflow_865` - :ref:`list_software_RInChI_509` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rising_652` - :ref:`list_software_rjags_535` - :ref:`list_software_RLCard_536` - :ref:`list_software_Rmath_508` - :ref:`list_software_rMATS-turbo_1024` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-Bloom_775` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_RNAmmer_658` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_RnBeads_671` - :ref:`list_software_Roary_525` - :ref:`list_software_ROCm_337` - :ref:`list_software_rocm-cmake_991` - :ref:`list_software_ROCm-CompilerSupport_1974` - :ref:`list_software_rocm-smi_807` - :ref:`list_software_rocminfo_861` - :ref:`list_software_ROCR-Runtime_1095` - :ref:`list_software_ROCT-Thunk-Interface_1837` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_root_numpy_1116` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_rstanarm_872` - :ref:`list_software_RStudio-Server_1390` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_ruamel.yaml_1127` - :ref:`list_software_Ruby_418` - :ref:`list_software_Ruby-Tk_654` - :ref:`list_software_ruffus_667` - :ref:`list_software_Rust_430` .. _list_software_R_82: @@ -40118,34 +41644,34 @@ R is a free software environment for statistical computing and graphics. *homepage*: https://www.r-project.org/ ========= ============================= =================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============================= =================================================== -``3.2.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` -``3.2.3`` ``-bare`` ``foss/2016a``, ``intel/2016a`` -``3.2.3`` ``-libX11-1.6.3`` ``intel/2016a`` -``3.3.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``3.3.3`` ``-X11-20160819`` ``foss/2016b``, ``intel/2016b`` -``3.3.3`` ``-X11-20170314`` ``intel/2017a`` -``3.4.0`` ``-X11-20170314`` ``intel/2017a`` -``3.4.1`` ``-X11-20160819`` ``foss/2016b`` -``3.4.3`` ``-X11-20171023`` ``foss/2017b``, ``intel/2017b`` -``3.4.3`` ``-X11-20171023-HDF5-1.8.19`` ``intel/2017b`` -``3.4.4`` ``-X11-20180131`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` -``3.5.0`` ``-X11-20180131`` ``iomkl/2018a`` -``3.5.1`` ``foss/2018b``, ``intel/2018b`` -``3.5.1`` ``-Python-2.7.15`` ``foss/2018b`` -``3.5.1`` ``-bare`` ``foss/2018b`` +``3.2.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` +``3.2.3`` ``-bare`` ``foss/2016a``, ``intel/2016a`` +``3.2.3`` ``-libX11-1.6.3`` ``intel/2016a`` +``3.3.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` +``3.3.3`` ``-X11-20160819`` ``foss/2016b``, ``intel/2016b`` +``3.3.3`` ``-X11-20170314`` ``intel/2017a`` +``3.4.0`` ``-X11-20170314`` ``intel/2017a`` +``3.4.1`` ``-X11-20160819`` ``foss/2016b`` +``3.4.3`` ``-X11-20171023`` ``foss/2017b``, ``intel/2017b`` +``3.4.3`` ``-X11-20171023-HDF5-1.8.19`` ``intel/2017b`` +``3.4.4`` ``-X11-20180131`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` +``3.5.0`` ``-X11-20180131`` ``iomkl/2018a`` +``3.5.1`` ``foss/2018b``, ``intel/2018b`` +``3.5.1`` ``-Python-2.7.15`` ``foss/2018b`` +``3.5.1`` ``-bare`` ``foss/2018b`` ``3.6.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``3.6.2`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``3.6.3`` ``foss/2020a`` -``4.0.0`` ``foss/2020a``, ``fosscuda/2020a`` -``4.0.3`` ``foss/2020b``, ``fosscuda/2020b`` -``4.0.4`` ``foss/2020b``, ``fosscuda/2020b`` -``4.0.5`` ``foss/2020b``, ``fosscuda/2020b`` -``4.1.0`` ``foss/2021a`` -``4.1.2`` ``foss/2021b`` -``4.2.0`` ``foss/2021b`` -``4.2.1`` ``foss/2022a`` +``3.6.3`` ``foss/2020a`` +``4.0.0`` ``foss/2020a``, ``fosscuda/2020a`` +``4.0.3`` ``foss/2020b``, ``fosscuda/2020b`` +``4.0.4`` ``foss/2020b``, ``fosscuda/2020b`` +``4.0.5`` ``foss/2020b``, ``fosscuda/2020b`` +``4.1.0`` ``foss/2021a`` +``4.1.2`` ``foss/2021b`` +``4.2.0`` ``foss/2021b`` +``4.2.1`` ``foss/2022a`` ========= ============================= =================================================== @@ -40159,24 +41685,24 @@ Bioconductor provides tools for the analysis and coprehension of high-throughpu *homepage*: https://bioconductor.org ======== ============= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ======== ============= =============================== ``3.2`` ``-R-3.2.3`` ``foss/2016a``, ``intel/2016a`` -``3.3`` ``-R-3.3.1`` ``intel/2016b`` -``3.5`` ``-R-3.4.0`` ``intel/2017a`` +``3.3`` ``-R-3.3.1`` ``intel/2016b`` +``3.5`` ``-R-3.4.0`` ``intel/2017a`` ``3.6`` ``-R-3.4.3`` ``foss/2017b``, ``intel/2017b`` -``3.6`` ``-R-3.4.4`` ``intel/2018a`` -``3.7`` ``-R-3.5.0`` ``iomkl/2018a`` -``3.7`` ``-R-3.5.1`` ``foss/2018b`` -``3.8`` ``-R-3.5.1`` ``foss/2018b`` -``3.9`` ``-R-3.6.0`` ``foss/2019a`` -``3.10`` ``foss/2019b`` -``3.11`` ``-R-4.0.0`` ``foss/2020a`` -``3.12`` ``-R-4.0.3`` ``foss/2020b`` -``3.13`` ``-R-4.1.0`` ``foss/2021a`` -``3.14`` ``-R-4.1.2`` ``foss/2021b`` -``3.15`` ``-R-4.2.0`` ``foss/2021b`` -``3.15`` ``-R-4.2.1`` ``foss/2022a`` +``3.6`` ``-R-3.4.4`` ``intel/2018a`` +``3.7`` ``-R-3.5.0`` ``iomkl/2018a`` +``3.7`` ``-R-3.5.1`` ``foss/2018b`` +``3.8`` ``-R-3.5.1`` ``foss/2018b`` +``3.9`` ``-R-3.6.0`` ``foss/2019a`` +``3.10`` ``foss/2019b`` +``3.11`` ``-R-4.0.0`` ``foss/2020a`` +``3.12`` ``-R-4.0.3`` ``foss/2020b`` +``3.13`` ``-R-4.1.0`` ``foss/2021a`` +``3.14`` ``-R-4.1.2`` ``foss/2021b`` +``3.15`` ``-R-4.2.0`` ``foss/2021b`` +``3.15`` ``-R-4.2.1`` ``foss/2022a`` ======== ============= =============================== @@ -40190,7 +41716,7 @@ R-INLA is a package in R that do approximate Bayesian inference for Latent Gauss *homepage*: https://www.r-inla.org ============ ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= ============== ``21.05.02`` ``-R-4.0.4`` ``foss/2020b`` ============ ============= ============== @@ -40206,9 +41732,9 @@ Interface to 'Keras' , a high-level neural networks 'API'. *homepage*: https://cran.r-project.org/web/packages/keras =========== ========================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ========================= ================================== -``2.1.6`` ``-R-3.4.4`` ``foss/2018a`` +``2.1.6`` ``-R-3.4.4`` ``foss/2018a`` ``2.2.5.0`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a``, ``fosscuda/2019a`` ``2.2.5.0`` ``-Python-3.7.4-R-3.6.2`` ``foss/2019b``, ``fosscuda/2019b`` ``2.4.0`` ``-R-4.0.4`` ``foss/2020b``, ``fosscuda/2020b`` @@ -40225,7 +41751,7 @@ Experimenting with computer vision and machine learning in R. This package expos *homepage*: https://cran.r-project.org/web/packages/opencv/ ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``0.2.0`` ``-R-4.0.0`` ``foss/2020a`` ========= ============= ============== @@ -40241,7 +41767,7 @@ The R extension for using tesseract *homepage*: https://cran.r-project.org/package=tesseract ======= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= ============== ``4.0`` ``-R-3.5.1`` ``foss/2018b`` ======= ============= ============== @@ -40257,14 +41783,14 @@ Ultrafast consensus module for raw de novo genome assembly of long uncorrected r *homepage*: https://github.com/lbcb-sci/racon ========== ====================================== -version toolchain +version toolchain ========== ====================================== -``1.3.2`` ``GCCcore/8.2.0`` -``1.4.7`` ``GCCcore/8.2.0``, ``gcccuda/2019b`` -``1.4.10`` ``GCC/7.3.0-2.30`` -``1.4.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.3.2`` ``GCCcore/8.2.0`` +``1.4.7`` ``GCCcore/8.2.0``, ``gcccuda/2019b`` +``1.4.10`` ``GCC/7.3.0-2.30`` +``1.4.13`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``1.4.21`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``1.5.0`` ``GCCcore/11.2.0`` +``1.5.0`` ``GCCcore/11.2.0`` ========== ====================================== @@ -40278,7 +41804,7 @@ View your GPU utilization, both for the total activity percent and individual bl *homepage*: https://github.com/clbr/radeontop ======= ================== -version toolchain +version toolchain ======= ================== ``1.3`` ``GCCcore/10.3.0`` ======= ================== @@ -40294,7 +41820,7 @@ A tool to order and orient genome assembly contigs via Minimap2 alignments to a *homepage*: https://github.com/malonge/RaGOO ======== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================= ============== ``1.11`` ``-Python-3.6.6`` ``foss/2018b`` ======== ================= ============== @@ -40310,7 +41836,7 @@ Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome-lev *homepage*: https://github.com/fenderglass/Ragout ======= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== ============== ``2.0`` ``-Python-2.7.12`` ``foss/2016b`` ``2.3`` ``foss/2020b`` @@ -40327,7 +41853,7 @@ RagTag is a collection of software tools for scaffolding and improving modern ge *homepage*: https://github.com/malonge/RagTag ========= ============== -version toolchain +version toolchain ========= ============== ``2.0.1`` ``foss/2020b`` ========= ============== @@ -40343,7 +41869,7 @@ Read Assignment, Mapping, and Phylogenetic Analysis in Real Time. *homepage*: https://github.com/artic-network/rampart/ ============ ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ============== ``1.2.0`` ``foss/2020b`` ``1.2.0rc3`` ``-Python-3.6.6`` ``foss/2018b`` @@ -40360,7 +41886,7 @@ Minimum free energy of folding randomization test software *homepage*: http://bioinformatics.psb.ugent.be/software/details/Randfold ========= =============================== -version toolchain +version toolchain ========= =============================== ``2.0.1`` ``foss/2018b``, ``intel/2016b`` ========= =============================== @@ -40376,7 +41902,7 @@ Xrandr protocol and ancillary headers *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== -version toolchain +version toolchain ========= =============================== ``1.5.0`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -40392,7 +41918,7 @@ A fast JSON parser/generator for C++ with both SAX/DOM style API *homepage*: https://rapidjson.org ========= ======================================================================================================================================= -version toolchain +version toolchain ========= ======================================================================================================================================= ``1.1.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ======================================================================================================================================= @@ -40408,7 +41934,7 @@ Rapidtide is a suite of python programs used to perform time delay analysis on f *homepage*: https://rapidtide.readthedocs.io ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``1.8.0`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================= =============== @@ -40424,7 +41950,7 @@ RAPSearch stands for Reduced Alphabet based Protein similarity Search *homepage*: https://omics.informatics.indiana.edu/mg/RAPSearch2 ======== ============= -version toolchain +version toolchain ======== ============= ``2.24`` ``GCC/9.3.0`` ======== ============= @@ -40440,7 +41966,7 @@ Rascaf (RnA-seq SCAFfolder) uses continuity and order information from paired-en *homepage*: https://github.com/mourisl/Rascaf ========= =============== -version toolchain +version toolchain ========= =============== ``1.0.2`` ``intel/2017a`` ========= =============== @@ -40456,10 +41982,10 @@ RASPA is a software package for simulating adsorption and diffusion of molecules *homepage*: https://iraspa.org/raspa/ ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``2.0.3`` ``-Python-2.7.12`` ``intel/2016b`` -``2.0.41`` ``foss/2020b`` +``2.0.41`` ``foss/2020b`` ========== ================== =============== @@ -40473,11 +41999,12 @@ Rasterio reads and writes geospatial raster data. *homepage*: https://github.com/mapbox/rasterio ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``1.1.7`` ``-Python-3.8.2`` ``foss/2020a`` ``1.2.3`` ``foss/2020b`` ``1.2.10`` ``foss/2021b`` +``1.3.4`` ``foss/2022a`` ========== ================= ============== @@ -40491,7 +42018,7 @@ rasterstats is a Python module for summarizing geospatial raster datasets based *homepage*: https://github.com/perrygeo/python-rasterstats ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.15.0`` ``-Python-3.8.2`` ``foss/2020a`` ========== ================= ============== @@ -40507,7 +42034,7 @@ Phased hybrid error correction of long reads using colored de Bruijn graphs *homepage*: https://github.com/DecodeGenetics/Ratatosk ======= ============== -version toolchain +version toolchain ======= ============== ``0.4`` ``GCC/10.2.0`` ======= ============== @@ -40523,16 +42050,16 @@ RAxML search algorithm for maximum likelihood based inference of phylogenetic tr *homepage*: https://github.com/stamatak/standard-RAxML ========== ================== ===================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ===================================================================================================================== -``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` -``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` -``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` -``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` +``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` +``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` +``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` +``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` ``8.2.12`` ``-hybrid-avx2`` ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``gompi/2021b``, ``iimpi/2019b``, ``intel/2018b``, ``intel/2019a`` -``8.2.12`` ``-pthreads-avx2`` ``GCC/10.2.0`` +``8.2.12`` ``-pthreads-avx2`` ``GCC/10.2.0`` ========== ================== ===================================================================================================================== @@ -40546,13 +42073,13 @@ RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML *homepage*: https://github.com/amkozlov/raxml-ng ========= ============================== -version toolchain +version toolchain ========= ============================== ``0.9.0`` ``GCC/8.3.0``, ``gompi/2019b`` -``1.0.1`` ``gompi/2019b`` -``1.0.2`` ``gompi/2020b`` -``1.0.3`` ``GCC/10.2.0`` -``1.1.0`` ``GCC/11.2.0`` +``1.0.1`` ``gompi/2019b`` +``1.0.2`` ``gompi/2020b`` +``1.0.3`` ``GCC/10.2.0`` +``1.1.0`` ``GCC/11.2.0`` ========= ============================== @@ -40566,7 +42093,7 @@ Parallel genome assemblies for parallel DNA sequencing *homepage*: http://denovoassembler.sourceforge.net/ ========= =============== -version toolchain +version toolchain ========= =============== ``2.3.1`` ``iimpi/2019a`` ========= =============== @@ -40582,11 +42109,11 @@ Ray is an open source project that makes it simple to scale any compute-intensiv *homepage*: https://www.ray.io/ ========== ================= ============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============================== -``0.8.4`` ``-Python-3.7.4`` ``foss/2019b`` -``1.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``1.9.2`` ``foss/2021b`` +``0.8.4`` ``-Python-3.7.4`` ``foss/2019b`` +``1.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.9.2`` ``foss/2021b`` ``1.13.0`` ``foss/2021a``, ``foss/2021b`` ========== ================= ============================== @@ -40601,9 +42128,9 @@ Raysect is an OOP ray-tracing framework for Python *homepage*: https://raysect.org ========= ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============================== -``0.6.0`` ``-Python-3.6.6`` ``intel/2018b`` +``0.6.0`` ``-Python-3.6.6`` ``intel/2018b`` ``0.7.1`` ``foss/2020b``, ``intel/2020b`` ========= ================= =============================== @@ -40618,7 +42145,7 @@ RBFOpt is a Python library for black-box optimization (also known as derivative- *homepage*: https://github.com/coin-or/rbfopt ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``4.1.1`` ``intel/2019a`` ``4.1.1`` ``-Python-3.6.6`` ``intel/2018b`` @@ -40635,7 +42162,7 @@ Rclone is a command line program to sync files and directories to and from a va *homepage*: https://rclone.org ========== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ========== ``1.42`` ``-amd64`` ``system`` ``1.54.1`` ``-amd64`` ``system`` @@ -40654,7 +42181,7 @@ Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for *homepage*: https://github.com/mourisl/Rcorrector ========= =============== -version toolchain +version toolchain ========= =============== ``1.0.2`` ``intel/2017a`` ========= =============== @@ -40670,7 +42197,7 @@ The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data stru *homepage*: https://cran.r-project.org/web/packages/RcppGSL ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``0.3.8`` ``-R-4.0.4`` ``foss/2020b`` ========= ============= ============== @@ -40686,7 +42213,7 @@ The rCUDA Framework enables the concurrent usage of CUDA-compatible devices remo *homepage*: http://www.rcuda.net/ ========= ============================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============================== ========== ``4.0.1`` ``_linux_64_Ubuntu10.04`` ``system`` ``5.0`` ``_linux_64_scientificLinux6`` ``system`` @@ -40702,13 +42229,13 @@ RDFLib is a Python library for working with RDF, a simple yet powerful language *homepage*: https://github.com/RDFLib/rdflib -========= ================================= -version toolchain -========= ================================= +========= ====================================== +version toolchain +========= ====================================== ``4.2.2`` ``GCCcore/8.3.0``, ``foss/2019a`` -``5.0.0`` ``GCCcore/10.2.0`` -``6.2.0`` ``GCCcore/10.3.0`` -========= ================================= +``5.0.0`` ``GCCcore/10.2.0`` +``6.2.0`` ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +========= ====================================== .. _list_software_RDKit_446: @@ -40721,14 +42248,14 @@ RDKit is a collection of cheminformatics and machine-learning software written i *homepage*: https://www.rdkit.org ============= ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ============= ================= =============================== -``2018.09.3`` ``-Python-3.6.6`` ``intel/2018b`` -``2019.09.3`` ``-Python-3.7.4`` ``foss/2019b`` +``2018.09.3`` ``-Python-3.6.6`` ``intel/2018b`` +``2019.09.3`` ``-Python-3.7.4`` ``foss/2019b`` ``2020.03.3`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``2020.09.3`` ``-Python-3.7.4`` ``foss/2019b`` -``2021.03.4`` ``foss/2021a`` -``2022.03.5`` ``foss/2021b`` +``2020.09.3`` ``-Python-3.7.4`` ``foss/2019b`` +``2021.03.4`` ``foss/2021a`` +``2022.03.5`` ``foss/2021b`` ============= ================= =============================== @@ -40742,7 +42269,7 @@ The RDP Classifier is a naive Bayesian classifier that can rapidly and accuratel *homepage*: http://sourceforge.net/projects/rdp-classifier ======== ================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================== ========== ``2.7`` ``-Java-1.7.0_60`` ``system`` ``2.12`` ``-Java-1.8`` ``system`` @@ -40761,12 +42288,12 @@ RE2 is a fast, safe, thread-friendly alternative to backtracking regular express *homepage*: https://github.com/google/re2 ============== ====================================== -version toolchain +version toolchain ============== ====================================== -``2020-07-01`` ``GCCcore/8.3.0`` -``2021-06-01`` ``GCCcore/10.2.0`` +``2020-07-01`` ``GCCcore/8.3.0`` +``2021-06-01`` ``GCCcore/10.2.0`` ``2022-02-01`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``2022-06-01`` ``GCCcore/11.3.0`` +``2022-06-01`` ``GCCcore/11.3.0`` ============== ====================================== @@ -40777,17 +42304,18 @@ version toolchain re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons. -*homepage*: https://re2c.org/ +*homepage*: https://re2c.org ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``1.1.1`` ``GCCcore/8.2.0`` -``1.2.1`` ``GCCcore/8.3.0`` -``1.3`` ``GCCcore/9.3.0`` -``2.0.3`` ``GCCcore/10.2.0`` -``2.1.1`` ``GCCcore/10.3.0`` +``1.1.1`` ``GCCcore/8.2.0`` +``1.2.1`` ``GCCcore/8.3.0`` +``1.3`` ``GCCcore/9.3.0`` +``2.0.3`` ``GCCcore/10.2.0`` +``2.1.1`` ``GCCcore/10.3.0`` ``2.2`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``3.0`` ``GCCcore/12.2.0`` ========= ====================================== @@ -40801,7 +42329,7 @@ reads2snp is a SNP and genotype caller: it predicts the genotype of distinct ind *homepage*: http://kimura.univ-montp2.fr/PopPhyl/index.php?section=tools ======= ========== -version toolchain +version toolchain ======= ========== ``2.0`` ``system`` ======= ========== @@ -40817,7 +42345,7 @@ A tool that evaluates the accuracy of a genome assembly using mapped paired end *homepage*: https://www.sanger.ac.uk/science/tools/reapr ========== ============== -version toolchain +version toolchain ========== ============== ``1.0.18`` ``foss/2019a`` ========== ============== @@ -40833,7 +42361,7 @@ Patched version of RECON to be used with RepeatModeler. *homepage*: https://www.repeatmasker.org/RepeatModeler/ ======== ============== -version toolchain +version toolchain ======== ============== ``1.08`` ``GCC/10.2.0`` ======== ============== @@ -40849,7 +42377,7 @@ Red (REpeat Detector) *homepage*: http://toolsmith.ens.utulsa.edu/ ============== ======================================== -version toolchain +version toolchain ============== ======================================== ``2015-05-22`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ============== ======================================== @@ -40865,7 +42393,7 @@ Redis is an open source (BSD licensed), in-memory data structure store, used as *homepage*: https://redis.io ========= ============================== -version toolchain +version toolchain ========= ============================== ``6.2.6`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========= ============================== @@ -40881,7 +42409,7 @@ The Python interface to the Redis key-value store. *homepage*: https://github.com/redis/redis-py ========= ============== -version toolchain +version toolchain ========= ============== ``4.3.1`` ``foss/2021a`` ``4.3.3`` ``foss/2021b`` @@ -40898,7 +42426,7 @@ Redundans is a pipeline that assists an assembly of heterozygous/polymorphic gen *homepage*: https://github.com/lpryszcz/redundans ========= =============== -version toolchain +version toolchain ========= =============== ``0.13c`` ``intel/2017b`` ========= =============== @@ -40914,7 +42442,7 @@ ReFrame is a framework for writing regression tests for HPC systems. *homepage*: https://github.com/eth-cscs/reframe ========== ========== -version toolchain +version toolchain ========== ========== ``2.18`` ``system`` ``2.19`` ``system`` @@ -40937,6 +42465,7 @@ version toolchain ``3.11.0`` ``system`` ``3.11.1`` ``system`` ``3.11.2`` ``system`` +``3.12.0`` ``system`` ========== ========== @@ -40949,12 +42478,12 @@ regionmask creates masks of geographical regions. It determines to which geograp *homepage*: https://regionmask.readthedocs.io -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== -``0.9.0`` ``foss/2021b`` +========= ================= ============================== +version versionsuffix toolchain +========= ================= ============================== +``0.9.0`` ``foss/2021b``, ``foss/2022a`` ``0.9.0`` ``-Python-3.8.2`` ``foss/2020a`` -========= ================= ============== +========= ================= ============================== .. _list_software_RegTools_815: @@ -40966,12 +42495,12 @@ RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help inter *homepage*: https://regtools.readthedocs.org -========= ============== -version toolchain -========= ============== +========= ============================== +version toolchain +========= ============================== ``0.4.2`` ``foss/2020b`` -``0.5.2`` ``foss/2020b`` -========= ============== +``0.5.2`` ``foss/2020b``, ``foss/2021b`` +========= ============================== .. _list_software_Relate_605: @@ -40984,7 +42513,7 @@ Software for estimating genome-wide genealogies for thousands of samples *homepage*: https://myersgroup.github.io/relate/ ============ ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= ============== ``20211123`` ``-R-4.0.3`` ``foss/2020b`` ============ ============= ============== @@ -41000,15 +42529,15 @@ RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-a *homepage*: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page ======================= ================ ============================================================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ======================= ================ ============================================================================================================ -``1.4`` ``intel/2016b`` -``1.4`` ``-single`` ``intel/2016b`` -``2.0.1`` ``intel/2016b`` +``1.4`` ``intel/2016b`` +``1.4`` ``-single`` ``intel/2016b`` +``2.0.1`` ``intel/2016b`` ``2.1`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``intel/2017b``, ``intelcuda/2017b`` -``2.1`` ``-CUDA-9.1.85`` ``foss/2018a`` -``3.0.4`` ``foss/2017b``, ``intel/2017b`` -``3.0_beta.2018.08.02`` ``fosscuda/2018a``, ``intel/2018a`` +``2.1`` ``-CUDA-9.1.85`` ``foss/2018a`` +``3.0.4`` ``foss/2017b``, ``intel/2017b`` +``3.0_beta.2018.08.02`` ``fosscuda/2018a``, ``intel/2018a`` ======================= ================ ============================================================================================================ @@ -41022,7 +42551,7 @@ Reads mapping against target sequences, checking mapping and consensus sequences *homepage*: https://github.com/B-UMMI/ReMatCh ======= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== ============== ``3.2`` ``-Python-2.7.12`` ``foss/2016b`` ======= ================== ============== @@ -41038,10 +42567,10 @@ REsource MOnitoring for Remote Applications *homepage*: https://github.com/TACC/remora ========= ================================================================ -version toolchain +version toolchain ========= ================================================================ ``1.8.2`` ``foss/2017a``, ``foss/2018a``, ``intel/2017a``, ``intel/2018a`` -``1.8.3`` ``gompi/2019a`` +``1.8.3`` ``gompi/2019a`` ========= ================================================================ @@ -41055,7 +42584,7 @@ Xrender protocol and ancillary headers *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ======== ================================================================== -version toolchain +version toolchain ======== ================================================================== ``0.11`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017b`` ======== ================================================================== @@ -41071,7 +42600,7 @@ The Repast Suite is a family of advanced, free, and open source agent-based mode *homepage*: https://repast.github.io/ ========= ============== -version toolchain +version toolchain ========= ============== ``2.2.0`` ``foss/2016a`` ========= ============== @@ -41087,12 +42616,12 @@ RepeatMasker is a program that screens DNA sequences for interspersed repeats a *homepage*: https://www.repeatmasker.org/ ============ ====================== ========================================================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ====================== ========================================================== ``4.0.8`` ``-Perl-5.26.0-HMMER`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` -``4.0.8`` ``-Perl-5.28.0-HMMER`` ``intel/2018b`` -``4.0.9-p2`` ``-HMMER`` ``gompi/2019b`` -``4.1.2-p1`` ``foss/2020b`` +``4.0.8`` ``-Perl-5.28.0-HMMER`` ``intel/2018b`` +``4.0.9-p2`` ``-HMMER`` ``gompi/2019b`` +``4.1.2-p1`` ``foss/2020b`` ============ ====================== ========================================================== @@ -41106,7 +42635,7 @@ RepeatModeler is a de novo transposable element (TE) family identification and m *homepage*: https://www.repeatmasker.org/ ========== ============== -version toolchain +version toolchain ========== ============== ``2.0.2a`` ``foss/2020b`` ========== ============== @@ -41122,7 +42651,7 @@ De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and te *homepage*: https://www.repeatmasker.org/ ========= ============== -version toolchain +version toolchain ========= ============== ``1.0.6`` ``GCC/10.2.0`` ========= ============== @@ -41138,7 +42667,7 @@ Request is designed to be the simplest way possible to make http calls. It *homepage*: https://github.com/request/request/ ========== =================== ================== -version versionsuffix toolchain +version versionsuffix toolchain ========== =================== ================== ``2.88.1`` ``-nodejs-12.19.0`` ``fosscuda/2020b`` ========== =================== ================== @@ -41154,12 +42683,12 @@ Python http for humans *homepage*: https://pypi.python.org/pypi/requests ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== -``2.10.0`` ``-Python-2.7.11`` ``foss/2016a`` -``2.10.0`` ``-Python-3.5.1`` ``foss/2016a`` -``2.11.1`` ``-Python-2.7.12`` ``intel/2016b`` -``2.11.1`` ``-Python-3.5.2`` ``intel/2016b`` +``2.10.0`` ``-Python-2.7.11`` ``foss/2016a`` +``2.10.0`` ``-Python-3.5.1`` ``foss/2016a`` +``2.11.1`` ``-Python-2.7.12`` ``intel/2016b`` +``2.11.1`` ``-Python-3.5.2`` ``intel/2016b`` ``2.13.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ========== ================== =============================== @@ -41174,12 +42703,28 @@ RERconverge is a set of software written in R that estimates the correlation be *homepage*: https://github.com/nclark-lab/RERconverge ========= ============= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= =============================== ``0.1.0`` ``-R-3.4.3`` ``foss/2017b``, ``intel/2017b`` ========= ============= =============================== +.. _list_software_resolos_775: + +*resolos* ++++++++++ + +Resolos is a toolkit written in Python for maintaining reproducible environments for scientific computations. It's main goal is to enable researchers to easily replicate environments through space (running code on HPC environment) and time (environment preservation for long term archival). For installation and detailed usage, check out the documentation. + +*homepage*: https://gitlab.unige.ch/resolos/resolos + +========= ================== +version toolchain +========= ================== +``0.3.5`` ``GCCcore/11.3.0`` +========= ================== + + .. _list_software_retworkx_902: *retworkx* @@ -41190,7 +42735,7 @@ retworkx is a general purpose graph library for python3 written in Rust to take *homepage*: https://github.com/Qiskit/retworkx ========= ============== -version toolchain +version toolchain ========= ============== ``0.9.0`` ``foss/2021a`` ========= ============== @@ -41206,7 +42751,7 @@ RevBayes provides an interactive environment for statistical computation in phy *homepage*: https://revbayes.github.io/ ========= ============================== -version toolchain +version toolchain ========= ============================== ``1.1.1`` ``GCC/10.2.0``, ``GCC/11.2.0`` ========= ============================== @@ -41222,7 +42767,7 @@ Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11 *homepage*: https://rgdal.r-forge.r-project.org/ ========== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ============== ``1.4-4`` ``-R-3.6.0`` ``foss/2019a`` ``1.4-8`` ``-R-3.6.2`` ``foss/2019b`` @@ -41243,13 +42788,13 @@ R interface to Geometry Engine - Open Source (GEOS) using the C API for topology *homepage*: https://cran.r-project.org/web/packages/rgeos/ ========== ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= =============== ``0.3-17`` ``-R-3.2.3`` ``intel/2016a`` -``0.5-1`` ``-R-3.6.0`` ``foss/2019a`` -``0.5-2`` ``-R-3.6.2`` ``foss/2019b`` -``0.5-5`` ``-R-4.0.0`` ``foss/2020a`` -``0.5-5`` ``-R-4.1.0`` ``foss/2021a`` +``0.5-1`` ``-R-3.6.0`` ``foss/2019a`` +``0.5-2`` ``-R-3.6.2`` ``foss/2019b`` +``0.5-5`` ``-R-4.0.0`` ``foss/2020a`` +``0.5-5`` ``-R-4.1.0`` ``foss/2021a`` ========== ============= =============== @@ -41263,7 +42808,7 @@ Gurobi Optimizer 9.5 interface *homepage*: https://www.gurobi.com ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``9.1.2`` ``-R-4.1.0`` ``foss/2021a`` ``9.5.0`` ``-R-4.1.0`` ``foss/2021a`` @@ -41280,7 +42825,7 @@ This R/Bioconductor package provides an interface between HDF5 and R. *homepage*: https://bioconductor.org/packages/release/bioc/html/rhdf5.html ========== ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= =============== ``2.16.0`` ``-R-3.2.3`` ``intel/2016a`` ``2.18.0`` ``-R-3.3.1`` ``intel/2016b`` @@ -41297,7 +42842,7 @@ RheoTool is an open-source toolbox based on OpenFOAM to simulate Generalized New *homepage*: https://github.com/fppimenta/rheoTool ======= ============== -version toolchain +version toolchain ======= ============== ``5.0`` ``foss/2019b`` ======= ============== @@ -41313,7 +42858,7 @@ Running and Analyzing OpenMM Jobs *homepage*: https://gitlab.com/Olllom/rickflow ================== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ================= =============== ``0.7.0`` ``-Python-3.7.4`` ``intel/2019b`` ``0.7.0-20200529`` ``-Python-3.7.4`` ``intel/2019b`` @@ -41330,7 +42875,7 @@ The reaction IUPAC International Chemical Identifier (RInChI TM) is a non-propri *homepage*: https://www.inchi-trust.org/ ======== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ======== ============= ========== ``1.00`` ``-x86_64`` ``system`` ======== ============= ========== @@ -41346,12 +42891,12 @@ geospatial xarray extension powered by rasterio *homepage*: https://github.com/corteva/rioxarray ========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============== ``0.0.12`` ``-Python-3.7.2`` ``intel/2019a`` -``0.0.24`` ``-Python-3.7.4`` ``foss/2019b`` -``0.1.1`` ``-Python-3.8.2`` ``foss/2020a`` -``0.11.1`` ``foss/2021b`` +``0.0.24`` ``-Python-3.7.4`` ``foss/2019b`` +``0.1.1`` ``-Python-3.8.2`` ``foss/2020a`` +``0.11.1`` ``foss/2021b`` ========== ================= =============== @@ -41364,12 +42909,13 @@ Provides everything needed for high performance data loading and augmentation in *homepage*: https://rising.rtfd.io/ -========= ================ ============== -version versionsuffix toolchain -========= ================ ============== -``0.2.2`` ``foss/2021a`` +========= ================ ============================== +version versionsuffix toolchain +========= ================ ============================== +``0.2.2`` ``foss/2021a``, ``foss/2022a`` ``0.2.2`` ``-CUDA-11.3.1`` ``foss/2021a`` -========= ================ ============== +``0.2.2`` ``-CUDA-11.7.0`` ``foss/2022a`` +========= ================ ============================== .. _list_software_rjags_535: @@ -41382,22 +42928,38 @@ The rjags package is an interface to the JAGS library. *homepage*: https://cran.r-project.org/web/packages/rjags ======== ============= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ======== ============= ================================== -``4-6`` ``-R-3.4.0`` ``intel/2017a`` -``4-6`` ``-R-3.4.3`` ``intel/2017b`` -``4-8`` ``-R-3.5.1`` ``foss/2018b`` -``4-9`` ``-R-3.6.0`` ``foss/2019a`` -``4-10`` ``foss/2019b`` -``4-10`` ``-R-4.0.0`` ``foss/2020a`` +``4-6`` ``-R-3.4.0`` ``intel/2017a`` +``4-6`` ``-R-3.4.3`` ``intel/2017b`` +``4-8`` ``-R-3.5.1`` ``foss/2018b`` +``4-9`` ``-R-3.6.0`` ``foss/2019a`` +``4-10`` ``foss/2019b`` +``4-10`` ``-R-4.0.0`` ``foss/2020a`` ``4-10`` ``-R-4.0.3`` ``foss/2020b``, ``fosscuda/2020b`` ``4-10`` ``-R-4.0.4`` ``foss/2020b``, ``fosscuda/2020b`` ``4-10`` ``-R-4.0.5`` ``foss/2020b``, ``fosscuda/2020b`` -``4-10`` ``-R-4.1.0`` ``foss/2021a`` -``4-12`` ``-R-4.1.2`` ``foss/2021b`` +``4-10`` ``-R-4.1.0`` ``foss/2021a`` +``4-12`` ``-R-4.1.2`` ``foss/2021b`` ======== ============= ================================== +.. _list_software_RLCard_536: + +*RLCard* +++++++++ + +RLCard is a toolkit for Reinforcement Learning (RL) in card games. + +*homepage*: https://www.rlcard.org + +========= ============== +version toolchain +========= ============== +``1.0.9`` ``foss/2022a`` +========= ============== + + .. _list_software_Rmath_508: *Rmath* @@ -41408,10 +42970,10 @@ Rmath is the standalone version of the R math library. Rmath can be used in you *homepage*: https://www.r-project.org/ ========= =============== -version toolchain +version toolchain ========= =============== ``3.3.1`` ``intel/2016b`` -``4.0.4`` ``foss/2020b`` +``4.0.4`` ``foss/2020b`` ========= =============== @@ -41425,7 +42987,7 @@ rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.source *homepage*: https://github.com/Xinglab/rmats-turbo ========= ============== -version toolchain +version toolchain ========= ============== ``4.1.1`` ``foss/2020b`` ========= ============== @@ -41441,9 +43003,9 @@ RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. T *homepage*: http://www.repeatmasker.org/RMBlast.html ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== -``2.2.28`` ``-Python-2.7.11`` ``foss/2016a`` +``2.2.28`` ``-Python-2.7.11`` ``foss/2016a`` ``2.9.0`` ``gompi/2019b`` ``2.10.0`` ``gompi/2019b`` ``2.11.0`` ``gompi/2020b`` @@ -41460,9 +43022,9 @@ RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. *homepage*: https://github.com/bcgsc/RNA-Bloom ========= ============== -version toolchain +version toolchain ========= ============== -``1.2.3`` ``GCC/8.3.0`` +``1.2.3`` ``GCC/8.3.0`` ``1.4.3`` ``GCC/11.2.0`` ========= ============== @@ -41477,10 +43039,10 @@ Fast, efficient RNA-Seq metrics for quality control and process optimization *homepage*: https://github.com/getzlab/rnaseqc ========= =================== ============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =================== ============================== -``1.1.8`` ``-Java-1.8`` ``foss/2018b`` -``1.1.8`` ``-Java-1.8.0_121`` ``foss/2016b`` +``1.1.8`` ``-Java-1.8`` ``foss/2018b`` +``1.1.8`` ``-Java-1.8.0_121`` ``foss/2016b`` ``2.4.2`` ``foss/2021a``, ``foss/2021b`` ========= =================== ============================== @@ -41495,7 +43057,7 @@ RNAclust is a perl script summarizing all the single steps required for clusteri *homepage*: http://www.bioinf.uni-leipzig.de/~kristin/Software/RNAclust/ ======= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= ============== ``1.3`` ``-Perl-5.24.0`` ``foss/2016b`` ``1.3`` ``-Python-3.6.6`` ``foss/2018b`` @@ -41512,7 +43074,7 @@ RNAcode - Analyze the protein coding potential in multiple sequence alignments *homepage*: https://wash.github.io/rnacode/ ======= ============== -version toolchain +version toolchain ======= ============== ``0.3`` ``foss/2017a`` ======= ============== @@ -41528,7 +43090,7 @@ RNAIndel calls coding indels and classifies them into somatic, germline, and ar *homepage*: https://github.com/stjude/RNAIndel ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.3.0`` ``-Python-3.6.6`` ``intel/2018b`` ``1.0.0`` ``-Python-3.6.6`` ``intel/2018b`` @@ -41545,7 +43107,7 @@ This is an example description. *homepage*: https://www.cbs.dtu.dk/services/RNAmmer ======= ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================ =============== ``1.2`` ``-Perl-5.28.0`` ``intel/2018b`` ======= ================ =============== @@ -41561,7 +43123,7 @@ rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and *homepage*: https://cab.spbu.ru/software/rnaquast/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``1.5.2`` ``-Python-2.7.15`` ``foss/2018b`` ``2.2.0`` ``-Python-3.8.2`` ``foss/2020a`` @@ -41579,7 +43141,7 @@ RNAz is a program for predicting structurally conserved and thermodynamically st *homepage*: http://www.tbi.univie.ac.at/~wash/RNAz/ ======= ============================== -version toolchain +version toolchain ======= ============================== ``2.1`` ``foss/2016b``, ``foss/2018b`` ======= ============================== @@ -41595,7 +43157,7 @@ RnBeads is an R package for comprehensive analysis of DNA methylation data obtai *homepage*: https://rnbeads.org ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``2.6.0`` ``-R-4.0.0`` ``foss/2020a`` ========= ============= ============== @@ -41611,10 +43173,10 @@ Rapid large-scale prokaryote pan genome analysis *homepage*: https://github.com/sanger-pathogens/Roary ========== ================ ============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================ ============================== -``3.12.0`` ``system`` -``3.12.0`` ``-Perl-5.26.1`` ``intel/2018a`` +``3.12.0`` ``system`` +``3.12.0`` ``-Perl-5.26.1`` ``intel/2018a`` ``3.13.0`` ``foss/2020a``, ``foss/2021a`` ========== ================ ============================== @@ -41629,7 +43191,7 @@ AMD ROCm is the first open-source software development platform for HPC/Hypersca *homepage*: https://rocmdocs.amd.com/en/latest/ ========= ================== -version toolchain +version toolchain ========= ================== ``4.5.0`` ``GCCcore/11.2.0`` ========= ================== @@ -41645,7 +43207,7 @@ ROCM cmake modules provides cmake modules for common build tasks needed for the *homepage*: https://github.com/RadeonOpenCompute/rocm-cmake ========= ================== -version toolchain +version toolchain ========= ================== ``4.5.0`` ``GCCcore/11.2.0`` ========= ================== @@ -41661,7 +43223,7 @@ The compiler support repository provides various Lightning Compiler related serv *homepage*: https://github.com/RadeonOpenCompute/ROCm-CompilerSupport ========= ================== -version toolchain +version toolchain ========= ================== ``4.5.0`` ``GCCcore/11.2.0`` ========= ================== @@ -41677,7 +43239,7 @@ The ROCm System Management Interface Library, or ROCm SMI library, is part of th *homepage*: https://github.com/RadeonOpenCompute/rocm_smi_lib ========= ================== -version toolchain +version toolchain ========= ================== ``4.5.0`` ``GCCcore/11.2.0`` ========= ================== @@ -41693,7 +43255,7 @@ ROCm Application for Reporting System Info *homepage*: https://github.com/RadeonOpenCompute/rocminfo ========= ================== -version toolchain +version toolchain ========= ================== ``4.5.0`` ``GCCcore/11.2.0`` ========= ================== @@ -41709,7 +43271,7 @@ The user-mode API interfaces and libraries necessary for host applications to la *homepage*: https://github.com/RadeonOpenCompute/ROCR-Runtime ========= ================== -version toolchain +version toolchain ========= ================== ``4.5.0`` ``GCCcore/11.2.0`` ========= ================== @@ -41725,7 +43287,7 @@ The user-mode API interfaces used to interact with the ROCk driver *homepage*: https://github.com/RadeonOpenCompute/ROCT-Thunk-Interface ========= ================== -version toolchain +version toolchain ========= ================== ``4.5.0`` ``GCCcore/11.2.0`` ========= ================== @@ -41741,7 +43303,7 @@ Repeat Orbit Interferometry PACkage (ROI_PAC), software for processing synthetic *homepage*: http://roipac.org/ ========= ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =============== ``3.0.1`` ``-Perl-5.24.1`` ``intel/2017a`` ========= ================ =============== @@ -41757,7 +43319,7 @@ The ROME (Refinement and Optimization via Machine Learning for cryo-EM) Softwar *homepage*: https://ipccsb.dfci.harvard.edu/rome ========= ================= -version toolchain +version toolchain ========= ================= ``1.1.2`` ``intel/2019.02`` ========= ================= @@ -41773,19 +43335,19 @@ The ROOT system provides a set of OO frameworks with all the functionality n *homepage*: http://root.cern.ch/drupal/ ============ ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============================== ``6.10.02`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``6.10.04`` ``-Python-2.7.13`` ``intel/2017a`` +``6.10.04`` ``-Python-2.7.13`` ``intel/2017a`` ``6.10.08`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``6.14.06`` ``-Python-2.7.15`` ``foss/2018b`` -``6.14.06`` ``-Python-3.6.6`` ``foss/2018b`` -``6.20.04`` ``-Python-3.7.4`` ``foss/2019b`` -``6.24.06`` ``foss/2021b`` -``v5.34.34`` ``-Python-2.7.11`` ``intel/2016a`` -``v5.34.36`` ``-Python-2.7.11`` ``intel/2016a`` -``v6.06.02`` ``-Python-2.7.12`` ``intel/2016b`` -``v6.08.02`` ``-Python-2.7.11`` ``foss/2016a`` +``6.14.06`` ``-Python-2.7.15`` ``foss/2018b`` +``6.14.06`` ``-Python-3.6.6`` ``foss/2018b`` +``6.20.04`` ``-Python-3.7.4`` ``foss/2019b`` +``6.24.06`` ``foss/2021b`` +``v5.34.34`` ``-Python-2.7.11`` ``intel/2016a`` +``v5.34.36`` ``-Python-2.7.11`` ``intel/2016a`` +``v6.06.02`` ``-Python-2.7.12`` ``intel/2016b`` +``v6.08.02`` ``-Python-2.7.11`` ``foss/2016a`` ============ ================== =============================== @@ -41799,7 +43361,7 @@ root_numpy is a Python extension module that provides an efficient interface bet *homepage*: https://scikit-hep.org/root_numpy/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``4.8.0`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== @@ -41815,7 +43377,7 @@ The rootpy project is a community-driven initiative aiming to provide a more pyt *homepage*: http://www.rootpy.org/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``0.8.0`` ``-Python-2.7.11`` ``foss/2016a`` ``1.0.1`` ``-Python-3.6.6`` ``foss/2018b`` @@ -41832,7 +43394,7 @@ Rosetta is the premier software suite for modeling macromolecular structures. As *homepage*: https://www.rosettacommons.org ================= ============== -version toolchain +version toolchain ================= ============== ``3.7`` ``foss/2016b`` ``2016.13.58602`` ``foss/2016a`` @@ -41850,7 +43412,7 @@ rpmrebuild is a tool to build an RPM file from a package that has already been *homepage*: http://rpmrebuild.sourceforge.net/ ======== ========== -version toolchain +version toolchain ======== ========== ``2.11`` ``system`` ======== ========== @@ -41866,12 +43428,12 @@ rpy2 is an interface to R running embedded in a Python process. *homepage*: https://rpy2.bitbucket.io/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== -``2.7.9`` ``-Python-2.7.12`` ``foss/2016b`` +``2.7.9`` ``-Python-2.7.12`` ``foss/2016b`` ``2.8.2`` ``-Python-2.7.13`` ``intel/2017a`` -``3.2.6`` ``-Python-3.7.4`` ``foss/2019b`` -``3.4.5`` ``foss/2021b`` +``3.2.6`` ``-Python-3.7.4`` ``foss/2019b`` +``3.4.5`` ``foss/2021b`` ========= ================== =============== @@ -41885,7 +43447,7 @@ RQGIS3 establishes an interface between R and QGIS3, i.e., it allows the user t *homepage*: https://github.com/r-spatial/RQGIS3 ============ ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= ============== ``20190903`` ``-R-3.6.0`` ``foss/2019a`` ============ ============= ============== @@ -41901,14 +43463,14 @@ RNA-Seq by Expectation-Maximization *homepage*: https://deweylab.github.io/RSEM/ ========== ================================================ -version toolchain +version toolchain ========== ================================================ -``1.2.26`` ``GNU/4.9.3-2.25`` -``1.2.30`` ``foss/2016a``, ``intel/2016b`` -``1.3.0`` ``foss/2016b``, ``intel/2017a`` +``1.2.26`` ``GNU/4.9.3-2.25`` +``1.2.30`` ``foss/2016a``, ``intel/2016b`` +``1.3.0`` ``foss/2016b``, ``intel/2017a`` ``1.3.1`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` -``1.3.2`` ``foss/2018b`` -``1.3.3`` ``foss/2019b`` +``1.3.2`` ``foss/2018b`` +``1.3.3`` ``foss/2019b`` ========== ================================================ @@ -41922,13 +43484,13 @@ RSeQC provides a number of useful modules that can comprehensively evaluate hig *homepage*: http://rseqc.sourceforge.net/ ========= ========================== ============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ========================== ============================== -``2.6.4`` ``-Python-2.7.12-R-3.3.1`` ``foss/2016b`` -``2.6.4`` ``-Python-2.7.14`` ``intel/2018a`` -``3.0.0`` ``-Python-3.6.6`` ``foss/2018b`` +``2.6.4`` ``-Python-2.7.12-R-3.3.1`` ``foss/2016b`` +``2.6.4`` ``-Python-2.7.14`` ``intel/2018a`` +``3.0.0`` ``-Python-3.6.6`` ``foss/2018b`` ``4.0.0`` ``foss/2021a``, ``foss/2021b`` -``4.0.0`` ``-Python-3.8.2`` ``foss/2020a`` +``4.0.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ========================== ============================== @@ -41942,10 +43504,10 @@ RStan is the R interface to Stan. Stan is a state-of-the-art platform for stat *homepage*: https://github.com/stan-dev/rstan ========== ============= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= =============================== ``2.18.2`` ``-R-3.4.3`` ``foss/2017b``, ``intel/2017b`` -``2.18.2`` ``-R-3.5.1`` ``foss/2018b`` +``2.18.2`` ``-R-3.5.1`` ``foss/2018b`` ========== ============= =============================== @@ -41959,7 +43521,7 @@ Estimates previously compiled regression models using the 'rstan' package, which *homepage*: https://r-forge.r-project.org/projects/rstanarm ========== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ============== ``2.19.3`` ``-R-3.6.2`` ``foss/2019b`` ========== ============= ============== @@ -41970,19 +43532,20 @@ version versionsuffix toolchain *RStudio-Server* ++++++++++++++++ -This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) +This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: rserver --server-daemonize=0 --www-port=8787 If you need a database config one can be created with: MYTMP=`mktemp -d` && echo -e "provider=sqlite\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" and then used with: rserver ... --database-config-file="${MYTMP}/db.conf" *homepage*: https://www.rstudio.com/ -============ ==================== ================== -version versionsuffix toolchain -============ ==================== ================== -``1.2.5033`` ``-Java-11`` ``fosscuda/2019b`` -``1.2.5042`` ``-Java-11`` ``foss/2019b`` -``1.3.959`` ``-Java-11-R-4.0.0`` ``foss/2020a`` -``1.3.1093`` ``-Java-11-R-4.0.0`` ``foss/2020a`` -``1.4.1717`` ``-Java-11-R-4.1.0`` ``foss/2021a`` -============ ==================== ================== +================= ==================== ================== +version versionsuffix toolchain +================= ==================== ================== +``1.2.5033`` ``-Java-11`` ``fosscuda/2019b`` +``1.2.5042`` ``-Java-11`` ``foss/2019b`` +``1.3.959`` ``-Java-11-R-4.0.0`` ``foss/2020a`` +``1.3.1093`` ``-Java-11-R-4.0.0`` ``foss/2020a`` +``1.4.1717`` ``-Java-11-R-4.1.0`` ``foss/2021a`` +``2022.07.2+576`` ``-Java-11-R-4.2.1`` ``foss/2022a`` +================= ==================== ================== .. _list_software_RTG-Tools_811: @@ -41995,7 +43558,7 @@ RTG Tools contains utilities to easily manipulate and accurately compare multipl *homepage*: https://www.realtimegenomics.com/products/rtg-tools ========= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========== ``3.9.1`` ``-Java-1.8`` ``system`` ========= ============= ========== @@ -42011,7 +43574,7 @@ Rtree is a ctypes Python wrapper of libspatialindex that provides a number of ad *homepage*: https://toblerity.org/rtree/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.8.3`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============== @@ -42026,11 +43589,11 @@ ruamel.yaml is a YAML 1.2 loader/dumper package for Python. *homepage*: https://sourceforge.net/projects/ruamel-yaml -=========== ====================================== -version toolchain -=========== ====================================== -``0.17.21`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -=========== ====================================== +=========== ========================================================== +version toolchain +=========== ========================================================== +``0.17.21`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +=========== ========================================================== .. _list_software_Ruby_418: @@ -42043,20 +43606,22 @@ Ruby is a dynamic, open source programming language with a focus on simplicity *homepage*: https://www.ruby-lang.org ========= ================================================ -version toolchain +version toolchain ========= ================================================ -``2.1.6`` ``system`` -``2.3.1`` ``intel/2016b``, ``system`` -``2.3.3`` ``system`` -``2.3.4`` ``system`` -``2.4.2`` ``foss/2017b`` +``2.1.6`` ``system`` +``2.3.1`` ``intel/2016b``, ``system`` +``2.3.3`` ``system`` +``2.3.4`` ``system`` +``2.4.2`` ``foss/2017b`` ``2.5.0`` ``foss/2018a``, ``intel/2017a``, ``intel/2017b`` -``2.5.1`` ``foss/2018a``, ``intel/2018a`` -``2.6.1`` ``GCCcore/7.3.0`` -``2.6.3`` ``GCCcore/8.2.0`` -``2.7.1`` ``GCCcore/8.3.0`` -``2.7.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``3.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.5.1`` ``foss/2018a``, ``intel/2018a`` +``2.6.1`` ``GCCcore/7.3.0`` +``2.6.3`` ``GCCcore/8.2.0`` +``2.7.1`` ``GCCcore/8.3.0`` +``2.7.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``3.0.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``3.0.3`` ``GCCcore/11.3.0`` +``3.0.5`` ``GCCcore/11.3.0`` ========= ================================================ @@ -42070,7 +43635,7 @@ Ruby Tk interface module using tcltklib *homepage*: https://github.com/ruby/tk ========= =============== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =============== =============================== ``0.2.0`` ``-Ruby-2.5.1`` ``foss/2018a``, ``intel/2018a`` ========= =============== =============================== @@ -42086,7 +43651,7 @@ Ruffus is a Computation Pipeline library for python. It is open-sourced, powerfu *homepage*: http://www.ruffus.org.uk/ ========= ============== -version toolchain +version toolchain ========= ============== ``2.8.4`` ``foss/2021b`` ========= ============== @@ -42102,23 +43667,24 @@ Rust is a systems programming language that runs blazingly fast, prevents segfau *homepage*: https://www.rust-lang.org ========== ========================================================================== -version toolchain +version toolchain ========== ========================================================================== -``1.8.0`` ``foss/2016a`` -``1.12.0`` ``foss/2016b`` -``1.12.1`` ``foss/2016b`` -``1.18.0`` ``foss/2017a`` -``1.21.0`` ``foss/2017b`` -``1.22.1`` ``GCCcore/6.4.0`` -``1.29.2`` ``GCCcore/7.3.0`` -``1.30.1`` ``GCCcore/6.4.0`` -``1.35.0`` ``GCCcore/8.2.0`` -``1.37.0`` ``GCCcore/8.3.0`` +``1.8.0`` ``foss/2016a`` +``1.12.0`` ``foss/2016b`` +``1.12.1`` ``foss/2016b`` +``1.18.0`` ``foss/2017a`` +``1.21.0`` ``foss/2017b`` +``1.22.1`` ``GCCcore/6.4.0`` +``1.29.2`` ``GCCcore/7.3.0`` +``1.30.1`` ``GCCcore/6.4.0`` +``1.35.0`` ``GCCcore/8.2.0`` +``1.37.0`` ``GCCcore/8.3.0`` ``1.42.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.52.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``1.54.0`` ``GCCcore/11.2.0`` -``1.56.0`` ``GCCcore/11.2.0`` -``1.60.0`` ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +``1.52.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``1.54.0`` ``GCCcore/11.2.0`` +``1.56.0`` ``GCCcore/11.2.0`` +``1.60.0`` ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +``1.65.0`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========== ========================================================================== @@ -42128,7 +43694,7 @@ version toolchain --- -:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_samplot_768` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAS_231` - :ref:`list_software_Satsuma2_784` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_SCGid_426` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_SCopeLoomR_963` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_scPred_609` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_ShengBTE_720` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_SHTns_464` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SISSO_401` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-pandas_1428` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_skorch_650` - :ref:`list_software_SlamDunk_799` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_slow5tools_1067` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_SMC++_313` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_smooth-topk_1157` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SoXt_398` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_SPM_240` - :ref:`list_software_spoa_435` - :ref:`list_software_SPOTPY_495` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-CCM+_613` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_stripy_683` - :ref:`list_software_STRique_685` - :ref:`list_software_Structure_977` - :ref:`list_software_STRUMPACK_698` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SURVIVOR_656` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_SWIPE_392` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` +:ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_samblaster_1070` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_samplot_768` - :ref:`list_software_SAMtools_786` - :ref:`list_software_sansa_534` - :ref:`list_software_SAP_228` - :ref:`list_software_SAS_231` - :ref:`list_software_Satsuma2_784` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_SBCL_292` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaFaCoS_707` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_scanpy_654` - :ref:`list_software_SCENIC_437` - :ref:`list_software_scGeneFit_888` - :ref:`list_software_SCGid_426` - :ref:`list_software_Schrodinger_1144` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-bio_1006` - :ref:`list_software_scikit-build_1220` - :ref:`list_software_scikit-cuda_1105` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-misc_1120` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_scikit-uplift_1352` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_SCopeLoomR_963` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_scPred_609` - :ref:`list_software_Scrappie_823` - :ref:`list_software_scVelo_620` - :ref:`list_software_scvi-tools_1043` - :ref:`list_software_Scythe_624` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL_227` - :ref:`list_software_SDL2_277` - :ref:`list_software_SDL2_image_887` - :ref:`list_software_SDL_image_837` - :ref:`list_software_SDSL_310` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_SECAPR_446` - :ref:`list_software_Seeder_600` - :ref:`list_software_segemehl_842` - :ref:`list_software_segmentation-models_1983` - :ref:`list_software_SeisSol_706` - :ref:`list_software_SelEstim_806` - :ref:`list_software_SELFIES_523` - :ref:`list_software_SentencePiece_1307` - :ref:`list_software_sep_328` - :ref:`list_software_SEPP_312` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_SeqKit_593` - :ref:`list_software_SeqLib_576` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_SeuratData_1006` - :ref:`list_software_SeuratDisk_1023` - :ref:`list_software_SeuratWrappers_1480` - :ref:`list_software_sf_217` - :ref:`list_software_sfftk_542` - :ref:`list_software_Shannon_725` - :ref:`list_software_SHAP_300` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_SHAPEIT4_578` - :ref:`list_software_Shapely_726` - :ref:`list_software_sharutils_991` - :ref:`list_software_Shasta_612` - :ref:`list_software_ShengBTE_720` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_SHTns_464` - :ref:`list_software_Sibelia_697` - :ref:`list_software_SICER2_424` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SignalP_686` - :ref:`list_software_silx_448` - :ref:`list_software_simint_660` - :ref:`list_software_SimNIBS_597` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singular_837` - :ref:`list_software_SiNVICT_576` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SISSO_401` - :ref:`list_software_SISSO++_487` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_sklearn-pandas_1428` - :ref:`list_software_sklearn-som_1132` - :ref:`list_software_skorch_650` - :ref:`list_software_SlamDunk_799` - :ref:`list_software_slamdunk_863` - :ref:`list_software_SLATEC_444` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_SLiM_341` - :ref:`list_software_slow5tools_1067` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_SMC++_313` - :ref:`list_software_smithwaterman_1412` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_smooth-topk_1157` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_SMV_246` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAP-HMM_577` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snp-sites_934` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SNPomatic_878` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SOCI_302` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_sonic_540` - :ref:`list_software_SoQt_391` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_SoX_282` - :ref:`list_software_SoXt_398` - :ref:`list_software_SpaceRanger_1099` - :ref:`list_software_Spack_498` - :ref:`list_software_spaCy_512` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spatialreg_1068` - :ref:`list_software_spdlog_649` - :ref:`list_software_SpectrA_690` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_speech_tools_1288` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_Sphinx-RTD-Theme_1457` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SplAdder_783` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_split-seq_930` - :ref:`list_software_splitRef_841` - :ref:`list_software_SPM_240` - :ref:`list_software_spoa_435` - :ref:`list_software_SPOOLES_549` - :ref:`list_software_SPOTPY_495` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_Squidpy_751` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SRST2_382` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSN_244` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_SSW_253` - :ref:`list_software_STACEY_457` - :ref:`list_software_Stack_502` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-CCM+_613` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_stars_557` - :ref:`list_software_Stata_509` - :ref:`list_software_Statistics-R_1194` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STEAK_376` - :ref:`list_software_STIR_322` - :ref:`list_software_stpipeline_1085` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_stripy_683` - :ref:`list_software_STRique_685` - :ref:`list_software_Structure_977` - :ref:`list_software_STRUMPACK_698` - :ref:`list_software_suave_548` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUMO_324` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SunPy_511` - :ref:`list_software_SuperLU_688` - :ref:`list_software_SuperLU_DIST_1091` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SURVIVOR_656` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_SVG_240` - :ref:`list_software_svist4get_941` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWAT+_362` - :ref:`list_software_swifter_772` - :ref:`list_software_SWIG_314` - :ref:`list_software_SWIPE_392` - :ref:`list_software_swissknife_1094` - :ref:`list_software_SymEngine_911` - :ref:`list_software_SymEngine-python_1630` - :ref:`list_software_SYMPHONY_647` - :ref:`list_software_sympy_578` - :ref:`list_software_SyRI_359` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: @@ -42141,7 +43707,7 @@ S-Lang is a multi-platform programmer's library designed to allow a developer t *homepage*: http://www.jedsoft.org/slang/ ========= ============= -version toolchain +version toolchain ========= ============= ``2.3.0`` ``GCC/4.9.2`` ========= ============= @@ -42157,7 +43723,7 @@ S4 stands for Stanford Stratified Structure Solver, a frequency domain code to *homepage*: https://web.stanford.edu/group/fan/S4 ================== ============== -version toolchain +version toolchain ================== ============== ``1.1.1-20180610`` ``foss/2017b`` ================== ============== @@ -42173,7 +43739,7 @@ S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is free software packa *homepage*: http://darwin.cwru.edu/sage/ ======= ========== -version toolchain +version toolchain ======= ========== ``6.3`` ``system`` ``6.4`` ``system`` @@ -42190,10 +43756,10 @@ Sailfish is a software tool that implements a novel, alignment-free algorithm fo *homepage*: http://www.cs.cmu.edu/~ckingsf/software/sailfish/ ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``0.10.1`` ``gompi/2019b`` -``0.10.1`` ``-Python-2.7.12`` ``foss/2016b`` +``0.10.1`` ``-Python-2.7.12`` ``foss/2016b`` ========== ================== =============== @@ -42207,7 +43773,7 @@ Sensitivity Analysis Library in Python (Numpy). Contains Sobol, Morris, Fraction *homepage*: https://SALib.github.io/SALib/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.1.3`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== @@ -42223,19 +43789,19 @@ Salmon is a wicked-fast program to produce a highly-accurate, transcript-level *homepage*: https://github.com/COMBINE-lab/salmon ========== ================== ================================ -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================================ -``0.8.2`` ``system`` -``0.8.2`` ``-Python-2.7.12`` ``foss/2016b`` -``0.11.2`` ``intel/2018a`` -``0.12.0`` ``foss/2018b`` -``0.14.1`` ``foss/2018b`` -``0.14.2`` ``gompi/2019a`` +``0.8.2`` ``system`` +``0.8.2`` ``-Python-2.7.12`` ``foss/2016b`` +``0.11.2`` ``intel/2018a`` +``0.12.0`` ``foss/2018b`` +``0.14.1`` ``foss/2018b`` +``0.14.2`` ``gompi/2019a`` ``1.0.0`` ``gompi/2019a``, ``gompi/2019b`` -``1.1.0`` ``gompi/2019b`` -``1.2.0`` ``gompi/2019b`` -``1.3.0`` ``gompi/2020a`` -``1.4.0`` ``GCC/11.2.0``, ``gompi/2020b`` +``1.1.0`` ``gompi/2019b`` +``1.2.0`` ``gompi/2019b`` +``1.3.0`` ``gompi/2020a`` +``1.4.0`` ``GCC/11.2.0``, ``gompi/2020b`` ========== ================== ================================ @@ -42249,7 +43815,7 @@ SALMON is an open-source computer program for ab-initio quantum-mechanical calcu *homepage*: https://salmon-tddft.jp ========= =============================== -version toolchain +version toolchain ========= =============================== ``1.2.1`` ``foss/2018b``, ``intel/2018b`` ========= =============================== @@ -42265,10 +43831,10 @@ Sambamba is a high performance modern robust and fast tool (and library), writt *homepage*: https://lomereiter.github.io/sambamba/ ========= ============== -version toolchain +version toolchain ========= ============== -``0.6.6`` ``system`` -``0.7.1`` ``system`` +``0.6.6`` ``system`` +``0.7.1`` ``system`` ``0.8.0`` ``GCC/10.2.0`` ``0.8.2`` ``GCC/10.3.0`` ========= ============== @@ -42284,9 +43850,9 @@ samblaster is a fast and flexible program for marking duplicates in read-id gro *homepage*: https://github.com/GregoryFaust/samblaster ========== ============================== -version toolchain +version toolchain ========== ============================== -``0.1.24`` ``foss/2018b`` +``0.1.24`` ``foss/2018b`` ``0.1.26`` ``GCC/10.2.0``, ``GCC/10.3.0`` ========== ============================== @@ -42301,7 +43867,7 @@ FEM solver solution suite for basic linear structures to advanced, flexible nonl *homepage*: http://www.plm.automation.siemens.com/en_us/products/lms/samtech/samcef-solver-suite/ =========== ========== -version toolchain +version toolchain =========== ========== ``17.0-03`` ``system`` =========== ========== @@ -42317,9 +43883,9 @@ Filter SAM file for soft and hard clipped alignments. *homepage*: https://github.com/tseemann/samclip ========= ================ ========================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ========================================================= -``0.2`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``0.2`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` ``0.4.0`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ========= ================ ========================================================= @@ -42334,7 +43900,7 @@ Plot structural variant signals from many BAMs and CRAMs. *homepage*: https://github.com/ryanlayer/samplot ========= ============== -version toolchain +version toolchain ========= ============== ``1.3.0`` ``foss/2021b`` ========= ============== @@ -42350,30 +43916,30 @@ SAM Tools provide various utilities for manipulating alignments in the SAM forma *homepage*: http://www.htslib.org/ ========== ================= ======================================================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ======================================================================================================================================= -``0.1.17`` ``intel/2017a`` -``0.1.19`` ``GCC/10.3.0``, ``foss/2016a``, ``foss/2016b`` -``0.1.20`` ``GCC/8.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b`` -``1.2`` ``foss/2016b`` -``1.3`` ``foss/2016a``, ``intel/2016a`` -``1.3.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``1.3.1`` ``-HTSlib-1.3.2`` ``intel/2016b`` -``1.4`` ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` -``1.4.1`` ``intel/2017a`` -``1.5`` ``foss/2016b``, ``intel/2017a`` -``1.6`` ``GCC/6.4.0-2.28``, ``foss/2017a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017b`` -``1.7`` ``foss/2018a``, ``intel/2018a`` -``1.8`` ``intel/2018a`` +``0.1.17`` ``intel/2017a`` +``0.1.19`` ``GCC/10.3.0``, ``foss/2016a``, ``foss/2016b`` +``0.1.20`` ``GCC/8.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b`` +``1.2`` ``foss/2016b`` +``1.3`` ``foss/2016a``, ``intel/2016a`` +``1.3.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``1.3.1`` ``-HTSlib-1.3.2`` ``intel/2016b`` +``1.4`` ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` +``1.4.1`` ``intel/2017a`` +``1.5`` ``foss/2016b``, ``intel/2017a`` +``1.6`` ``GCC/6.4.0-2.28``, ``foss/2017a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017b`` +``1.7`` ``foss/2018a``, ``intel/2018a`` +``1.8`` ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` -``1.10`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` -``1.11`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` -``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` -``1.13`` ``GCC/10.3.0`` -``1.14`` ``GCC/11.2.0`` -``1.15`` ``GCC/11.2.0`` -``1.15.1`` ``GCC/11.2.0``, ``GCC/11.3.0`` -``1.16.1`` ``GCC/11.2.0``, ``GCC/11.3.0`` +``1.10`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` +``1.11`` ``GCC/10.2.0``, ``GCC/9.3.0``, ``iccifort/2020.4.304`` +``1.12`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/9.3.0`` +``1.13`` ``GCC/10.3.0``, ``GCC/11.3.0`` +``1.14`` ``GCC/11.2.0`` +``1.15`` ``GCC/11.2.0`` +``1.15.1`` ``GCC/11.2.0``, ``GCC/11.3.0`` +``1.16.1`` ``GCC/11.2.0``, ``GCC/11.3.0`` ========== ================= ======================================================================================================================================= @@ -42387,12 +43953,28 @@ Structural variant (SV) annotation, a companion to the 'dolly' tool. *homepage*: https://github.com/dellytools/sansa/ ========= =============== -version toolchain +version toolchain ========= =============== ``0.0.7`` ``gompi/2020b`` ========= =============== +.. _list_software_SAP_228: + +*SAP* ++++++ + +SAP is a pairwise structure alignment via double dynamic programming + +*homepage*: https://github.com/mathbio-nimr-mrc-ac-uk/SAP + +========= ============== +version toolchain +========= ============== +``1.1.3`` ``GCC/11.3.0`` +========= ============== + + .. _list_software_SAS_231: *SAS* @@ -42403,7 +43985,7 @@ SAS is a software suite for advanced analytics, multivariate analyses, business *homepage*: https://www.sas.com ======= ========== -version toolchain +version toolchain ======= ========== ``9.4`` ``system`` ======= ========== @@ -42419,7 +44001,7 @@ Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and *homepage*: https://github.com/bioinfologics/satsuma2 ============ ============== -version toolchain +version toolchain ============ ============== ``20220304`` ``GCC/11.3.0`` ============ ============== @@ -42435,7 +44017,7 @@ Interface to various variant calling formats. *homepage*: https://github.com/statgen/savvy ========= ==================== -version toolchain +version toolchain ========= ==================== ``1.3.0`` ``GCC/8.2.0-2.31.1`` ========= ==================== @@ -42451,7 +44033,7 @@ Open Source SAXON XSLT processor developed by Saxonica Limited. *homepage*: http://saxon.sourceforge.net ============ =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ============ =================== ========== ``9.7.0.4`` ``-Java-1.7.0_79`` ``system`` ``9.7.0.21`` ``-Java-1.8.0_162`` ``system`` @@ -42469,9 +44051,9 @@ Steel Bank Common Lisp (SBCL) is a high performance Common Lisp compiler. It is *homepage*: http://sbcl.sourceforge.net/ ========= ================== -version toolchain +version toolchain ========= ================== -``2.0.9`` ``GCCcore/9.3.0`` +``2.0.9`` ``GCCcore/9.3.0`` ``2.2.1`` ``GCCcore/10.3.0`` ========= ================== @@ -42486,7 +44068,7 @@ sbt is a build tool for Scala, Java, and more. *homepage*: http://www.scala-sbt.org/ ========== =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== =================== ========== ``1.0.2`` ``-Java-1.8.0_152`` ``system`` ``1.3.13`` ``-Java-1.8`` ``system`` @@ -42503,7 +44085,7 @@ ScaFaCoS is a library of scalable fast coulomb solvers. *homepage*: http://www.scafacos.de/ ========= =============================================================================== -version toolchain +version toolchain ========= =============================================================================== ``1.0.1`` ``foss/2020a``, ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``intel/2020a`` ========= =============================================================================== @@ -42519,26 +44101,26 @@ The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines *homepage*: https://www.netlib.org/scalapack/ ========= ================================= ============================================================================================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================================= ============================================================================================================================================ -``2.0.2`` ``gompi/2019b``, ``gompic/2019b`` -``2.0.2`` ``-BLIS-0.3.2`` ``gompi/2018b`` -``2.0.2`` ``-OpenBLAS-0.2.13-LAPACK-3.5.0`` ``gmvapich2/1.7.20`` -``2.0.2`` ``-OpenBLAS-0.2.15-LAPACK-3.6.0`` ``gmpich/2016a``, ``gmvapich2/2016a``, ``gompi/2016a`` -``2.0.2`` ``-OpenBLAS-0.2.18-LAPACK-3.6.0`` ``gompi/2016.04``, ``gompi/2016.06`` -``2.0.2`` ``-OpenBLAS-0.2.18-LAPACK-3.6.1`` ``gompi/2016.07``, ``gompi/2016b`` -``2.0.2`` ``-OpenBLAS-0.2.19-LAPACK-3.6.1`` ``gompi/2016.09`` -``2.0.2`` ``-OpenBLAS-0.2.19-LAPACK-3.7.0`` ``gompi/2017a`` +``2.0.2`` ``gompi/2019b``, ``gompic/2019b`` +``2.0.2`` ``-BLIS-0.3.2`` ``gompi/2018b`` +``2.0.2`` ``-OpenBLAS-0.2.13-LAPACK-3.5.0`` ``gmvapich2/1.7.20`` +``2.0.2`` ``-OpenBLAS-0.2.15-LAPACK-3.6.0`` ``gmpich/2016a``, ``gmvapich2/2016a``, ``gompi/2016a`` +``2.0.2`` ``-OpenBLAS-0.2.18-LAPACK-3.6.0`` ``gompi/2016.04``, ``gompi/2016.06`` +``2.0.2`` ``-OpenBLAS-0.2.18-LAPACK-3.6.1`` ``gompi/2016.07``, ``gompi/2016b`` +``2.0.2`` ``-OpenBLAS-0.2.19-LAPACK-3.6.1`` ``gompi/2016.09`` +``2.0.2`` ``-OpenBLAS-0.2.19-LAPACK-3.7.0`` ``gompi/2017a`` ``2.0.2`` ``-OpenBLAS-0.2.20`` ``gimpi/2017b``, ``gimpi/2018a``, ``gimpic/2017b``, ``gmpich/2017.08``, ``gompi/2017b``, ``gompi/2018a``, ``gompic/2017b``, ``gompic/2018a`` -``2.0.2`` ``-OpenBLAS-0.3.1`` ``gompi/2018b``, ``gompic/2018b`` -``2.0.2`` ``-OpenBLAS-0.3.3`` ``gompi/2018.08`` -``2.0.2`` ``-OpenBLAS-0.3.5`` ``gompi/2019a``, ``gompic/2019a`` -``2.1.0`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b`` -``2.1.0`` ``-bf`` ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2020b`` -``2.1.0`` ``-bl`` ``gompi/2020b`` -``2.1.0`` ``-fb`` ``gompi/2021a``, ``gompi/2021b`` -``2.2`` ``-amd`` ``gompi/2020a`` -``2.2.0`` ``-fb`` ``gompi/2022.05``, ``gompi/2022a`` +``2.0.2`` ``-OpenBLAS-0.3.1`` ``gompi/2018b``, ``gompic/2018b`` +``2.0.2`` ``-OpenBLAS-0.3.3`` ``gompi/2018.08`` +``2.0.2`` ``-OpenBLAS-0.3.5`` ``gompi/2019a``, ``gompic/2019a`` +``2.1.0`` ``gompi/2020a``, ``gompi/2020b``, ``gompic/2020a``, ``gompic/2020b`` +``2.1.0`` ``-bf`` ``gompi/2020a``, ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2020b`` +``2.1.0`` ``-bl`` ``gompi/2020b`` +``2.1.0`` ``-fb`` ``gompi/2021a``, ``gompi/2021b`` +``2.2`` ``-amd`` ``gompi/2020a`` +``2.2.0`` ``-fb`` ``gompi/2022.05``, ``gompi/2022.10``, ``gompi/2022a``, ``gompi/2022b``, ``nvompi/2022.07`` ========= ================================= ============================================================================================================================================ @@ -42552,10 +44134,10 @@ Scalasca is a software tool that supports the performance optimization of paral *homepage*: https://www.scalasca.org/ ======= ================================= -version toolchain +version toolchain ======= ================================= -``2.3`` ``foss/2016a`` -``2.5`` ``gompi/2019a``, ``gompi/2020a`` +``2.3`` ``foss/2016a`` +``2.5`` ``gompi/2019a``, ``gompi/2020a`` ``2.6`` ``gompi/2021a``, ``gompic/2020b`` ======= ================================= @@ -42570,7 +44152,7 @@ SCALCE [skeɪlz] is a FASTQ compression tool that uses locally consistet parsing *homepage*: http://scalce.sourceforge.net/Home ======= ============= -version toolchain +version toolchain ======= ============= ``2.7`` ``GCC/4.8.2`` ======= ============= @@ -42586,11 +44168,12 @@ Scanpy is a scalable toolkit for analyzing single-cell gene expression data buil *homepage*: https://scanpy.readthedocs.io/en/stable/ ========= ============================== -version toolchain +version toolchain ========= ============================== -``1.7.2`` ``foss/2020b`` +``1.7.2`` ``foss/2020b`` ``1.8.1`` ``foss/2020b``, ``foss/2021a`` -``1.8.2`` ``foss/2021b`` +``1.8.2`` ``foss/2021b`` +``1.9.1`` ``foss/2021b`` ========= ============================== @@ -42604,7 +44187,7 @@ SCENIC Suite is a set of tools to study and decipher gene regulation. *homepage*: https://scenic.aertslab.org ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.2.4`` ``-R-4.1.0`` ``foss/2021a`` ========= ============= ============== @@ -42620,7 +44203,7 @@ Python code for genetic marker selection using linear programming. *homepage*: https://github.com/solevillar/scGeneFit-python ========= ============== -version toolchain +version toolchain ========= ============== ``1.0.2`` ``foss/2021a`` ========= ============== @@ -42636,7 +44219,7 @@ A consensus approach to contig filtering and genome prediction from single-cell *homepage*: https://github.com/amsesk/SCGid ========= ============== -version toolchain +version toolchain ========= ============== ``0.9b0`` ``foss/2021b`` ========= ============== @@ -42652,7 +44235,7 @@ Schrodinger aims to provide integrated software solutions and services that tr *homepage*: https://www.schrodinger.com/ ========== ========== -version toolchain +version toolchain ========== ========== ``2020-4`` ``system`` ``2021-4`` ``system`` @@ -42672,7 +44255,7 @@ An R package for inferring the subclonal architecture of tumors *homepage*: https://github.com/genome/sciclone ======= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= ============== ``1.1`` ``-R-3.5.1`` ``foss/2018b`` ======= ============= ============== @@ -42688,7 +44271,7 @@ ScientificPython is a collection of Python modules for scientific computing. It *homepage*: http://dirac.cnrs-orleans.fr/ScientificPython ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== ``2.9.4`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ========= ================== =============================== @@ -42704,7 +44287,7 @@ This package provides utilities for exploratory analysis of large scale genetic *homepage*: https://scikit-allel.readthedocs.io/en/latest/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``1.1.8`` ``-Python-2.7.13`` ``foss/2017a`` ``1.2.1`` ``-Python-3.8.2`` ``foss/2020a`` @@ -42722,12 +44305,12 @@ scikit-bio is an open-source, BSD-licensed Python 3 package providing data struc *homepage*: http://scikit-bio.org -========= ================= ============== -version versionsuffix toolchain -========= ================= ============== +========= ================= ============================================== +version versionsuffix toolchain +========= ================= ============================================== ``0.5.6`` ``-Python-3.8.2`` ``foss/2020a`` -``0.5.7`` ``foss/2021b`` -========= ================= ============== +``0.5.7`` ``foss/2020b``, ``foss/2021b``, ``foss/2022a`` +========= ================= ============================================== .. _list_software_scikit-build_1220: @@ -42740,12 +44323,12 @@ Scikit-Build, or skbuild, is an improved build system generator for CPython C/C+ *homepage*: https://scikit-build.readthedocs.io/en/latest ========== ================= ================================================================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================================================================================================ -``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``0.10.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.10.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` ``0.11.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -``0.15.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``0.15.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ================= ================================================================================================================ @@ -42759,7 +44342,7 @@ SciKit-cuda, a.k.a. skcuda, provides Python interfaces to many of the functions *homepage*: https://github.com/lebedov/scikit-cuda ========= ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================== ``0.5.3`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ================= ================== @@ -42775,25 +44358,26 @@ scikit-image is a collection of algorithms for image processing. *homepage*: https://scikit-image.org/ ========== ================== ======================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ======================================================================== -``0.12.3`` ``-Python-2.7.11`` ``foss/2016a`` -``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` -``0.12.3`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``0.13.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.13.0`` ``-Python-3.6.1`` ``intel/2017a`` -``0.13.0`` ``-Python-3.6.3`` ``foss/2017b`` -``0.13.1`` ``-Python-2.7.14`` ``intel/2017b`` -``0.13.1`` ``-Python-3.6.3`` ``foss/2017b`` -``0.13.1`` ``-Python-3.6.4`` ``foss/2018a`` -``0.14.0`` ``-Python-3.6.4`` ``intel/2018a`` -``0.14.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``0.15.0`` ``-Python-3.7.2`` ``foss/2019a`` -``0.16.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``0.17.1`` ``-Python-3.8.2`` ``foss/2020a`` +``0.12.3`` ``-Python-2.7.11`` ``foss/2016a`` +``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` +``0.12.3`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``0.13.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.13.0`` ``-Python-3.6.1`` ``intel/2017a`` +``0.13.0`` ``-Python-3.6.3`` ``foss/2017b`` +``0.13.1`` ``-Python-2.7.14`` ``intel/2017b`` +``0.13.1`` ``-Python-3.6.3`` ``foss/2017b`` +``0.13.1`` ``-Python-3.6.4`` ``foss/2018a`` +``0.14.0`` ``-Python-3.6.4`` ``intel/2018a`` +``0.14.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``0.15.0`` ``-Python-3.7.2`` ``foss/2019a`` +``0.16.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``0.17.1`` ``-Python-3.8.2`` ``foss/2020a`` ``0.18.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -``0.18.3`` ``foss/2021a`` -``0.19.1`` ``foss/2021b`` +``0.18.3`` ``foss/2021a`` +``0.19.1`` ``foss/2021b`` +``0.19.3`` ``foss/2022a`` ========== ================== ======================================================================== @@ -42807,42 +44391,58 @@ Scikit-learn integrates machine learning algorithms in the tightly-knit scientif *homepage*: https://scikit-learn.org/stable/index.html ========== ================================= ======================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================================= ======================================================================== -``0.16.1`` ``-Python-2.7.13`` ``foss/2017a`` -``0.17.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``0.17.1`` ``-Python-2.7.11-freetype-2.6.3`` ``intel/2016a`` -``0.17.1`` ``-Python-2.7.12`` ``intel/2016b`` -``0.17.1`` ``-Python-3.5.1`` ``foss/2016a``, ``intel/2016a`` -``0.18`` ``-Python-2.7.12`` ``intel/2016b`` -``0.18`` ``-Python-3.5.2`` ``intel/2016b`` -``0.18.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``0.18.1`` ``-Python-2.7.13`` ``intel/2017a`` -``0.18.1`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``0.18.1`` ``-Python-3.6.1`` ``intel/2017a`` -``0.18.2`` ``-Python-3.6.1`` ``intel/2017a`` -``0.19.0`` ``-Python-3.6.1`` ``intel/2017a`` -``0.19.1`` ``-Python-2.7.13`` ``foss/2017a`` +``0.16.1`` ``-Python-2.7.13`` ``foss/2017a`` +``0.17.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``0.17.1`` ``-Python-2.7.11-freetype-2.6.3`` ``intel/2016a`` +``0.17.1`` ``-Python-2.7.12`` ``intel/2016b`` +``0.17.1`` ``-Python-3.5.1`` ``foss/2016a``, ``intel/2016a`` +``0.18`` ``-Python-2.7.12`` ``intel/2016b`` +``0.18`` ``-Python-3.5.2`` ``intel/2016b`` +``0.18.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``0.18.1`` ``-Python-2.7.13`` ``intel/2017a`` +``0.18.1`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``0.18.1`` ``-Python-3.6.1`` ``intel/2017a`` +``0.18.2`` ``-Python-3.6.1`` ``intel/2017a`` +``0.19.0`` ``-Python-3.6.1`` ``intel/2017a`` +``0.19.1`` ``-Python-2.7.13`` ``foss/2017a`` ``0.19.1`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``0.19.1`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``0.19.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``0.20.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``0.20.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``0.20.2`` ``-Python-2.7.15`` ``foss/2018b`` -``0.20.2`` ``-Python-3.6.6`` ``foss/2018b`` -``0.20.3`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` -``0.20.4`` ``-Python-2.7.16`` ``intel/2019b`` -``0.20.4`` ``-Python-2.7.18`` ``foss/2020b`` -``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``0.19.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.20.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.20.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``0.20.2`` ``-Python-2.7.15`` ``foss/2018b`` +``0.20.2`` ``-Python-3.6.6`` ``foss/2018b`` +``0.20.3`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` +``0.20.4`` ``-Python-2.7.16`` ``intel/2019b`` +``0.20.4`` ``-Python-2.7.18`` ``foss/2020b`` +``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ``0.23.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``0.23.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -``0.24.2`` ``foss/2021a``, ``intel/2021a`` -``1.0.1`` ``foss/2021b``, ``intel/2021b`` -``1.0.2`` ``foss/2021b`` -``1.1.2`` ``foss/2022a``, ``intel/2022a`` +``0.24.2`` ``foss/2021a``, ``intel/2021a`` +``1.0.1`` ``foss/2021b``, ``intel/2021b`` +``1.0.2`` ``foss/2021b`` +``1.1.2`` ``foss/2022a``, ``intel/2022a`` ========== ================================= ======================================================================== +.. _list_software_scikit-misc_1120: + +*scikit-misc* ++++++++++++++ + +Miscellaneous tools for data analysis and scientific computing + +*homepage*: https://github.com/has2k1/scikit-misc + +========= ============== +version toolchain +========= ============== +``0.1.4`` ``foss/2021a`` +========= ============== + + .. _list_software_scikit-multilearn_1777: *scikit-multilearn* @@ -42853,7 +44453,7 @@ Scikit-multilearn is a BSD-licensed library for multi-label classification that *homepage*: http://scikit.ml ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.2.0`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== @@ -42869,12 +44469,12 @@ Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) *homepage*: https://scikit-optimize.github.io ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.5.2`` ``-Python-3.6.6`` ``intel/2018b`` -``0.7.4`` ``-Python-3.7.4`` ``foss/2019b`` -``0.8.1`` ``-Python-3.8.2`` ``foss/2020a`` -``0.9.0`` ``foss/2021a`` +``0.7.4`` ``-Python-3.7.4`` ``foss/2019b`` +``0.8.1`` ``-Python-3.8.2`` ``foss/2020a`` +``0.9.0`` ``foss/2021a`` ========= ================= =============== @@ -42888,7 +44488,7 @@ scikit-uplift is a Python module for classic approaches for uplift modeling buil *homepage*: https://github.com/maks-sh/scikit-uplift ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.2.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -42904,7 +44504,7 @@ Single-cell mutation identification via phylogenetic inference (SCIPhI) is a new *homepage*: https://github.com/cbg-ethz/SCIPhI ========= =============== -version toolchain +version toolchain ========= =============== ``0.1.3`` ``intel/2018b`` ========= =============== @@ -42920,11 +44520,11 @@ SciPy is a collection of mathematical algorithms and convenience functions buil *homepage*: https://www.scipy.org ========== ================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ================================== -``0.16.0`` ``-Python-2.7.12`` ``intel/2016b`` -``0.17.0`` ``-Python-2.7.11`` ``intel/2016a`` -``0.19.0`` ``-Python-3.5.2`` ``intel/2016b`` +``0.16.0`` ``-Python-2.7.12`` ``intel/2016b`` +``0.17.0`` ``-Python-2.7.11`` ``intel/2016a`` +``0.19.0`` ``-Python-3.5.2`` ``intel/2016b`` ``1.4.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========== ================== ================================== @@ -42939,20 +44539,20 @@ Bundle of Python packages for scientific software *homepage*: https://python.org/ =========== ================== ======================================================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ======================================================================== ``2019.03`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` -``2019.10`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``2019.10`` ``-Python-3.7.2`` ``intel/2019a`` +``2019.10`` ``-Python-2.7.16`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``2019.10`` ``-Python-3.7.2`` ``intel/2019a`` ``2019.10`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` -``2020.03`` ``-Python-2.7.18`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` +``2020.03`` ``-Python-2.7.18`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` ``2020.03`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a``, ``intelcuda/2020a`` ``2020.11`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b``, ``intelcuda/2020b`` -``2020.11`` ``-Python-2.7.18`` ``foss/2020b`` -``2021.05`` ``foss/2021a``, ``intel/2021a`` -``2021.10`` ``foss/2021b``, ``intel/2021b`` -``2021.10`` ``-Python-2.7.18`` ``foss/2021b`` -``2022.05`` ``foss/2022.05``, ``foss/2022a``, ``intel/2022.05``, ``intel/2022a`` +``2020.11`` ``-Python-2.7.18`` ``foss/2020b`` +``2021.05`` ``foss/2021a``, ``gomkl/2021a``, ``intel/2021a`` +``2021.10`` ``foss/2021b``, ``intel/2021b`` +``2021.10`` ``-Python-2.7.18`` ``foss/2021b`` +``2022.05`` ``foss/2022.05``, ``foss/2022a``, ``intel/2022.05``, ``intel/2022a`` =========== ================== ======================================================================== @@ -42966,7 +44566,7 @@ This package implements SCnorm — a method to normalize single-cell RNA-seq dat *homepage*: https://bioconductor.org/packages/SCnorm ========== ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= =============== ``0.99.7`` ``-R-3.4.0`` ``intel/2017a`` ========== ============= =============== @@ -42982,8 +44582,9 @@ Microbial pan-GWAS using the output from Roary *homepage*: https://github.com/AdmiralenOla/Scoary ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== +``1.6.16`` ``foss/2021a`` ``1.6.16`` ``-Python-2.7.14`` ``intel/2018a`` ========== ================== =============== @@ -42998,27 +44599,28 @@ SCons is a software construction tool. *homepage*: https://www.scons.org/ =============== ======================= ================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain =============== ======================= ================================================================================= -``2.4.1`` ``-Python-2.7.11`` ``foss/2016a`` -``2.5.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.5.1`` ``intel/2017a`` -``2.5.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2.5.1`` ``-Python-2.7.13`` ``intel/2017a`` +``2.4.1`` ``-Python-2.7.11`` ``foss/2016a`` +``2.5.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``2.5.1`` ``intel/2017a`` +``2.5.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``2.5.1`` ``-Python-2.7.13`` ``intel/2017a`` ``3.0.1`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a``, ``iomkl/2018a`` -``3.0.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` -``3.0.1`` ``-Python-2.7.15-bare`` ``GCCcore/7.3.0`` -``3.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``3.0.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``3.0.4`` ``-Python-2.7.15`` ``foss/2018b`` -``3.0.5`` ``GCCcore/8.2.0`` -``3.0.5`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` -``3.0.5`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``3.1.1`` ``GCCcore/8.3.0`` -``3.1.2`` ``GCCcore/9.3.0`` -``4.0.1`` ``GCCcore/10.2.0`` -``4.1.0.post1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``4.2.0`` ``GCCcore/11.2.0`` +``3.0.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` +``3.0.1`` ``-Python-2.7.15-bare`` ``GCCcore/7.3.0`` +``3.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``3.0.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``3.0.4`` ``-Python-2.7.15`` ``foss/2018b`` +``3.0.5`` ``GCCcore/8.2.0`` +``3.0.5`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` +``3.0.5`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``3.1.1`` ``GCCcore/8.3.0`` +``3.1.2`` ``GCCcore/9.3.0`` +``4.0.1`` ``GCCcore/10.2.0`` +``4.1.0.post1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``4.2.0`` ``GCCcore/11.2.0`` +``4.4.0`` ``GCCcore/11.3.0`` =============== ======================= ================================================================================= @@ -43032,13 +44634,13 @@ SCOOP (Scalable COncurrent Operations in Python) is a distributed task module a *homepage*: http://code.google.com/p/scoop/ =========== ================== ================= -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ================= -``0.6.2`` ``-Python-2.7.12`` ``intel/2016b`` +``0.6.2`` ``-Python-2.7.12`` ``intel/2016b`` ``0.7.1.1`` ``GCCcore/8.2.0`` -``0.7.1.1`` ``-Python-2.7.11`` ``intel/2016a`` -``0.7.1.1`` ``-Python-2.7.14`` ``intel/2017b`` -``0.7.1.1`` ``-Python-3.5.1`` ``intel/2016a`` +``0.7.1.1`` ``-Python-2.7.11`` ``intel/2016a`` +``0.7.1.1`` ``-Python-2.7.14`` ``intel/2017b`` +``0.7.1.1`` ``-Python-3.5.1`` ``intel/2016a`` =========== ================== ================= @@ -43052,7 +44654,7 @@ An R package (compatible with SCope) to create generic .loom files and extend th *homepage*: https://github.com/aertslab/SCopeLoomR ========== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ============== ``0.13.0`` ``-R-4.1.2`` ``foss/2021b`` ========== ============= ============== @@ -43068,12 +44670,13 @@ The Score-P measurement infrastructure is a highly scalable and easy-to-use too *homepage*: https://www.score-p.org ========= ================ ================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ================================================== -``2.0.1`` ``foss/2016a`` +``2.0.1`` ``foss/2016a`` ``6.0`` ``gompi/2019a``, ``gompi/2020a``, ``gompic/2019b`` -``7.0`` ``gompi/2021a``, ``gompic/2020b`` -``7.1`` ``-CUDA-11.3.1`` ``gompi/2021a`` +``7.0`` ``gompi/2021a``, ``gompic/2020b`` +``7.1`` ``-CUDA-11.3.1`` ``gompi/2021a`` +``8.0`` ``gompi/2022a`` ========= ================ ================================================== @@ -43087,16 +44690,16 @@ Software package and libraries for sequential and parallel graph partitioning, s *homepage*: https://www.labri.fr/perso/pelegrin/scotch/ =================== ============= ===================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain =================== ============= ===================================================================================================================================================== -``5.1.12b_esmumps`` ``foss/2017b`` +``5.1.12b_esmumps`` ``foss/2017b`` ``6.0.4`` ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``6.0.4`` ``-64bitint`` ``foss/2017b`` -``6.0.6`` ``foss/2018a``, ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2018a`` -``6.0.9`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` -``6.1.0`` ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2020b`` -``6.1.2`` ``gompi/2021b``, ``iimpi/2021b`` -``7.0.1`` ``gompi/2022a`` +``6.0.4`` ``-64bitint`` ``foss/2017b`` +``6.0.6`` ``foss/2018a``, ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2018a`` +``6.0.9`` ``gompi/2019b``, ``gompi/2020a``, ``iimpi/2019b``, ``iimpi/2020a``, ``iimpic/2019b`` +``6.1.0`` ``gompi/2020b``, ``gompi/2021a``, ``iimpi/2020b``, ``iimpi/2021a`` +``6.1.2`` ``gompi/2021b``, ``iimpi/2021b`` +``7.0.1`` ``gompi/2022a``, ``iimpi/2022a`` =================== ============= ===================================================================================================================================================== @@ -43110,7 +44713,7 @@ The scp.py module uses a paramiko transport to send and recieve files via the sc *homepage*: https://github.com/jbardin/scp.py ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``0.10.2`` ``-Python-2.7.12`` ``intel/2016b`` ``0.13.1`` ``-Python-2.7.15`` ``intel/2018b`` @@ -43128,7 +44731,7 @@ scPred package for cell type prediction from scRNA-seq data *homepage*: https://github.com/powellgenomicslab/scPred ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.9.2`` ``-R-4.1.2`` ``foss/2021b`` ========= ============= ============== @@ -43144,7 +44747,7 @@ Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithm *homepage*: https://github.com/nanoporetech/scrappie ========= =============== -version toolchain +version toolchain ========= =============== ``1.3.2`` ``intel/2018a`` ========= =============== @@ -43160,13 +44763,30 @@ scVelo is a scalable toolkit for estimating and analyzing RNA velocities in sing *homepage*: https://scvelo.org ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.1.24`` ``-Python-3.7.4`` ``foss/2019b`` ``0.2.3`` ``foss/2021a`` ========== ================= ============== +.. _list_software_scvi-tools_1043: + +*scvi-tools* +++++++++++++ + +scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData. + +*homepage*: https://github.com/scverse/scvi-tools + +========== ================ ============== +version versionsuffix toolchain +========== ================ ============== +``0.16.4`` ``foss/2021a`` +``0.16.4`` ``-CUDA-11.3.1`` ``foss/2021a`` +========== ================ ============== + + .. _list_software_Scythe_624: *Scythe* @@ -43177,7 +44797,7 @@ Scythe uses a Naive Bayesian approach to classify contaminant substrings in seq *homepage*: https://github.com/ucdavis-bioinformatics/scythe ========= ================= -version toolchain +version toolchain ========= ================= ``0.994`` ``GCCcore/9.3.0`` ========= ================= @@ -43193,7 +44813,7 @@ SDCC is a retargettable, optimizing ANSI - C compiler suite that targets the In *homepage*: http://sdcc.sourceforge.net/ ========= ========== -version toolchain +version toolchain ========= ========== ``3.3.0`` ``system`` ========= ========== @@ -43209,7 +44829,7 @@ SDL: Simple DirectMedia Layer, a cross-platform multimedia library *homepage*: https://www.libsdl.org/ ========== ================= -version toolchain +version toolchain ========== ================= ``1.2.15`` ``GCCcore/6.4.0`` ========== ================= @@ -43225,15 +44845,15 @@ SDL: Simple DirectMedia Layer, a cross-platform multimedia library *homepage*: http://www.libsdl.org/ ========== ====================================================================== -version toolchain +version toolchain ========== ====================================================================== -``2.0.4`` ``intel/2016b`` -``2.0.8`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` +``2.0.4`` ``intel/2016b`` +``2.0.8`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``2.0.9`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``2.0.10`` ``GCCcore/8.3.0`` -``2.0.14`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.0.20`` ``GCCcore/11.2.0`` -``2.0.22`` ``GCCcore/11.3.0`` +``2.0.10`` ``GCCcore/8.3.0`` +``2.0.14`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +``2.0.20`` ``GCCcore/11.2.0`` +``2.0.22`` ``GCCcore/11.3.0`` ========== ====================================================================== @@ -43247,7 +44867,7 @@ SDL_image is an image file loading library. *homepage*: https://www.libsdl.org/projects/SDL_image/ ========= ================= -version toolchain +version toolchain ========= ================= ``2.0.3`` ``GCCcore/6.4.0`` ========= ================= @@ -43263,7 +44883,7 @@ SDL_image is an image file loading library. *homepage*: https://www.libsdl.org/projects/SDL_image/release-1.2.html ========== ================= -version toolchain +version toolchain ========== ================= ``1.2.12`` ``GCCcore/6.4.0`` ========== ================= @@ -43279,7 +44899,7 @@ The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 libr *homepage*: https://github.com/simongog/sdsl-lite ================== ================= -version toolchain +version toolchain ================== ================= ``2.1.1-20191211`` ``GCCcore/8.3.0`` ================== ================= @@ -43295,24 +44915,25 @@ Seaborn is a Python visualization library based on matplotlib. It provides a hi *homepage*: https://seaborn.pydata.org/ ========== ================== ========================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ========================================================================================= -``0.7.1`` ``-Python-2.7.12`` ``intel/2016b`` -``0.8.1`` ``-Python-2.7.13`` ``foss/2017a`` -``0.8.1`` ``-Python-2.7.14`` ``intel/2018a`` +``0.7.1`` ``-Python-2.7.12`` ``intel/2016b`` +``0.8.1`` ``-Python-2.7.13`` ``foss/2017a`` +``0.8.1`` ``-Python-2.7.14`` ``intel/2018a`` ``0.9.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a``, ``intelcuda/2017b`` -``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` -``0.9.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``0.9.0`` ``-Python-3.6.4`` ``intel/2018a`` -``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.9.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``0.9.1`` ``-Python-2.7.16`` ``foss/2019b`` -``0.9.1`` ``-Python-2.7.18`` ``foss/2020b`` -``0.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``0.10.1`` ``intel/2020b`` -``0.10.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``0.11.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``0.11.2`` ``foss/2021a``, ``foss/2021b`` +``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` +``0.9.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``0.9.0`` ``-Python-3.6.4`` ``intel/2018a`` +``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.9.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``0.9.1`` ``-Python-2.7.16`` ``foss/2019b`` +``0.9.1`` ``-Python-2.7.18`` ``foss/2020b`` +``0.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.10.1`` ``intel/2020b`` +``0.10.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.11.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``0.11.2`` ``foss/2021a``, ``foss/2021b`` +``0.12.1`` ``foss/2022a`` ========== ================== ========================================================================================= @@ -43326,7 +44947,7 @@ SearchGUI is a user-friendly open-source graphical user interface for configurin *homepage*: https://github.com/compomics/searchgui ========= =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= =================== ========== ``3.3.3`` ``-Java-1.8.0_152`` ``system`` ========= =================== ========== @@ -43342,7 +44963,7 @@ SECAPR is a bioinformatics pipeline for the rapid and user-friendly processing o *homepage*: https://github.com/AntonelliLab/seqcap_processor ========== ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ============== ``1.1.15`` ``-Python-2.7.16`` ``foss/2019b`` ========== ================== ============== @@ -43358,7 +44979,7 @@ Seeder is a framework for DNA motif discovery. *homepage*: https://metacpan.org/pod/Seeder ======== ================ ================= -version versionsuffix toolchain +version versionsuffix toolchain ======== ================ ================= ``0.01`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` ======== ================ ================= @@ -43374,9 +44995,9 @@ segemehl is a software to map short sequencer reads to reference genomes. Unli *homepage*: http://www.bioinf.uni-leipzig.de/Software/segemehl/ ========= ============================================================================= -version toolchain +version toolchain ========= ============================================================================= -``0.2.0`` ``foss/2016b``, ``intel/2017b``, ``intel/2018a`` +``0.2.0`` ``foss/2016b``, ``intel/2017b``, ``intel/2018a`` ``0.3.4`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.3.0``, ``foss/2018b`` ========= ============================================================================= @@ -43391,7 +45012,7 @@ Python library with Neural Networks for Image Segmentation based on Keras and Te *homepage*: https://github.com/qubvel/segmentation_models ========= ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================================== ``1.0.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========= ================= ================================== @@ -43407,7 +45028,7 @@ SeisSol is a software package for simulating wave propagation and dynamic ruptur *homepage*: http://www.seissol.org ========== ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ============== ``201703`` ``-Python-2.7.15`` ``foss/2018b`` ========== ================== ============== @@ -43423,12 +45044,28 @@ SelEstim is aimed at distinguishing neutral from selected polymorphisms and esti *homepage*: http://www1.montpellier.inra.fr/CBGP/software/selestim/index.html ========= ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ========== ``1.1.4`` ``-Linux-64bits`` ``system`` ========= ================= ========== +.. _list_software_SELFIES_523: + +*SELFIES* ++++++++++ + +Robust representation of semantically constrained graphs, in particular for molecules in chemistry + +*homepage*: https://github.com/aspuru-guzik-group/selfies + +========= ============== +version toolchain +========= ============== +``2.1.1`` ``GCC/11.2.0`` +========= ============== + + .. _list_software_SentencePiece_1307: *SentencePiece* @@ -43438,13 +45075,14 @@ Unsupervised text tokenizer for Neural Network-based text generation. *homepage*: https://github.com/google/sentencepiece -========== ================= ============== -version versionsuffix toolchain -========== ================= ============== -``0.1.85`` ``-Python-3.7.4`` ``GCC/8.3.0`` -``0.1.94`` ``-Python-3.8.2`` ``GCC/9.3.0`` -``0.1.96`` ``GCC/10.2.0`` -========== ================= ============== +========== ================= ============================== +version versionsuffix toolchain +========== ================= ============================== +``0.1.85`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``0.1.94`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``0.1.96`` ``GCC/10.2.0``, ``GCC/10.3.0`` +``0.1.97`` ``GCC/11.3.0`` +========== ================= ============================== .. _list_software_sep_328: @@ -43457,7 +45095,7 @@ Python and C library for Source Extraction and Photometry. (this easyconfig pro *homepage*: https://sep.readthedocs.io ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== ``1.0.3`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ========= ================== =============================== @@ -43473,7 +45111,7 @@ SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic plac *homepage*: https://github.com/smirarab/sepp ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``4.3.10`` ``-Python-3.7.4`` ``foss/2019b`` ``4.3.10`` ``-Python-3.8.2`` ``foss/2020a`` @@ -43493,7 +45131,7 @@ Seq-Gen is a program that will simulate the evolution of nucleotide or amino aci *homepage*: http://tree.bio.ed.ac.uk/software/Seq-Gen ========= =============== -version toolchain +version toolchain ========= =============== ``1.3.4`` ``intel/2017b`` ========= =============== @@ -43509,10 +45147,10 @@ In-silico method written in Python and R to determine HLA genotypes of a sample. *homepage*: https://github.com/TRON-Bioinformatics/seq2HLA ======= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== =============== ``2.3`` ``-Python-2.7.14`` ``intel/2018a`` -``2.3`` ``-Python-2.7.15`` ``foss/2018b`` +``2.3`` ``-Python-2.7.15`` ``foss/2018b`` ======= ================== =============== @@ -43526,10 +45164,10 @@ SeqAn is an open source C++ library of efficient algorithms and data structures *homepage*: https://www.seqan.de/ ========= ============= =================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= =================================================================================================================================== -``1.4.2`` ``-library`` ``system`` -``2.3.2`` ``foss/2016b`` +``1.4.2`` ``-library`` ``system`` +``2.3.2`` ``foss/2016b`` ``2.4.0`` ``GCC/8.2.0-2.31.1``, ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018b``, ``intel/2018b`` ========= ============= =================================================================================================================================== @@ -43544,7 +45182,7 @@ SeqAn is an open source C++ library of efficient algorithms and data structure *homepage*: https://github.com/seqan/seqan3 ========= ========== -version toolchain +version toolchain ========= ========== ``3.0.0`` ``system`` ========= ========== @@ -43560,7 +45198,7 @@ SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation *homepage*: https://bioinf.shenwei.me/seqkit/ ========== ========== -version toolchain +version toolchain ========== ========== ``0.8.1`` ``system`` ``0.13.2`` ``system`` @@ -43578,11 +45216,11 @@ C++ interface to HTSlib, BWA-MEM and Fermi. *homepage*: https://github.com/walaj/SeqLib -========= ============================================= -version toolchain -========= ============================================= -``1.2.0`` ``GCC/10.2.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` -========= ============================================= +========= ============================================================= +version toolchain +========= ============================================================= +``1.2.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` +========= ============================================================= .. _list_software_Seqmagick_917: @@ -43595,7 +45233,7 @@ We often have to convert between sequence formats and do little tasks on them, *homepage*: https://fhcrc.github.io/seqmagick/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``0.6.1`` ``-Python-2.7.11`` ``foss/2016a`` ``0.6.2`` ``-Python-2.7.15`` ``foss/2018b`` @@ -43612,7 +45250,7 @@ Tool for stripping adaptors and/or merging paired reads with overlap into single *homepage*: https://github.com/jstjohn/SeqPrep ========= ================= -version toolchain +version toolchain ========= ================= ``1.3.2`` ``GCCcore/7.3.0`` ========= ================= @@ -43628,9 +45266,9 @@ Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FA *homepage*: https://github.com/lh3/seqtk/ ======= ================================================================================================================================== -version toolchain +version toolchain ======= ================================================================================================================================== -``1.2`` ``foss/2016b``, ``intel/2017a`` +``1.2`` ``foss/2016b``, ``intel/2017a`` ``1.3`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``foss/2018a``, ``foss/2018b`` ======= ================================================================================================================================== @@ -43644,11 +45282,11 @@ The serf library is a high performance C-based HTTP client library built upon t *homepage*: http://serf.apache.org/ -========= ===================================================================================================================================================================== -version toolchain -========= ===================================================================================================================================================================== -``1.3.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``intel/2017b``, ``iomkl/2018a`` -========= ===================================================================================================================================================================== +========= ========================================================================================================================================================================================= +version toolchain +========= ========================================================================================================================================================================================= +``1.3.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/9.3.0``, ``foss/2017b``, ``intel/2017b``, ``iomkl/2018a`` +========= ========================================================================================================================================================================================= .. _list_software_setuptools_1122: @@ -43661,7 +45299,7 @@ Easily download, build, install, upgrade, and uninstall Python packages *homepage*: https://pypi.org/project/setuptools ========== ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ========== ``1.4.2`` ``system`` ``41.0.1`` ``-py3`` ``system`` @@ -43678,15 +45316,17 @@ Seurat is an R package designed for QC, analysis, and exploration of single cell *homepage*: https://satijalab.org/seurat ============ ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= =============== ``1.4.0.16`` ``-R-3.4.0`` ``intel/2017a`` ``2.3.4`` ``-R-3.4.4`` ``intel/2018a`` -``2.3.4`` ``-R-3.5.1`` ``foss/2018b`` -``3.1.2`` ``-R-3.6.0`` ``foss/2019a`` -``3.1.5`` ``-R-4.0.0`` ``foss/2020a`` -``4.0.1`` ``-R-4.0.3`` ``foss/2020b`` -``4.0.3`` ``-R-4.0.3`` ``foss/2020b`` +``2.3.4`` ``-R-3.5.1`` ``foss/2018b`` +``3.1.2`` ``-R-3.6.0`` ``foss/2019a`` +``3.1.5`` ``-R-4.0.0`` ``foss/2020a`` +``4.0.1`` ``-R-4.0.3`` ``foss/2020b`` +``4.0.3`` ``-R-4.0.3`` ``foss/2020b`` +``4.2.0`` ``-R-4.2.1`` ``foss/2022a`` +``4.3.0`` ``-R-4.1.2`` ``foss/2021b`` ============ ============= =============== @@ -43700,12 +45340,28 @@ SeuratData is a mechanism for distributing datasets in the form of Seurat object *homepage*: https://github.com/satijalab/seurat-data ============ ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= ============== ``20210514`` ``-R-4.0.3`` ``foss/2020b`` ============ ============= ============== +.. _list_software_SeuratDisk_1023: + +*SeuratDisk* +++++++++++++ + +Interfaces for HDF5-based Single Cell File Formats + +*homepage*: https://github.com/mojaveazure/seurat-disk + +============== ============= ============== +version versionsuffix toolchain +============== ============= ============== +``0.0.0.9020`` ``-R-4.2.1`` ``foss/2022a`` +============== ============= ============== + + .. _list_software_SeuratWrappers_1480: *SeuratWrappers* @@ -43716,7 +45372,7 @@ SeuratWrappers is a collection of community-provided methods and extensions for *homepage*: https://github.com/satijalab/seurat-wrappers ============ ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= ============== ``20210528`` ``-R-4.0.3`` ``foss/2020b`` ============ ============= ============== @@ -43732,12 +45388,28 @@ Support for simple features, a standardized way to encode spatial vector data. B *homepage*: https://cran.r-project.org/package=sf ========= ========================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ========================= ============== ``0.9-5`` ``-R-4.0.0-Python-3.8.2`` ``foss/2020a`` ========= ========================= ============== +.. _list_software_sfftk_542: + +*sfftk* ++++++++ + +sfftk is a set of utilities that facilitate creation, conversion and modification of Electron Microscopy Data Bank - Segmentation File Format (EMDB-SFF) files. EMDB-SFF is an open, community-driven file format to handle annotated segmentations and subtomogram averages that facilitates segmentation file interchange. It is written in Python and provides both a command-line suite of commands and a Python API. + +*homepage*: https://emdb-empiar.github.io/EMDB-SFF/ + +========= ============== +version toolchain +========= ============== +``0.7.4`` ``foss/2021a`` +========= ============== + + .. _list_software_Shannon_725: *Shannon* @@ -43748,7 +45420,7 @@ Shannon is a program for assembling transcripts from RNA-Seq data *homepage*: https://sreeramkannan.github.io/Shannon/ ============ ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============== ``20170511`` ``-Python-2.7.13`` ``intel/2017a`` ============ ================== =============== @@ -43764,7 +45436,7 @@ SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the *homepage*: https://github.com/slundberg/shap ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.35.0`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================= ============== @@ -43780,7 +45452,7 @@ An R package for the extraction, analysis and classification of (not only) archa *homepage*: https://github.com/ISAAKiel/shapAAR ================== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ============= ============== ``0.1.0-20180425`` ``-R-3.6.0`` ``foss/2019a`` ================== ============= ============== @@ -43796,7 +45468,7 @@ SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing *homepage*: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html ========== =============== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== =============== ========== ``2.r837`` ``.GLIBCv2.12`` ``system`` ``2.r904`` ``.glibcv2.17`` ``system`` @@ -43813,11 +45485,11 @@ SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing *homepage*: https://odelaneau.github.io/shapeit4/ ========= ============================================== -version toolchain +version toolchain ========= ============================================== -``4.1.3`` ``foss/2019b`` +``4.1.3`` ``foss/2019b`` ``4.2.0`` ``foss/2019b``, ``foss/2020a``, ``foss/2020b`` -``4.2.2`` ``foss/2020b``, ``foss/2021a`` +``4.2.2`` ``foss/2020b``, ``foss/2021a`` ========= ============================================== @@ -43831,13 +45503,13 @@ Shapely is a BSD-licensed Python package for manipulation and analysis of planar *homepage*: https://github.com/Toblerity/Shapely =============== ================= ======================================================= -version versionsuffix toolchain +version versionsuffix toolchain =============== ================= ======================================================= -``1.7.0`` ``-Python-3.7.2`` ``foss/2019a`` -``1.7.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` -``1.7.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` -``1.8.1.post1`` ``GCC/11.2.0`` -``1.8.2`` ``foss/2021b`` +``1.7.0`` ``-Python-3.7.2`` ``foss/2019a`` +``1.7.0`` ``-Python-3.7.4`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` +``1.7.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``1.8.1.post1`` ``GCC/11.2.0`` +``1.8.2`` ``foss/2021b``, ``foss/2022a`` ``1.8a1`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``iccifort/2020.4.304`` =============== ================= ======================================================= @@ -43852,7 +45524,7 @@ GNU shar makes so-called shell archives out of many files, preparing them for tr *homepage*: https://www.gnu.org/software/sharutils/ ======== ================= -version toolchain +version toolchain ======== ================= ``4.15`` ``GCCcore/6.3.0`` ======== ================= @@ -43868,7 +45540,7 @@ The goal of the Shasta long read assembler is to rapidly produce accurate assemb *homepage*: https://github.com/chanzuckerberg/shasta ========= ============== -version toolchain +version toolchain ========= ============== ``0.8.0`` ``foss/2020b`` ========= ============== @@ -43884,7 +45556,7 @@ A solver for the Boltzmann transport equation for phonons. *homepage*: https://bitbucket.org/sousaw/shengbte ========= ============== -version toolchain +version toolchain ========= ============== ``1.1.1`` ``foss/2021a`` ========= ============== @@ -43900,7 +45572,7 @@ Shift is a framework for Self-Healing Independent File Transfer that provides hi *homepage*: http://people.nas.nasa.gov/~kolano/projects/shift.html ======= =============== -version toolchain +version toolchain ======= =============== ``4.0`` ``intel/2016a`` ======= =============== @@ -43916,7 +45588,7 @@ SHORE, for Short Read, is a mapping and analysis pipeline for short read data pr *homepage*: http://1001genomes.org/software/shore.html ========= ============== -version toolchain +version toolchain ========= ============== ``0.9.3`` ``foss/2016a`` ========= ============== @@ -43932,7 +45604,7 @@ Sensitive Short Read Homology Search for Paired-End Reads *homepage*: https://sourceforge.net/projects/short-pair ============ ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ============== ``20170125`` ``foss/2021b`` ``20170125`` ``-Python-2.7.15`` ``foss/2018b`` @@ -43949,10 +45621,10 @@ Faster SPAdes assembly of Illumina reads *homepage*: https://github.com/tseemann/shovill ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== -``0.9.0`` ``-Python-2.7.14`` ``foss/2018a`` -``1.0.4`` ``-Python-2.7.15`` ``foss/2018b`` +``0.9.0`` ``-Python-2.7.14`` ``foss/2018a`` +``1.0.4`` ``-Python-2.7.15`` ``foss/2018b`` ``1.1.0`` ``gompi/2021b`` ========= ================== =============== @@ -43967,9 +45639,9 @@ A std::streambuf wrapper for compression formats. *homepage*: https://github.com/jonathonl/shrinkwrap ============== ================== -version toolchain +version toolchain ============== ================== -``1.0.0-beta`` ``GCCcore/8.2.0`` +``1.0.0-beta`` ``GCCcore/8.2.0`` ``1.1.0`` ``GCCcore/10.2.0`` ============== ================== @@ -43984,7 +45656,7 @@ Spherical Harmonic Transform library aimed at high performance numerical simulat *homepage*: https://bitbucket.org/nschaeff/shtns ========= ============== -version toolchain +version toolchain ========= ============== ``2.7`` ``foss/2021b`` ``3.5.1`` ``foss/2021b`` @@ -44001,9 +45673,9 @@ Sibelia: A comparative genomics tool: It assists biologists in analysing the g *homepage*: http://bioinf.spbau.ru/en/sibelia ========= ============================== -version toolchain +version toolchain ========= ============================== -``3.0.6`` ``foss/2016b`` +``3.0.6`` ``foss/2016b`` ``3.0.7`` ``foss/2018b``, ``foss/2020b`` ========= ============================== @@ -44018,7 +45690,7 @@ Redesigned and improved ChIP-seq broad peak calling tool SICER *homepage*: https://zanglab.github.io/SICER2/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.0.3`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -44034,7 +45706,7 @@ Windowed Adaptive Trimming for fastq files using quality *homepage*: https://github.com/najoshi/sickle ======== =============================== -version toolchain +version toolchain ======== =============================== ``1.33`` ``foss/2017a``, ``intel/2018a`` ======== =============================== @@ -44049,18 +45721,18 @@ SIESTA is both a method and its computer program implementation, to perform effi *homepage*: http://departments.icmab.es/leem/siesta -=============== ============= =============================================================== -version versionsuffix toolchain -=============== ============= =============================================================== -``4.0`` ``foss/2017b``, ``intel/2017a`` -``4.0.1`` ``intel/2017a`` -``4.1-b2`` ``intel/2017a`` -``4.1-b3`` ``intel/2017a`` -``4.1-b4`` ``foss/2018b``, ``intel/2018b`` -``4.1-MaX-1.0`` ``intel/2019b`` -``4.1-MaX-1.0`` ``-PEXSI`` ``intel/2019b`` -``4.1.5`` ``foss/2020a``, ``foss/2021a``, ``foss/2021b``, ``intel/2020a`` -=============== ============= =============================================================== +=============== ============= ================================================================================================ +version versionsuffix toolchain +=============== ============= ================================================================================================ +``4.0`` ``foss/2017b``, ``intel/2017a`` +``4.0.1`` ``intel/2017a`` +``4.1-b2`` ``intel/2017a`` +``4.1-b3`` ``intel/2017a`` +``4.1-b4`` ``foss/2018b``, ``intel/2018b`` +``4.1-MaX-1.0`` ``intel/2019b`` +``4.1-MaX-1.0`` ``-PEXSI`` ``intel/2019b`` +``4.1.5`` ``foss/2020a``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``intel/2020a``, ``intel/2022a`` +=============== ============= ================================================================================================ .. _list_software_SignalP_686: @@ -44072,11 +45744,13 @@ SignalP predicts the presence and location of signal peptide cleavage sites i *homepage*: https://services.healthtech.dtu.dk/software.php -======== ============= ========== -version versionsuffix toolchain -======== ============= ========== -``5.0b`` ``-Linux`` ``system`` -======== ============= ========== +======== ===================== ============== +version versionsuffix toolchain +======== ===================== ============== +``5.0b`` ``-Linux`` ``system`` +``6.0g`` ``-fast`` ``foss/2022a`` +``6.0g`` ``-fast-CUDA-11.7.0`` ``foss/2022a`` +======== ===================== ============== .. _list_software_silx_448: @@ -44089,13 +45763,29 @@ The silx project provides a collection of Python packages to support the develo *homepage*: http://www.silx.org/ ========== ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================== ``0.13.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``0.14.0`` ``foss/2020b``, ``fosscuda/2020b`` ========== ================= ================================== +.. _list_software_simint_660: + +*simint* +++++++++ + +Simint is a vectorized implementation of the Obara-Saika (OS) method of calculating electron repulsion integrals. Speedup is gained by vectorizing the primitive loop of the OS algorithm, with additional vectorization and optimizations left to the compiler. + +*homepage*: https://www.bennyp.org/research/simint/ + +======= ======================== ============== +version versionsuffix toolchain +======= ======================== ============== +``0.7`` ``-lmax-5-vec-avx-psi4`` ``GCC/11.2.0`` +======= ======================== ============== + + .. _list_software_SimNIBS_597: *SimNIBS* @@ -44106,7 +45796,7 @@ SimNIBS is a free and open source software package for the Simulation of Non-inv *homepage*: https://simnibs.github.io/simnibs ========= ============== -version toolchain +version toolchain ========= ============== ``3.2.4`` ``foss/2020b`` ========= ============== @@ -44121,12 +45811,13 @@ Simulation and Parameter Estimation in Geophysics: a python package for simulati *homepage*: https://simpeg.xyz -========== ================== =============== -version versionsuffix toolchain -========== ================== =============== +========== ================== =============================== +version versionsuffix toolchain +========== ================== =============================== ``0.3.1`` ``-Python-2.7.12`` ``intel/2016b`` ``0.14.1`` ``-Python-3.8.2`` ``intel/2020a`` -========== ================== =============== +``0.18.1`` ``foss/2021b``, ``intel/2021b`` +========== ================== =============================== .. _list_software_SIMPLE_458: @@ -44139,7 +45830,7 @@ Single-particle IMage Processing Linux Engine SIMPLE is an open-source software *homepage*: https://simplecryoem.com/ ========= ============== -version toolchain +version toolchain ========= ============== ``2.5`` ``foss/2018a`` ``3.0.0`` ``foss/2020b`` @@ -44156,7 +45847,7 @@ Multi-lingual medical image registration library. *homepage*: https://simpleelastix.github.io ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``0.10.0`` ``-Python-3.6.3`` ``foss/2017b`` ``0.10.0`` ``-Python-3.6.4`` ``foss/2018a`` @@ -44173,17 +45864,17 @@ SimpleITK is a simplified programming interface to the algorithms and data struc *homepage*: https://www.simpleitk.org -=========== ================== ============== -version versionsuffix toolchain -=========== ================== ============== +=========== ================== ============================== +version versionsuffix toolchain +=========== ================== ============================== ``1.1.0`` ``-Python-2.7.15`` ``foss/2018b`` ``1.1.0`` ``-Python-3.6.4`` ``foss/2018a`` ``1.1.0`` ``-Python-3.6.6`` ``foss/2018b`` ``1.2.4`` ``-Python-3.7.4`` ``foss/2019b`` ``2.1.0`` ``foss/2020b`` ``2.1.1`` ``foss/2021a`` -``2.1.1.2`` ``foss/2021b`` -=========== ================== ============== +``2.1.1.2`` ``foss/2021b``, ``foss/2022a`` +=========== ================== ============================== .. _list_software_simpy_562: @@ -44196,7 +45887,7 @@ SimPy is a process-based discrete-event simulation framework based on standard P *homepage*: https://simpy.readthedocs.io ========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============== ``3.0.11`` ``intel/2019a`` ``3.0.11`` ``-Python-3.6.6`` ``intel/2018b`` @@ -44213,7 +45904,7 @@ SimVascular is an open source software suite for cardiovascular simulation, prov *homepage*: http://simvascular.github.io/ ============= =============== -version toolchain +version toolchain ============= =============== ``2.16.0406`` ``intel/2016b`` ============= =============== @@ -44229,7 +45920,7 @@ SingleM is a tool to find the abundances of discrete operational taxonomic units *homepage*: https://github.com/wwood/singlem ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``0.12.1`` ``-Python-2.7.15`` ``intel/2019a`` ========== ================== =============== @@ -44245,7 +45936,7 @@ Singular is a computer algebra system for polynomial computations, with special *homepage*: https://www.singular.uni-kl.de/ ========= ================================ -version toolchain +version toolchain ========= ================================ ``4.1.2`` ``GCC/8.2.0-2.31.1``, ``system`` ========= ================================ @@ -44261,7 +45952,7 @@ SiNVICT is a tool for the detection of SNVs and indels from cfDNA/ctDNA samples *homepage*: https://github.com/sfu-compbio/sinvict ================ ============= -version toolchain +version toolchain ================ ============= ``1.0-20180817`` ``GCC/9.3.0`` ================ ============= @@ -44277,15 +45968,15 @@ SIONlib is a scalable I/O library for parallel access to task-local files. The *homepage*: https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html ========= ============= ============================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============================================================================ -``1.6.1`` ``foss/2016a`` -``1.6.1`` ``-tools`` ``foss/2016a`` -``1.7.1`` ``foss/2017a`` -``1.7.1`` ``-tools`` ``foss/2017a`` -``1.7.4`` ``-tools`` ``GCCcore/8.2.0`` +``1.6.1`` ``foss/2016a`` +``1.6.1`` ``-tools`` ``foss/2016a`` +``1.7.1`` ``foss/2017a`` +``1.7.1`` ``-tools`` ``foss/2017a`` +``1.7.4`` ``-tools`` ``GCCcore/8.2.0`` ``1.7.6`` ``-tools`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.7.7`` ``-tools`` ``GCCcore/11.3.0`` +``1.7.7`` ``-tools`` ``GCCcore/11.3.0`` ========= ============= ============================================================================ @@ -44299,16 +45990,16 @@ SIP is a tool that makes it very easy to create Python bindings for C and C++ li *homepage*: http://www.riverbankcomputing.com/software/sip/ =========== ================== ================================================================ -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ================================================================ -``4.18`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``4.18.1`` ``-Python-2.7.11`` ``foss/2016a`` -``4.18.1`` ``-Python-2.7.12`` ``intel/2016b`` -``4.19`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``4.19.2`` ``-Python-2.7.13`` ``intel/2017a`` +``4.18`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``4.18.1`` ``-Python-2.7.11`` ``foss/2016a`` +``4.18.1`` ``-Python-2.7.12`` ``intel/2016b`` +``4.19`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``4.19.2`` ``-Python-2.7.13`` ``intel/2017a`` ``4.19.8`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``4.19.8`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``4.19.13`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``4.19.8`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``4.19.13`` ``-Python-2.7.15`` ``fosscuda/2018b`` =========== ================== ================================================================ @@ -44322,13 +46013,29 @@ A data-driven method combining symbolic regression and compressed sensing toward *homepage*: https://github.com/rouyang2017/SISSO ================ =============== -version toolchain +version toolchain ================ =============== ``3.0.2`` ``iimpi/2021b`` ``3.1-20220324`` ``iimpi/2021b`` ================ =============== +.. _list_software_SISSO++_487: + +*SISSO++* ++++++++++ + +C++ implementation of SISSO with built in Python bindings for an efficient python interface + +*homepage*: https://gitlab.com/sissopp_developers/sissopp + +======= ============== +version toolchain +======= ============== +``1.1`` ``foss/2021b`` +======= ============== + + .. _list_software_SKESA_375: *SKESA* @@ -44339,10 +46046,10 @@ SKESA is a de-novo sequence read assembler for cultured single isolate genomes b *homepage*: https://github.com/ncbi/SKESA ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== -``2.2`` ``foss/2018a`` -``2.3.0`` ``foss/2018b`` +``2.2`` ``foss/2018a`` +``2.3.0`` ``foss/2018b`` ``2.4.0`` ``_saute.1.3.0_1`` ``gompi/2021b`` ========= ================== =============== @@ -44357,7 +46064,7 @@ Sketch-map is a dimensionality reduction algorithm that is particularly well sui *homepage*: http://sketchmap.org/ ============ =============== -version toolchain +version toolchain ============ =============== ``20170130`` ``intel/2016b`` ============ =============== @@ -44373,7 +46080,7 @@ skewer implements the bit-masked k-difference matching algorithm dedicated to th *homepage*: https://github.com/relipmoc/skewer ========= =============== -version toolchain +version toolchain ========= =============== ``0.2.2`` ``intel/2016b`` ========= =============== @@ -44389,7 +46096,7 @@ This module provides a bridge between Scikit-Learn's machine learning methods an *homepage*: https://github.com/scikit-learn-contrib/sklearn-pandas ========= ============== -version toolchain +version toolchain ========= ============== ``2.2.0`` ``foss/2021b`` ========= ============== @@ -44405,7 +46112,7 @@ A simple, planar self-organizing map with methods similar to clustering methods *homepage*: https://github.com/rileypsmith/sklearn-som ========= ============== -version toolchain +version toolchain ========= ============== ``1.1.0`` ``foss/2020b`` ========= ============== @@ -44421,7 +46128,7 @@ A scikit-learn compatible neural network library that wraps PyTorch. *homepage*: https://skorch.readthedocs.io/ ========== =================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== =================== ============== ``0.11.0`` ``-PyTorch-1.10.0`` ``foss/2021a`` ========== =================== ============== @@ -44437,7 +46144,23 @@ SlamDunk is a novel, fully automated software tool for automated, robust, scalab *homepage*: https://t-neumann.github.io/slamdunk ========= ============== -version toolchain +version toolchain +========= ============== +``0.4.3`` ``foss/2021b`` +========= ============== + + +.. _list_software_slamdunk_863: + +*slamdunk* +++++++++++ + +SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis. + +*homepage*: https://t-neumann.github.io/slamdunk/ + +========= ============== +version toolchain ========= ============== ``0.4.3`` ``foss/2021b`` ========= ============== @@ -44453,7 +46176,7 @@ SLATEC Common Mathematical Library, a comprehensive software library containing *homepage*: https://www.netlib.org/slatec/ ======= ========================================================================= -version toolchain +version toolchain ======= ========================================================================= ``4.1`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` ======= ========================================================================= @@ -44469,16 +46192,17 @@ SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software libra *homepage*: https://www.grycap.upv.es/slepc/ ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== -``3.8.3`` ``foss/2017b`` -``3.9.2`` ``foss/2018a`` -``3.11.0`` ``foss/2018b`` -``3.12.2`` ``-Python-2.7.16`` ``intel/2019b`` +``3.8.3`` ``foss/2017b`` +``3.9.2`` ``foss/2018a`` +``3.11.0`` ``foss/2018b`` +``3.12.2`` ``-Python-2.7.16`` ``intel/2019b`` ``3.12.2`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ``3.12.2`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``3.14.2`` ``foss/2020b`` -``3.15.1`` ``foss/2021a`` +``3.14.2`` ``foss/2020b`` +``3.15.1`` ``foss/2021a`` +``3.17.2`` ``foss/2022a`` ========== ================== =============================== @@ -44492,7 +46216,7 @@ Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computati *homepage*: https://bitbucket.org/slepc/slepc4py ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``3.9.0`` ``-Python-3.6.4`` ``foss/2018a`` ``3.12.0`` ``-Python-3.7.4`` ``foss/2019b`` @@ -44510,10 +46234,10 @@ Investigate RNA-Seq transcript abundance from kallisto and perform differential *homepage*: http://pachterlab.github.io/sleuth ========== ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= =============== ``0.29.0`` ``-R-3.4.0`` ``intel/2017a`` -``0.30.0`` ``-R-3.5.1`` ``foss/2018b`` +``0.30.0`` ``-R-3.5.1`` ``foss/2018b`` ========== ============= =============== @@ -44527,7 +46251,7 @@ slidingwindow is a simple little Python library for computing a set of windows i *homepage*: https://github.com/adamrehn/slidingwindow ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``0.0.13`` ``-Python-2.7.15`` ``intel/2018b`` ``0.0.13`` ``-Python-3.6.6`` ``intel/2018b`` @@ -44544,7 +46268,7 @@ SLiM is an evolutionary simulation framework that combines a powerful engine for *homepage*: https://messerlab.org/slim ======= ============= -version toolchain +version toolchain ======= ============= ``3.4`` ``GCC/9.3.0`` ======= ============= @@ -44560,7 +46284,7 @@ slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, *homepage*: https://hasindu2008.github.io/slow5tools ========= =============== -version toolchain +version toolchain ========= =============== ``0.4.0`` ``gompi/2021b`` ========= =============== @@ -44576,7 +46300,7 @@ Smafa attempts to align or cluster pre-aligned biological sequences, handling se *homepage*: https://github.com/wwood/smafa ========= ================= -version toolchain +version toolchain ========= ================= ``0.4.0`` ``GCCcore/8.2.0`` ========= ================= @@ -44592,7 +46316,7 @@ The smallgenomeutilities are a collection of scripts that is useful for dealing *homepage*: https://github.com/cbg-ethz/smallgenomeutilities ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.2.1`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== @@ -44608,7 +46332,7 @@ SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It *homepage*: https://github.com/ruanjue/smartdenovo ============ ============== -version toolchain +version toolchain ============ ============== ``20180219`` ``foss/2018b`` ============ ============== @@ -44624,7 +46348,7 @@ SMC++ is a program for estimating the size history of populations from whole gen *homepage*: https://github.com/popgenmethods/smcpp ========== ============== -version toolchain +version toolchain ========== ============== ``1.15.4`` ``foss/2022a`` ========== ============== @@ -44640,7 +46364,7 @@ smith-waterman-gotoh alignment algorithm. *homepage*: https://github.com/ekg/smithwaterman ============ ============================================================================= -version toolchain +version toolchain ============ ============================================================================= ``20160702`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ============ ============================================================================= @@ -44656,7 +46380,7 @@ Smoldyn is a computer program for cell-scale biochemical simulations. It simulat *homepage*: http://www.smoldyn.org/ ======== ============== -version toolchain +version toolchain ======== ============== ``2.48`` ``foss/2016a`` ======== ============== @@ -44672,7 +46396,7 @@ Smooth Loss Functions for Deep Top-k Classification *homepage*: https://github.com/oval-group/smooth-topk ================ ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ================ ================ ============== ``1.0-20210817`` ``foss/2021a`` ``1.0-20210817`` ``-CUDA-11.3.1`` ``foss/2021a`` @@ -44689,7 +46413,7 @@ PacBio’s open-source SMRT Analysis software suite is designed for use with Sin *homepage*: https://www.pacb.com/support/software-downloads/ =============== =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain =============== =================== ========== ``5.1.0.26412`` ``-cli-tools-only`` ``system`` ``6.0.0.47841`` ``-cli-tools-only`` ``system`` @@ -44706,7 +46430,7 @@ Smokeview is a visualization program that displays output of FDS and CFAST simul *homepage*: https://github.com/firemodels/smv ========== ======================= -version toolchain +version toolchain ========== ======================= ``6.7.17`` ``iccifort/2020.4.304`` ========== ======================= @@ -44722,15 +46446,15 @@ The Snakemake workflow management system is a tool to create reproducible and sc *homepage*: https://snakemake.readthedocs.io ========== ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============================== -``5.2.2`` ``-Python-3.6.4`` ``intel/2018a`` +``5.2.2`` ``-Python-3.6.4`` ``intel/2018a`` ``5.2.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``5.7.1`` ``-Python-3.7.2`` ``foss/2019a`` -``5.26.1`` ``-Python-3.8.2`` ``intel/2020a`` -``6.1.0`` ``foss/2020b`` -``6.6.1`` ``foss/2021a`` -``6.10.0`` ``foss/2021b`` +``5.7.1`` ``-Python-3.7.2`` ``foss/2019a`` +``5.26.1`` ``-Python-3.8.2`` ``intel/2020a`` +``6.1.0`` ``foss/2020b`` +``6.6.1`` ``foss/2021a`` +``6.10.0`` ``foss/2021b`` ========== ================= =============================== @@ -44741,12 +46465,13 @@ version versionsuffix toolchain Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data -*homepage*: http://snap.cs.berkeley.edu/ +*homepage*: https://www.microsoft.com/en-us/research/project/snap ============== =============== -version toolchain +version toolchain ============== =============== ``1.0beta.23`` ``intel/2017b`` +``2.0.1`` ``GCC/12.2.0`` ============== =============== @@ -44760,10 +46485,10 @@ SNAP is a general purpose gene finding program suitable for both eukaryotic and *homepage*: https://korflab.github.io/ ============== ========================================================================= -version toolchain +version toolchain ============== ========================================================================= ``2013-11-29`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` -``20190603`` ``GCC/10.2.0`` +``20190603`` ``GCC/10.2.0`` ============== ========================================================================= @@ -44777,7 +46502,7 @@ SNAPE-pooled computes the probability distribution for the frequency of the mino *homepage*: https://code.google.com/archive/p/snape-pooled/ ======= ============== -version toolchain +version toolchain ======= ============== ``r32`` ``foss/2016a`` ======= ============== @@ -44793,7 +46518,7 @@ SNAPHU is an implementation of the Statistical-cost, Network-flow Algorithm for *homepage*: https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/ ========= =================================================== -version toolchain +version toolchain ========= =================================================== ``1.4.2`` ``GCCcore/6.3.0``, ``intel/2016b``, ``intel/2017a`` ========= =================================================== @@ -44809,14 +46534,14 @@ Snappy is a compression/decompression library. It does not aim for maximum compr *homepage*: https://github.com/google/snappy ========= ============================================================================================================ -version toolchain +version toolchain ========= ============================================================================================================ -``1.1.2`` ``GCC/4.9.2`` -``1.1.3`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25`` -``1.1.6`` ``system`` +``1.1.2`` ``GCC/4.9.2`` +``1.1.3`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25`` +``1.1.6`` ``system`` ``1.1.7`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``intel/2017b`` -``1.1.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` -``1.1.9`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.1.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +``1.1.9`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========= ============================================================================================================ @@ -44830,11 +46555,11 @@ Rapid haploid variant calling and core genome alignment *homepage*: https://github.com/tseemann/snippy ========= ========================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ========================= ============== ``4.4.1`` ``-Perl-5.28.0`` ``foss/2018b`` ``4.6.0`` ``GCC/10.2.0`` -``4.6.0`` ``-Java-13-Python-3.8.2`` ``GCC/9.3.0`` +``4.6.0`` ``-Java-13-Python-3.8.2`` ``GCC/9.3.0`` ``4.6.0`` ``-R-4.1.2`` ``foss/2021b`` ========= ========================= ============== @@ -44849,7 +46574,7 @@ Finds SNP sites from a multi-FASTA alignment file. *homepage*: https://sanger-pathogens.github.io/snp-sites/ ========= ============================================================================= -version toolchain +version toolchain ========= ============================================================================= ``2.5.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ========= ============================================================================= @@ -44865,13 +46590,13 @@ SnpEff is a variant annotation and effect prediction tool. It annotates and pre *homepage*: https://pcingola.github.io/SnpEff/ ======== ========================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ======== ========================= ================== -``3.6`` ``-Java-1.7.0_80`` ``system`` -``4.1d`` ``-Java-1.7.0_80`` ``system`` -``4.3t`` ``-Java-1.8`` ``system`` -``5.0`` ``-Java-13`` ``system`` -``5.0`` ``-Java-13-Python-3.8.2`` ``GCCcore/9.3.0`` +``3.6`` ``-Java-1.7.0_80`` ``system`` +``4.1d`` ``-Java-1.7.0_80`` ``system`` +``4.3t`` ``-Java-1.8`` ``system`` +``5.0`` ``-Java-13`` ``system`` +``5.0`` ``-Java-13-Python-3.8.2`` ``GCCcore/9.3.0`` ``5.0e`` ``-Java-11`` ``GCCcore/11.2.0`` ``5.0e`` ``-Java-13`` ``GCCcore/10.2.0`` ======== ========================= ================== @@ -44887,7 +46612,7 @@ SNPhylo: a pipeline to generate a phylogenetic tree from huge SNP data *homepage*: http://chibba.pgml.uga.edu/snphylo/ ============ ========================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ========================== =============================== ``20140701`` ``foss/2016a``, ``intel/2016a`` ``20160204`` ``-Python-2.7.14-R-3.4.3`` ``foss/2017b``, ``intel/2017b`` @@ -44904,7 +46629,7 @@ High throughput sequencing technologies generate large amounts of short reads. *homepage*: https://github.com/magnusmanske/snpomatic ======= ================= -version toolchain +version toolchain ======= ================= ``1.0`` ``GCCcore/9.3.0`` ======= ================= @@ -44920,7 +46645,7 @@ SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Pack *homepage*: http://soap.genomics.org.cn/soapaligner.html ======== ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================= ========== ``2.21`` ``_Linux-x86_64`` ``system`` ======== ================= ========== @@ -44936,7 +46661,7 @@ SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo f *homepage*: http://soap.genomics.org.cn/SOAPdenovo-Trans.html ========= =============== -version toolchain +version toolchain ========= =============== ``1.0.4`` ``intel/2017a`` ========= =============== @@ -44952,9 +46677,9 @@ SOAPdenovo is a novel short-read assembly method that can build a de novo draf *homepage*: http://soap.genomics.org.cn/index.html ======== =========================================================================================== -version toolchain +version toolchain ======== =========================================================================================== -``r240`` ``GCC/5.4.0-2.26`` +``r240`` ``GCC/5.4.0-2.26`` ``r241`` ``GCC/6.4.0-2.28``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2018a`` ======== =========================================================================================== @@ -44969,7 +46694,7 @@ SOAPfuse is an open source tool developed for genome-wide detection of fusion t *homepage*: https://sourceforge.net/p/soapfuse/wiki/Home/ ======== ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================ ============== ``1.27`` ``-Perl-5.24.0`` ``foss/2016b`` ``1.27`` ``-Perl-5.28.0`` ``foss/2018b`` @@ -44986,7 +46711,7 @@ socat is a relay for bidirectional data transfer between two independent data ch *homepage*: http://www.dest-unreach.org/socat =========== ================= -version toolchain +version toolchain =========== ================= ``1.7.3.3`` ``GCCcore/8.2.0`` =========== ================= @@ -45002,11 +46727,11 @@ SOCI is a database access library for C++ that makes the illusion of embedding S *homepage*: http://soci.sourceforge.net/ ========= ================================= -version toolchain +version toolchain ========= ================================= ``4.0.1`` ``GCC/10.2.0``, ``GCCcore/9.3.0`` -``4.0.2`` ``GCC/10.3.0`` -``4.0.3`` ``GCC/11.2.0`` +``4.0.2`` ``GCC/10.3.0`` +``4.0.3`` ``GCC/11.2.0``, ``GCC/11.3.0`` ========= ================================= @@ -45020,7 +46745,7 @@ SolexaQA calculates sequence quality statistics and creates visual representatio *homepage*: http://solexaqa.sourceforge.net ========= ============== -version toolchain +version toolchain ========= ============== ``3.1.5`` ``foss/2016b`` ========= ============== @@ -45036,7 +46761,7 @@ Sonic is a simple algorithm for speeding up or slowing down speech. However, it *homepage*: https://github.com/espeak-ng/sonic ============ =============== -version toolchain +version toolchain ============ =============== ``20180202`` ``gompi/2020a`` ============ =============== @@ -45052,7 +46777,7 @@ SoQt is a library which provides the glue between Systems in Motion's Coin high *homepage*: https://coin3d.github.io/SoQt/html/ ========= ============================== -version toolchain +version toolchain ========= ============================== ``1.6.0`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========= ============================== @@ -45068,7 +46793,7 @@ SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU- *homepage*: http://bioinfo.lifl.fr/RNA/sortmerna/ ======= ============== -version toolchain +version toolchain ======= ============== ``2.1`` ``foss/2016a`` ======= ============== @@ -45084,7 +46809,7 @@ Sound eXchange, the Swiss Army knife of audio manipulation *homepage*: http://sox.sourceforge.net/ ========== ================================= -version toolchain +version toolchain ========== ================================= ``14.4.2`` ``GCC/8.3.0``, ``GCCcore/11.3.0`` ========== ================================= @@ -45100,7 +46825,7 @@ SoXt is an Xt/Motif glue library for Coin. It can also be used on top of the SG *homepage*: https://coin3d.github.io/SoXt/html/ ========= ============== -version toolchain +version toolchain ========= ============== ``1.4.0`` ``GCC/11.2.0`` ========= ============== @@ -45116,12 +46841,13 @@ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq *homepage*: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger ========= ============== -version toolchain +version toolchain ========= ============== -``1.1.0`` ``GCC/9.3.0`` -``1.2.2`` ``GCC/9.3.0`` +``1.1.0`` ``GCC/9.3.0`` +``1.2.2`` ``GCC/9.3.0`` ``1.3.0`` ``GCC/10.3.0`` ``1.3.1`` ``GCC/11.2.0`` +``2.0.0`` ``GCC/11.2.0`` ========= ============== @@ -45135,7 +46861,7 @@ Spack is a package manager for supercomputers, Linux, and macOS. It makes instal *homepage*: https://spack.io/ ========== ========== -version toolchain +version toolchain ========== ========== ``0.10.0`` ``system`` ``0.11.2`` ``system`` @@ -45146,6 +46872,22 @@ version toolchain ========== ========== +.. _list_software_spaCy_512: + +*spaCy* ++++++++ + +Industrial-strength Natural Language Processing (NLP) in Python. + +*homepage*: https://spacy.io/ + +========= ============== +version toolchain +========= ============== +``3.4.4`` ``foss/2022a`` +========= ============== + + .. _list_software_SPAdes_544: *SPAdes* @@ -45156,20 +46898,20 @@ Genome assembler for single-cell and isolates data sets *homepage*: http://bioinf.spbau.ru/en/spades ========== ================== ============================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ============================================== -``3.9.0`` ``foss/2016a``, ``foss/2016b`` -``3.10.1`` ``foss/2016b``, ``foss/2017a`` -``3.11.1`` ``foss/2017b``, ``foss/2018a`` +``3.9.0`` ``foss/2016a``, ``foss/2016b`` +``3.10.1`` ``foss/2016b``, ``foss/2017a`` +``3.11.1`` ``foss/2017b``, ``foss/2018a`` ``3.12.0`` ``foss/2016b``, ``foss/2018a``, ``foss/2018b`` -``3.13.0`` ``GCC/10.3.0``, ``foss/2018b`` -``3.13.1`` ``GCC/8.2.0-2.31.1`` -``3.14.0`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` -``3.14.0`` ``-Python-3.7.4`` ``GCC/8.3.0`` -``3.14.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` -``3.15.2`` ``GCC/10.2.0`` -``3.15.2`` ``-Python-2.7.18`` ``GCC/10.2.0`` -``3.15.3`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``3.13.0`` ``GCC/10.3.0``, ``foss/2018b`` +``3.13.1`` ``GCC/8.2.0-2.31.1`` +``3.14.0`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` +``3.14.0`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``3.14.1`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``3.15.2`` ``GCC/10.2.0`` +``3.15.2`` ``-Python-2.7.18`` ``GCC/10.2.0`` +``3.15.3`` ``GCC/10.3.0``, ``GCC/11.2.0`` ========== ================== ============================================== @@ -45183,11 +46925,11 @@ Spaln (space-efficient spliced alignment) is a stand-alone program that maps an *homepage*: https://github.com/ogotoh/spaln ========== ======================================== -version toolchain +version toolchain ========== ======================================== ``2.3.3c`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2.4.03`` ``iccifort/2019.5.281`` -``2.4.12`` ``GCC/10.2.0`` +``2.4.03`` ``iccifort/2019.5.281`` +``2.4.12`` ``GCC/10.2.0``, ``GCC/11.2.0`` ========== ======================================== @@ -45201,28 +46943,28 @@ Spark is Hadoop MapReduce done in memory *homepage*: https://spark.apache.org ========= =========================================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =========================================== ================================== -``1.3.0`` ``system`` -``1.4.1`` ``system`` -``1.5.0`` ``system`` -``1.6.0`` ``system`` -``1.6.1`` ``system`` -``2.0.0`` ``system`` -``2.0.2`` ``system`` -``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_144`` ``system`` -``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_152`` ``system`` -``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3`` ``intel/2017b`` -``2.3.0`` ``-Hadoop-2.7-Java-1.8.0_162`` ``system`` -``2.4.0`` ``-Hadoop-2.7-Java-1.8`` ``system`` -``2.4.0`` ``-Hadoop-2.7-Java-1.8-Python-3.6.6`` ``intel/2018b`` -``2.4.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``2.4.0`` ``-Python-3.6.6`` ``intel/2018b`` -``2.4.5`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` -``3.0.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``1.3.0`` ``system`` +``1.4.1`` ``system`` +``1.5.0`` ``system`` +``1.6.0`` ``system`` +``1.6.1`` ``system`` +``2.0.0`` ``system`` +``2.0.2`` ``system`` +``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_144`` ``system`` +``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_152`` ``system`` +``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3`` ``intel/2017b`` +``2.3.0`` ``-Hadoop-2.7-Java-1.8.0_162`` ``system`` +``2.4.0`` ``-Hadoop-2.7-Java-1.8`` ``system`` +``2.4.0`` ``-Hadoop-2.7-Java-1.8-Python-3.6.6`` ``intel/2018b`` +``2.4.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``2.4.0`` ``-Python-3.6.6`` ``intel/2018b`` +``2.4.5`` ``-Python-3.7.4-Java-1.8`` ``intel/2019b`` +``3.0.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``3.1.1`` ``foss/2020b``, ``fosscuda/2020b`` -``3.1.1`` ``-Python-3.8.2`` ``foss/2020a`` -``3.2.1`` ``foss/2021b`` +``3.1.1`` ``-Python-3.8.2`` ``foss/2020a`` +``3.2.1`` ``foss/2021b`` ========= =========================================== ================================== @@ -45236,11 +46978,11 @@ An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! T *homepage*: https://github.com/sparsehash/sparsehash ========= ============================================================================================================================== -version toolchain +version toolchain ========= ============================================================================================================================== -``2.0.2`` ``foss/2016a`` +``2.0.2`` ``foss/2016a`` ``2.0.3`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``intel/2017a`` -``2.0.4`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.0.4`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================================== @@ -45254,7 +46996,7 @@ A collection of all the estimation functions for spatial cross-sectional models *homepage*: https://cran.r-project.org/package=spatialreg ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.1-5`` ``-R-3.6.2`` ``foss/2019b`` ``1.1-8`` ``-R-4.1.0`` ``foss/2021a`` @@ -45271,7 +47013,7 @@ Very fast, header-only/compiled, C++ logging library. *homepage*: https://github.com/gabime/spdlog ========= ================== -version toolchain +version toolchain ========= ================== ``1.9.2`` ``GCCcore/10.3.0`` ========= ================== @@ -45287,9 +47029,9 @@ Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. *homepage*: https://spectralib.org/ ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``1.0.0`` ``GCC/10.2.0`` +``1.0.0`` ``GCC/10.2.0`` ``1.0.1`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ====================================== @@ -45304,7 +47046,7 @@ Contains some implementations of Singular Spectrum Analysis (SSA) for the gapfil *homepage*: https://cran.r-project.org/web/packages/spectral.methods ============= ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ============= ============= =============== ``0.7.2.133`` ``-R-3.4.3`` ``intel/2017b`` ``0.7.2.133`` ``-R-3.4.4`` ``intel/2018a`` @@ -45321,7 +47063,7 @@ The Edinburgh Speech Tools Library is a collection of C++ class, functions and r *homepage*: ['http://festvox.org/festival/'] ========= ================= -version toolchain +version toolchain ========= ================= ``2.5.0`` ``GCCcore/9.3.0`` ========= ================= @@ -45337,12 +47079,12 @@ Spglib is a library for finding and handling crystal symmetries written in C. *homepage*: https://atztogo.github.io/spglib/ ========== ========================= -version toolchain +version toolchain ========== ========================= ``1.9.2`` ``intel/2016.02-GCC-4.9`` -``1.9.9`` ``intel/2017b`` -``1.16.1`` ``GCCcore/10.2.0`` -``1.16.2`` ``GCCcore/10.3.0`` +``1.9.9`` ``intel/2017b`` +``1.16.1`` ``GCCcore/10.2.0`` +``1.16.2`` ``GCCcore/10.3.0`` ========== ========================= @@ -45356,20 +47098,20 @@ Spglib for Python. Spglib is a library for finding and handling crystal symmetri *homepage*: https://pypi.python.org/pypi/spglib ================ ================== ======================================================== -version versionsuffix toolchain +version versionsuffix toolchain ================ ================== ======================================================== -``1.9.4.2`` ``-Python-2.7.12`` ``intel/2016b`` -``1.9.5`` ``-Python-2.7.12`` ``intel/2016b`` -``1.9.9.38`` ``-Python-2.7.13`` ``intel/2017a`` -``1.10.0.2`` ``-Python-2.7.14`` ``intel/2017b`` -``1.10.0.2`` ``-Python-3.6.3`` ``intel/2017b`` -``1.14.1.post0`` ``-Python-3.7.2`` ``intel/2019a`` -``1.16.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``1.9.4.2`` ``-Python-2.7.12`` ``intel/2016b`` +``1.9.5`` ``-Python-2.7.12`` ``intel/2016b`` +``1.9.9.38`` ``-Python-2.7.13`` ``intel/2017a`` +``1.10.0.2`` ``-Python-2.7.14`` ``intel/2017b`` +``1.10.0.2`` ``-Python-3.6.3`` ``intel/2017b`` +``1.14.1.post0`` ``-Python-3.7.2`` ``intel/2019a`` +``1.16.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` ``1.16.0`` ``-Python-3.7.4`` ``fosscuda/2019b``, ``intel/2019b``, ``intelcuda/2019b`` -``1.16.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``1.16.1`` ``foss/2021a``, ``intel/2021a`` -``1.16.3`` ``foss/2021b``, ``intel/2021b`` -``2.0.0`` ``foss/2022a``, ``intel/2022a`` +``1.16.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.16.1`` ``foss/2021a``, ``gomkl/2021a``, ``intel/2021a`` +``1.16.3`` ``foss/2021b``, ``intel/2021b`` +``2.0.0`` ``foss/2022a``, ``intel/2022a`` ================ ================== ======================================================== @@ -45383,19 +47125,35 @@ Sphinx is a tool that makes it easy to create intelligent and beautiful document *homepage*: http://sphinx.pocoo.org/ ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``1.4.8`` ``-Python-2.7.11`` ``foss/2016a`` -``1.4.8`` ``-Python-3.5.1`` ``foss/2016a`` +``1.4.8`` ``-Python-2.7.11`` ``foss/2016a`` +``1.4.8`` ``-Python-3.5.1`` ``foss/2016a`` ``1.8.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``1.8.1`` ``-Python-2.7.15`` ``foss/2018b`` +``1.8.1`` ``-Python-2.7.15`` ``foss/2018b`` ``1.8.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.8.1`` ``-Python-3.6.4`` ``foss/2018a`` +``1.8.1`` ``-Python-3.6.4`` ``foss/2018a`` ``1.8.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``1.8.3`` ``-Python-3.6.4`` ``intel/2018a`` +``1.8.3`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================== =============================== +.. _list_software_Sphinx-RTD-Theme_1457: + +*Sphinx-RTD-Theme* +++++++++++++++++++ + +Sphinx theme designed to provide a great reader experience for documentation users on both desktop and mobile devices. + +*homepage*: https://sphinx-rtd-theme.readthedocs.io + +========= ================== +version toolchain +========= ================== +``1.1.1`` ``GCCcore/10.2.0`` +========= ================== + + .. _list_software_SpiceyPy_822: *SpiceyPy* @@ -45406,12 +47164,12 @@ SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65) *homepage*: https://github.com/AndrewAnnex/SpiceyPy ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``1.1.0`` ``-Python-2.7.12`` ``intel/2016b`` -``1.1.1`` ``-Python-3.6.1`` ``intel/2017a`` +``1.1.0`` ``-Python-2.7.12`` ``intel/2016b`` +``1.1.1`` ``-Python-3.6.1`` ``intel/2017a`` ``2.1.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``2.1.0`` ``-Python-3.6.4`` ``foss/2018a`` +``2.1.0`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================== =============================== @@ -45425,7 +47183,7 @@ Sparse InversE Covariance estimation for Ecological Association and Statistical *homepage*: https://github.com/zdk123/SpiecEasi ============ ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= =============== ``1.0.0`` ``-R-3.4.4`` ``intel/2018a`` ``20160830`` ``-R-3.3.1`` ``intel/2016b`` @@ -45442,7 +47200,7 @@ Splicing Adder is a toolbox for alternative splicing analysis based on RNA-Seq a *homepage*: https://github.com/ratschlab/spladder ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``2.4.2`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -45458,7 +47216,7 @@ SPLASH is a free and open source visualisation tool for Smoothed Particle Hydro *homepage*: http://users.monash.edu.au/~dprice/splash/index.html ========= ============== -version toolchain +version toolchain ========= ============== ``2.8.0`` ``foss/2018b`` ========= ============== @@ -45474,7 +47232,7 @@ SpliceMap is a de novo splice junction discovery and alignment tool. It offers *homepage*: https://web.stanford.edu/group/wonglab/SpliceMap/ =========== ================== -version toolchain +version toolchain =========== ================== ``3.3.5.2`` ``GCC/7.3.0-2.30`` =========== ================== @@ -45490,7 +47248,7 @@ Analysis tools for split-seq. *homepage*: https://github.com/yjzhang/split-seq-pipeline ============ ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ============== ``20190717`` ``-Python-3.6.6`` ``foss/2018b`` ============ ================= ============== @@ -45506,7 +47264,7 @@ splitRef splits a reference haplotype file into smaller files with subsets of *homepage*: http://www.sph.umich.edu/csg/yli/splitRef/index.html ========= ========== -version toolchain +version toolchain ========= ========== ``0.0.2`` ``system`` ========= ========== @@ -45522,7 +47280,7 @@ SPM (Statistical Parametric Mapping) refers to the construction and assessment *homepage*: https://www.fil.ion.ucl.ac.uk/spm ============== ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================= ========== ``12.5_r7771`` ``-MATLAB-2021a`` ``system`` ``12.5_r7771`` ``-MATLAB-2021b`` ``system`` @@ -45539,15 +47297,31 @@ Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) alg *homepage*: https://github.com/rvaser/spoa ========= ============================================== -version toolchain +version toolchain ========= ============================================== -``3.0.1`` ``GCC/7.3.0-2.30`` -``3.4.0`` ``GCC/10.2.0`` -``4.0.0`` ``GCC/8.3.0`` +``3.0.1`` ``GCC/7.3.0-2.30`` +``3.4.0`` ``GCC/10.2.0`` +``4.0.0`` ``GCC/8.3.0`` ``4.0.7`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0`` ========= ============================================== +.. _list_software_SPOOLES_549: + +*SPOOLES* ++++++++++ + +SPOOLES is a library for solving sparse real and complex linear systems of equations, written in the C language using object oriented design. + +*homepage*: https://netlib.org/linalg/spooles/spooles.2.2.html + +======= =============== +version toolchain +======= =============== +``2.2`` ``gompi/2021a`` +======= =============== + + .. _list_software_SPOTPY_495: *SPOTPY* @@ -45558,7 +47332,7 @@ SPOTPY is a Python framework that enables the use of Computational optimization *homepage*: https://spotpy.readthedocs.io ========== =============== -version toolchain +version toolchain ========== =============== ``1.5.14`` ``intel/2021b`` ========== =============== @@ -45574,7 +47348,7 @@ Scalable Parallel Pseudo Random Number Generators Library *homepage*: http://www.sprng.org/ ======== ============== -version toolchain +version toolchain ======== ============== ``2.0b`` ``foss/2016a`` ======== ============== @@ -45590,13 +47364,13 @@ Spyder is an interactive Python development environment providing MATLAB-like fe *homepage*: https://github.com/spyder-ide/spyder ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``3.1.4`` ``-Python-2.7.13`` ``intel/2017a`` -``3.3.1`` ``-Python-3.6.4`` ``foss/2018a`` -``3.3.2`` ``-Python-3.6.6`` ``foss/2018b`` -``4.1.5`` ``-Python-3.7.2`` ``foss/2019a`` -``4.1.5`` ``-Python-3.8.2`` ``foss/2020a`` +``3.3.1`` ``-Python-3.6.4`` ``foss/2018a`` +``3.3.2`` ``-Python-3.6.6`` ``foss/2018b`` +``4.1.5`` ``-Python-3.7.2`` ``foss/2019a`` +``4.1.5`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================== =============== @@ -45610,26 +47384,27 @@ SQLite: SQL Database Engine in a C Library *homepage*: http://www.sqlite.org/ ============ ==================================================================================================================================================================== -version toolchain +version toolchain ============ ==================================================================================================================================================================== -``3.8.8.1`` ``GCC/4.8.4``, ``GCC/4.9.2`` -``3.8.10.2`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``gimkl/2.11.5`` -``3.9.2`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` +``3.8.8.1`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``3.8.10.2`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``gimkl/2.11.5`` +``3.9.2`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``3.13.0`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016b`` -``3.14.1`` ``GCCcore/4.9.3`` -``3.17.0`` ``GCCcore/6.3.0`` -``3.20.1`` ``GCCcore/6.4.0`` -``3.21.0`` ``GCCcore/6.4.0`` -``3.23.0`` ``GCCcore/6.4.0`` -``3.24.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``3.26.0`` ``GCCcore/8.2.0`` -``3.27.2`` ``GCCcore/8.2.0`` -``3.29.0`` ``GCCcore/8.3.0`` -``3.31.1`` ``GCCcore/9.3.0`` -``3.33.0`` ``GCCcore/10.2.0`` -``3.35.4`` ``GCCcore/10.3.0`` -``3.36`` ``GCCcore/11.2.0`` -``3.38.3`` ``GCCcore/11.3.0`` +``3.14.1`` ``GCCcore/4.9.3`` +``3.17.0`` ``GCCcore/6.3.0`` +``3.20.1`` ``GCCcore/6.4.0`` +``3.21.0`` ``GCCcore/6.4.0`` +``3.23.0`` ``GCCcore/6.4.0`` +``3.24.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``3.26.0`` ``GCCcore/8.2.0`` +``3.27.2`` ``GCCcore/8.2.0`` +``3.29.0`` ``GCCcore/8.3.0`` +``3.31.1`` ``GCCcore/9.3.0`` +``3.33.0`` ``GCCcore/10.2.0`` +``3.35.4`` ``GCCcore/10.3.0`` +``3.36`` ``GCCcore/11.2.0`` +``3.38.3`` ``GCCcore/11.3.0`` +``3.39.4`` ``GCCcore/12.2.0`` ============ ==================================================================================================================================================================== @@ -45643,7 +47418,7 @@ SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, *homepage*: https://github.com/jtamames/SqueezeMeta ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``0.4.3`` ``-Python-2.7.15`` ``foss/2018b`` ``1.0.0`` ``-Python-2.7.15`` ``foss/2018b`` @@ -45651,6 +47426,22 @@ version versionsuffix toolchain ========= ================== ============== +.. _list_software_Squidpy_751: + +*Squidpy* ++++++++++ + +Squidpy is a tool for the analysis and visualization of spatial molecular data. + +*homepage*: https://squidpy.readthedocs.io + +========= ============== +version toolchain +========= ============== +``1.2.2`` ``foss/2021b`` +========= ============== + + .. _list_software_SRA-Toolkit_1017: *SRA-Toolkit* @@ -45661,21 +47452,21 @@ The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will all *homepage*: https://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software =========== =================== =============== -version versionsuffix toolchain +version versionsuffix toolchain =========== =================== =============== -``2.3.5`` ``-centos_linux64`` ``system`` -``2.5.4-1`` ``-centos_linux64`` ``system`` -``2.5.7`` ``-centos_linux64`` ``system`` -``2.8.2-1`` ``-centos_linux64`` ``system`` -``2.9.0`` ``-centos_linux64`` ``system`` -``2.9.2`` ``-ubuntu64`` ``system`` -``2.9.4`` ``-centos_linux64`` ``system`` -``2.9.6-1`` ``-centos_linux64`` ``system`` +``2.3.5`` ``-centos_linux64`` ``system`` +``2.5.4-1`` ``-centos_linux64`` ``system`` +``2.5.7`` ``-centos_linux64`` ``system`` +``2.8.2-1`` ``-centos_linux64`` ``system`` +``2.9.0`` ``-centos_linux64`` ``system`` +``2.9.2`` ``-ubuntu64`` ``system`` +``2.9.4`` ``-centos_linux64`` ``system`` +``2.9.6-1`` ``-centos_linux64`` ``system`` ``2.10.4`` ``gompi/2019b`` -``2.10.5`` ``-centos_linux64`` ``system`` +``2.10.5`` ``-centos_linux64`` ``system`` ``2.10.8`` ``gompi/2020a`` ``2.10.9`` ``gompi/2020b`` -``3.0.0`` ``-centos_linux64`` ``system`` +``3.0.0`` ``-centos_linux64`` ``system`` =========== =================== =============== @@ -45689,10 +47480,10 @@ Single Read Paired Read Indel Substitution Minimizer *homepage*: https://github.com/ncbi/SRPRISM ========= ============= ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ================== -``3.0.0`` ``foss/2018b`` -``3.1.1`` ``-Java-11`` ``GCCcore/8.2.0`` +``3.0.0`` ``foss/2018b`` +``3.1.1`` ``-Java-11`` ``GCCcore/8.2.0`` ``3.1.2`` ``GCCcore/10.2.0`` ========= ============= ================== @@ -45707,7 +47498,7 @@ Short Read Sequence Typing for Bacterial Pathogens *homepage*: https://katholt.github.io/srst2 ================== ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ================== ================== ============== ``0.2.0-20210620`` ``-Python-2.7.18`` ``foss/2020b`` ================== ================== ============== @@ -45723,7 +47514,7 @@ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequ *homepage*: http://www.sanger.ac.uk/resources/software/ssaha2/ ========= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========== ``2.5.5`` ``-i686`` ``system`` ``2.5.5`` ``-x86_64`` ``system`` @@ -45740,7 +47531,7 @@ Spatial statistical modeling and prediction for data on stream networks, includi *homepage*: https://cran.r-project.org/web/packages/SSN ========== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= ============== ``1.1.14`` ``-R-3.6.0`` ``foss/2019a`` ========== ============= ============== @@ -45756,11 +47547,11 @@ SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension *homepage*: https://github.com/nsoranzo/sspace_basic ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``2.1.1`` ``-Perl-5.24.1`` ``intel/2017a`` ``2.1.1`` ``-Perl-5.26.0`` ``intel/2017b`` -``2.1.1`` ``-Python-2.7.18`` ``GCC/10.2.0`` +``2.1.1`` ``-Python-2.7.18`` ``GCC/10.2.0`` ========= ================== =============== @@ -45773,11 +47564,11 @@ SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Si *homepage*: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library -======= ========================================================= -version toolchain -======= ========================================================= -``1.1`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -======= ========================================================= +======= ============================================================================= +version toolchain +======= ============================================================================= +``1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +======= ============================================================================= .. _list_software_STACEY_457: @@ -45790,7 +47581,7 @@ The BEAST2 package STACEY can be used for species delimitation and species tree *homepage*: http://www.indriid.com/software.html ========= ============== -version toolchain +version toolchain ========= ============== ``1.2.5`` ``GCC/10.2.0`` ========= ============== @@ -45806,7 +47597,7 @@ Stack is a cross-platform program for developing Haskell projects. It is intende *homepage*: https://docs.haskellstack.org ========= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========== ``2.3.3`` ``-x86_64`` ``system`` ========= ============= ========== @@ -45822,28 +47613,28 @@ Stacks is a software pipeline for building loci from short-read sequences, such *homepage*: https://catchenlab.life.illinois.edu/stacks/ ============== ============================================================================== -version toolchain +version toolchain ============== ============================================================================== -``1.40`` ``foss/2016a`` -``1.42`` ``foss/2016a`` -``1.44`` ``foss/2016a`` -``1.45`` ``foss/2016a`` -``1.46`` ``intel/2017a`` -``1.47`` ``foss/2016a`` -``1.48`` ``intel/2017b``, ``intel/2018b`` -``2.0`` ``foss/2018a``, ``intel/2018a`` -``2.0Beta7c`` ``intel/2017b`` -``2.0Beta8c`` ``intel/2017b`` -``2.0Beta9`` ``intel/2018a`` -``2.0Beta10a`` ``foss/2018a`` -``2.2`` ``foss/2018a`` -``2.3b`` ``foss/2018a`` -``2.3e`` ``foss/2018b`` -``2.5`` ``iccifort/2019.5.281`` +``1.40`` ``foss/2016a`` +``1.42`` ``foss/2016a`` +``1.44`` ``foss/2016a`` +``1.45`` ``foss/2016a`` +``1.46`` ``intel/2017a`` +``1.47`` ``foss/2016a`` +``1.48`` ``intel/2017b``, ``intel/2018b`` +``2.0`` ``foss/2018a``, ``intel/2018a`` +``2.0Beta7c`` ``intel/2017b`` +``2.0Beta8c`` ``intel/2017b`` +``2.0Beta9`` ``intel/2018a`` +``2.0Beta10a`` ``foss/2018a`` +``2.2`` ``foss/2018a`` +``2.3b`` ``foss/2018a`` +``2.3e`` ``foss/2018b`` +``2.5`` ``iccifort/2019.5.281`` ``2.41`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2.53`` ``foss/2019b``, ``iccifort/2019.5.281`` -``2.54`` ``foss/2020a`` -``2.62`` ``foss/2022a`` +``2.53`` ``foss/2019b``, ``iccifort/2019.5.281`` +``2.54`` ``foss/2020a`` +``2.62`` ``foss/2022a`` ============== ============================================================================== @@ -45857,9 +47648,9 @@ STAMP is a tool for characterizing similarities between transcription factor bin *homepage*: http://www.benoslab.pitt.edu/stamp/ ======= ================================ -version toolchain +version toolchain ======= ================================ -``1.2`` ``intel/2016a`` +``1.2`` ``intel/2016a`` ``1.3`` ``intel/2016a``, ``intel/2016b`` ======= ================================ @@ -45874,7 +47665,7 @@ A software package to extract ground displacements from time series of synthetic *homepage*: http://homepages.see.leeds.ac.uk/~earahoo/stamps/ ========= ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =============== ``3.3b1`` ``-Perl-5.24.1`` ``intel/2017a`` ========= ================ =============== @@ -45890,7 +47681,7 @@ Stampy is a package for the mapping of short reads from illumina sequencing mach *homepage*: http://www.well.ox.ac.uk/stampy ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== ``1.0.31`` ``-Python-2.7.12`` ``intel/2016b`` ``1.0.32`` ``-Python-2.7.14`` ``intel/2018a`` @@ -45907,28 +47698,28 @@ STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays *homepage*: https://github.com/alexdobin/STAR ======================== ============================================================== -version toolchain +version toolchain ======================== ============================================================== -``2.4.2a`` ``foss/2018b`` -``2.5.0a`` ``GNU/4.9.3-2.25`` -``2.5.2a`` ``foss/2016a`` -``2.5.2b`` ``intel/2016b`` +``2.4.2a`` ``foss/2018b`` +``2.5.0a`` ``GNU/4.9.3-2.25`` +``2.5.2a`` ``foss/2016a`` +``2.5.2b`` ``intel/2016b`` ``2.5.3a`` ``GCC/8.3.0``, ``GCC/9.3.0``, ``intel/2017a``, ``intel/2017b`` -``2.5.4b`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` -``2.6.0c`` ``foss/2018a``, ``intel/2018a`` -``2.6.1c`` ``foss/2018b`` -``2.7.0d`` ``foss/2018b`` -``2.7.0f`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` -``2.7.1a`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` -``2.7.2b`` ``GCC/8.3.0`` -``2.7.3a`` ``GCC/8.3.0``, ``GCC/9.3.0`` -``2.7.4a`` ``GCC/9.3.0`` -``2.7.5b`` ``GCC/9.3.0`` -``2.7.6a`` ``GCC/10.2.0``, ``GCC/9.3.0`` -``2.7.7a`` ``GCC/10.2.0``, ``GCC/9.3.0`` -``2.7.8a`` ``GCC/10.2.0`` -``2.7.9a`` ``GCC/10.3.0``, ``GCC/11.2.0`` -``2.7.10a_alpha_220601`` ``GCC/10.3.0`` +``2.5.4b`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` +``2.6.0c`` ``foss/2018a``, ``intel/2018a`` +``2.6.1c`` ``foss/2018b`` +``2.7.0d`` ``foss/2018b`` +``2.7.0f`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` +``2.7.1a`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` +``2.7.2b`` ``GCC/8.3.0`` +``2.7.3a`` ``GCC/8.3.0``, ``GCC/9.3.0`` +``2.7.4a`` ``GCC/9.3.0`` +``2.7.5b`` ``GCC/9.3.0`` +``2.7.6a`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``2.7.7a`` ``GCC/10.2.0``, ``GCC/9.3.0`` +``2.7.8a`` ``GCC/10.2.0`` +``2.7.9a`` ``GCC/10.3.0``, ``GCC/11.2.0`` +``2.7.10a_alpha_220601`` ``GCC/10.3.0`` ======================== ============================================================== @@ -45942,13 +47733,15 @@ STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the *homepage*: https://mdx.plm.automation.siemens.com/star-ccm-plus ============= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ============= ============= ========== ``13.04.011`` ``system`` ``17.02.008`` ``system`` ``17.02.008`` ``-r8`` ``system`` ``17.04.008`` ``system`` ``17.04.008`` ``-r8`` ``system`` +``17.06.007`` ``system`` +``17.06.007`` ``-r8`` ``system`` ============= ============= ========== @@ -45962,11 +47755,11 @@ STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supp *homepage*: https://github.com/STAR-Fusion/STAR-Fusion ========= ============================= ==================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============================= ==================== -``1.5.0`` ``-Perl-5.28.0`` ``foss/2018b`` +``1.5.0`` ``-Perl-5.28.0`` ``foss/2018b`` ``1.6.0`` ``-Perl-5.28.1-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` -``1.8.1`` ``-Python-3.7.4`` ``foss/2019b`` +``1.8.1`` ``-Python-3.7.4`` ``foss/2019b`` ========= ============================= ==================== @@ -45980,7 +47773,7 @@ Reading, manipulating, writing and plotting spatiotemporal arrays (raster and ve *homepage*: https://cran.r-project.org/package=stars ========= ========================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ========================= ============== ``0.4-3`` ``-R-4.0.0-Python-3.8.2`` ``foss/2020a`` ========= ========================= ============== @@ -45996,7 +47789,7 @@ Stata is a complete, integrated statistical software package that provides every *homepage*: https://www.stata.com/ ======= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ======= ============= ========== ``15`` ``system`` ``16`` ``-legacy`` ``system`` @@ -46014,7 +47807,7 @@ Perl interface with the R statistical program *homepage*: https://metacpan.org/pod/Statistics::R ======== ============== -version toolchain +version toolchain ======== ============== ``0.34`` ``foss/2020a`` ======== ============== @@ -46030,21 +47823,21 @@ Statsmodels is a Python module that provides classes and functions for the esti *homepage*: https://www.statsmodels.org ========== ================== =================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =================================================== -``0.6.1`` ``-Python-2.7.13`` ``foss/2017a`` -``0.6.1`` ``-Python-3.5.1`` ``intel/2016a`` -``0.6.1`` ``-Python-3.5.2`` ``intel/2016b`` -``0.8.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``0.9.0`` ``-Python-2.7.16`` ``intel/2019b`` -``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.10.1`` ``foss/2019a`` -``0.11.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``0.11.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.6.1`` ``-Python-2.7.13`` ``foss/2017a`` +``0.6.1`` ``-Python-3.5.1`` ``intel/2016a`` +``0.6.1`` ``-Python-3.5.2`` ``intel/2016b`` +``0.8.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` +``0.9.0`` ``-Python-2.7.16`` ``intel/2019b`` +``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.10.1`` ``foss/2019a`` +``0.11.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.11.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ``0.12.1`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``0.12.2`` ``foss/2021a`` -``0.13.1`` ``foss/2021b``, ``intel/2021b`` +``0.12.2`` ``foss/2021a`` +``0.13.1`` ``foss/2021b``, ``foss/2022a``, ``intel/2021b`` ========== ================== =================================================== @@ -46058,7 +47851,7 @@ Detects integrations of any sort in high-throughput sequencing (HTS) data. STEA *homepage*: https://omictools.com/steak-tool ============== ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================== ============== ``2019.09.12`` ``foss/2021b`` ``2019.09.12`` ``-Python-2.7.16`` ``foss/2019b`` @@ -46075,7 +47868,7 @@ Software for Tomographic Image Reconstruction *homepage*: http://stir.sourceforge.net/ ======= =============== -version toolchain +version toolchain ======= =============== ``3.0`` ``intel/2018a`` ======= =============== @@ -46091,7 +47884,7 @@ The ST Pipeline contains the tools and scripts needed to process and analyze th *homepage*: https://github.com/SpatialTranscriptomicsResearch/st_pipeline ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``1.7.3`` ``-Python-2.7.15`` ``foss/2018b`` ``1.7.6`` ``-Python-3.7.2`` ``foss/2019a`` @@ -46109,7 +47902,7 @@ The STREAM benchmark is a simple synthetic benchmark program that measures susta *homepage*: https://www.cs.virginia.edu/stream/ ======== ================================================================================================================== -version toolchain +version toolchain ======== ================================================================================================================== ``5.10`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``GCC/9.3.0``, ``iccifort/2020.1.217``, ``intel/2016b``, ``intel/2018b`` ======== ================================================================================================================== @@ -46125,10 +47918,10 @@ Strelka2 is a fast and accurate small variant caller optimized for analysis of *homepage*: https://github.com/Illumina/strelka ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== -``2.9.7`` ``intel/2018a`` -``2.9.9`` ``foss/2018b`` +``2.9.7`` ``intel/2018a`` +``2.9.9`` ``foss/2018b`` ``2.9.10`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ========== ================== =============================== @@ -46143,19 +47936,19 @@ StringTie is a fast and highly efficient assembler of RNA-Seq alignments into po *homepage*: https://ccb.jhu.edu/software/stringtie/ ========== ================================== -version toolchain +version toolchain ========== ================================== -``1.3.0`` ``intel/2016b`` +``1.3.0`` ``intel/2016b`` ``1.3.3`` ``GCCcore/6.4.0``, ``intel/2017a`` -``1.3.3b`` ``foss/2016b`` -``1.3.5`` ``GCCcore/8.2.0``, ``foss/2018b`` -``2.0.3`` ``GCCcore/7.3.0`` -``2.1.0`` ``foss/2018b`` -``2.1.1`` ``GCC/8.3.0`` -``2.1.3`` ``GCC/8.3.0``, ``GCC/9.3.0`` -``2.1.4`` ``GCC/8.3.0``, ``GCC/9.3.0`` -``2.1.7`` ``GCC/10.3.0`` -``2.2.1`` ``GCC/11.2.0`` +``1.3.3b`` ``foss/2016b`` +``1.3.5`` ``GCCcore/8.2.0``, ``foss/2018b`` +``2.0.3`` ``GCCcore/7.3.0`` +``2.1.0`` ``foss/2018b`` +``2.1.1`` ``GCC/8.3.0`` +``2.1.3`` ``GCC/8.3.0``, ``GCC/9.3.0`` +``2.1.4`` ``GCC/8.3.0``, ``GCC/9.3.0`` +``2.1.7`` ``GCC/10.3.0`` +``2.2.1`` ``GCC/11.2.0`` ========== ================================== @@ -46169,7 +47962,7 @@ A Python interface to TRIPACK and STRIPACK Fortran code for (constrained) triang *homepage*: https://github.com/underworldcode/stripy ========= ============== -version toolchain +version toolchain ========= ============== ``2.1.0`` ``foss/2021a`` ========= ============== @@ -46185,7 +47978,7 @@ STRique is a python package to analyze repeat expansion and methylation states o *homepage*: https://github.com/giesselmann/STRique ========= ============== -version toolchain +version toolchain ========= ============== ``0.4.2`` ``foss/2021b`` ========= ============== @@ -46201,7 +47994,7 @@ The program structure is a free software package for using multi-locus genotype *homepage*: https://web.stanford.edu/group/pritchardlab/structure.html ========= ===================================================================================== -version toolchain +version toolchain ========= ===================================================================================== ``2.3.4`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.3.199-GCC-8.3.0-2.32``, ``iccifort/2019.5.281`` ========= ===================================================================================== @@ -46217,7 +48010,7 @@ STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner *homepage*: https://fastmath-scidac.llnl.gov/software/strumpack.html ========= =============================== -version toolchain +version toolchain ========= =============================== ``6.1.0`` ``foss/2020b``, ``intel/2020b`` ========= =============================== @@ -46233,7 +48026,7 @@ suave is an interactive web application to visualize read depth ratios between t *homepage*: https://github.com/dellytools/suave ============ ============== -version toolchain +version toolchain ============ ============== ``20160529`` ``foss/2020b`` ============ ============== @@ -46249,13 +48042,13 @@ High performance read alignment, quantification and mutation discovery *homepage*: http://subread.sourceforge.net/ ============ ============================================= -version toolchain +version toolchain ============ ============================================= -``1.5.0-p1`` ``foss/2016a``, ``foss/2016b`` -``1.6.3`` ``foss/2018b`` -``1.6.4`` ``foss/2018b`` -``2.0.0`` ``GCC/7.3.0-2.30``, ``GCC/8.3.0`` -``2.0.2`` ``GCC/10.2.0`` +``1.5.0-p1`` ``foss/2016a``, ``foss/2016b`` +``1.6.3`` ``foss/2018b`` +``1.6.4`` ``foss/2018b`` +``2.0.0`` ``GCC/7.3.0-2.30``, ``GCC/8.3.0`` +``2.0.2`` ``GCC/10.2.0`` ``2.0.3`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` ============ ============================================= @@ -46270,13 +48063,13 @@ Subversion is an open source version control system. *homepage*: http://subversion.apache.org/ ========== ====================================== -version toolchain +version toolchain ========== ====================================== -``1.9.7`` ``iomkl/2018a`` -``1.9.9`` ``GCCcore/7.3.0`` -``1.10.0`` ``foss/2017b``, ``intel/2017b`` -``1.12.0`` ``GCCcore/8.2.0`` -``1.14.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.9.7`` ``iomkl/2018a`` +``1.9.9`` ``GCCcore/7.3.0`` +``1.10.0`` ``foss/2017b``, ``intel/2017b`` +``1.12.0`` ``GCCcore/8.2.0`` +``1.14.0`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``1.14.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========== ====================================== @@ -46291,7 +48084,7 @@ Lightweight SOAP client *homepage*: https://pypi.python.org/pypi/suds-py3 =========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================= =============== ``1.3.3.0`` ``-Python-3.6.4`` ``intel/2018a`` =========== ================= =============== @@ -46307,24 +48100,24 @@ SuiteSparse is a collection of libraries manipulate sparse matrices. *homepage*: https://faculty.cse.tamu.edu/davis/suitesparse.html ========== ============================ ================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ============================ ================================================================================================= -``4.5.1`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` -``4.5.2`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` -``4.5.3`` ``-METIS-5.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` -``4.5.3`` ``-ParMETIS-4.0.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``4.5.5`` ``-METIS-5.1.0`` ``foss/2017a``, ``intel/2017a`` -``4.5.5`` ``-ParMETIS-4.0.3`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``4.5.6`` ``-METIS-5.1.0`` ``foss/2017b`` +``4.5.1`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` +``4.5.2`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` +``4.5.3`` ``-METIS-5.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` +``4.5.3`` ``-ParMETIS-4.0.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` +``4.5.5`` ``-METIS-5.1.0`` ``foss/2017a``, ``intel/2017a`` +``4.5.5`` ``-ParMETIS-4.0.3`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``4.5.6`` ``-METIS-5.1.0`` ``foss/2017b`` ``5.1.2`` ``-METIS-5.1.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` -``5.1.2`` ``-ParMETIS-4.0.3`` ``foss/2017b``, ``intel/2017b`` -``5.4.0`` ``-METIS-5.1.0`` ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` -``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b``, ``intel/2019b`` -``5.7.1`` ``-METIS-5.1.0`` ``foss/2020a``, ``intel/2020a`` -``5.8.1`` ``-METIS-5.1.0`` ``foss/2020b``, ``intel/2020b`` -``5.10.1`` ``-METIS-5.1.0`` ``foss/2021a``, ``foss/2021b`` -``5.10.1`` ``-METIS-5.1.0-CUDA-11.3.1`` ``foss/2021a`` -``5.13.0`` ``-METIS-5.1.0`` ``foss/2022a`` +``5.1.2`` ``-ParMETIS-4.0.3`` ``foss/2017b``, ``intel/2017b`` +``5.4.0`` ``-METIS-5.1.0`` ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` +``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b``, ``intel/2019b`` +``5.7.1`` ``-METIS-5.1.0`` ``foss/2020a``, ``intel/2020a`` +``5.8.1`` ``-METIS-5.1.0`` ``foss/2020b``, ``intel/2020b`` +``5.10.1`` ``-METIS-5.1.0`` ``foss/2021a``, ``foss/2021b`` +``5.10.1`` ``-METIS-5.1.0-CUDA-11.3.1`` ``foss/2021a`` +``5.13.0`` ``-METIS-5.1.0`` ``foss/2022a`` ========== ============================ ================================================================================================= @@ -46338,7 +48131,7 @@ SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. *homepage*: http://metabarcoding.org/sumatra ========== ============== -version toolchain +version toolchain ========== ============== ``1.0.20`` ``foss/2016a`` ========== ============== @@ -46354,7 +48147,7 @@ SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. *homepage*: http://metabarcoding.org/sumatra ========== ============== -version toolchain +version toolchain ========== ============== ``1.0.20`` ``foss/2016a`` ========== ============== @@ -46370,12 +48163,12 @@ Simulation of Urban MObility" (SUMO) is an open source, highly portable, microsc *homepage*: https://www.eclipse.org/sumo/ ========== ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================= ``1.3.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``1.7.0`` ``-Python-3.8.2`` ``foss/2020a`` -``1.12.0`` ``foss/2021b`` -``1.14.1`` ``foss/2021b`` +``1.7.0`` ``-Python-3.8.2`` ``foss/2020a`` +``1.12.0`` ``foss/2021b`` +``1.14.1`` ``foss/2021b`` ========== ================= ================= @@ -46389,13 +48182,13 @@ SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers *homepage*: https://computation.llnl.gov/projects/sundials ========= ================================================================================================================================== -version toolchain +version toolchain ========= ================================================================================================================================== -``2.6.2`` ``intel/2016b``, ``intel/2018b`` +``2.6.2`` ``intel/2016b``, ``intel/2018b`` ``2.7.0`` ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``5.1.0`` ``foss/2019b``, ``intel/2019b`` -``5.7.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``6.3.0`` ``foss/2021b``, ``foss/2022a`` +``5.1.0`` ``foss/2019b``, ``intel/2019b`` +``5.7.0`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``6.3.0`` ``foss/2021b``, ``foss/2022a`` ========= ================================================================================================================================== @@ -46409,7 +48202,7 @@ The community-developed, free and open-source solar data analysis environment fo *homepage*: https://sunpy.org/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.1.3`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -46425,11 +48218,11 @@ SuperLU is a general purpose library for the direct solution of large, sparse, *homepage*: https://crd-legacy.lbl.gov/~xiaoye/SuperLU/ ========= ================================================================================ -version toolchain +version toolchain ========= ================================================================================ -``5.1.1`` ``foss/2016a``, ``intel/2016a`` -``5.2.1`` ``foss/2017b``, ``intel/2017b`` -``5.2.2`` ``foss/2020a``, ``intel/2020a`` +``5.1.1`` ``foss/2016a``, ``intel/2016a`` +``5.2.1`` ``foss/2017b``, ``intel/2017b`` +``5.2.2`` ``foss/2020a``, ``intel/2020a`` ``5.3.0`` ``foss/2020b``, ``foss/2021a``, ``foss/2022a``, ``intel/2020b``, ``intel/2022a`` ========= ================================================================================ @@ -46444,10 +48237,11 @@ SuperLU is a general purpose library for the direct solution of large, sparse, n *homepage*: https://crd-legacy.lbl.gov/~xiaoye/SuperLU/ ========= =================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =================== =============================== -``5.4.0`` ``-trisolve-merge`` ``intel/2020a`` +``5.4.0`` ``-trisolve-merge`` ``intel/2020a`` ``6.4.0`` ``foss/2020a``, ``intel/2020a`` +``8.1.0`` ``foss/2022a`` ========= =================== =============================== @@ -46461,7 +48255,7 @@ Very simple MPI sanity code. Nothing more, nothing less. *homepage*: https://github.com/hpc/supermagic ============ =============================== -version toolchain +version toolchain ============ =============================== ``20170824`` ``foss/2017a``, ``gompi/2019b`` ============ =============================== @@ -46477,7 +48271,7 @@ Supernova is a software package for de novo assembly from Chromium Linked-Reads *homepage*: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome ========= ========== -version toolchain +version toolchain ========= ========== ``2.0.1`` ``system`` ``2.1.1`` ``system`` @@ -46494,7 +48288,7 @@ Toolset for SV simulation, comparison and filtering *homepage*: https://github.com/fritzsedlazeck/SURVIVOR ===================== ============== -version toolchain +version toolchain ===================== ============== ``1.0.7-19-ged1ca51`` ``GCC/11.2.0`` ===================== ============== @@ -46510,7 +48304,7 @@ SVDetect is a application for the isolation and the type prediction of intra- an *homepage*: http://svdetect.sourceforge.net/Site/Home.html ======== ================ ========================================================== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================ ========================================================== ``0.8b`` ``-Perl-5.26.0`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ======== ================ ========================================================== @@ -46526,7 +48320,7 @@ SVDquartets-based species trees *homepage*: https://github.com/pranjalv123/SVDquest ============ =============== -version toolchain +version toolchain ============ =============== ``20190627`` ``gompi/2019a`` ============ =============== @@ -46542,12 +48336,28 @@ Perl binding for SVG *homepage*: https://metacpan.org/pod/SVG ======== ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================ ============== ``2.84`` ``-Perl-5.30.0`` ``foss/2019b`` ======== ================ ============== +.. _list_software_svist4get_941: + +*svist4get* ++++++++++++ + +Svist4get is a simple bioinformatics tool for visualization of genomic signal tracks in user-defined genomic windows, either arbitrary selected by genomic coordinates or anchored to particular transcripts or genes. + +*homepage*: https://github.com/art-egorov/svist4get + +========= ============== +version toolchain +========= ============== +``1.3.1`` ``foss/2020b`` +========= ============== + + .. _list_software_swarm_554: *swarm* @@ -46558,7 +48368,7 @@ A robust and fast clustering method for amplicon-based studies *homepage*: https://github.com/torognes/swarm ========= ============== -version toolchain +version toolchain ========= ============== ``2.2.2`` ``foss/2018b`` ========= ============== @@ -46574,10 +48384,10 @@ SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostat *homepage*: http://swash.sourceforge.net/ ======== ============= ================================ -version versionsuffix toolchain +version versionsuffix toolchain ======== ============= ================================ ``3.14`` ``-mpi`` ``intel/2016b``, ``intel/2017a`` -``4.01`` ``-mpi`` ``intel/2017a`` +``4.01`` ``-mpi`` ``intel/2017a`` ======== ============= ================================ @@ -46591,9 +48401,9 @@ The Soil & Water Assessment Tool (SWAT) is a small watershed to river basin-scal *homepage*: https://swatplus.gitbook.io ========== ======================= -version toolchain +version toolchain ========== ======================= -``60.4.1`` ``GCC/9.3.0`` +``60.4.1`` ``GCC/9.3.0`` ``60.5.1`` ``iccifort/2020.4.304`` ========== ======================= @@ -46608,7 +48418,7 @@ A package which efficiently applies any function to a pandas dataframe or series *homepage*: https://github.com/jmcarpenter2/swifter ========= ================================== -version toolchain +version toolchain ========= ================================== ``1.0.9`` ``foss/2020b``, ``fosscuda/2020b`` ========= ================================== @@ -46624,25 +48434,25 @@ SWIG is a software development tool that connects programs written in C and C++ *homepage*: http://www.swig.org/ ========== ============================ ============================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============================ ============================================================================== -``3.0.8`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``3.0.8`` ``-Python-3.5.1`` ``foss/2016a`` -``3.0.10`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.0.10`` ``-Python-2.7.12-PCRE-8.39`` ``intel/2016b`` -``3.0.11`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``3.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``3.0.12`` ``-Python-2.7.13`` ``intel/2017a`` -``3.0.12`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``3.0.12`` ``-Python-2.7.14-bare`` ``GCCcore/6.4.0`` -``3.0.12`` ``-Python-2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``intel/2018b`` -``3.0.12`` ``-Python-3.6.1`` ``intel/2017a`` -``3.0.12`` ``-Python-3.6.2`` ``foss/2017b``, ``intel/2018.00`` -``3.0.12`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.01`` -``3.0.12`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` -``3.0.12`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``3.0.12`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -``4.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``3.0.8`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``3.0.8`` ``-Python-3.5.1`` ``foss/2016a`` +``3.0.10`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.0.10`` ``-Python-2.7.12-PCRE-8.39`` ``intel/2016b`` +``3.0.11`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``3.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.0.12`` ``-Python-2.7.13`` ``intel/2017a`` +``3.0.12`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` +``3.0.12`` ``-Python-2.7.14-bare`` ``GCCcore/6.4.0`` +``3.0.12`` ``-Python-2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``intel/2018b`` +``3.0.12`` ``-Python-3.6.1`` ``intel/2017a`` +``3.0.12`` ``-Python-3.6.2`` ``foss/2017b``, ``intel/2018.00`` +``3.0.12`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.01`` +``3.0.12`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` +``3.0.12`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``3.0.12`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` +``4.0.1`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ``4.0.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ============================ ============================================================================== @@ -46657,7 +48467,7 @@ Smith-Waterman database searches with inter-sequence SIMD parallelisation *homepage*: https://github.com/torognes/swipe ========= ============== -version toolchain +version toolchain ========= ============== ``2.1.1`` ``GCC/10.3.0`` ========= ============== @@ -46673,7 +48483,7 @@ Perl module for reading and writing UniProtKB data in plain text format. *homepage*: https://sourceforge.net/projects/swissknife/ ======== ================= -version toolchain +version toolchain ======== ================= ``1.80`` ``GCCcore/8.3.0`` ======== ================= @@ -46689,11 +48499,11 @@ SymEngine is a standalone fast C++ symbolic manipulation library *homepage*: https://github.com/symengine/symengine ========= ============= ==================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ==================== -``0.3.0`` ``-20181006`` ``intel/2018a`` +``0.3.0`` ``-20181006`` ``intel/2018a`` ``0.4.0`` ``GCC/8.2.0-2.31.1`` -``0.7.0`` ``GCC/10.3.0`` +``0.7.0`` ``GCC/10.3.0`` ========= ============= ==================== @@ -46707,7 +48517,7 @@ Python wrappers to the C++ library SymEngine, a fast C++ symbolic manipulation l *homepage*: https://github.com/symengine/symengine.py ========= ============== -version toolchain +version toolchain ========= ============== ``0.7.2`` ``GCC/10.3.0`` ========= ============== @@ -46723,7 +48533,7 @@ SYMPHONY is an open-source solver for mixed-integer linear programs (MILPs) writ *homepage*: https://projects.coin-or.org/SYMPHONY ========== ============== -version toolchain +version toolchain ========== ============== ``5.6.16`` ``foss/2018b`` ========== ============== @@ -46739,21 +48549,21 @@ SymPy is a Python library for symbolic mathematics. It aims to become a full-fe *homepage*: https://sympy.org/ ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== ``1.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``1.3`` ``-Python-2.7.14`` ``intel/2018a`` -``1.3`` ``-Python-2.7.15`` ``foss/2018b`` -``1.3`` ``-Python-3.6.4`` ``intel/2018a`` -``1.3`` ``-Python-3.6.6`` ``foss/2018b`` +``1.3`` ``-Python-2.7.14`` ``intel/2018a`` +``1.3`` ``-Python-2.7.15`` ``foss/2018b`` +``1.3`` ``-Python-3.6.4`` ``intel/2018a`` +``1.3`` ``-Python-3.6.6`` ``foss/2018b`` ``1.4`` ``foss/2019a``, ``intel/2019a`` -``1.5.1`` ``-Python-3.7.4`` ``foss/2019b`` -``1.6.2`` ``-Python-3.8.2`` ``foss/2020a`` +``1.5.1`` ``-Python-3.7.4`` ``foss/2019b`` +``1.6.2`` ``-Python-3.8.2`` ``foss/2020a`` ``1.7.1`` ``foss/2020b``, ``intel/2020b`` -``1.8`` ``foss/2021a`` -``1.9`` ``foss/2021b`` -``1.10.1`` ``foss/2022a`` -``1.11.1`` ``foss/2022a`` +``1.8`` ``foss/2021a`` +``1.9`` ``foss/2021b`` +``1.10.1`` ``foss/2022a`` +``1.11.1`` ``foss/2022a`` ========== ================== =============================== @@ -46767,7 +48577,7 @@ Synteny and Rearrangement Identifier (SyRI). *homepage*: https://schneebergerlab.github.io/syri/ ======= ============== -version toolchain +version toolchain ======= ============== ``1.4`` ``foss/2021a`` ======= ============== @@ -46783,10 +48593,10 @@ Szip compression software, providing lossless compression of scientific data *homepage*: https://www.hdfgroup.org/doc_resource/SZIP/ ========= ============================================================================================================================================================================================================================================================================================= -version toolchain +version toolchain ========= ============================================================================================================================================================================================================================================================================================= ``2.1`` ``GCC/4.8.1``, ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``gmpolf/2017.10``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========= ============================================================================================================================================================================================================================================================================================= @@ -46796,7 +48606,7 @@ version toolchain --- -:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TALYS_397` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_TELEMAC-MASCARET_1144` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboard_1187` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_termcolor_983` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_ThemisPy_819` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmap_434` - :ref:`list_software_tmux_462` - :ref:`list_software_TN93_270` - :ref:`list_software_TOBIAS_450` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_topaz_558` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchdata_954` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` +:ref:`list_software_tabix_536` - :ref:`list_software_tabixpp_760` - :ref:`list_software_taco_423` - :ref:`list_software_TagDust_700` - :ref:`list_software_TagLib_563` - :ref:`list_software_Taiyaki_716` - :ref:`list_software_TALON_382` - :ref:`list_software_TALYS_397` - :ref:`list_software_TAMkin_548` - :ref:`list_software_task-spooler_1252` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_TBA_215` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_TCLAP_372` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_TELEMAC-MASCARET_1144` - :ref:`list_software_Telescope_932` - :ref:`list_software_Teneto_623` - :ref:`list_software_tensorboard_1187` - :ref:`list_software_tensorboardX_1275` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_TensorFlow-Datasets_1913` - :ref:`list_software_tensorflow-probability_2337` - :ref:`list_software_TensorRT_801` - :ref:`list_software_terastructure_1437` - :ref:`list_software_termcolor_983` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_TEtranscripts_1366` - :ref:`list_software_texinfo_765` - :ref:`list_software_texlive_769` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_TFEA_288` - :ref:`list_software_Theano_607` - :ref:`list_software_ThemisPy_819` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_tidybayes_974` - :ref:`list_software_tidymodels_1086` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_TinyXML_661` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tMAE_327` - :ref:`list_software_tmap_434` - :ref:`list_software_tmux_462` - :ref:`list_software_TN93_270` - :ref:`list_software_TOBIAS_450` - :ref:`list_software_ToFu_382` - :ref:`list_software_Togl_406` - :ref:`list_software_tokenizers_1102` - :ref:`list_software_Tombo_513` - :ref:`list_software_TOML-Fortran_1093` - :ref:`list_software_topaz_558` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchaudio_1074` - :ref:`list_software_torchdata_954` - :ref:`list_software_torchinfo_972` - :ref:`list_software_torchsampler_1300` - :ref:`list_software_torchtext_997` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TranscriptClean_1549` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transformers_1286` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TRAVIS-Analyzer_1356` - :ref:`list_software_treatSens_953` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_trimesh_764` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TRUST4_470` - :ref:`list_software_Trycycler_961` - :ref:`list_software_tsne_442` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` - :ref:`list_software_TWL-NINJA_660` - :ref:`list_software_typing-extensions_1816` .. _list_software_tabix_536: @@ -46809,7 +48619,7 @@ Generic indexer for TAB-delimited genome position files *homepage*: http://samtools.sourceforge.net ========= ==================================================================================================================================================================== -version toolchain +version toolchain ========= ==================================================================================================================================================================== ``0.2.6`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``intel/2016a``, ``intel/2016b`` ========= ==================================================================================================================================================================== @@ -46825,7 +48635,7 @@ C++ wrapper to tabix indexer *homepage*: https://github.com/ekg/tabixpp ========= ============================================================= -version toolchain +version toolchain ========= ============================================================= ``1.1.0`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0`` ========= ============================================================= @@ -46841,7 +48651,7 @@ Multi-sample transcriptome assembly from RNA-Seq *homepage*: http://tacorna.github.io ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.5.1`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== @@ -46857,7 +48667,7 @@ Raw sequences produced by next generation sequencing (NGS) machines may contain *homepage*: http://tagdust.sourceforge.net/ ======== ===================================== -version toolchain +version toolchain ======== ===================================== ``2.33`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0`` ======== ===================================== @@ -46873,7 +48683,7 @@ TagLib is a library for reading and editing the meta-data of several popular aud *homepage*: https://taglib.org/ ========== ================= -version toolchain +version toolchain ========== ================= ``1.11.1`` ``GCCcore/8.2.0`` ========== ================= @@ -46889,7 +48699,7 @@ Taiyaki is research software for training models for basecalling Oxford Nanopore *homepage*: https://github.com/nanoporetech/taiyaki ================== =============================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ================== =============================== ================================== ``5.1.0-20200617`` ``-Python-3.7.2-PyTorch-1.2.0`` ``foss/2019a``, ``fosscuda/2019a`` ================== =============================== ================================== @@ -46905,7 +48715,7 @@ TALON is a Python package for identifying and quantifying known and novel genes/ *homepage*: https://github.com/mortazavilab/TALON ======= ============== -version toolchain +version toolchain ======= ============== ``5.0`` ``foss/2020b`` ======= ============== @@ -46921,7 +48731,7 @@ TALYS is a nuclear reaction program. *homepage*: https://tendl.web.psi.ch/tendl_2019/talys.html ======== ===================================== -version toolchain +version toolchain ======== ===================================== ``1.95`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` ======== ===================================== @@ -46937,7 +48747,7 @@ TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry a *homepage*: https://molmod.github.io/tamkin/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.0.9`` ``-Python-2.7.11`` ``intel/2016a`` ``1.2.4`` ``-Python-2.7.14`` ``intel/2017b`` @@ -46946,6 +48756,22 @@ version versionsuffix toolchain ========= ================== =============== +.. _list_software_task-spooler_1252: + +*task-spooler* +++++++++++++++ + +task spooler is a Unix batch system where the tasks spooled run one after the other. + +*homepage*: http://viric.name/soft/ts/ + +========= ================== +version toolchain +========= ================== +``1.0.2`` ``GCCcore/11.3.0`` +========= ================== + + .. _list_software_taxator-tk_1039: *taxator-tk* @@ -46956,12 +48782,28 @@ A set of programs for the taxonomic analysis of nucleotide sequence data *homepage*: https://github.com/fungs/taxator-tk ========= =============================================== -version toolchain +version toolchain ========= =============================================== ``1.3.3`` ``GCC/10.2.0``, ``foss/2018b``, ``gompi/2019a`` ========= =============================================== +.. _list_software_TBA_215: + +*TBA* ++++++ + +TBA (a Transcription factor Binding Analysis): TBA is a multi-functional machine learning tool for identifying transcription factors associated with genomic features + +*homepage*: https://github.com/jenhantao/tba + +======= ============== +version toolchain +======= ============== +``1.0`` ``foss/2020b`` +======= ============== + + .. _list_software_tbb_312: *tbb* @@ -46972,28 +48814,28 @@ Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ *homepage*: https://software.intel.com/en-us/articles/intel-tbb/ ============== ========================================================== -version toolchain +version toolchain ============== ========================================================== -``4.0.0.233`` ``system`` -``4.0.5.339`` ``system`` -``4.3.6.211`` ``system`` -``4.4.2.152`` ``system`` -``2017.2.132`` ``system`` -``2017.4.174`` ``system`` -``2017.6.196`` ``system`` -``2017_U5`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2017a`` -``2017_U6`` ``GCCcore/6.3.0``, ``intel/2017a`` -``2018_U1`` ``GCCcore/6.4.0`` -``2018_U2`` ``GCCcore/6.4.0`` -``2018_U3`` ``GCCcore/6.4.0`` -``2018_U5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2019_U4`` ``GCCcore/8.2.0`` -``2019_U9`` ``GCCcore/8.3.0`` -``2020.1`` ``GCCcore/9.3.0`` -``2020.2`` ``GCCcore/8.3.0`` +``4.0.0.233`` ``system`` +``4.0.5.339`` ``system`` +``4.3.6.211`` ``system`` +``4.4.2.152`` ``system`` +``2017.2.132`` ``system`` +``2017.4.174`` ``system`` +``2017.6.196`` ``system`` +``2017_U5`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2017a`` +``2017_U6`` ``GCCcore/6.3.0``, ``intel/2017a`` +``2018_U1`` ``GCCcore/6.4.0`` +``2018_U2`` ``GCCcore/6.4.0`` +``2018_U3`` ``GCCcore/6.4.0`` +``2018_U5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2019_U4`` ``GCCcore/8.2.0`` +``2019_U9`` ``GCCcore/8.3.0`` +``2020.1`` ``GCCcore/9.3.0`` +``2020.2`` ``GCCcore/8.3.0`` ``2020.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``2021.4.0`` ``GCCcore/11.2.0`` -``2021.5.0`` ``GCCcore/11.3.0`` +``2021.4.0`` ``GCCcore/11.2.0`` +``2021.5.0`` ``GCCcore/11.3.0`` ============== ========================================================== @@ -47007,7 +48849,7 @@ Tbl2asn is a command-line program that automates the creation of sequence recor *homepage*: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ============ ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= ========== ``25.8`` ``-linux64`` ``system`` ``20180227`` ``-linux64`` ``system`` @@ -47026,7 +48868,7 @@ The Tiny C Compiler (aka TCC, tCc, or TinyCC) is an x86 and x86-64 C compiler c *homepage*: http://bellard.org/tcc/ ========== ========== -version toolchain +version toolchain ========== ========== ``0.9.26`` ``system`` ========== ========== @@ -47042,19 +48884,19 @@ Tcl (Tool Command Language) is a very powerful but easy to learn dynamic progra *homepage*: https://www.tcl.tk/ ========== ========================================================================================================================================================================= -version toolchain +version toolchain ========== ========================================================================================================================================================================= -``8.5.19`` ``foss/2017a`` -``8.6.3`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``8.5.19`` ``foss/2017a`` +``8.6.3`` ``GCC/4.8.4``, ``GCC/4.9.2`` ``8.6.4`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``8.6.5`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016b`` -``8.6.6`` ``GCCcore/4.9.3``, ``GCCcore/6.3.0`` -``8.6.7`` ``GCCcore/6.4.0`` -``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` -``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``8.6.10`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``8.6.11`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``8.6.12`` ``GCCcore/11.3.0`` +``8.6.5`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016b`` +``8.6.6`` ``GCCcore/4.9.3``, ``GCCcore/6.3.0`` +``8.6.7`` ``GCCcore/6.4.0`` +``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` +``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``8.6.10`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``8.6.11`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``8.6.12`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========== ========================================================================================================================================================================= @@ -47068,10 +48910,10 @@ TCLAP is a small, flexible library that provides a simple interface for defining *homepage*: http://tclap.sourceforge.net/ ========= ====================================== -version toolchain +version toolchain ========= ====================================== -``1.2.2`` ``GCCcore/8.3.0`` -``1.2.4`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.2.2`` ``GCCcore/8.3.0`` +``1.2.4`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``1.2.5`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ====================================== @@ -47086,14 +48928,14 @@ Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C sh *homepage*: https://www.tcsh.org =========== ======================================================= -version toolchain +version toolchain =========== ======================================================= -``6.19.00`` ``intel/2016a`` +``6.19.00`` ``intel/2016a`` ``6.20.00`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``6.22.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``6.22.03`` ``GCCcore/10.2.0`` -``6.22.04`` ``GCCcore/10.3.0`` -``6.24.01`` ``GCCcore/11.2.0`` +``6.22.03`` ``GCCcore/10.2.0`` +``6.22.04`` ``GCCcore/10.3.0`` +``6.24.01`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` =========== ======================================================= @@ -47107,7 +48949,7 @@ Quickly plot and animate your CFD results exactly the way you want. Analyze comp *homepage*: http://www.tecplot.com/products/tecplot-360/ =========== ========== -version toolchain +version toolchain =========== ========== ``linux64`` ``system`` =========== ========== @@ -47123,7 +48965,7 @@ TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free- *homepage*: http://www.opentelemac.org ========= ============== -version toolchain +version toolchain ========= ============== ``8p3r1`` ``foss/2021b`` ========= ============== @@ -47139,7 +48981,7 @@ Single locus resolution of Transposable ELEment expression using next-generation *homepage*: https://github.com/mlbendall/telescope ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.0.3`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -47155,7 +48997,7 @@ Teneto is package for deriving, analysing and plotting temporal network represen *homepage*: https://teneto.readthedocs.io ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.5.1`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -47171,7 +49013,7 @@ TensorBoard is a suite of web applications for inspecting and understanding your *homepage*: https://github.com/tensorflow/tensorboard ========== ============== -version toolchain +version toolchain ========== ============== ``2.8.0`` ``foss/2021a`` ``2.10.0`` ``foss/2022a`` @@ -47187,13 +49029,14 @@ Tensorboard for PyTorch. *homepage*: https://github.com/lanpa/tensorboardX -======= ================== ================================== -version versionsuffix toolchain -======= ================== ================================== -``2.0`` ``-Python-3.7.4`` ``foss/2019b`` -``2.1`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` -``2.2`` ``-PyTorch-1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` -======= ================== ================================== +========= ================== ================================== +version versionsuffix toolchain +========= ================== ================================== +``2.0`` ``-Python-3.7.4`` ``foss/2019b`` +``2.1`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` +``2.2`` ``-PyTorch-1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` +``2.5.1`` ``foss/2022a`` +========= ================== ================================== .. _list_software_TensorFlow_1043: @@ -47206,67 +49049,84 @@ An open-source software library for Machine Intelligence *homepage*: https://www.tensorflow.org/ ========== ============================= =================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============================= =================================================== -``0.12.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``0.12.1`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` -``1.0.1`` ``-Python-2.7.12`` ``intel/2016b`` -``1.0.1`` ``-Python-3.5.2`` ``intel/2016b`` -``1.1.0`` ``-Python-2.7.13`` ``intel/2017a`` -``1.1.0`` ``-Python-3.6.1`` ``intel/2017a`` -``1.2.0`` ``-Python-3.6.1`` ``intel/2017a`` -``1.2.1`` ``-GPU-Python-3.5.2`` ``foss/2016b`` -``1.2.1`` ``-Python-3.5.2`` ``foss/2016b`` -``1.3.0`` ``-Python-2.7.13`` ``intel/2017a`` -``1.3.0`` ``-Python-3.6.1`` ``intel/2017a`` -``1.3.0`` ``-Python-3.6.3`` ``intel/2017b`` -``1.4.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.4.1`` ``-Python-3.6.3`` ``foss/2017b`` -``1.5.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.6.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.6.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` -``1.7.0`` ``-Python-3.6.4`` ``foss/2018a`` -``1.7.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` -``1.8.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b`` -``1.8.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b`` +``0.12.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``0.12.1`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` +``1.0.1`` ``-Python-2.7.12`` ``intel/2016b`` +``1.0.1`` ``-Python-3.5.2`` ``intel/2016b`` +``1.1.0`` ``-Python-2.7.13`` ``intel/2017a`` +``1.1.0`` ``-Python-3.6.1`` ``intel/2017a`` +``1.2.0`` ``-Python-3.6.1`` ``intel/2017a`` +``1.2.1`` ``-GPU-Python-3.5.2`` ``foss/2016b`` +``1.2.1`` ``-Python-3.5.2`` ``foss/2016b`` +``1.3.0`` ``-Python-2.7.13`` ``intel/2017a`` +``1.3.0`` ``-Python-3.6.1`` ``intel/2017a`` +``1.3.0`` ``-Python-3.6.3`` ``intel/2017b`` +``1.4.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``1.4.1`` ``-Python-3.6.3`` ``foss/2017b`` +``1.5.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``1.6.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.6.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` +``1.7.0`` ``-Python-3.6.4`` ``foss/2018a`` +``1.7.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` +``1.8.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b`` +``1.8.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b`` ``1.8.0`` ``-Python-3.6.4`` ``foss/2018a``, ``fosscuda/2018a``, ``intel/2018a`` -``1.10.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``1.10.1`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``1.10.1`` ``-Python-3.6.6`` ``foss/2018b`` -``1.11.0`` ``-Python-3.6.6`` ``foss/2018b`` -``1.12.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``1.12.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``1.13.1`` ``-Python-3.6.6`` ``foss/2018b`` -``1.13.1`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` -``1.14.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` -``1.15.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``1.15.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``1.15.5`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``1.15.5`` ``-Python-3.7.4-nompi`` ``fosscuda/2019b`` -``2.0.0`` ``-Python-3.7.2`` ``foss/2019a`` -``2.0.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``2.0.1`` ``-Python-3.7.2`` ``foss/2019a`` -``2.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``2.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``2.2.2`` ``-Python-3.7.4`` ``foss/2019b`` -``2.2.3`` ``foss/2020b`` -``2.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``2.3.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` -``2.4.1`` ``foss/2020b``, ``fosscuda/2020b`` -``2.4.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``2.4.4`` ``foss/2021a`` -``2.5.0`` ``foss/2020b``, ``fosscuda/2020b`` -``2.5.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` -``2.5.3`` ``foss/2021a`` -``2.5.3`` ``-CUDA-11.3.1`` ``foss/2021a`` -``2.6.0`` ``foss/2021a`` -``2.6.0`` ``-CUDA-11.3.1`` ``foss/2021a`` -``2.7.1`` ``foss/2021b`` -``2.7.1`` ``-CUDA-11.4.1`` ``foss/2021b`` +``1.10.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``1.10.1`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``1.10.1`` ``-Python-3.6.6`` ``foss/2018b`` +``1.11.0`` ``-Python-3.6.6`` ``foss/2018b`` +``1.12.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``1.12.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``1.13.1`` ``-Python-3.6.6`` ``foss/2018b`` +``1.13.1`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` +``1.14.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` +``1.15.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.15.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``1.15.5`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.15.5`` ``-Python-3.7.4-nompi`` ``fosscuda/2019b`` +``2.0.0`` ``-Python-3.7.2`` ``foss/2019a`` +``2.0.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2.0.1`` ``-Python-3.7.2`` ``foss/2019a`` +``2.0.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2.1.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.2.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.2.2`` ``-Python-3.7.4`` ``foss/2019b`` +``2.2.3`` ``foss/2020b`` +``2.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` +``2.3.1`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a`` +``2.4.1`` ``foss/2020b``, ``fosscuda/2020b`` +``2.4.1`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2.4.4`` ``foss/2021a`` +``2.5.0`` ``foss/2020b``, ``fosscuda/2020b`` +``2.5.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``2.5.3`` ``foss/2021a`` +``2.5.3`` ``-CUDA-11.3.1`` ``foss/2021a`` +``2.6.0`` ``foss/2021a`` +``2.6.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +``2.7.1`` ``foss/2021b`` +``2.7.1`` ``-CUDA-11.4.1`` ``foss/2021b`` +``2.8.4`` ``foss/2021b`` ========== ============================= =================================================== +.. _list_software_TensorFlow-Datasets_1913: + +*TensorFlow-Datasets* ++++++++++++++++++++++ + +TensorFlow Datasets is a collection of datasets ready to use, with TensorFlow or other Python ML frameworks, such as Jax. All datasets are exposed as tf.data.Datasets , enabling easy-to-use and high-performance input pipelines. + +*homepage*: https://www.tensorflow.org/datasets + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``4.7.0`` ``-CUDA-11.3.1`` ``foss/2021a`` +========= ================ ============== + + .. _list_software_tensorflow-probability_2337: *tensorflow-probability* @@ -47277,10 +49137,11 @@ TensorFlow Probability (TFP) is a library for probabilistic reasoning and statis *homepage*: https://www.tensorflow.org/probability ========== ================= ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================== -``0.9.0`` ``-Python-3.7.4`` ``foss/2019b`` +``0.9.0`` ``-Python-3.7.4`` ``foss/2019b`` ``0.12.1`` ``foss/2020b``, ``fosscuda/2020b`` +``0.16.0`` ``foss/2021b`` ========== ================= ================================== @@ -47294,7 +49155,7 @@ NVIDIA TensorRT is a platform for high-performance deep learning inference *homepage*: https://developer.nvidia.com/tensorrt =========== ================== ================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== ================== ``4.0.1.6`` ``-Python-2.7.15`` ``fosscuda/2018b`` =========== ================== ================== @@ -47310,7 +49171,7 @@ TeraStructure is a new algorithm to fit Bayesian models of genetic variation in *homepage*: https://github.com/StoreyLab/terastructure ======= ============= -version toolchain +version toolchain ======= ============= ``1.0`` ``GCC/8.3.0`` ======= ============= @@ -47326,7 +49187,7 @@ Termcolor is a header-only C++ library for printing colored messages to the ter *homepage*: https://termcolor.readthedocs.io/ ========= ========== -version toolchain +version toolchain ========= ========== ``2.0.0`` ``system`` ========= ========== @@ -47342,7 +49203,7 @@ The Tesla Deployment Kit is a set of tools provided primarily for the NVIDIA Tes *homepage*: https://developer.nvidia.com/tesla-deployment-kit ============ ========== -version toolchain +version toolchain ============ ========== ``5.319.43`` ``system`` ============ ========== @@ -47358,10 +49219,11 @@ Tesseract is an optical character recognition engine *homepage*: https://github.com/tesseract-ocr/tesseract ========= ===================================== -version toolchain +version toolchain ========= ===================================== -``4.0.0`` ``GCCcore/7.3.0`` +``4.0.0`` ``GCCcore/7.3.0`` ``4.1.0`` ``GCCcore/10.3.0``, ``GCCcore/8.2.0`` +``5.3.0`` ``GCCcore/11.3.0`` ========= ===================================== @@ -47375,12 +49237,12 @@ Test utilities for code working with files and commands *homepage*: https://github.com/jupyter/testpath ======= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== =============================== ``0.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``0.3`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``0.3`` ``-Python-3.5.1`` ``foss/2016a`` -``0.3`` ``-Python-3.5.2`` ``intel/2016b`` +``0.3`` ``-Python-3.5.1`` ``foss/2016a`` +``0.3`` ``-Python-3.5.2`` ``intel/2016b`` ======= ================== =============================== @@ -47394,9 +49256,9 @@ A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator *homepage*: http://wias-berlin.de/software/index.jsp?id=TetGen ========= ================== -version toolchain +version toolchain ========= ================== -``1.5.0`` ``GCCcore/6.4.0`` +``1.5.0`` ``GCCcore/6.4.0`` ``1.6.0`` ``GCCcore/10.2.0`` ========= ================== @@ -47411,7 +49273,7 @@ Tools for estimating differential enrichment of Transposable Elements and other *homepage*: http://hammelllab.labsites.cshl.edu/software/#TEToolkit ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``1.5.1`` ``-Python-2.7.11`` ``foss/2016a`` ========= ================== ============== @@ -47427,7 +49289,7 @@ TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates reads t *homepage*: https://github.com/mhammell-laboratory/TEtranscripts ========= ============== -version toolchain +version toolchain ========= ============== ``2.2.0`` ``foss/2020a`` ========= ============== @@ -47443,14 +49305,15 @@ Texinfo is the official documentation format of the GNU project. *homepage*: https://www.gnu.org/software/texinfo/ ========= ======================================================== -version toolchain +version toolchain ========= ======================================================== -``4.13a`` ``system`` -``5.2`` ``GCC/4.8.2`` -``6.4`` ``GCCcore/5.4.0`` -``6.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``6.6`` ``GCCcore/8.2.0`` +``4.13a`` ``system`` +``5.2`` ``GCC/4.8.2`` +``6.4`` ``GCCcore/5.4.0`` +``6.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``6.6`` ``GCCcore/8.2.0`` ``6.7`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``6.8`` ``GCCcore/11.2.0`` ========= ======================================================== @@ -47464,11 +49327,11 @@ TeX is a typesetting language. Instead of visually formatting your text, you ent *homepage*: https://tug.org ============ ============================== -version toolchain +version toolchain ============ ============================== -``20200406`` ``GCCcore/8.3.0`` +``20200406`` ``GCCcore/8.3.0`` ``20210324`` ``GCC/10.3.0``, ``GCC/11.2.0`` -``20220321`` ``GCC/11.2.0`` +``20220321`` ``GCC/11.2.0`` ============ ============================== @@ -47482,12 +49345,28 @@ Text-CSV parser *homepage*: https://metacpan.org/pod/Text::CSV ======== ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ================ ============== ``1.33`` ``-Perl-5.22.1`` ``foss/2016a`` ======== ================ ============== +.. _list_software_TFEA_288: + +*TFEA* +++++++ + +Transcription Factor Enrichment Analysis + +*homepage*: https://github.com/Dowell-Lab/TFEA + +========= ================== ============== +version versionsuffix toolchain +========= ================== ============== +``1.1.4`` ``-muMerge-1.1.0`` ``foss/2020b`` +========= ================== ============== + + .. _list_software_Theano_607: *Theano* @@ -47498,26 +49377,26 @@ Theano is a Python library that allows you to define, optimize, and evaluate mat *homepage*: https://deeplearning.net/software/theano ========= ================== ==================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ==================================================================================== -``0.8.2`` ``-Python-2.7.11`` ``foss/2016a`` -``0.8.2`` ``-Python-3.5.1`` ``foss/2016a`` -``0.8.2`` ``-Python-3.5.2`` ``intel/2016b`` -``0.9.0`` ``-Python-2.7.13`` ``intel/2017a`` -``0.9.0`` ``-Python-3.6.1`` ``intel/2017a`` -``1.0.0`` ``-Python-2.7.14`` ``intel/2017b`` -``1.0.0`` ``-Python-3.6.3`` ``intel/2017b`` -``1.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` -``1.0.2`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` -``1.0.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``1.0.2`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intelcuda/2017b`` -``1.0.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``1.0.4`` ``foss/2019a``, ``fosscuda/2019a`` -``1.0.4`` ``-Python-3.6.4`` ``foss/2018a`` -``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` -``1.0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` -``1.0.4`` ``-Python-3.8.2`` ``foss/2020a`` +``0.8.2`` ``-Python-2.7.11`` ``foss/2016a`` +``0.8.2`` ``-Python-3.5.1`` ``foss/2016a`` +``0.8.2`` ``-Python-3.5.2`` ``intel/2016b`` +``0.9.0`` ``-Python-2.7.13`` ``intel/2017a`` +``0.9.0`` ``-Python-3.6.1`` ``intel/2017a`` +``1.0.0`` ``-Python-2.7.14`` ``intel/2017b`` +``1.0.0`` ``-Python-3.6.3`` ``intel/2017b`` +``1.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` +``1.0.2`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``1.0.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``1.0.2`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intelcuda/2017b`` +``1.0.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``1.0.4`` ``foss/2019a``, ``fosscuda/2019a`` +``1.0.4`` ``-Python-3.6.4`` ``foss/2018a`` +``1.0.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``1.0.4`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` +``1.0.4`` ``-Python-3.8.2`` ``foss/2020a`` ``1.1.2`` ``-PyMC`` ``foss/2020b``, ``foss/2021b``, ``fosscuda/2020b``, ``intel/2020b``, ``intel/2021b`` ========= ================== ==================================================================================== @@ -47532,7 +49411,7 @@ A header-only C++ library for L-BFGS and L-BFGS-B algorithms *homepage*: https://github.com/aeb/ThemisPy ========= ============== -version toolchain +version toolchain ========= ============== ``0.3.0`` ``foss/2021a`` ========= ============== @@ -47548,7 +49427,7 @@ Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate th *homepage*: https://github.com/raphael-group/THetA ======= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================== ============== ``0.7`` ``-Python-2.7.15`` ``foss/2018b`` ======= ================== ============== @@ -47564,7 +49443,7 @@ Fit Thurstonian IRT models in R using Stan, lavaan, or Mplus *homepage*: https://github.com/paul-buerkner/thurstonianIRT ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``0.9.0`` ``-R-3.6.0`` ``foss/2019a`` ========= ============= ============== @@ -47580,9 +49459,9 @@ TiCC utils is a collection of generic C++ software which is used in a lot of pro *homepage*: https://github.com/LanguageMachines/ticcutils ======== ================================ -version toolchain +version toolchain ======== ================================ -``0.11`` ``foss/2016a`` +``0.11`` ``foss/2016a`` ``0.21`` ``iimpi/2019a``, ``intel/2018b`` ======== ================================ @@ -47597,7 +49476,7 @@ Compose data for and extract, manipulate, and visualize posterior draws from Bay *homepage*: https://cran.r-project.org/package=tidybayes ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``2.1.1`` ``-R-4.0.0`` ``foss/2020a`` ========= ============= ============== @@ -47613,7 +49492,7 @@ The tidy modeling "verse" is a collection of packages for modeling and statistic *homepage*: https://cran.r-project.org/package=tidymodels ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``0.1.0`` ``-R-4.0.0`` ``foss/2020a`` ========= ============= ============== @@ -47629,7 +49508,7 @@ The Apache Tika toolkit detects and extracts metadata and text from over a thous *homepage*: https://tika.apache.org/ ======== ========== -version toolchain +version toolchain ======== ========== ``1.16`` ``system`` ======== ========== @@ -47645,9 +49524,9 @@ TiMBL (Tilburg Memory Based Learner) is an open source software package impleme *homepage*: http://ilk.uvt.nl/timbl/ ========== ================================ -version toolchain +version toolchain ========== ================================ -``6.4.7`` ``foss/2016a`` +``6.4.7`` ``foss/2016a`` ``6.4.13`` ``iimpi/2019a``, ``intel/2018b`` ========== ================================ @@ -47661,12 +49540,12 @@ The `time' command runs another program, then displays information about the res *homepage*: https://www.gnu.org/software/time/ -======= =================================================================================================================== -version toolchain -======= =================================================================================================================== -``1.7`` ``system`` -``1.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -======= =================================================================================================================== +======= ======================================================================================================================================= +version toolchain +======= ======================================================================================================================================= +``1.7`` ``system`` +``1.9`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +======= ======================================================================================================================================= .. _list_software_TINKER_461: @@ -47679,7 +49558,7 @@ The TINKER molecular modeling software is a complete and general package for mol *homepage*: https://dasher.wustl.edu/tinker ========= ============== -version toolchain +version toolchain ========= ============== ``8.6.1`` ``foss/2018b`` ``8.7.2`` ``foss/2019b`` @@ -47697,12 +49576,28 @@ TinyDB is a lightweight document oriented database optimized for your happiness *homepage*: https://tinydb.readthedocs.io/ ========== ================= -version toolchain +version toolchain ========== ================= ``3.15.2`` ``GCCcore/8.3.0`` ========== ================= +.. _list_software_TinyXML_661: + +*TinyXML* ++++++++++ + +TinyXML is a simple, small, minimal, C++ XML parser that can be easily integrating into other programs. It reads XML and creates C++ objects representing the XML document. The objects can be manipulated, changed, and saved again as XML. + +*homepage*: https://sourceforge.net/projects/tinyxml + +========= ====================================== +version toolchain +========= ====================================== +``2.6.2`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ====================================== + + .. _list_software_Tk_191: *Tk* @@ -47713,20 +49608,20 @@ Tk is an open source, cross-platform widget toolchain that provides a library of *homepage*: https://www.tcl.tk/ ========== ================= ================================================================================================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ================================================================================================================================================ -``8.6.3`` ``-no-X11`` ``GCC/4.8.4``, ``GCC/4.9.2`` -``8.6.4`` ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` -``8.6.4`` ``-libX11-1.6.3`` ``intel/2016a`` -``8.6.4`` ``-no-X11`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a`` +``8.6.3`` ``-no-X11`` ``GCC/4.8.4``, ``GCC/4.9.2`` +``8.6.4`` ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` +``8.6.4`` ``-libX11-1.6.3`` ``intel/2016a`` +``8.6.4`` ``-no-X11`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a`` ``8.6.5`` ``GCC/5.4.0-2.26``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016b`` -``8.6.6`` ``foss/2017a``, ``intel/2017a`` -``8.6.7`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2018a``, ``iomkl/2018a`` -``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` -``8.6.10`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``8.6.11`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``8.6.12`` ``GCCcore/11.3.0`` +``8.6.6`` ``foss/2017a``, ``intel/2017a`` +``8.6.7`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2018a``, ``iomkl/2018a`` +``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``8.6.10`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``8.6.11`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``8.6.12`` ``GCCcore/11.3.0`` ========== ================= ================================================================================================================================================ @@ -47740,26 +49635,26 @@ Tkinter module, built with the Python buildsystem *homepage*: https://python.org/ ========== ================== ========================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ========================================================================================================= -``2.7.13`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` +``2.7.13`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` ``2.7.14`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a``, ``intelcuda/2017b`` -``2.7.15`` ``GCCcore/8.2.0`` -``2.7.15`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` -``2.7.16`` ``GCCcore/8.3.0`` -``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -``3.6.1`` ``-Python-3.6.1`` ``foss/2017a``, ``intel/2017a`` -``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` -``3.6.3`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``3.6.4`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018.02``, ``iomkl/2018a`` -``3.6.6`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` -``3.7.2`` ``GCCcore/8.2.0`` -``3.7.4`` ``GCCcore/8.3.0`` -``3.8.2`` ``GCCcore/9.3.0`` -``3.8.6`` ``GCCcore/10.2.0`` -``3.9.5`` ``GCCcore/10.3.0`` -``3.9.6`` ``GCCcore/11.2.0`` -``3.10.4`` ``GCCcore/11.3.0`` +``2.7.15`` ``GCCcore/8.2.0`` +``2.7.15`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` +``2.7.16`` ``GCCcore/8.3.0`` +``2.7.18`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +``3.6.1`` ``-Python-3.6.1`` ``foss/2017a``, ``intel/2017a`` +``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` +``3.6.3`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` +``3.6.4`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018.02``, ``iomkl/2018a`` +``3.6.6`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` +``3.7.2`` ``GCCcore/8.2.0`` +``3.7.4`` ``GCCcore/8.3.0`` +``3.8.2`` ``GCCcore/9.3.0`` +``3.8.6`` ``GCCcore/10.2.0`` +``3.9.5`` ``GCCcore/10.3.0`` +``3.9.6`` ``GCCcore/11.2.0`` +``3.10.4`` ``GCCcore/11.3.0`` ========== ================== ========================================================================================================= @@ -47773,9 +49668,10 @@ This package unifies protein structure alignment and RNA structure alignment in *homepage*: https://zhanglab.ccmb.med.umich.edu/RNA-align/TMalign/ ============ =============================== -version toolchain +version toolchain ============ =============================== ``20180426`` ``foss/2018b``, ``intel/2019a`` +``20190822`` ``GCC/11.3.0`` ============ =============================== @@ -47789,7 +49685,7 @@ Package containing functions to: perform a negative binomial test on allele *homepage*: https://github.com/mumichae/tMAE ========= ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ============== ``1.0.0`` ``-R-4.0.3`` ``foss/2020b`` ``1.0.1`` ``-R-4.1.2`` ``foss/2021b`` @@ -47806,7 +49702,7 @@ tmap is a very fast visualization library for large, high-dimensional data sets. *homepage*: https://tmap.gdb.tools ============ ============== -version toolchain +version toolchain ============ ============== ``20220502`` ``GCC/11.2.0`` ============ ============== @@ -47822,14 +49718,15 @@ tmux is a terminal multiplexer: it enables a number of terminals to be created, *homepage*: https://github.com/tmux/tmux/ ======== ================================================== -version toolchain +version toolchain ======== ================================================== -``1.9a`` ``GCC/4.9.2`` -``2.2`` ``GCCcore/4.9.3`` -``2.3`` ``GCC/5.4.0-2.26``, ``system`` -``3.1c`` ``GCCcore/8.3.0`` -``3.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``1.9a`` ``GCC/4.9.2`` +``2.2`` ``GCCcore/4.9.3`` +``2.3`` ``GCC/5.4.0-2.26``, ``system`` +``3.1c`` ``GCCcore/8.3.0`` +``3.2`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``3.2a`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``system`` +``3.3a`` ``GCCcore/11.3.0`` ======== ================================================== @@ -47843,7 +49740,7 @@ This is a simple program meant to compute pairwise distances between aligned nu *homepage*: https://github.com/veg/tn93 ========= ================== -version toolchain +version toolchain ========= ================== ``1.0.7`` ``GCCcore/10.3.0`` ========= ================== @@ -47854,14 +49751,15 @@ version toolchain *TOBIAS* ++++++++ -TOBIAS is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data, and includes: Correction of Tn5 insertion bias; Calculation of footprint scores within regulatory regions; Estimation of bound/unbound transcription factor binding sites; and Visualization of footprints within and across different conditions +TOBIAS is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data. *homepage*: https://github.com/loosolab/TOBIAS =========== ============== -version toolchain +version toolchain =========== ============== ``0.12.12`` ``foss/2021b`` +``0.14.0`` ``foss/2020b`` =========== ============== @@ -47875,10 +49773,10 @@ Tomography for Fusion. *homepage*: https://github.com/ToFuProject/tofu ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== -``1.3.17`` ``-Python-2.7.14`` ``foss/2018a`` -``1.3.17`` ``-Python-3.6.4`` ``foss/2018a`` +``1.3.17`` ``-Python-2.7.14`` ``foss/2018a`` +``1.3.17`` ``-Python-3.6.4`` ``foss/2018a`` ``1.4.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``1.4.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.4.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` @@ -47896,12 +49794,28 @@ A Tcl/Tk widget for OpenGL rendering. *homepage*: https://sourceforge.net/projects/togl/ ======= ========================================================= -version toolchain +version toolchain ======= ========================================================= ``2.0`` ``GCCcore/10.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` ======= ========================================================= +.. _list_software_tokenizers_1102: + +*tokenizers* +++++++++++++ + +Fast State-of-the-Art Tokenizers optimized for Research and Production + +*homepage*: https://github.com/huggingface/tokenizers + +========== ================== +version toolchain +========== ================== +``0.12.1`` ``GCCcore/10.3.0`` +========== ================== + + .. _list_software_Tombo_513: *Tombo* @@ -47912,7 +49826,7 @@ Tombo is a suite of tools primarily for the identification of modified nucleotid *homepage*: https://github.com/nanoporetech/tombo ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.5.1`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -47928,9 +49842,10 @@ TOML parser for Fortran projects *homepage*: https://github.com/toml-f/toml-f ========= ======================================= -version toolchain +version toolchain ========= ======================================= ``0.2.2`` ``GCC/10.2.0``, ``iccifort/2020.4.304`` +``0.3.1`` ``GCC/11.2.0`` ========= ======================================= @@ -47944,7 +49859,7 @@ A pipeline for particle detection in cryo-electron microscopy images using conv *homepage*: https://github.com/tbepler/topaz ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``0.2.5`` ``foss/2021a`` ``0.2.5`` ``-CUDA-11.3.1`` ``foss/2021a`` @@ -47961,12 +49876,12 @@ TopHat is a fast splice junction mapper for RNA-Seq reads. *homepage*: http://ccb.jhu.edu/software/tophat/ ========= ================== ================================================================================ -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================================================================================ -``2.1.0`` ``-Python-2.7.14`` ``intel/2018a`` +``2.1.0`` ``-Python-2.7.14`` ``intel/2018a`` ``2.1.1`` ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``2.1.2`` ``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` -``2.1.2`` ``-Python-2.7.18`` ``GCC/10.2.0`` +``2.1.2`` ``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` +``2.1.2`` ``-Python-2.7.18`` ``GCC/10.2.0`` ========= ================== ================================================================================ @@ -47980,7 +49895,7 @@ Data manipulation and transformation for audio signal processing, powered by PyT *homepage*: https://github.com/pytorch/audio ========= =============================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =============================== ================================== ``0.5.0`` ``-Python-3.7.4-PyTorch-1.4.0`` ``foss/2019b``, ``fosscuda/2019b`` ========= =============================== ================================== @@ -47996,7 +49911,7 @@ TorchData is a prototype library of common modular data loading primitives for e *homepage*: https://github.com/pytorch/data ========= =============================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= =============================== ============== ``0.3.0`` ``-PyTorch-1.11.0-CUDA-11.3.1`` ``foss/2021a`` ========= =============================== ============== @@ -48012,12 +49927,29 @@ version versionsuffix toolchain *homepage*: https://github.com/TylerYep/torchinfo ========= ================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================================== ``1.5.2`` ``-PyTorch-1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` ========= ================== ================================== +.. _list_software_torchsampler_1300: + +*torchsampler* +++++++++++++++ + +A (PyTorch) imbalanced dataset sampler for oversampling low classes and undersampling high frequent ones. + +*homepage*: https://github.com/ufoym/imbalanced-dataset-sampler + +========= ================ ============== +version versionsuffix toolchain +========= ================ ============== +``0.1.2`` ``foss/2022a`` +``0.1.2`` ``-CUDA-11.7.0`` ``foss/2022a`` +========= ================ ============== + + .. _list_software_torchtext_997: *torchtext* @@ -48028,13 +49960,13 @@ Data loaders and abstractions for text and NLP *homepage*: https://github.com/pytorch/text ========== =============================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== =============================== ================================== -``0.5.0`` ``-PyTorch-1.4.0-Python-3.7.4`` ``fosscuda/2019b`` +``0.5.0`` ``-PyTorch-1.4.0-Python-3.7.4`` ``fosscuda/2019b`` ``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` -``0.8.1`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` -``0.9.1`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` -``0.10.0`` ``-PyTorch-1.9.0`` ``fosscuda/2020b`` +``0.8.1`` ``-PyTorch-1.7.1`` ``fosscuda/2020b`` +``0.9.1`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` +``0.10.0`` ``-PyTorch-1.9.0`` ``fosscuda/2020b`` ========== =============================== ================================== @@ -48048,28 +49980,29 @@ Datasets, Transforms and Models specific to Computer Vision *homepage*: https://github.com/pytorch/vision ========== ==================================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ==================================== ================================== -``0.2.0`` ``-Python-3.6.4`` ``intel/2018a`` -``0.2.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` +``0.2.0`` ``-Python-3.6.4`` ``intel/2018a`` +``0.2.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` ``0.2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` -``0.4.2`` ``-PyTorch-1.3.1`` ``fosscuda/2020b`` +``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` +``0.4.2`` ``-PyTorch-1.3.1`` ``fosscuda/2020b`` ``0.4.2`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` -``0.5.0`` ``-Python-3.7.4-PyTorch-1.4.0`` ``fosscuda/2019b`` +``0.5.0`` ``-Python-3.7.4-PyTorch-1.4.0`` ``fosscuda/2019b`` ``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0`` ``foss/2019b``, ``fosscuda/2019b`` -``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0-imkl`` ``fosscuda/2019b`` +``0.7.0`` ``-Python-3.7.4-PyTorch-1.6.0-imkl`` ``fosscuda/2019b`` ``0.8.2`` ``-PyTorch-1.7.1`` ``foss/2020b``, ``fosscuda/2020b`` -``0.8.2`` ``-Python-3.7.4-PyTorch-1.7.1`` ``fosscuda/2019b`` -``0.9.1`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` -``0.9.1`` ``-Python-3.7.4-PyTorch-1.8.1`` ``fosscuda/2019b`` -``0.10.0`` ``-PyTorch-1.9.0`` ``fosscuda/2020b`` -``0.11.1`` ``foss/2021a`` -``0.11.1`` ``-CUDA-11.3.1`` ``foss/2021a`` -``0.11.3`` ``foss/2021a`` -``0.11.3`` ``-CUDA-11.3.1`` ``foss/2021a`` -``0.12.0`` ``-PyTorch-1.11.0-CUDA-11.3.1`` ``foss/2021a`` -``0.13.1`` ``-CUDA-11.7.0`` ``foss/2022a`` +``0.8.2`` ``-Python-3.7.4-PyTorch-1.7.1`` ``fosscuda/2019b`` +``0.9.1`` ``-PyTorch-1.8.1`` ``fosscuda/2020b`` +``0.9.1`` ``-Python-3.7.4-PyTorch-1.8.1`` ``fosscuda/2019b`` +``0.10.0`` ``-PyTorch-1.9.0`` ``fosscuda/2020b`` +``0.11.1`` ``foss/2021a`` +``0.11.1`` ``-CUDA-11.3.1`` ``foss/2021a`` +``0.11.3`` ``foss/2021a`` +``0.11.3`` ``-CUDA-11.3.1`` ``foss/2021a`` +``0.12.0`` ``-PyTorch-1.11.0-CUDA-11.3.1`` ``foss/2021a`` +``0.13.1`` ``foss/2022a`` +``0.13.1`` ``-CUDA-11.7.0`` ``foss/2022a`` ========== ==================================== ================================== @@ -48083,7 +50016,7 @@ TotalView is a GUI-based source code defect analysis tool that gives you unprece *homepage*: http://www.roguewave.com/products/totalview.aspx ============ ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ========== ``8.11.0-0`` ``-linux-x86-64`` ``system`` ``8.11.0-2`` ``-linux-x86-64`` ``system`` @@ -48101,22 +50034,22 @@ A fast, extensible progress bar for Python and CLI *homepage*: https://github.com/tqdm/tqdm ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== -``4.24.0`` ``-Python-2.7.15`` ``foss/2018b`` -``4.24.0`` ``-Python-3.5.1`` ``foss/2016a`` -``4.29.0`` ``-Python-3.6.4`` ``intel/2018a`` -``4.32.1`` ``GCCcore/8.2.0`` -``4.41.1`` ``GCCcore/8.3.0`` +``4.24.0`` ``-Python-2.7.15`` ``foss/2018b`` +``4.24.0`` ``-Python-3.5.1`` ``foss/2016a`` +``4.29.0`` ``-Python-3.6.4`` ``intel/2018a`` +``4.32.1`` ``GCCcore/8.2.0`` +``4.41.1`` ``GCCcore/8.3.0`` ``4.41.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``4.47.0`` ``GCCcore/9.3.0`` -``4.51.0`` ``-Python-3.8.2`` ``intel/2020a`` -``4.56.2`` ``GCCcore/10.2.0`` -``4.60.0`` ``GCCcore/10.2.0`` -``4.61.1`` ``GCCcore/10.3.0`` -``4.61.2`` ``GCCcore/10.3.0`` -``4.62.3`` ``GCCcore/11.2.0`` -``4.64.0`` ``GCCcore/11.3.0`` +``4.47.0`` ``GCCcore/9.3.0`` +``4.51.0`` ``-Python-3.8.2`` ``intel/2020a`` +``4.56.2`` ``GCCcore/10.2.0`` +``4.60.0`` ``GCCcore/10.2.0`` +``4.61.1`` ``GCCcore/10.3.0`` +``4.61.2`` ``GCCcore/10.3.0`` +``4.62.3`` ``GCCcore/11.2.0`` +``4.64.0`` ``GCCcore/11.3.0`` ========== ================== =============================== @@ -48130,7 +50063,7 @@ Tracer is a graphical tool for visualization and diagnostics of MCMC output. *homepage*: https://github.com/beast-dev/tracer ========= ================= -version toolchain +version toolchain ========= ================= ``1.7.1`` ``GCCcore/8.2.0`` ========= ================= @@ -48146,7 +50079,7 @@ TranscriptClean is a Python program that corrects mismatches, microindels, and n *homepage*: https://github.com/mortazavilab/TranscriptClean ========= ============== -version toolchain +version toolchain ========= ============== ``2.0.2`` ``foss/2020b`` ========= ============== @@ -48162,7 +50095,7 @@ TransDecoder identifies candidate coding regions within transcript sequences, s *homepage*: https://github.com/TransDecoder/TransDecoder/wiki ========= ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =============== ``2.1.0`` ``-Perl-5.24.1`` ``intel/2017a`` ========= ================ =============== @@ -48178,11 +50111,12 @@ State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0 *homepage*: https://github.com/huggingface/transformers ========== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ============== ``4.2.1`` ``-Python-3.8.2`` ``foss/2020a`` ``4.20.1`` ``foss/2021a`` ``4.21.1`` ``foss/2021b`` +``4.24.0`` ``foss/2022a`` ========== ================= ============== @@ -48196,7 +50130,7 @@ Transrate is software for de-novo transcriptome assembly quality analysis. It e *homepage*: http://hibberdlab.com/transrate/ ========= ========== -version toolchain +version toolchain ========= ========== ``1.0.3`` ``system`` ========= ========== @@ -48212,7 +50146,7 @@ Travis CI Client (CLI and Ruby library) *homepage*: https://github.com/travis-ci/travis.rb ========= =============== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= =============== ========== ``1.8.2`` ``-Ruby-2.3.1`` ``system`` ``1.8.4`` ``-Ruby-2.3.3`` ``system`` @@ -48229,7 +50163,7 @@ TRAVIS is a free tool for analyzing and visualizing trajectories from all kinds *homepage*: http://www.travis-analyzer.de/ ========== ============== -version toolchain +version toolchain ========== ============== ``210521`` ``GCC/10.3.0`` ========== ============== @@ -48245,7 +50179,7 @@ Utilities to investigate sensitivity to unmeasured confounding in parametric mod *homepage*: https://github.com/vdorie/treatSens ================ ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ================ ============= ============== ``3.0-20201002`` ``-R-4.0.0`` ``foss/2020a`` ================ ============= ============== @@ -48261,7 +50195,7 @@ TreeMix is a method for inferring the patterns of population splits and mixtures *homepage*: http://bitbucket.org/nygcresearch/treemix ======== =============================================== -version toolchain +version toolchain ======== =============================================== ``1.13`` ``GCC/10.3.0``, ``GCC/11.2.0``, ``intel/2018a`` ======== =============================================== @@ -48277,7 +50211,7 @@ TreeShrink is an algorithm for detecting abnormally long branches in one or more *homepage*: https://github.com/uym2/TreeShrink ========= ================= ==================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ==================== ``1.3.2`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` ========= ================= ==================== @@ -48292,12 +50226,12 @@ Tandem Repeats Finder: a program to analyze DNA sequences. *homepage*: https://tandem.bu.edu/trf/trf.html -========== ============= ========================================================= -version versionsuffix toolchain -========== ============= ========================================================= -``4.09`` ``-linux64`` ``system`` -``4.09.1`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` -========== ============= ========================================================= +========== ============= ========================================================================= +version versionsuffix toolchain +========== ============= ========================================================================= +``4.09`` ``-linux64`` ``system`` +``4.09.1`` ``GCC/10.3.0``, ``GCCcore/10.2.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` +========== ============= ========================================================================= .. _list_software_Triangle_822: @@ -48310,7 +50244,7 @@ Triangle generates exact Delaunay triangulations, constrained Delaunay triangula *homepage*: http://www.cs.cmu.edu/~quake/triangle.html ======= ==================================================================================================== -version toolchain +version toolchain ======= ==================================================================================================== ``1.6`` ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2018a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a`` ======= ==================================================================================================== @@ -48326,11 +50260,11 @@ The Trilinos Project is an effort to develop algorithms and enabling technologie *homepage*: https://trilinos.org =========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== =============================== ``12.12.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``12.12.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``12.12.1`` ``-Python-3.7.4`` ``foss/2019b`` +``12.12.1`` ``-Python-3.7.4`` ``foss/2019b`` =========== ================== =============================== @@ -48344,23 +50278,23 @@ Trim Galore! is a wrapper script to automate quality and adapter trimming as wel *homepage*: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ ========= ========================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ========================= =============================== -``0.4.2`` ``foss/2016b`` +``0.4.2`` ``foss/2016b`` ``0.4.4`` ``foss/2016b``, ``intel/2017a`` -``0.5.0`` ``foss/2018b`` -``0.5.0`` ``-Python-3.6.6`` ``intel/2018b`` -``0.6.0`` ``-Python-2.7.15`` ``foss/2018b`` -``0.6.0`` ``-Python-3.6.6`` ``foss/2018b`` -``0.6.1`` ``-Python-2.7.15`` ``foss/2018b`` -``0.6.1`` ``-Python-3.6.6`` ``foss/2018b`` -``0.6.2`` ``-Java-11`` ``GCCcore/8.2.0`` -``0.6.2`` ``-Python-2.7.15`` ``foss/2018b`` -``0.6.2`` ``-Python-3.6.6`` ``foss/2018b`` -``0.6.5`` ``-Java-11-Python-3.7.4`` ``GCCcore/8.3.0`` -``0.6.6`` ``-Python-2.7.18`` ``GCC/10.2.0`` -``0.6.6`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` -``0.6.7`` ``GCCcore/10.3.0`` +``0.5.0`` ``foss/2018b`` +``0.5.0`` ``-Python-3.6.6`` ``intel/2018b`` +``0.6.0`` ``-Python-2.7.15`` ``foss/2018b`` +``0.6.0`` ``-Python-3.6.6`` ``foss/2018b`` +``0.6.1`` ``-Python-2.7.15`` ``foss/2018b`` +``0.6.1`` ``-Python-3.6.6`` ``foss/2018b`` +``0.6.2`` ``-Java-11`` ``GCCcore/8.2.0`` +``0.6.2`` ``-Python-2.7.15`` ``foss/2018b`` +``0.6.2`` ``-Python-3.6.6`` ``foss/2018b`` +``0.6.5`` ``-Java-11-Python-3.7.4`` ``GCCcore/8.3.0`` +``0.6.6`` ``-Python-2.7.18`` ``GCC/10.2.0`` +``0.6.6`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``0.6.7`` ``GCCcore/10.3.0`` ========= ========================= =============================== @@ -48374,12 +50308,28 @@ A tool for automated alignment trimming in large-scale phylogenetic analyses *homepage*: http://trimal.cgenomics.org/ ========= ============================================================================ -version toolchain +version toolchain ========= ============================================================================ ``1.4.1`` ``GCC/8.2.0-2.31.1``, ``GCCcore/10.3.0``, ``GCCcore/9.3.0``, ``intel/2018a`` ========= ============================================================================ +.. _list_software_trimesh_764: + +*trimesh* ++++++++++ + +Trimesh is a Python (2.7- 3.3+) library for loading and using triangular meshes with an emphasis on watertight meshes. The goal of the library is to provide a fully featured Trimesh object which allows for easy manipulation and analysis, in the style of the excellent Polygon object in the Shapely library. + +*homepage*: https://trimsh.org/ + +========== ============== +version toolchain +========== ============== +``3.17.1`` ``foss/2022a`` +========== ============== + + .. _list_software_Trimmomatic_1158: *Trimmomatic* @@ -48390,7 +50340,7 @@ Trimmomatic performs a variety of useful trimming tasks for illumina paired-en *homepage*: http://www.usadellab.org/cms/?page=trimmomatic ======== =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ======== =================== ========== ``0.32`` ``-Java-1.7.0_80`` ``system`` ``0.36`` ``-Java-1.8.0_92`` ``system`` @@ -48411,18 +50361,19 @@ Trinity represents a novel method for the efficient and robust de novo reconstru *homepage*: https://trinityrnaseq.github.io ========== ================== ======================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ======================================== -``2.2.0`` ``foss/2016a`` -``2.4.0`` ``foss/2017a`` -``2.5.1`` ``intel/2017a``, ``intel/2017b`` -``2.6.6`` ``intel/2018a`` -``2.8.4`` ``foss/2018b`` +``2.2.0`` ``foss/2016a`` +``2.4.0`` ``foss/2017a`` +``2.5.1`` ``intel/2017a``, ``intel/2017b`` +``2.6.6`` ``intel/2018a`` +``2.8.4`` ``foss/2018b`` ``2.8.5`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2.8.5`` ``-Java-11`` ``GCC/8.3.0`` -``2.9.1`` ``-Python-2.7.16`` ``foss/2019b`` -``2.9.1`` ``-Python-3.7.4`` ``foss/2019b`` -``2.10.0`` ``-Python-3.7.4`` ``foss/2019b`` +``2.8.5`` ``-Java-11`` ``GCC/8.3.0`` +``2.9.1`` ``foss/2020b`` +``2.9.1`` ``-Python-2.7.16`` ``foss/2019b`` +``2.9.1`` ``-Python-3.7.4`` ``foss/2019b`` +``2.10.0`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================== ======================================== @@ -48436,7 +50387,7 @@ TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific pro *homepage*: https://triqs.github.io/triqs ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ``2.2.1`` ``-Python-2.7.15`` ``foss/2019a`` @@ -48455,7 +50406,7 @@ TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific pro *homepage*: https://triqs.github.io/cthyb/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` @@ -48473,7 +50424,7 @@ TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific pro *homepage*: https://triqs.github.io/dft_tools/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` @@ -48491,7 +50442,7 @@ TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific pro *homepage*: https://triqs.github.io/tprf ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ``3.0.0`` ``-Python-3.8.2`` ``foss/2020a`` @@ -48509,7 +50460,7 @@ Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analy *homepage*: https://bitbucket.org/liulab/trust ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``3.0.2`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============== @@ -48525,9 +50476,9 @@ Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analy *homepage*: https://github.com/liulab-dfci/TRUST4 =========== ============== -version toolchain +version toolchain =========== ============== -``1.0.5.1`` ``system`` +``1.0.5.1`` ``system`` ``1.0.6`` ``GCC/11.2.0`` ``1.0.7`` ``GCC/11.3.0`` =========== ============== @@ -48543,7 +50494,7 @@ Trycycler is a tool for generating consensus long-read assemblies for bacterial *homepage*: https://github.com/rrwick/Trycycler ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``0.3.3`` ``-Python-3.8.2`` ``foss/2020a`` ``0.5.2`` ``foss/2021a`` @@ -48561,7 +50512,7 @@ Python library containing T-SNE algorithms. *homepage*: https://github.com/danielfrg/tsne ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.1.8`` ``-Python-2.7.16`` ``intel/2019b`` ========= ================== =============== @@ -48577,9 +50528,9 @@ TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to pro *homepage*: https://www.turbovnc.org ========= ================== -version toolchain +version toolchain ========= ================== -``2.2.3`` ``GCCcore/8.2.0`` +``2.2.3`` ``GCCcore/8.2.0`` ``3.0.1`` ``GCCcore/11.3.0`` ========= ================== @@ -48594,7 +50545,7 @@ The Virtual Brain will deliver the first open simulation of the human brain bas *homepage*: http://thevirtualbrain.org ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``1.4.1`` ``-Python-2.7.11`` ``intel/2016a`` ``1.5`` ``-Python-2.7.11`` ``intel/2016a`` @@ -48611,7 +50562,7 @@ The Virtual Brain Project (TVB Project) has the purpose of offering some modern *homepage*: http://www.thevirtualbrain.org/ ============ ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============== ``1.5`` ``-Python-2.7.11`` ``intel/2016a`` ``20150915`` ``-Python-2.7.11`` ``intel/2016a`` @@ -48628,7 +50579,7 @@ Bundle of dependency Python packages for TVB (The Virtual Brain) *homepage*: https://thevirtualbrain.org ============ ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============== ``20160618`` ``-Python-2.7.11`` ``intel/2016a`` ============ ================== =============== @@ -48644,7 +50595,7 @@ The Virtual Brain Project (TVB Project) has the purpose of offering some modern *homepage*: http://www.thevirtualbrain.org/ ============ ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============== ``1.5`` ``-Python-2.7.11`` ``intel/2016a`` ``20150921`` ``-Python-2.7.11`` ``intel/2016a`` @@ -48661,7 +50612,7 @@ The Virtual Brain Project (TVB Project) has the purpose of offering some modern *homepage*: http://www.thevirtualbrain.org/ ============ ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============== ``1.5`` ``-Python-2.7.11`` ``intel/2016a`` ``20150922`` ``-Python-2.7.11`` ``intel/2016a`` @@ -48678,7 +50629,7 @@ Nearly Infinite Neighbor Joining Application. *homepage*: https://github.com/TravisWheelerLab/NINJA ===================== ============== -version toolchain +version toolchain ===================== ============== ``0.97-cluster_only`` ``GCC/10.2.0`` ===================== ============== @@ -48689,19 +50640,20 @@ version toolchain *typing-extensions* +++++++++++++++++++ -Typing Extensions – Backported and Experimental Type Hints for Python +Typing Extensions - Backported and Experimental Type Hints for Python *homepage*: https://github.com/python/typing/blob/master/typing_extensions/README.rst ============ ================= ================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ================== ``3.7.4.3`` ``GCCcore/10.2.0`` -``3.7.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` -``3.7.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` +``3.7.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` +``3.7.4.3`` ``-Python-3.8.2`` ``GCCcore/9.3.0`` ``3.10.0.0`` ``GCCcore/10.3.0`` ``3.10.0.2`` ``GCCcore/11.2.0`` ``4.3.0`` ``GCCcore/11.3.0`` +``4.4.0`` ``GCCcore/10.3.0`` ============ ================= ================== @@ -48711,7 +50663,7 @@ version versionsuffix toolchain --- -:ref:`list_software_UCC_219` - :ref:`list_software_UCC-CUDA_549` - :ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_UCX-CUDA_570` - :ref:`list_software_ucx-py_614` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_uncertainty-calibration_2411` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_unimap_650` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_UShER_423` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` +:ref:`list_software_UCC_219` - :ref:`list_software_UCC-CUDA_549` - :ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_UCX-CUDA_570` - :ref:`list_software_ucx-py_614` - :ref:`list_software_UCX-ROCm_622` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_umap-learn_1010` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umi4cPackage_1166` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_uncertainty-calibration_2411` - :ref:`list_software_Unicycler_942` - :ref:`list_software_Unidecode_912` - :ref:`list_software_unimap_650` - :ref:`list_software_units_563` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_UQTk_357` - :ref:`list_software_USEARCH_523` - :ref:`list_software_UShER_423` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` .. _list_software_UCC_219: @@ -48724,9 +50676,10 @@ UCC (Unified Collective Communication) is a collective communication operations *homepage*: https://www.openucx.org/ ========= ================== -version toolchain +version toolchain ========= ================== ``1.0.0`` ``GCCcore/11.3.0`` +``1.1.0`` ``GCCcore/12.2.0`` ========= ================== @@ -48740,7 +50693,7 @@ UCC (Unified Collective Communication) is a collective communication operations *homepage*: https://www.openucx.org/ ========= ================ ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ================== ``1.0.0`` ``-CUDA-11.7.0`` ``GCCcore/11.3.0`` ========= ================ ================== @@ -48756,7 +50709,7 @@ UCLUST: Extreme high-speed sequence clustering, alignment and database search. *homepage*: https://www.drive5.com/usearch/index.html =========== =============== ========== -version versionsuffix toolchain +version versionsuffix toolchain =========== =============== ========== ``1.2.22q`` ``-i86linux64`` ``system`` =========== =============== ========== @@ -48772,23 +50725,23 @@ Unified Communication X An open-source production grade communication framework *homepage*: http://www.openucx.org/ ============ ================ ======================================================= -version versionsuffix toolchain +version versionsuffix toolchain ============ ================ ======================================================= -``1.3.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``1.3.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.5.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` -``1.5.0rc1`` ``-hpcx`` ``GCCcore/8.2.0`` -``1.5.1`` ``GCCcore/8.2.0`` -``1.6.1`` ``GCCcore/8.3.0`` -``1.8.0`` ``GCCcore/9.3.0`` -``1.8.0`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` -``1.9.0`` ``GCCcore/10.2.0`` -``1.9.0`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` -``1.9.0`` ``-CUDA-11.2.1`` ``GCCcore/10.2.0`` -``1.10.0`` ``GCCcore/10.3.0`` -``1.11.0`` ``GCCcore/11.2.0`` -``1.11.2`` ``GCCcore/11.2.0`` -``1.12.1`` ``GCCcore/11.3.0`` -``1.13.1`` ``GCCcore/12.2.0`` +``1.5.0rc1`` ``-hpcx`` ``GCCcore/8.2.0`` +``1.5.1`` ``GCCcore/8.2.0`` +``1.6.1`` ``GCCcore/8.3.0`` +``1.8.0`` ``GCCcore/9.3.0`` +``1.8.0`` ``-CUDA-11.0.2`` ``GCCcore/9.3.0`` +``1.9.0`` ``GCCcore/10.2.0`` +``1.9.0`` ``-CUDA-11.1.1`` ``GCCcore/10.2.0`` +``1.9.0`` ``-CUDA-11.2.1`` ``GCCcore/10.2.0`` +``1.10.0`` ``GCCcore/10.3.0`` +``1.11.0`` ``GCCcore/11.2.0`` +``1.11.2`` ``GCCcore/11.2.0`` +``1.12.1`` ``GCCcore/11.3.0`` +``1.13.1`` ``GCCcore/12.2.0`` ============ ================ ======================================================= @@ -48802,12 +50755,13 @@ Unified Communication X An open-source production grade communication framework *homepage*: http://www.openucx.org/ ========== ================ ================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================ ================== ``1.10.0`` ``-CUDA-11.3.1`` ``GCCcore/10.3.0`` ``1.11.0`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` ``1.11.2`` ``-CUDA-11.4.1`` ``GCCcore/11.2.0`` ``1.12.1`` ``-CUDA-11.7.0`` ``GCCcore/11.3.0`` +``1.13.1`` ``-CUDA-12.0.0`` ``GCCcore/12.2.0`` ========== ================ ================== @@ -48821,12 +50775,28 @@ UCX-Py is the Python interface for UCX, a low-level high-performance networking *homepage*: https://ucx-py.readthedocs.io ========== ============== -version toolchain +version toolchain ========== ============== ``0.21.0`` ``foss/2020b`` ========== ============== +.. _list_software_UCX-ROCm_622: + +*UCX-ROCm* +++++++++++ + +Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX ROCm support. + +*homepage*: http://www.openucx.org/ + +========== =============== ================== +version versionsuffix toolchain +========== =============== ================== +``1.11.2`` ``-ROCm-4.5.0`` ``GCCcore/11.2.0`` +========== =============== ================== + + .. _list_software_udocker_749: *udocker* @@ -48837,9 +50807,9 @@ A basic user tool to execute simple docker containers in batch or interactive s *homepage*: https://github.com/indigo-dc/udocker ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== -``1.1.1`` ``-Python-2.7.14`` ``foss/2017b`` +``1.1.1`` ``-Python-2.7.14`` ``foss/2017b`` ``1.1.3`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============== @@ -48854,13 +50824,13 @@ UDUNITS supports conversion of unit specifications between formatted and binary *homepage*: https://www.unidata.ucar.edu/software/udunits/ ========== =============================================================================================================================================================================================== -version toolchain +version toolchain ========== =============================================================================================================================================================================================== -``2.2.20`` ``foss/2016a``, ``intel/2016b`` -``2.2.24`` ``intel/2017a`` -``2.2.25`` ``foss/2017b``, ``intel/2017b`` +``2.2.20`` ``foss/2016a``, ``intel/2016b`` +``2.2.24`` ``intel/2017a`` +``2.2.25`` ``foss/2017b``, ``intel/2017b`` ``2.2.26`` ``GCCcore/10.2.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2018a``, ``foss/2018b``, ``foss/2020a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``2.2.28`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``2.2.28`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== =============================================================================================================================================================================================== @@ -48874,7 +50844,7 @@ The Unified Form Language (UFL) is a domain specific language for declaration *homepage*: https://bitbucket.org/fenics-project/ufl ============ ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================= ============== ``2018.1.0`` ``-Python-3.6.4`` ``foss/2018a`` ``2019.1.0`` ``-Python-3.7.4`` ``foss/2019b`` @@ -48890,12 +50860,12 @@ Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction te *homepage*: https://umap-learn.readthedocs.io/en/latest/ -========= ================== -version toolchain -========= ================== +========= ============================== +version toolchain +========= ============================== ``0.4.6`` ``fosscuda/2020b`` -``0.5.3`` ``foss/2021a`` -========= ================== +``0.5.3`` ``foss/2021a``, ``foss/2021b`` +========= ============================== .. _list_software_UMI-tools_841: @@ -48908,7 +50878,7 @@ Tools for handling Unique Molecular Identifiers in NGS data sets *homepage*: https://umi-tools.readthedocs.io ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.0.0`` ``-Python-3.6.6`` ``foss/2018b`` ``1.0.1`` ``-Python-3.7.4`` ``foss/2019b`` @@ -48926,7 +50896,7 @@ umi4cPackage is a processing and analysis pipeline for UMI-4C experiment. *homepage*: https://github.com/tanaylab/umi4cpackage ============ ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= ============== ``20200116`` ``-R-4.0.0`` ``foss/2020a`` ============ ============= ============== @@ -48942,7 +50912,7 @@ Package for estimating UMI counts in Transcript Tag Counting data. *homepage*: https://github.com/vals/umis ========= =============== -version toolchain +version toolchain ========= =============== ``1.0.3`` ``intel/2019a`` ========= =============== @@ -48958,7 +50928,7 @@ The UNAFold package contains several programs for performing energy minimization *homepage*: http://mfold.rna.albany.edu/?q=DINAMelt/software ======= ================ =============== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================ =============== ``3.8`` ``-Perl-5.24.1`` ``intel/2017a`` ======= ================ =============== @@ -48974,7 +50944,7 @@ Python library to measure the calibration error of models, including confidence *homepage*: https://github.com/p-lambda/verified_calibration ========= ============== -version toolchain +version toolchain ========= ============== ``0.0.9`` ``foss/2021b`` ========= ============== @@ -48990,9 +50960,9 @@ Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumin *homepage*: https://github.com/rrwick/Unicycler ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== -``0.4.7`` ``-Python-3.7.2`` ``foss/2019a`` +``0.4.7`` ``-Python-3.7.2`` ``foss/2019a`` ``0.4.8`` ``-Python-3.8.2`` ``gompi/2020a`` ``0.4.9`` ``gompi/2021a`` ``0.5.0`` ``gompi/2021b`` @@ -49009,7 +50979,7 @@ Python library for lossy ASCII transliterations of Unicode text (port of Text::U *homepage*: https://github.com/avian2/unidecode ========= ================= ================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ================= ``1.1.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========= ================= ================= @@ -49025,7 +50995,7 @@ Unimap is a fork of minimap2 optimized for assembly-to-reference alignment. It i *homepage*: https://github.com/lh3/unimap ======= ================== -version toolchain +version toolchain ======= ================== ``0.1`` ``GCCcore/10.2.0`` ======= ================== @@ -49041,7 +51011,7 @@ GNU Units converts quantities expressed in various systems of measurement to the *homepage*: https://www.gnu.org/software/units/ ======== ================= -version toolchain +version toolchain ======== ================= ``2.19`` ``GCCcore/8.2.0`` ======== ================= @@ -49057,7 +51027,7 @@ unixODBC provides a uniform interface between application and database driver *homepage*: https://www.unixodbc.org ========= ============== -version toolchain +version toolchain ========= ============== ``2.3.7`` ``foss/2018b`` ========= ============== @@ -49073,10 +51043,10 @@ RAR is a powerful archive manager. *homepage*: https://www.rarlab.com/ ========= ================== -version toolchain +version toolchain ========= ================== -``5.6.1`` ``GCCcore/7.3.0`` -``5.7.3`` ``GCCcore/8.2.0`` +``5.6.1`` ``GCCcore/7.3.0`` +``5.7.3`` ``GCCcore/8.2.0`` ``6.0.2`` ``GCCcore/10.2.0`` ========= ================== @@ -49090,11 +51060,11 @@ UnZip is an extraction utility for archives compressed in .zip format (also call *homepage*: http://www.info-zip.org/UnZip.html -======= ========================================================================================================================================================================================= -version toolchain -======= ========================================================================================================================================================================================= -``6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` -======= ========================================================================================================================================================================================= +======= ============================================================================================================================================================================================================= +version toolchain +======= ============================================================================================================================================================================================================= +``6.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``system`` +======= ============================================================================================================================================================================================================= .. _list_software_UQTk_357: @@ -49107,7 +51077,7 @@ The UQ Toolkit (UQTk) is a collection of libraries and tools for the quantifica *homepage*: https://www.sandia.gov/UQToolkit/ ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``3.1.0`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================= =============== @@ -49123,7 +51093,7 @@ USEARCH is a unique sequence analysis tool which offers search and clustering al *homepage*: http://www.drive5.com/usearch/index.html =================== =============== ========== -version versionsuffix toolchain +version versionsuffix toolchain =================== =============== ========== ``5.2.236`` ``-i86linux32`` ``system`` ``5.2.236-6.1.544`` ``-i86linux32`` ``system`` @@ -49142,7 +51112,7 @@ UShER is now a package consisting of a family of programs for rapid phylogeneti *homepage*: https://github.com/yatisht/usher ========= =============== -version toolchain +version toolchain ========= =============== ``0.4.1`` ``gompi/2020b`` ``0.5.0`` ``gompi/2021b`` @@ -49159,7 +51129,7 @@ USPEX (Universal Structure Predictor: Evolutionary Xtallography... and in Russi *homepage*: http://uspex-team.org/uspex/overview ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``9.4.4`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== @@ -49175,13 +51145,13 @@ utf8proc is a small, clean C library that provides Unicode normalization, case-f *homepage*: https://github.com/JuliaStrings/utf8proc ========= ======================================================== -version toolchain +version toolchain ========= ======================================================== -``2.2.0`` ``GCCcore/6.4.0`` -``2.3.0`` ``GCCcore/8.2.0`` +``2.2.0`` ``GCCcore/6.4.0`` +``2.3.0`` ``GCCcore/8.2.0`` ``2.5.0`` ``GCCcore/10.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``2.6.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` -``2.7.0`` ``GCCcore/11.3.0`` +``2.6.1`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` +``2.7.0`` ``GCCcore/11.3.0`` ========= ======================================================== @@ -49195,25 +51165,26 @@ Set of Linux utilities *homepage*: https://www.kernel.org/pub/linux/utils/util-linux ========== ====================================== -version toolchain +version toolchain ========== ====================================== -``2.27.1`` ``foss/2016a``, ``intel/2016a`` -``2.28`` ``foss/2016a``, ``intel/2016a`` -``2.28.1`` ``intel/2016b`` -``2.29`` ``foss/2016b``, ``intel/2016b`` -``2.29.2`` ``GCCcore/6.3.0``, ``intel/2017a`` -``2.30`` ``GCCcore/6.4.0`` -``2.30.1`` ``GCCcore/6.3.0``, ``foss/2017a`` -``2.31`` ``GCCcore/6.4.0`` -``2.31.1`` ``GCCcore/6.4.0`` -``2.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` -``2.32.1`` ``GCCcore/7.3.0`` -``2.33`` ``GCCcore/8.2.0`` -``2.34`` ``GCCcore/8.3.0`` -``2.35`` ``GCCcore/9.3.0`` +``2.27.1`` ``foss/2016a``, ``intel/2016a`` +``2.28`` ``foss/2016a``, ``intel/2016a`` +``2.28.1`` ``intel/2016b`` +``2.29`` ``foss/2016b``, ``intel/2016b`` +``2.29.2`` ``GCCcore/6.3.0``, ``intel/2017a`` +``2.30`` ``GCCcore/6.4.0`` +``2.30.1`` ``GCCcore/6.3.0``, ``foss/2017a`` +``2.31`` ``GCCcore/6.4.0`` +``2.31.1`` ``GCCcore/6.4.0`` +``2.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` +``2.32.1`` ``GCCcore/7.3.0`` +``2.33`` ``GCCcore/8.2.0`` +``2.34`` ``GCCcore/8.3.0`` +``2.35`` ``GCCcore/9.3.0`` ``2.36`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``2.37`` ``GCCcore/11.2.0`` -``2.38`` ``GCCcore/11.3.0`` +``2.37`` ``GCCcore/11.2.0`` +``2.38`` ``GCCcore/11.3.0`` +``2.38.1`` ``GCCcore/12.2.0`` ========== ====================================== @@ -49236,12 +51207,12 @@ R interface to Google's open source JavaScript engine *homepage*: https://cran.r-project.org/web/packages/V8/ ========= ============= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= =============================== -``2.2`` ``-R-3.5.1`` ``foss/2018b`` +``2.2`` ``-R-3.5.1`` ``foss/2018b`` ``2.3`` ``-R-3.6.0`` ``foss/2019a``, ``intel/2019a`` -``3.2.0`` ``-R-3.6.2`` ``foss/2019b`` -``3.4.0`` ``-R-4.0.0`` ``foss/2020a`` +``3.2.0`` ``-R-3.6.2`` ``foss/2019b`` +``3.4.0`` ``-R-4.0.0`` ``foss/2020a`` ========= ============= =============================== @@ -49255,7 +51226,7 @@ Vala is a programming language using modern high level abstractions without impo *homepage*: https://wiki.gnome.org/Projects/Vala ========== ================== -version toolchain +version toolchain ========== ================== ``0.52.4`` ``GCCcore/10.3.0`` ========== ================== @@ -49271,15 +51242,16 @@ Valgrind: Debugging and profiling tools *homepage*: https://valgrind.org ========== ================================================================================= -version toolchain +version toolchain ========== ================================================================================= -``3.11.0`` ``foss/2016a``, ``intel/2016a`` +``3.11.0`` ``foss/2016a``, ``intel/2016a`` ``3.13.0`` ``foss/2017b``, ``foss/2018a``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` -``3.14.0`` ``foss/2018b`` -``3.16.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020a`` -``3.17.0`` ``gompi/2021a`` -``3.18.1`` ``gompi/2021b``, ``iimpi/2021b`` -``3.19.0`` ``gompi/2022a`` +``3.14.0`` ``foss/2018b`` +``3.16.1`` ``gompi/2019b``, ``gompi/2020a``, ``gompi/2020b``, ``iimpi/2020a`` +``3.17.0`` ``gompi/2021a`` +``3.18.1`` ``gompi/2021b``, ``iimpi/2021b`` +``3.19.0`` ``gompi/2022a`` +``3.20.0`` ``gompi/2022a`` ========== ================================================================================= @@ -49293,7 +51265,7 @@ The Vampir software tool provides an easy-to-use framework that enables develop *homepage*: http://www.vampir.eu ========= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========== ``8.4.1`` ``system`` ``8.4.1`` ``-demo`` ``system`` @@ -49310,7 +51282,7 @@ The Vampire Theorem Prover. *homepage*: https://vprover.github.io/ ========= ================== -version toolchain +version toolchain ========= ================== ``4.5.1`` ``GCCcore/10.2.0`` ========= ================== @@ -49326,7 +51298,7 @@ VarDict is an ultra sensitive variant caller for both single and paired sample *homepage*: https://github.com/AstraZeneca-NGS/VarDict ========= ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ ============== ``1.5.7`` ``-Perl-5.28.0`` ``foss/2018b`` ========= ================ ============== @@ -49342,7 +51314,7 @@ Variant tools is a software tool for the manipulation, annotation, selection, si *homepage*: https://vatlab.github.io/vat-docs/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``3.1.3`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -49358,7 +51330,7 @@ VariantMetaCaller automatically integrates variant calling pipelines into a bett *homepage*: http://bioinformatics.mit.bme.hu/VariantMetaCaller/ ======= =============== -version toolchain +version toolchain ======= =============== ``1.0`` ``intel/2017a`` ======= =============== @@ -49374,7 +51346,7 @@ Variant calling and somatic mutation/CNV detection for next-generation sequencin *homepage*: https://github.com/dkoboldt/varscan ========= ================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ========== ``2.3.6`` ``-Java-1.7.0_80`` ``system`` ``2.4.1`` ``-Java-1.7.0_80`` ``system`` @@ -49393,7 +51365,7 @@ Command line utility that provides tools for processing and analyzing astronom *homepage*: https://www.astro.princeton.edu/~jhartman/vartools.html ======== =============================== -version toolchain +version toolchain ======== =============================== ``1.35`` ``foss/2016b``, ``intel/2016b`` ======== =============================== @@ -49409,7 +51381,7 @@ The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic *homepage*: http://www.vasp.at ========= ========================= -version toolchain +version toolchain ========= ========================= ``5.4.1`` ``intel/2016.02-GCC-4.9`` ========= ========================= @@ -49425,7 +51397,7 @@ VAtools is a python package that includes several tools to annotate VCF files w *homepage*: https://vatools.readthedocs.io/en/latest/ ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``3.0.1`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== @@ -49441,7 +51413,7 @@ An awk-like VCF parser *homepage*: https://github.com/cc2qe/vawk ========= ================== ================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ================== ``0.0.1`` ``-Python-2.7.18`` ``GCCcore/10.2.0`` ========= ================== ================== @@ -49457,7 +51429,7 @@ VBZ compression HDF5 plugin for nanopolish *homepage*: https://github.com/nanoporetech/vbz_compression ========= =============== -version toolchain +version toolchain ========= =============== ``1.0.1`` ``gompi/2020b`` ========= =============== @@ -49473,7 +51445,7 @@ VCF-kit is a command-line based collection of utilities for performing analysis *homepage*: https://github.com/AndersenLab/VCF-kit ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``0.1.6`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============== @@ -49489,11 +51461,12 @@ vcflib provides methods to manipulate and interpret sequence variation as it can *homepage*: https://github.com/vcflib/vcflib ========= ================= ============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============================== ``1.0.2`` ``GCC/10.2.0``, ``GCC/10.3.0`` -``1.0.2`` ``-Python-3.8.2`` ``GCC/9.3.0`` -``1.0.3`` ``-R-4.1.2`` ``foss/2021b`` +``1.0.2`` ``-Python-3.8.2`` ``GCC/9.3.0`` +``1.0.3`` ``-R-4.1.0`` ``foss/2021a`` +``1.0.3`` ``-R-4.1.2`` ``foss/2021b`` ========= ================= ============================== @@ -49507,7 +51480,7 @@ Load data from a VCF (variant call format) file into numpy arrays, and (option *homepage*: https://github.com/alimanfoo/vcfnp ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.3.0`` ``-Python-2.7.11`` ``foss/2016a`` ========= ================== ============== @@ -49523,14 +51496,14 @@ The aim of VCFtools is to provide easily accessible methods for working with c *homepage*: https://vcftools.github.io ========== ================ ===================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================ ===================================================================================================================== -``0.1.14`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` -``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` -``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` +``0.1.14`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` +``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` +``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` ``0.1.16`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/11.3.0``, ``GCC/8.3.0``, ``GCC/9.3.0``, ``iccifort/2019.5.281`` -``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` +``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` ========== ================ ===================================================================================================================== @@ -49544,7 +51517,7 @@ VEGAS (Versatile Gene-based Association Study) is a free program for performing *homepage*: http://gump.qimr.edu.au/VEGAS/ ========== ========== -version toolchain +version toolchain ========== ========== ``0.8.27`` ``system`` ========== ========== @@ -49560,9 +51533,9 @@ Velocyto is a library for the analysis of RNA velocity. *homepage*: https://velocyto.org/velocyto.py/ =========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================= =============== -``0.17.17`` ``foss/2021a`` +``0.17.17`` ``foss/2021a`` ``0.17.17`` ``-Python-3.8.2`` ``intel/2020a`` =========== ================= =============== @@ -49577,10 +51550,10 @@ Sequence assembler for very short reads *homepage*: http://www.ebi.ac.uk/~zerbino/velvet/ ========== ================ ============================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========== ================ ============================================================= ``1.2.10`` ``-mt-kmer_191`` ``GCC/11.2.0``, ``GCC/8.3.0``, ``foss/2018a``, ``foss/2018b`` -``1.2.10`` ``-mt-kmer_37`` ``intel/2017a`` +``1.2.10`` ``-mt-kmer_37`` ``intel/2017a`` ========== ================ ============================================================= @@ -49594,16 +51567,16 @@ Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, in *homepage*: https://www.ensembl.org/info/docs/tools/vep ========= ================ =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================ =============================== -``93.4`` ``-Perl-5.26.1`` ``intel/2018a`` -``94.0`` ``-Perl-5.28.0`` ``foss/2018b`` +``93.4`` ``-Perl-5.26.1`` ``intel/2018a`` +``94.0`` ``-Perl-5.28.0`` ``foss/2018b`` ``94.5`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``95.0`` ``-Perl-5.28.0`` ``foss/2018b`` -``96.0`` ``-Perl-5.28.1`` ``foss/2019a`` -``103.1`` ``GCC/10.2.0`` -``105`` ``GCC/11.2.0`` -``107`` ``GCC/11.3.0`` +``95.0`` ``-Perl-5.28.0`` ``foss/2018b`` +``96.0`` ``-Perl-5.28.1`` ``foss/2019a`` +``103.1`` ``GCC/10.2.0`` +``105`` ``GCC/11.2.0`` +``107`` ``GCC/11.3.0`` ========= ================ =============================== @@ -49617,7 +51590,7 @@ verifyBamID is a software that verifies whether the reads in particular file mat *homepage*: http://csg.sph.umich.edu/kang/verifyBamID/index.html ========= ============== -version toolchain +version toolchain ========= ============== ``1.1.3`` ``foss/2016a`` ========= ============== @@ -49633,7 +51606,7 @@ A versatile and efficient RNA-Seq read counting tool *homepage*: https://github.com/qinzhu/VERSE ========= ============== -version toolchain +version toolchain ========= ============== ``0.1.5`` ``foss/2016b`` ========= ============== @@ -49649,7 +51622,7 @@ VESTA is a 3D visualization program for structured models, volumetric data su *homepage*: http://www.jp-minerals.org/vesta ========= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========== ``3.5.8`` ``-gtk3`` ``system`` ========= ============= ========== @@ -49665,16 +51638,16 @@ The Vienna RNA Package consists of a C code library and several stand-alone prog *homepage*: https://www.tbi.univie.ac.at/RNA/ ========== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============================== -``2.2.3`` ``intel/2016b`` -``2.3.4`` ``foss/2016b`` -``2.3.5`` ``intel/2017a`` +``2.2.3`` ``intel/2016b`` +``2.3.4`` ``foss/2016b`` +``2.3.5`` ``intel/2017a`` ``2.4.10`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` -``2.4.11`` ``-Python-3.6.6`` ``foss/2018b`` -``2.4.14`` ``-Python-3.6.6`` ``foss/2018b`` -``2.5.0`` ``foss/2021b`` -``2.5.1`` ``foss/2021b`` +``2.4.11`` ``-Python-3.6.6`` ``foss/2018b`` +``2.4.14`` ``-Python-3.6.6`` ``foss/2018b`` +``2.5.0`` ``foss/2021b`` +``2.5.1`` ``foss/2021b`` ========== ================== =============================== @@ -49687,13 +51660,14 @@ Vim is an advanced text editor that seeks to provide the power of the de-facto *homepage*: http://www.vim.org -============ ================== ================= -version versionsuffix toolchain -============ ================== ================= -``8.0`` ``-Python-2.7.11`` ``foss/2016a`` -``8.1.0483`` ``-Python-2.7.15`` ``foss/2018b`` +============ ================== ================== +version versionsuffix toolchain +============ ================== ================== +``8.0`` ``-Python-2.7.11`` ``foss/2016a`` +``8.1.0483`` ``-Python-2.7.15`` ``foss/2018b`` ``8.1.1209`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` -============ ================== ================= +``9.0.0950`` ``GCCcore/11.3.0`` +============ ================== ================== .. _list_software_VirSorter_944: @@ -49706,7 +51680,7 @@ VirSorter: mining viral signal from microbial genomic data. *homepage*: https://github.com/simroux/VirSorter ============ ================ ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================ ============== ``20160601`` ``-Perl-5.22.1`` ``foss/2016a`` ============ ================ ============== @@ -49722,11 +51696,11 @@ VirtualGL is an open source toolkit that gives any Linux or Unix remote display *homepage*: https://virtualgl.org/ ========= ================= -version toolchain +version toolchain ========= ================= -``2.6.1`` ``foss/2018b`` +``2.6.1`` ``foss/2018b`` ``2.6.2`` ``GCCcore/9.3.0`` -``3.0`` ``GCC/11.2.0`` +``3.0`` ``GCC/11.2.0`` ========= ================= @@ -49740,7 +51714,7 @@ Virtuoso is a high-performance and scalable Multi-Model RDBMS, Data Integration *homepage*: https://github.com/openlink/virtuoso-opensource =========== ============== -version toolchain +version toolchain =========== ============== ``7.2.6.1`` ``GCC/10.3.0`` =========== ============== @@ -49756,7 +51730,7 @@ VisPy is a high-performance interactive 2D/3D data visualization library levera *homepage*: https://vispy.org ========= =============================== -version toolchain +version toolchain ========= =============================== ``0.6.6`` ``foss/2020b``, ``intel/2020b`` ========= =============================== @@ -49772,14 +51746,14 @@ VMD is a molecular visualization program for displaying, animating, and analyzin *homepage*: https://www.ks.uiuc.edu/Research/vmd ============ ================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== ================================== -``1.9.3`` ``-Python-2.7.12`` ``intel/2016b`` -``1.9.3`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2018a`` -``1.9.3`` ``-Python-2.7.15`` ``intel/2018b`` -``1.9.4a43`` ``-Python-3.7.4`` ``fosscuda/2019b`` +``1.9.3`` ``-Python-2.7.12`` ``intel/2016b`` +``1.9.3`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2018a`` +``1.9.3`` ``-Python-2.7.15`` ``intel/2018b`` +``1.9.4a43`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``1.9.4a51`` ``foss/2020b``, ``fosscuda/2020b`` -``1.9.4a57`` ``foss/2022a`` +``1.9.4a57`` ``foss/2022a`` ============ ================== ================================== @@ -49793,7 +51767,7 @@ vmtk is a collection of libraries and tools for 3D reconstruction, geometric ana *homepage*: https://vmtk.org ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.4.0`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================= ============== @@ -49809,7 +51783,7 @@ CUDA-accelerated numpy 3D affine transformations *homepage*: https://github.com/the-lay/voltools ========= ============== -version toolchain +version toolchain ========= ============== ``0.4.2`` ``foss/2020b`` ========= ============== @@ -49825,7 +51799,7 @@ Command-line tools for creating and playing Ogg Vorbis files. *homepage*: https://xiph.org/vorbis/ ========= ========================================================== -version toolchain +version toolchain ========= ========================================================== ``1.4.2`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ========= ========================================================== @@ -49841,7 +51815,7 @@ Voro++ is a software library for carrying out three-dimensional computations of *homepage*: http://math.lbl.gov/voro++/ ========= ================================================================================================================================================================== -version toolchain +version toolchain ========= ================================================================================================================================================================== ``0.4.6`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/6.4.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2019b``, ``intel/2016a``, ``intel/2019b`` ========= ================================================================================================================================================================== @@ -49857,21 +51831,21 @@ Basic Python libraries used by UGent's HPC group *homepage*: http://hpcugent.github.com/vsc-base/ ========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== =============== -``1.6.9`` ``system`` -``1.7.3`` ``system`` -``2.0.4`` ``system`` -``2.1.2`` ``system`` -``2.4.2`` ``system`` +``1.6.9`` ``system`` +``1.7.3`` ``system`` +``2.0.4`` ``system`` +``2.1.2`` ``system`` +``2.4.2`` ``system`` ``2.4.17`` ``-Python-2.7.11`` ``intel/2016a`` -``2.5.1`` ``system`` +``2.5.1`` ``system`` ``2.5.1`` ``-Python-2.7.11`` ``intel/2016a`` ``2.5.1`` ``-Python-2.7.12`` ``intel/2016b`` -``2.5.8`` ``system`` -``2.8.0`` ``system`` -``2.8.1`` ``system`` -``2.8.3`` ``system`` +``2.5.8`` ``system`` +``2.8.0`` ``system`` +``2.8.1`` ``system`` +``2.8.3`` ``system`` ========== ================== =============== @@ -49885,17 +51859,17 @@ vsc-install provides shared setuptools functions and classes for Python librarie *homepage*: https://pypi.python.org/pypi/vsc-install =========== ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================== =============== ``0.9.18`` ``-Python-2.7.11`` ``intel/2016a`` -``0.10.6`` ``system`` +``0.10.6`` ``system`` ``0.10.6`` ``-Python-2.7.11`` ``intel/2016a`` ``0.10.11`` ``-Python-2.7.11`` ``intel/2016a`` ``0.10.11`` ``-Python-2.7.12`` ``intel/2016b`` -``0.10.25`` ``system`` -``0.10.26`` ``system`` -``0.11.1`` ``system`` -``0.11.2`` ``system`` +``0.10.25`` ``system`` +``0.10.26`` ``system`` +``0.11.1`` ``system`` +``0.11.2`` ``system`` =========== ================== =============== @@ -49909,35 +51883,35 @@ mympirun is a tool to make it easier for users of HPC clusters to run MPI progra *homepage*: https://github.com/hpcugent/vsc-mympirun =========== ================================== =============== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================================== =============== -``3.2.1`` ``system`` -``3.3.0`` ``system`` -``3.4.2`` ``system`` +``3.2.1`` ``system`` +``3.3.0`` ``system`` +``3.4.2`` ``system`` ``3.4.2`` ``-Python-2.7.11-vsc-base-2.4.17`` ``intel/2016a`` ``3.4.2`` ``-Python-2.7.11-vsc-base-2.5.1`` ``intel/2016a`` -``3.4.2`` ``-vsc-base-2.4.2`` ``system`` +``3.4.2`` ``-vsc-base-2.4.2`` ``system`` ``3.4.3`` ``-Python-2.7.12`` ``intel/2016b`` -``4.0.0`` ``system`` -``4.0.0b0`` ``system`` -``4.0.1`` ``system`` -``4.0.2`` ``system`` -``4.1.4`` ``system`` -``4.1.5`` ``system`` -``4.1.6`` ``system`` -``4.1.8`` ``system`` -``4.1.9`` ``system`` -``5.1.0`` ``system`` -``5.2.0`` ``system`` -``5.2.2`` ``system`` -``5.2.3`` ``system`` -``5.2.4`` ``system`` -``5.2.5`` ``system`` -``5.2.6`` ``system`` -``5.2.7`` ``system`` -``5.2.9`` ``system`` -``5.2.10`` ``system`` -``5.2.11`` ``system`` +``4.0.0`` ``system`` +``4.0.0b0`` ``system`` +``4.0.1`` ``system`` +``4.0.2`` ``system`` +``4.1.4`` ``system`` +``4.1.5`` ``system`` +``4.1.6`` ``system`` +``4.1.8`` ``system`` +``4.1.9`` ``system`` +``5.1.0`` ``system`` +``5.2.0`` ``system`` +``5.2.2`` ``system`` +``5.2.3`` ``system`` +``5.2.4`` ``system`` +``5.2.5`` ``system`` +``5.2.6`` ``system`` +``5.2.7`` ``system`` +``5.2.9`` ``system`` +``5.2.10`` ``system`` +``5.2.11`` ``system`` =========== ================================== =============== @@ -49951,7 +51925,7 @@ VSC-tools is a set of Python libraries and scripts that are commonly used within *homepage*: http://hpcugent.github.com/vsc-mympirun/ ========= ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============== ``3.4.1`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== @@ -49967,7 +51941,7 @@ vsc-processcontrol is a module to abstract process control like scheduler settin *homepage*: http://hpcugent.github.com/vsc-processcontrol/ ======= =================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ======= =================== ========== ``1.0`` ``system`` ``1.0`` ``-vsc-base-2.1.2`` ``system`` @@ -49984,13 +51958,13 @@ VSEARCH supports de novo and reference based chimera detection, clustering, ful *homepage*: https://github.com/torognes/vsearch ========== ======================================== -version toolchain +version toolchain ========== ======================================== -``2.9.1`` ``foss/2018b`` +``2.9.1`` ``foss/2018b`` ``2.13.4`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` -``2.15.0`` ``GCC/9.3.0`` -``2.18.0`` ``GCC/10.2.0`` -``2.21.1`` ``GCC/10.3.0`` +``2.15.0`` ``GCC/9.3.0`` +``2.18.0`` ``GCC/10.2.0`` +``2.21.1`` ``GCC/10.3.0`` ========== ======================================== @@ -50004,7 +51978,7 @@ A tool set for short variant discovery in genetic sequence data. *homepage*: http://genome.sph.umich.edu/wiki/Vt =========== ============================================================================= -version toolchain +version toolchain =========== ============================================================================= ``0.57721`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``GCC/9.3.0``, ``foss/2018b`` =========== ============================================================================= @@ -50020,27 +51994,28 @@ The Visualization Toolkit (VTK) is an open-source, freely available software sys *homepage*: https://www.vtk.org ============= ================== =================================================== -version versionsuffix toolchain +version versionsuffix toolchain ============= ================== =================================================== -``6.3.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``6.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``7.0.0`` ``-Python-2.7.12`` ``intel/2016b`` -``7.1.0`` ``-Python-2.7.12`` ``intel/2016b`` -``7.1.1`` ``-Python-2.7.13`` ``intel/2017a`` -``8.0.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` -``8.1.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` -``8.1.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` -``8.1.1`` ``-Python-2.7.15`` ``foss/2018b`` -``8.1.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` -``8.2.0`` ``foss/2021a`` -``8.2.0`` ``-Python-2.7.15`` ``foss/2019a`` -``8.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` -``8.2.0`` ``-Python-3.7.4`` ``foss/2019b`` +``6.3.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` +``6.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` +``7.0.0`` ``-Python-2.7.12`` ``intel/2016b`` +``7.1.0`` ``-Python-2.7.12`` ``intel/2016b`` +``7.1.1`` ``-Python-2.7.13`` ``intel/2017a`` +``8.0.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` +``8.1.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` +``8.1.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` +``8.1.1`` ``-Python-2.7.15`` ``foss/2018b`` +``8.1.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``8.2.0`` ``foss/2021a`` +``8.2.0`` ``-Python-2.7.15`` ``foss/2019a`` +``8.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` +``8.2.0`` ``-Python-3.7.4`` ``foss/2019b`` ``8.2.0`` ``-Python-3.8.2`` ``foss/2020a``, ``fosscuda/2020a``, ``intel/2020a`` -``9.0.1`` ``foss/2020b``, ``foss/2021a`` -``9.1.0`` ``foss/2021b`` -``9.2.0.rc2`` ``foss/2022a`` +``9.0.1`` ``foss/2020b``, ``foss/2021a`` +``9.1.0`` ``foss/2021b`` +``9.2.0.rc2`` ``foss/2022a`` +``9.2.2`` ``foss/2022a`` ============= ================== =================================================== @@ -50054,7 +52029,7 @@ Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, For *homepage*: https://software.intel.com/en-us/vtune ================= ========== -version toolchain +version toolchain ================= ========== ``2013_update6`` ``system`` ``2013_update8`` ``system`` @@ -50092,7 +52067,7 @@ VV is an open-source and cross platform image viewer, designed for fast and sim *homepage*: https://www.creatis.insa-lyon.fr/rio/vv ============== ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============== ================= ============== ``2018.09.19`` ``-Python-3.6.6`` ``foss/2018b`` ============== ================= ============== @@ -50108,7 +52083,7 @@ A multi-platform collection of C++ software libraries for Computer Vision and Im *homepage*: https://sf.net/projects/vxl ========== ============== -version toolchain +version toolchain ========== ============== ``1.18.0`` ``foss/2018a`` ========== ============== @@ -50120,7 +52095,7 @@ version toolchain --- -:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_Wayland_720` - :ref:`list_software_Waylandpp_944` - :ref:`list_software_WCT_238` - :ref:`list_software_wcwidth_762` - :ref:`list_software_webin-cli_890` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wgsim_551` - :ref:`list_software_WHAM_301` - :ref:`list_software_WhatsHap_800` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` +:ref:`list_software_wandb_524` - :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_Wayland_720` - :ref:`list_software_Waylandpp_944` - :ref:`list_software_WCT_238` - :ref:`list_software_wcwidth_762` - :ref:`list_software_webin-cli_890` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wgsim_551` - :ref:`list_software_WHAM_301` - :ref:`list_software_WhatsHap_800` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WildMagic_881` - :ref:`list_software_Winnowmap_960` - :ref:`list_software_WisecondorX_1141` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_wpebackend-fdo_1402` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wtdbg2_586` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` .. _list_software_wandb_524: @@ -50132,11 +52107,13 @@ CLI and Python API for Weights and Biases (wandb), a tool for visualizing and tr *homepage*: https://www.wandb.com/ -========== ================= ================= -version versionsuffix toolchain -========== ================= ================= +========== ================= ================== +version versionsuffix toolchain +========== ================= ================== ``0.8.30`` ``-Python-3.7.4`` ``gcccuda/2019b`` -========== ================= ================= +``0.13.4`` ``GCCcore/11.3.0`` +``0.13.6`` ``GCC/11.3.0`` +========== ================= ================== .. _list_software_Wannier90_829: @@ -50149,13 +52126,13 @@ A tool for obtaining maximally-localised Wannier functions *homepage*: http://www.wannier.org =========== ============= ==================================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ============= ==================================================================================================================================================================== -``1.2`` ``intel/2016.02-GCC-4.9`` -``2.0.1`` ``intel/2016.02-GCC-4.9``, ``intel/2016a`` -``2.0.1.1`` ``-abinit`` ``intel/2018b`` -``2.1.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` -``3.0.0`` ``intel/2018b`` +``1.2`` ``intel/2016.02-GCC-4.9`` +``2.0.1`` ``intel/2016.02-GCC-4.9``, ``intel/2016a`` +``2.0.1.1`` ``-abinit`` ``intel/2018b`` +``2.1.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` +``3.0.0`` ``intel/2018b`` ``3.1.0`` ``foss/2020b``, ``foss/2021a``, ``foss/2021b``, ``foss/2022a``, ``gomkl/2021a``, ``intel/2020a``, ``intel/2020b``, ``intel/2021a``, ``intel/2021b``, ``intel/2022a`` =========== ============= ==================================================================================================================================================================== @@ -50170,7 +52147,7 @@ WannierTools is an open source software that studies the physical properties of *homepage*: http://www.wanniertools.com ========= =============== -version toolchain +version toolchain ========= =============== ``2.3.0`` ``intel/2018a`` ``2.5.1`` ``intel/2020b`` @@ -50186,12 +52163,12 @@ Wayland is a project to define a protocol for a compositor to talk to its clien *homepage*: https://wayland.freedesktop.org/ -========== ================== -version toolchain -========== ================== +========== ====================================== +version toolchain +========== ====================================== ``1.20.0`` ``GCCcore/11.3.0`` -``1.21.0`` ``GCCcore/11.2.0`` -========== ================== +``1.21.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========== ====================================== .. _list_software_Waylandpp_944: @@ -50199,15 +52176,15 @@ version toolchain *Waylandpp* +++++++++++ -Wayland is an object oriented display protocol, which features request and events. Requests can be seen as method calls on certain objects, whereas events can be seen as signals of an object. This makes the Wayland protocol a perfect candidate for a C++ binding. The goal of this library is to create such a C++ binding for Wayland using the most modern C++ technology currently available, providing an easy to use C++ API to Wayland. +Wayland is an object oriented display protocol, which features request and events. Requests can be seen as method calls on certain objects, whereas events can be seen as signals of an object. This makes the Wayland protocol a perfect candidate for a C++ binding. The goal of this library is to create such a C++ binding for Wayland using the most modern C++ technology currently available, providing an easy to use C++ API to Wayland. *homepage*: https://github.com/NilsBrause/waylandpp -========= ================== -version toolchain -========= ================== -``1.0.0`` ``GCCcore/11.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.0.0`` ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +========= ====================================== .. _list_software_WCT_238: @@ -50220,7 +52197,7 @@ NOAA's Weather and Climate Toolkit (WCT) is free, platform independent software *homepage*: https://www.ncdc.noaa.gov/wct/index.php ========= ============= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= ========== ``4.6.0`` ``-Java-11`` ``system`` ========= ============= ========== @@ -50236,12 +52213,12 @@ wcwidth is a low-level Python library to simplify Terminal emulation. *homepage*: https://github.com/jquast/wcwidth ========= ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== =============================== -``0.1.7`` ``-Python-2.7.11`` ``foss/2016a`` +``0.1.7`` ``-Python-2.7.11`` ``foss/2016a`` ``0.1.7`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``0.1.7`` ``-Python-3.5.1`` ``foss/2016a`` -``0.1.7`` ``-Python-3.5.2`` ``intel/2016b`` +``0.1.7`` ``-Python-3.5.1`` ``foss/2016a`` +``0.1.7`` ``-Python-3.5.2`` ``intel/2016b`` ========= ================== =============================== @@ -50255,7 +52232,7 @@ The Webin command line submission interface can be used to validate, upload and *homepage*: https://github.com/enasequence/webin-cli ========= ========== -version toolchain +version toolchain ========= ========== ``1.8.9`` ``system`` ========= ========== @@ -50266,15 +52243,16 @@ version toolchain *WebKitGTK+* ++++++++++++ -WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers. It offers WebKit’s full functionality and is useful in a wide range of systems from desktop computers to embedded systems like phones, tablets, and televisions. +WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers. It offers WebKit's full functionality and is useful in a wide range of systems from desktop computers to embedded systems like phones, tablets, and televisions. *homepage*: https://webkitgtk.org/ ========== ============================= -version toolchain +version toolchain ========== ============================= -``2.24.1`` ``GCC/8.2.0-2.31.1`` +``2.24.1`` ``GCC/8.2.0-2.31.1`` ``2.27.4`` ``GCC/10.3.0``, ``GCC/8.3.0`` +``2.37.1`` ``GCC/11.2.0`` ========== ============================= @@ -50288,7 +52266,7 @@ WebSocket++ is an open source (BSD license) header only C++ library that implem *homepage*: https://www.zaphoyd.com/websocketpp/ ========= =============== -version toolchain +version toolchain ========= =============== ``0.8.1`` ``gompi/2019a`` ========= =============== @@ -50304,7 +52282,7 @@ Weka is a collection of machine learning algorithms for data mining tasks. The *homepage*: http://www.cs.waikato.ac.nz/ml/weka/index.html ========== ================== ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ========== ``3.6.12`` ``-Java-1.7.0_80`` ``system`` ``3.7.0`` ``-Java-1.7.0_80`` ``system`` @@ -50321,14 +52299,14 @@ GNU Wget is a free software package for retrieving files using HTTP, HTTPS and F *homepage*: https://www.gnu.org/software/wget ========== ===================================== -version toolchain +version toolchain ========== ===================================== -``1.17.1`` ``foss/2016a``, ``foss/2016b`` -``1.19.4`` ``GCCcore/6.4.0`` -``1.20.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` +``1.17.1`` ``foss/2016a``, ``foss/2016b`` +``1.19.4`` ``GCCcore/6.4.0`` +``1.20.1`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ``1.20.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``1.21.1`` ``GCCcore/10.3.0`` -``1.21.2`` ``GCCcore/11.2.0`` +``1.21.1`` ``GCCcore/10.3.0`` +``1.21.2`` ``GCCcore/11.2.0`` ========== ===================================== @@ -50342,7 +52320,7 @@ Wgsim is a small tool for simulating sequence reads from a reference genome. *homepage*: https://github.com/lh3/wgsim/ ============ ============================== -version toolchain +version toolchain ============ ============================== ``20111017`` ``GCC/10.2.0``, ``GCC/11.2.0`` ============ ============================== @@ -50358,7 +52336,7 @@ An implementation of WHAM: the Weighted Histogram Analysis Method *homepage*: http://membrane.urmc.rochester.edu/?page_id=126 ============ ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= =============== ``2.0.9.1`` ``intel/2019a`` ``2.0.9.1`` ``-kj_mol`` ``intel/2019a`` @@ -50377,10 +52355,10 @@ WhatsHap is a software for phasing genomic variants using DNA sequencing reads, *homepage*: https://whatshap.readthedocs.io ======= ============================== -version toolchain +version toolchain ======= ============================== ``1.1`` ``foss/2020b``, ``foss/2021a`` -``1.4`` ``foss/2021b`` +``1.4`` ``foss/2021b`` ======= ============================== @@ -50394,17 +52372,17 @@ A built-package format for Python. *homepage*: https://pypi.python.org/pypi/wheel ========== ================== ======================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================== ======================================================================== -``0.29.0`` ``-Python-2.7.11`` ``foss/2016a`` -``0.29.0`` ``-Python-3.5.1`` ``foss/2016a`` +``0.29.0`` ``-Python-2.7.11`` ``foss/2016a`` +``0.29.0`` ``-Python-3.5.1`` ``foss/2016a`` ``0.30.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``0.30.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` -``0.30.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` -``0.31.0`` ``-Python-2.7.14`` ``fosscuda/2018a``, ``intel/2018a`` -``0.31.0`` ``-Python-3.6.4`` ``foss/2018a``, ``fosscuda/2018a`` -``0.31.1`` ``-Python-2.7.15`` ``fosscuda/2018b`` -``0.31.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` +``0.30.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` +``0.31.0`` ``-Python-2.7.14`` ``fosscuda/2018a``, ``intel/2018a`` +``0.31.0`` ``-Python-3.6.4`` ``foss/2018a``, ``fosscuda/2018a`` +``0.31.1`` ``-Python-2.7.15`` ``fosscuda/2018b`` +``0.31.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ========== ================== ======================================================================== @@ -50418,13 +52396,13 @@ The program package WIEN2k allows to perform electronic structure calculations o *homepage*: http://www.wien2k.at/ ======== ================================================ -version toolchain +version toolchain ======== ================================================ ``17.1`` ``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` ``18.1`` ``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` -``19.1`` ``intel/2019a`` -``19.2`` ``intel/2020b`` -``21.1`` ``intel/2021a`` +``19.1`` ``intel/2019a`` +``19.2`` ``intel/2020b`` +``21.1`` ``intel/2021a`` ======== ================================================ @@ -50438,7 +52416,7 @@ Wild Magic 5.17 *homepage*: https://www.geometrictools.com/index.html ======== ================================== -version toolchain +version toolchain ======== ================================== ``5.17`` ``GCCcore/10.3.0``, ``foss/2018b`` ======== ================================== @@ -50454,7 +52432,7 @@ Winnowmap is a long-read mapping algorithm, and a result of our exploration int *homepage*: https://github.com/marbl/Winnowmap ======= ============= -version toolchain +version toolchain ======= ============= ``1.0`` ``GCC/8.3.0`` ======= ============= @@ -50470,7 +52448,7 @@ WisecondorX -- an evolved WISECONDOR *homepage*: https://github.com/CenterForMedicalGeneticsGhent/WisecondorX ========= ================= ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ============== ``1.1.6`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= ============== @@ -50486,7 +52464,7 @@ A within-sample comparison approach to detect copy number variations in whole ex *homepage*: https://github.com/VUmcCGP/wisexome ============ ================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============== ``20180517`` ``-Python-2.7.14`` ``intel/2018a`` ============ ================== =============== @@ -50502,7 +52480,7 @@ wkhtmltopdf and wkhtmltoimage are open source (LGPLv3) command line tools to ren *homepage*: http://wkhtmltopdf.org/ ========== ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= ========== ``0.12.3`` ``-Linux-x86_64`` ``system`` ========== ================= ========== @@ -50518,22 +52496,38 @@ The Worker framework has been developed to help deal with parameter exploration *homepage*: https://github.com/gjbex/worker ========== ================ ============================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================ ============================== -``1.6.4`` ``intel/2016a`` -``1.6.5`` ``intel/2016a`` -``1.6.6`` ``intel/2016b`` -``1.6.7`` ``-intel-2016b`` ``system`` -``1.6.7`` ``-intel-2017a`` ``system`` -``1.6.7`` ``-intel-2017b`` ``system`` -``1.6.8`` ``-intel-2018a`` ``system`` -``1.6.8`` ``-intel-2018b`` ``system`` -``1.6.11`` ``intel/2019b`` +``1.6.4`` ``intel/2016a`` +``1.6.5`` ``intel/2016a`` +``1.6.6`` ``intel/2016b`` +``1.6.7`` ``-intel-2016b`` ``system`` +``1.6.7`` ``-intel-2017a`` ``system`` +``1.6.7`` ``-intel-2017b`` ``system`` +``1.6.8`` ``-intel-2018a`` ``system`` +``1.6.8`` ``-intel-2018b`` ``system`` +``1.6.11`` ``intel/2019b`` ``1.6.12`` ``foss/2019a``, ``foss/2021b`` -``1.6.13`` ``iimpi/2021b`` +``1.6.13`` ``iimpi/2021b`` ========== ================ ============================== +.. _list_software_wpebackend-fdo_1402: + +*wpebackend-fdo* +++++++++++++++++ + +WPE WebKit allows embedders to create simple and performant systems based on Web platform technologies. It is a WebKit port designed with flexibility and hardware acceleration in mind, leveraging common 3D graphics APIs for best performance. + +*homepage*: https://wpewebkit.org/ + +========== ================== +version toolchain +========== ================== +``1.13.1`` ``GCCcore/11.2.0`` +========== ================== + + .. _list_software_WPS_250: *WPS* @@ -50544,15 +52538,16 @@ WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WR *homepage*: http://www.wrf-model.org ========= ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= =============== ``3.8.0`` ``-dmpar`` ``intel/2016a`` -``3.9.1`` ``-dmpar`` ``foss/2020b`` +``3.9.1`` ``-dmpar`` ``foss/2020b`` ``4.0.1`` ``-dmpar`` ``intel/2018b`` -``4.0.2`` ``-dmpar`` ``foss/2018b`` +``4.0.2`` ``-dmpar`` ``foss/2018b`` ``4.1`` ``-dmpar`` ``intel/2019b`` -``4.2`` ``-dmpar`` ``foss/2020b`` -``4.3.1`` ``-dmpar`` ``foss/2021a`` +``4.2`` ``-dmpar`` ``foss/2020b`` +``4.3.1`` ``-dmpar`` ``foss/2021a`` +``4.4`` ``-dmpar`` ``foss/2022a`` ========= ============= =============== @@ -50566,16 +52561,17 @@ The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale *homepage*: https://www.wrf-model.org =========== ============= ================================================================ -version versionsuffix toolchain +version versionsuffix toolchain =========== ============= ================================================================ -``3.8.0`` ``-dmpar`` ``intel/2016a``, ``intel/2016b`` +``3.8.0`` ``-dmpar`` ``intel/2016a``, ``intel/2016b`` ``3.9.1.1`` ``-dmpar`` ``foss/2020a``, ``foss/2020b``, ``intel/2020a``, ``intel/2020b`` -``4.0.1`` ``-dmpar`` ``intel/2018b`` -``4.0.2`` ``-dmpar`` ``foss/2018b`` -``4.1.3`` ``-dm+sm`` ``intel/2019b`` -``4.1.3`` ``-dmpar`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b`` -``4.2.2`` ``-dmpar`` ``foss/2020b`` -``4.3`` ``-dmpar`` ``foss/2021a`` +``4.0.1`` ``-dmpar`` ``intel/2018b`` +``4.0.2`` ``-dmpar`` ``foss/2018b`` +``4.1.3`` ``-dm+sm`` ``intel/2019b`` +``4.1.3`` ``-dmpar`` ``foss/2019b``, ``foss/2020a``, ``intel/2019b`` +``4.2.2`` ``-dmpar`` ``foss/2020b`` +``4.3`` ``-dmpar`` ``foss/2021a`` +``4.4`` ``-dmpar`` ``foss/2022a`` =========== ============= ================================================================ @@ -50589,7 +52585,7 @@ WRF-Fire combines the Weather Research and Forecasting model (WRF) with a fire c *homepage*: http://www.openwfm.org/wiki/WRF-SFIRE ============ ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= =============== ``20170221`` ``-dmpar`` ``intel/2016b`` ============ ============= =============== @@ -50605,7 +52601,7 @@ A collection of diagnostic and interpolation routines for use with output from *homepage*: https://wrf-python.readthedocs.io ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``1.2.0`` ``-Python-3.6.4`` ``intel/2018a`` ``1.3.1`` ``-Python-3.6.6`` ``intel/2018b`` @@ -50622,9 +52618,9 @@ Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio *homepage*: https://github.com/ruanjue/wtdbg2 ======= ===================================== -version toolchain +version toolchain ======= ===================================== -``2.3`` ``GCC/7.3.0-2.30`` +``2.3`` ``GCC/7.3.0-2.30`` ``2.5`` ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ======= ===================================== @@ -50639,7 +52635,7 @@ wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is *homepage*: http://wxpropgrid.sourceforge.net/ ========== ============= -version toolchain +version toolchain ========== ============= ``1.4.15`` ``GCC/4.9.2`` ========== ============= @@ -50655,17 +52651,18 @@ Wraps the wxWidgets C++ toolkit and provides access to the user interface portio *homepage*: https://www.wxpython.org/ =============== ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain =============== ================== =============================== ``3.0.2.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` -``3.0.2.0`` ``-Python-2.7.12`` ``intel/2016b`` -``3.0.2.0`` ``-Python-2.7.13`` ``intel/2017a`` -``3.0.2.0`` ``-Python-2.7.14`` ``intel/2017b`` -``3.0.2.0`` ``-Python-2.7.15`` ``foss/2018b`` -``4.0.4`` ``-Python-2.7.15`` ``GCC/8.2.0-2.31.1`` -``4.0.4`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` -``4.0.7.post2`` ``-Python-3.7.4`` ``GCC/8.3.0`` -``4.1.1`` ``foss/2021a`` +``3.0.2.0`` ``-Python-2.7.12`` ``intel/2016b`` +``3.0.2.0`` ``-Python-2.7.13`` ``intel/2017a`` +``3.0.2.0`` ``-Python-2.7.14`` ``intel/2017b`` +``3.0.2.0`` ``-Python-2.7.15`` ``foss/2018b`` +``4.0.4`` ``-Python-2.7.15`` ``GCC/8.2.0-2.31.1`` +``4.0.4`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` +``4.0.7.post2`` ``-Python-3.7.4`` ``GCC/8.3.0`` +``4.1.1`` ``foss/2021a`` +``4.2.0`` ``foss/2021b`` =============== ================== =============================== @@ -50679,14 +52676,15 @@ wxWidgets is a C++ library that lets developers create applications for Windows, *homepage*: https://www.wxwidgets.org ========= ============================== -version toolchain +version toolchain ========= ============================== -``3.0.3`` ``foss/2018a`` -``3.0.4`` ``GCC/8.2.0-2.31.1`` -``3.1.3`` ``GCC/8.3.0`` -``3.1.4`` ``GCC/10.2.0`` +``3.0.3`` ``foss/2018a`` +``3.0.4`` ``GCC/8.2.0-2.31.1`` +``3.1.3`` ``GCC/8.3.0`` +``3.1.4`` ``GCC/10.2.0`` ``3.1.5`` ``GCC/10.3.0``, ``GCC/11.2.0`` -``3.2.1`` ``GCC/11.3.0`` +``3.2.0`` ``GCC/11.2.0`` +``3.2.1`` ``GCC/11.3.0`` ========= ============================== @@ -50696,7 +52694,7 @@ version toolchain --- -:ref:`list_software_X11_186` - :ref:`list_software_x13as_432` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_XGrafix_697` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-Compile_999` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_XPLOR-NIH_673` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtensor_787` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_xxd_340` - :ref:`list_software_xxHash_628` - :ref:`list_software_XZ_178` +:ref:`list_software_X11_186` - :ref:`list_software_x13as_432` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_XALT_313` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCFun_452` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xESMF_419` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_XGrafix_697` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XlsxWriter_1068` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_xmitgcm_761` - :ref:`list_software_XML-Compile_999` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_XPLOR-NIH_673` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtb_334` - :ref:`list_software_xtensor_787` - :ref:`list_software_xtrans_672` - :ref:`list_software_Xvfb_406` - :ref:`list_software_xxd_340` - :ref:`list_software_xxHash_628` - :ref:`list_software_XZ_178` .. _list_software_X11_186: @@ -50709,21 +52707,22 @@ The X Window System (X11) is a windowing system for bitmap displays *homepage*: https://www.x.org ============ ================================================== -version toolchain +version toolchain ============ ================================================== ``20160819`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` -``20170129`` ``GCCcore/6.3.0``, ``gimkl/2017a`` -``20170314`` ``GCCcore/6.3.0`` -``20171023`` ``GCCcore/6.4.0`` -``20180131`` ``GCCcore/6.4.0`` -``20180604`` ``GCCcore/7.3.0`` -``20190311`` ``GCCcore/8.2.0`` -``20190717`` ``GCCcore/8.3.0`` -``20200222`` ``GCCcore/9.3.0`` -``20201008`` ``GCCcore/10.2.0`` -``20210518`` ``GCCcore/10.3.0`` -``20210802`` ``GCCcore/11.2.0`` -``20220504`` ``GCCcore/11.3.0`` +``20170129`` ``GCCcore/6.3.0``, ``gimkl/2017a`` +``20170314`` ``GCCcore/6.3.0`` +``20171023`` ``GCCcore/6.4.0`` +``20180131`` ``GCCcore/6.4.0`` +``20180604`` ``GCCcore/7.3.0`` +``20190311`` ``GCCcore/8.2.0`` +``20190717`` ``GCCcore/8.3.0`` +``20200222`` ``GCCcore/9.3.0`` +``20201008`` ``GCCcore/10.2.0`` +``20210518`` ``GCCcore/10.3.0`` +``20210802`` ``GCCcore/11.2.0`` +``20220504`` ``GCCcore/11.3.0`` +``20221110`` ``GCCcore/12.2.0`` ============ ================================================== @@ -50737,7 +52736,7 @@ X-13ARIMA-SEATS is seasonal adjustment software produced, distributed, and main *homepage*: https://www.census.gov/data/software/x13as.About_X-13.html =========== ====================================== -version toolchain +version toolchain =========== ====================================== ``1-1-b59`` ``GCCcore/10.2.0``, ``GCCcore/11.2.0`` =========== ====================================== @@ -50753,25 +52752,25 @@ x264 is a free software library and application for encoding video streams into *homepage*: https://www.videolan.org/developers/x264.html ============ ================================= -version toolchain +version toolchain ============ ================================= ``20160114`` ``gimkl/2.11.5``, ``intel/2016a`` -``20160430`` ``foss/2016a``, ``intel/2016a`` -``20160614`` ``foss/2016b``, ``intel/2016b`` -``20170406`` ``gimkl/2017a`` -``20170721`` ``GCCcore/6.4.0`` -``20170913`` ``intel/2017a`` -``20171217`` ``foss/2017b``, ``intel/2017b`` -``20180128`` ``GCCcore/6.4.0`` -``20180325`` ``GCCcore/6.4.0`` -``20181203`` ``GCCcore/7.3.0`` -``20190413`` ``GCCcore/8.2.0`` -``20190925`` ``GCCcore/8.3.0`` -``20191217`` ``GCCcore/9.3.0`` -``20201026`` ``GCCcore/10.2.0`` -``20210414`` ``GCCcore/10.3.0`` -``20210613`` ``GCCcore/11.2.0`` -``20220620`` ``GCCcore/11.3.0`` +``20160430`` ``foss/2016a``, ``intel/2016a`` +``20160614`` ``foss/2016b``, ``intel/2016b`` +``20170406`` ``gimkl/2017a`` +``20170721`` ``GCCcore/6.4.0`` +``20170913`` ``intel/2017a`` +``20171217`` ``foss/2017b``, ``intel/2017b`` +``20180128`` ``GCCcore/6.4.0`` +``20180325`` ``GCCcore/6.4.0`` +``20181203`` ``GCCcore/7.3.0`` +``20190413`` ``GCCcore/8.2.0`` +``20190925`` ``GCCcore/8.3.0`` +``20191217`` ``GCCcore/9.3.0`` +``20201026`` ``GCCcore/10.2.0`` +``20210414`` ``GCCcore/10.3.0`` +``20210613`` ``GCCcore/11.2.0`` +``20220620`` ``GCCcore/11.3.0`` ============ ================================= @@ -50785,16 +52784,16 @@ x265 is a free software library and application for encoding video streams into *homepage*: https://x265.org/ ======= ========================================================== -version toolchain +version toolchain ======= ========================================================== -``2.4`` ``foss/2016b`` -``2.5`` ``intel/2017a`` -``2.6`` ``GCCcore/6.4.0``, ``intel/2017b`` -``2.7`` ``GCCcore/6.4.0`` -``2.9`` ``GCCcore/7.3.0`` -``3.0`` ``GCCcore/8.2.0`` -``3.2`` ``GCCcore/8.3.0`` -``3.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` +``2.4`` ``foss/2016b`` +``2.5`` ``intel/2017a`` +``2.6`` ``GCCcore/6.4.0``, ``intel/2017b`` +``2.7`` ``GCCcore/6.4.0`` +``2.9`` ``GCCcore/7.3.0`` +``3.0`` ``GCCcore/8.2.0`` +``3.2`` ``GCCcore/8.3.0`` +``3.3`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` ``3.5`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ======= ========================================================== @@ -50809,7 +52808,7 @@ XALT 2 is a tool to allow a site to track user executables and library usage o *homepage*: https://github.com/xalt/xalt ========= ========== -version toolchain +version toolchain ========= ========== ``2.8.4`` ``system`` ========= ========== @@ -50824,25 +52823,27 @@ xarray (formerly xray) is an open source project and Python package that aims to *homepage*: https://github.com/pydata/xarray -========== ================== =================================================== -version versionsuffix toolchain -========== ================== =================================================== -``0.9.5`` ``-Python-2.7.13`` ``intel/2017a`` -``0.9.5`` ``-Python-3.6.1`` ``intel/2017a`` -``0.9.6`` ``-Python-2.7.13`` ``intel/2017a`` -``0.10.0`` ``-Python-2.7.14`` ``intel/2017b`` -``0.10.0`` ``-Python-3.6.3`` ``intel/2017b`` -``0.10.3`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.4`` ``-Python-3.6.4`` ``intel/2018a`` -``0.10.8`` ``-Python-3.6.4`` ``intel/2018a`` -``0.12.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` -``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` -``0.15.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``0.16.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` -``0.16.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` -``0.19.0`` ``foss/2021a`` -``0.20.1`` ``foss/2021b``, ``intel/2021b`` -========== ================== =================================================== +============ ================== =================================================== +version versionsuffix toolchain +============ ================== =================================================== +``0.9.5`` ``-Python-2.7.13`` ``intel/2017a`` +``0.9.5`` ``-Python-3.6.1`` ``intel/2017a`` +``0.9.6`` ``-Python-2.7.13`` ``intel/2017a`` +``0.10.0`` ``-Python-2.7.14`` ``intel/2017b`` +``0.10.0`` ``-Python-3.6.3`` ``intel/2017b`` +``0.10.3`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.4`` ``-Python-3.6.4`` ``intel/2018a`` +``0.10.8`` ``-Python-3.6.4`` ``intel/2018a`` +``0.12.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` +``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` +``0.15.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``0.16.1`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``0.16.2`` ``foss/2020b``, ``fosscuda/2020b``, ``intel/2020b`` +``0.19.0`` ``foss/2021a`` +``0.20.1`` ``foss/2021b``, ``intel/2021b`` +``2022.6.0`` ``foss/2022a``, ``intel/2022a`` +``2022.9.0`` ``foss/2022a`` +============ ================== =================================================== .. _list_software_xbitmaps_872: @@ -50855,10 +52856,10 @@ provides bitmaps for x *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =========================================== -version toolchain +version toolchain ========= =========================================== ``1.1.1`` ``foss/2016a``, ``intel/2016a``, ``system`` -``1.1.2`` ``system`` +``1.1.2`` ``system`` ========= =========================================== @@ -50872,7 +52873,7 @@ The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a sm *homepage*: https://xcb.freedesktop.org/ ======== ========== -version toolchain +version toolchain ======== ========== ``1.11`` ``system`` ``1.13`` ``system`` @@ -50889,7 +52890,7 @@ The xcb-util package provides additional extensions to the XCB library, many th *homepage*: http://xcb.freedesktop.org/ ========= =============================== -version toolchain +version toolchain ========= =============================== ``0.4.0`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -50905,7 +52906,7 @@ The xcb-util-image package provides additional extensions to the XCB library. *homepage*: http://xcb.freedesktop.org/ ========= =============================== -version toolchain +version toolchain ========= =============================== ``0.4.0`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -50921,7 +52922,7 @@ The xcb-util-keysyms package contains a library for handling standard X key con *homepage*: http://xcb.freedesktop.org/ ========= =============================== -version toolchain +version toolchain ========= =============================== ``0.4.0`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -50937,7 +52938,7 @@ The xcb-util-renderutil package provides additional extensions to the XCB librar *homepage*: http://xcb.freedesktop.org/ ========= =============================== -version toolchain +version toolchain ========= =============================== ``0.3.9`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -50953,7 +52954,7 @@ The xcb-util-wm package contains libraries which provide client and window-manag *homepage*: http://xcb.freedesktop.org/ ========= =============================== -version toolchain +version toolchain ========= =============================== ``0.4.1`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -50969,7 +52970,7 @@ xCell is a gene signatures-based method learned from thousands of pure cell type *homepage*: https://github.com/dviraran/xCell ======== ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ======== ============= ============== ``1.12`` ``-R-3.5.1`` ``foss/2018b`` ======== ============= ============== @@ -50984,14 +52985,14 @@ XCFun is a library of DFT exchange-correlation (XC) functionals. It is based on *homepage*: http://dftlibs.org/xcfun/ -============ ================== ====================================== -version versionsuffix toolchain -============ ================== ====================================== -``2.1.0`` ``GCCcore/9.3.0`` -``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` -``20180122`` ``-Python-2.7.14`` ``intel/2017b`` -``20190127`` ``-Python-3.7.2`` ``foss/2019a`` -============ ================== ====================================== +============ ================== ========================================================== +version versionsuffix toolchain +============ ================== ========================================================== +``2.1.0`` ``GCCcore/9.3.0`` +``2.1.1`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.3.0`` +``20180122`` ``-Python-2.7.14`` ``intel/2017b`` +``20190127`` ``-Python-3.7.2`` ``foss/2019a`` +============ ================== ========================================================== .. _list_software_XCrySDen_752: @@ -51004,9 +53005,9 @@ XCrySDen is a crystalline and molecular structure visualisation program aiming a *homepage*: http://www.xcrysden.org/ ========== ================================================================================ -version toolchain +version toolchain ========== ================================================================================ -``1.5.60`` ``intel/2019a`` +``1.5.60`` ``intel/2019a`` ``1.6.2`` ``foss/2019b``, ``foss/2020b``, ``foss/2022a``, ``intel/2019b``, ``intel/2022a`` ========== ================================================================================ @@ -51021,11 +53022,11 @@ Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerce *homepage*: https://xerces.apache.org/xerces-c/ ========= ============================================================================= -version toolchain +version toolchain ========= ============================================================================= -``3.1.4`` ``GCCcore/6.4.0`` -``3.2.0`` ``GCCcore/7.3.0`` -``3.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``3.1.4`` ``GCCcore/6.4.0`` +``3.2.0`` ``GCCcore/7.3.0`` +``3.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.2.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/9.3.0`` ========= ============================================================================= @@ -51040,10 +53041,10 @@ xESMF: Universal Regridder for Geospatial Data *homepage*: https://xesmf.readthedocs.io ========= ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= =============== ``0.3.0`` ``intel/2020b`` -``0.3.0`` ``-Python-3.8.2`` ``foss/2020a`` +``0.3.0`` ``-Python-3.8.2`` ``foss/2020a`` ========= ================= =============== @@ -51057,7 +53058,7 @@ XExtProto protocol headers. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================================== -version toolchain +version toolchain ========= ================================================================== ``7.3.0`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017b`` ========= ================================================================== @@ -51073,7 +53074,7 @@ X11 XFree86 video mode extension protocol headers. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== -version toolchain +version toolchain ========= =============================== ``2.3.1`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -51089,15 +53090,17 @@ XGBoost is an optimized distributed gradient boosting library designed to be hig *homepage*: https://github.com/dmlc/xgboost ============ =================== =============== -version versionsuffix toolchain +version versionsuffix toolchain ============ =================== =============== ``0.6a2`` ``-Python-2.7.12`` ``intel/2016b`` ``0.6a2`` ``-Python-3.5.2`` ``intel/2016b`` ``0.6a2`` ``-Python-3.6.1`` ``intel/2017a`` ``0.72.1`` ``-Python-2.7.14`` ``intel/2017b`` -``0.90`` ``-Python-3.7.4`` ``foss/2019b`` -``1.2.0`` ``-Python-3.8.2`` ``foss/2020a`` -``1.5.0`` ``foss/2021a`` +``0.90`` ``-Python-3.7.4`` ``foss/2019b`` +``1.2.0`` ``-Python-3.8.2`` ``foss/2020a`` +``1.5.0`` ``foss/2021a`` +``1.7.2`` ``foss/2022a`` +``1.7.2`` ``-CUDA-11.7.0`` ``foss/2022a`` ``20171120`` ``-Java-1.8.0_152`` ``intel/2017b`` ============ =================== =============== @@ -51112,7 +53115,7 @@ A graphics library and controller for physics simulation programs. 3-d surface p *homepage*: https://ptsg.egr.msu.edu/ ======== ================= -version toolchain +version toolchain ======== ================= ``2.41`` ``GCCcore/9.3.0`` ======== ================= @@ -51128,7 +53131,7 @@ X protocol and ancillary headers for xinerama *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== -version toolchain +version toolchain ========= =============================== ``1.2.1`` ``foss/2016a``, ``intel/2016a`` ========= =============================== @@ -51144,7 +53147,7 @@ The non-arch keyboard configuration database for X Window. The goal is to provi *homepage*: http://www.freedesktop.org/wiki/Software/XKeyboardConfig/ ======== =============================== -version toolchain +version toolchain ======== =============================== ``2.17`` ``foss/2016a``, ``intel/2016a`` ======== =============================== @@ -51160,7 +53163,7 @@ A Python module for creating Excel XLSX files *homepage*: https://xlsxwriter.readthedocs.io/ ========= ================== -version toolchain +version toolchain ========= ================== ``1.4.0`` ``GCCcore/10.2.0`` ``1.4.4`` ``GCCcore/10.3.0`` @@ -51178,7 +53181,7 @@ The purpose of XMDS2 is to simplify the process of creating simulations that so *homepage*: http://www.xmds.org/ ========= ================== ============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ================== ============== ``2.2.3`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== ============== @@ -51194,12 +53197,30 @@ Scipion is an image processing framework to obtain 3D models of macromolecular c *homepage*: https://github.com/I2PC/scipion/wiki ================== ================== ================================== -version versionsuffix toolchain +version versionsuffix toolchain ================== ================== ================================== ``3.19.04-Apollo`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a`` +``3.22.07-Helios`` ``foss/2022a`` +``3.22.07-Helios`` ``-CUDA-11.7.0`` ``foss/2022a`` ================== ================== ================================== +.. _list_software_xmitgcm_761: + +*xmitgcm* ++++++++++ + +xmitgcm is a python package for reading MITgcm binary MDS files into xarray data structures. By storing data in dask arrays, xmitgcm enables parallel, out-of-core analysis of MITgcm output data. + +*homepage*: https://github.com/MITgcm/xmitgcm + +========= ============== +version toolchain +========= ============== +``0.5.2`` ``foss/2022a`` +========= ============== + + .. _list_software_XML-Compile_999: *XML-Compile* @@ -51210,7 +53231,7 @@ Perl module for compilation based XML processing *homepage*: https://metacpan.org/pod/XML::Compile ======== ================== -version toolchain +version toolchain ======== ================== ``1.63`` ``GCCcore/11.2.0`` ======== ================== @@ -51226,17 +53247,17 @@ Perl binding for libxml2 *homepage*: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod ========== ================ ========================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================ ========================================================== -``2.0132`` ``-Perl-5.24.0`` ``foss/2016b``, ``intel/2016b`` -``2.0132`` ``-Perl-5.24.1`` ``intel/2017a`` -``2.0132`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` -``2.0132`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``2.0132`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -``2.0200`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` -``2.0201`` ``GCCcore/8.3.0`` -``2.0205`` ``GCCcore/9.3.0`` -``2.0206`` ``GCCcore/10.2.0`` +``2.0132`` ``-Perl-5.24.0`` ``foss/2016b``, ``intel/2016b`` +``2.0132`` ``-Perl-5.24.1`` ``intel/2017a`` +``2.0132`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` +``2.0132`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``2.0132`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``2.0200`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` +``2.0201`` ``GCCcore/8.3.0`` +``2.0205`` ``GCCcore/9.3.0`` +``2.0206`` ``GCCcore/10.2.0`` ``2.0207`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========== ================ ========================================================== @@ -51251,17 +53272,17 @@ This is a Perl extension interface to James Clark's XML parser, expat. *homepage*: https://search.cpan.org/~toddr/XML-Parser-2.46/ =========== ================ ====================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain =========== ================ ====================================================================================== -``2.41`` ``-Perl-5.20.3`` ``intel/2016a`` -``2.44`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` +``2.41`` ``-Perl-5.20.3`` ``intel/2016a`` +``2.44`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` ``2.44_01`` ``-Perl-5.24.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` -``2.44_01`` ``-Perl-5.24.1`` ``GCCcore/6.3.0``, ``intel/2017a`` -``2.44_01`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` -``2.44_01`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` -``2.44_01`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` -``2.46`` ``-Perl-5.32.1`` ``GCCcore/10.3.0`` -``2.46`` ``-Perl-5.34.1`` ``GCCcore/11.3.0`` +``2.44_01`` ``-Perl-5.24.1`` ``GCCcore/6.3.0``, ``intel/2017a`` +``2.44_01`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` +``2.44_01`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` +``2.44_01`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` +``2.46`` ``-Perl-5.32.1`` ``GCCcore/10.3.0`` +``2.46`` ``-Perl-5.34.1`` ``GCCcore/11.3.0`` =========== ================ ====================================================================================== @@ -51275,9 +53296,9 @@ xmlf90 is a basic XML parsing library written in Fortran. *homepage*: https://launchpad.net/xmlf90 ========= ============================================================================================================================================================ -version toolchain +version toolchain ========= ============================================================================================================================================================ -``1.5.3`` ``foss/2016b``, ``foss/2017a`` +``1.5.3`` ``foss/2016b``, ``foss/2017a`` ``1.5.4`` ``GCC/10.2.0``, ``GCC/10.3.0``, ``GCC/11.2.0``, ``iccifort/2019.5.281``, ``iccifort/2020.4.304``, ``intel-compilers/2021.2.0``, ``intel-compilers/2021.4.0`` ========= ============================================================================================================================================================ @@ -51292,7 +53313,7 @@ XML Security Library is a C library based on LibXML2, supporting major XML secu *homepage*: https://www.aleksey.com/xmlsec/index.html ========== ================= -version toolchain +version toolchain ========== ================= ``1.2.26`` ``GCCcore/6.4.0`` ========== ================= @@ -51308,7 +53329,7 @@ Command line XML tool *homepage*: http://xmlstar.sourceforge.net ========= ================================= -version toolchain +version toolchain ========= ================================= ``1.6.1`` ``GCCcore/6.4.0``, ``foss/2016a`` ========= ================================= @@ -51324,7 +53345,7 @@ Xonsh is a Python-ish, BASHwards-looking shell language and command prompt. *homepage*: https://xon.sh/ ========= =============== -version toolchain +version toolchain ========= =============== ``0.3.2`` ``intel/2016a`` ========= =============== @@ -51340,12 +53361,12 @@ X.org macros utilities. *homepage*: https://cgit.freedesktop.org/xorg/util/macros ========== ==================================================================================================================================== -version toolchain +version toolchain ========== ==================================================================================================================================== -``1.19.0`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` -``1.19.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` +``1.19.0`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` +``1.19.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.19.2`` ``GCCcore/10.2.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0`` -``1.19.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.19.3`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========== ==================================================================================================================================== @@ -51359,7 +53380,7 @@ A System for X-ray Crystallography and NMR *homepage*: https://nmr.cit.nih.gov/xplor-nih/ ======= ================= ========== -version versionsuffix toolchain +version versionsuffix toolchain ======= ================= ========== ``3.4`` ``-Linux_x86_64`` ``system`` ======= ================= ========== @@ -51375,13 +53396,13 @@ The xprop utility is for displaying window and font properties in an X server. *homepage*: https://www.x.org/wiki/ ========= ================= ======================================================================================================================= -version versionsuffix toolchain +version versionsuffix toolchain ========= ================= ======================================================================================================================= ``1.2.2`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` -``1.2.2`` ``-X11-20180131`` ``GCCcore/6.4.0`` -``1.2.3`` ``GCCcore/7.3.0`` -``1.2.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``1.2.2`` ``-X11-20180131`` ``GCCcore/6.4.0`` +``1.2.3`` ``GCCcore/7.3.0`` +``1.2.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.2.5`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ================= ======================================================================================================================= @@ -51395,10 +53416,10 @@ X protocol and ancillary headers *homepage*: https://www.freedesktop.org/wiki/Software/xlibs ========== ============================================================================================================================================================================= -version toolchain +version toolchain ========== ============================================================================================================================================================================= -``7.0.28`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` -``7.0.29`` ``intel/2016a`` +``7.0.28`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` +``7.0.29`` ``intel/2016a`` ``7.0.31`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ========== ============================================================================================================================================================================= @@ -51413,7 +53434,7 @@ CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C++ data b *homepage*: https://www.codesynthesis.com/products/xsd/ ========= ================= -version toolchain +version toolchain ========= ================= ``4.0.0`` ``GCCcore/8.2.0`` ========= ================= @@ -51429,7 +53450,7 @@ X!Tandem open source is software that can match tandem mass spectra with peptid *homepage*: https://www.thegpm.org/tandem ============== ========================================================== -version toolchain +version toolchain ============== ========================================================== ``17.02.01.4`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ============== ========================================================== @@ -51445,10 +53466,10 @@ Semiempirical Extended Tight-Binding Program Package. *homepage*: https://xtb-docs.readthedocs.io ================ ================= =============================== -version versionsuffix toolchain +version versionsuffix toolchain ================ ================= =============================== -``6.2.2-hotfix`` ``-Python-3.6.3`` ``intel/2017b`` -``6.2.3`` ``foss/2019b`` +``6.2.2-hotfix`` ``-Python-3.6.3`` ``intel/2017b`` +``6.2.3`` ``foss/2019b`` ``6.4.1`` ``foss/2021b``, ``intel/2021a`` ================ ================= =============================== @@ -51463,7 +53484,7 @@ xtensor is a C++ library meant for numerical analysis with multi-dimensional arr *homepage*: https://github.com/xtensor-stack/xtensor ========== ============== -version toolchain +version toolchain ========== ============== ``0.24.0`` ``foss/2021b`` ========== ============== @@ -51479,7 +53500,7 @@ xtrans includes a number of routines to make X implementations transport-indepen *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ===================================================================== -version toolchain +version toolchain ========= ===================================================================== ``1.3.5`` ``GCCcore/11.3.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ===================================================================== @@ -51495,13 +53516,13 @@ Xvfb is an X server that can run on machines with no display hardware and no phy *homepage*: https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml =========== ===================================== -version toolchain +version toolchain =========== ===================================== -``1.20.8`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` +``1.20.8`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``1.20.9`` ``GCCcore/10.2.0``, ``GCCcore/9.3.0`` -``1.20.11`` ``GCCcore/10.3.0`` -``1.20.13`` ``GCCcore/11.2.0`` -``21.1.3`` ``GCCcore/11.3.0`` +``1.20.11`` ``GCCcore/10.3.0`` +``1.20.13`` ``GCCcore/11.2.0`` +``21.1.3`` ``GCCcore/11.3.0`` =========== ===================================== @@ -51515,7 +53536,7 @@ xxd is part of the VIM package and this will only install xxd, not vim! xxd conv *homepage*: https://www.vim.org ============ ========================================================== -version toolchain +version toolchain ============ ========================================================== ``8.2.4220`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0`` ============ ========================================================== @@ -51531,7 +53552,7 @@ xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM spe *homepage*: https://cyan4973.github.io/xxHash ========= ================== -version toolchain +version toolchain ========= ================== ``0.8.0`` ``GCCcore/11.2.0`` ========= ================== @@ -51547,15 +53568,16 @@ xz: XZ utilities *homepage*: https://tukaani.org/xz/ ========= =================== =========================================================================================================================================================== -version versionsuffix toolchain +version versionsuffix toolchain ========= =================== =========================================================================================================================================================== -``5.0.5`` ``GCC/4.8.2`` -``5.2.0`` ``GCC/4.9.2`` +``5.0.5`` ``GCC/4.8.2`` +``5.2.0`` ``GCC/4.9.2`` ``5.2.2`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` -``5.2.2`` ``-gettext-0.19.7`` ``foss/2016a``, ``intel/2016a`` -``5.2.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``gimkl/2017a`` -``5.2.4`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` -``5.2.5`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +``5.2.2`` ``-gettext-0.19.7`` ``foss/2016a``, ``intel/2016a`` +``5.2.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``gimkl/2017a`` +``5.2.4`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` +``5.2.5`` ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/9.3.0`` +``5.2.7`` ``GCCcore/12.2.0`` ========= =================== =========================================================================================================================================================== @@ -51577,11 +53599,11 @@ YACS was created as a lightweight library to define and manage system configurat *homepage*: https://github.com/rbgirshick/yacs -========= ============================================================================= -version toolchain -========= ============================================================================= -``0.1.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/8.3.0`` -========= ============================================================================= +========= ================================================================================================= +version toolchain +========= ================================================================================================= +``0.1.8`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/8.3.0`` +========= ================================================================================================= .. _list_software_Yade_387: @@ -51594,12 +53616,12 @@ Yade is an extensible open-source framework for discrete numerical models, foc *homepage*: https://yade-dem.org/doc/ ============ ================== =============================== -version versionsuffix toolchain +version versionsuffix toolchain ============ ================== =============================== ``1.20.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``2016.06a`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` -``2017.01a`` ``-Python-2.7.12`` ``intel/2016b`` -``2018.02b`` ``-Python-2.7.14`` ``intel/2018a`` +``2017.01a`` ``-Python-2.7.12`` ``intel/2016b`` +``2018.02b`` ``-Python-2.7.14`` ``intel/2018a`` ============ ================== =============================== @@ -51613,20 +53635,20 @@ Yaff stands for 'Yet another force field'. It is a pythonic force-field code. *homepage*: https://molmod.github.io/yaff/ ==================== ============================== ================================================ -version versionsuffix toolchain +version versionsuffix toolchain ==================== ============================== ================================================ -``1.0.develop.2.15`` ``-Python-2.7.12-HDF5-1.8.18`` ``intel/2016b`` -``1.1.2`` ``-Python-2.7.13`` ``intel/2017a`` -``1.1.3`` ``-Python-2.7.13`` ``intel/2017a`` +``1.0.develop.2.15`` ``-Python-2.7.12-HDF5-1.8.18`` ``intel/2016b`` +``1.1.2`` ``-Python-2.7.13`` ``intel/2017a`` +``1.1.3`` ``-Python-2.7.13`` ``intel/2017a`` ``1.4.2`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` -``1.4.2`` ``-Python-3.6.3`` ``intel/2017b`` -``1.4.5`` ``-Python-2.7.15`` ``intel/2018b`` -``1.5.0`` ``-Python-2.7.15`` ``intel/2018b`` -``1.5.0`` ``-Python-3.7.2`` ``intel/2019a`` -``1.6.0`` ``foss/2020b`` -``1.6.0`` ``-Python-3.7.2`` ``intel/2019a`` -``1.6.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` -``1.6.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` +``1.4.2`` ``-Python-3.6.3`` ``intel/2017b`` +``1.4.5`` ``-Python-2.7.15`` ``intel/2018b`` +``1.5.0`` ``-Python-2.7.15`` ``intel/2018b`` +``1.5.0`` ``-Python-3.7.2`` ``intel/2019a`` +``1.6.0`` ``foss/2020b`` +``1.6.0`` ``-Python-3.7.2`` ``intel/2019a`` +``1.6.0`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` +``1.6.0`` ``-Python-3.8.2`` ``foss/2020a``, ``intel/2020a`` ==================== ============================== ================================================ @@ -51640,10 +53662,10 @@ Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecula *homepage*: http://www.yambo-code.org ========= ========================= -version toolchain +version toolchain ========= ========================= ``3.4.2`` ``intel/2016.02-GCC-4.9`` -``5.0.4`` ``intel/2021a`` +``5.0.4`` ``intel/2021a`` ========= ========================= @@ -51656,11 +53678,12 @@ yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec *homepage*: https://github.com/jbeder/yaml-cpp -========= ================= -version toolchain -========= ================= +========= ================== +version toolchain +========= ================== ``0.6.3`` ``GCCcore/8.3.0`` -========= ================= +``0.7.0`` ``GCCcore/11.3.0`` +========= ================== .. _list_software_YANK_307: @@ -51673,7 +53696,7 @@ A GPU-accelerated Python framework for exploring algorithms for alchemical free *homepage*: http://getyank.org/ ========== ================= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ================= =============== ``0.25.2`` ``-Python-3.8.2`` ``intel/2020a`` ========== ================= =============== @@ -51689,9 +53712,9 @@ YAPS - Yet Another Positioning Solver *homepage*: https://github.com/baktoft/yaps ========= ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========= ============= =============== -``1.1.0`` ``-R-3.5.1`` ``foss/2018b`` +``1.1.0`` ``-R-3.5.1`` ``foss/2018b`` ``1.1.0`` ``-R-3.6.0`` ``intel/2019a`` ========= ============= =============== @@ -51706,7 +53729,7 @@ Yasm: Complete rewrite of the NASM assembler with BSD license *homepage*: http://www.tortall.net/projects/yasm/ ========= =================================================================================================================================================================================================================================================================================================================== -version toolchain +version toolchain ========= =================================================================================================================================================================================================================================================================================================================== ``1.3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ========= =================================================================================================================================================================================================================================================================================================================== @@ -51722,15 +53745,15 @@ Yet Another eXchange Tool *homepage*: https://www.dkrz.de/redmine/projects/yaxt =========== ================================================= -version toolchain +version toolchain =========== ================================================= ``0.5.1`` ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``0.6.0`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` -``0.6.2`` ``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` -``0.9.0`` ``gompi/2020b`` -``0.9.1`` ``gompi/2021a`` -``0.9.2`` ``iimpi/2021b`` -``0.9.2.1`` ``gompi/2021b`` +``0.6.2`` ``foss/2018b``, ``gompi/2019b``, ``iimpi/2019b`` +``0.9.0`` ``gompi/2020b`` +``0.9.1`` ``gompi/2021a`` +``0.9.2`` ``iimpi/2021b`` +``0.9.2.1`` ``gompi/2021b`` =========== ================================================= @@ -51744,7 +53767,7 @@ Yices 2 is an SMT solver that decides the satisfiability of formulas containing *homepage*: https://yices.csl.sri.com/index.html ========= ================== -version toolchain +version toolchain ========= ================== ``2.6.2`` ``GCCcore/10.2.0`` ========= ================== @@ -51769,14 +53792,14 @@ Z3 is a theorem prover from Microsoft Research. *homepage*: https://github.com/Z3Prover/z3 ========== ==================================== -version toolchain +version toolchain ========== ==================================== ``4.8.9`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.8.10`` ``GCCcore/10.2.0`` -``4.8.11`` ``GCCcore/10.3.0`` -``4.8.12`` ``GCCcore/11.2.0`` -``4.8.16`` ``GCCcore/11.3.0`` -``4.10.2`` ``GCCcore/11.3.0`` +``4.8.10`` ``GCCcore/10.2.0`` +``4.8.11`` ``GCCcore/10.3.0`` +``4.8.12`` ``GCCcore/11.2.0`` +``4.8.16`` ``GCCcore/11.3.0`` +``4.10.2`` ``GCCcore/11.3.0`` ========== ==================================== @@ -51789,14 +53812,15 @@ Zarr is a Python package providing an implementation of compressed, chunked, N-d *homepage*: https://zarr.readthedocs.io/en/stable/ -========== ================== ============== -version versionsuffix toolchain -========== ================== ============== +========== ================== ============================== +version versionsuffix toolchain +========== ================== ============================== ``2.1.4`` ``-Python-2.7.13`` ``foss/2017a`` ``2.4.0`` ``-Python-3.8.2`` ``foss/2020a`` ``2.8.1`` ``foss/2020b`` ``2.10.1`` ``foss/2021a`` -========== ================== ============== +``2.13.3`` ``foss/2021b``, ``foss/2022a`` +========== ================== ============================== .. _list_software_ZeroMQ_574: @@ -51809,16 +53833,16 @@ ZeroMQ looks like an embeddable networking library but acts like a concurrency f *homepage*: https://www.zeromq.org/ ========= ========================================================================================================= -version toolchain +version toolchain ========= ========================================================================================================= -``4.1.4`` ``foss/2016a``, ``intel/2016a`` -``4.1.5`` ``intel/2016b`` -``4.2.0`` ``foss/2016b``, ``intel/2016b`` +``4.1.4`` ``foss/2016a``, ``intel/2016a`` +``4.1.5`` ``intel/2016b`` +``4.2.0`` ``foss/2016b``, ``intel/2016b`` ``4.2.2`` ``foss/2017a``, ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` -``4.2.5`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` -``4.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``4.3.3`` ``GCCcore/10.2.0`` -``4.3.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` +``4.2.5`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` +``4.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``4.3.3`` ``GCCcore/10.2.0`` +``4.3.4`` ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0`` ========= ========================================================================================================= @@ -51831,12 +53855,12 @@ zfp is a compressed format for representing multidimensional floating-point and *homepage*: https://github.com/LLNL/zfp -========= ================== -version toolchain -========= ================== +========= ===================================== +version toolchain +========= ===================================== ``0.5.5`` ``GCCcore/10.2.0`` -``1.0.0`` ``GCCcore/9.3.0`` -========= ================== +``1.0.0`` ``GCCcore/10.3.0``, ``GCCcore/9.3.0`` +========= ===================================== .. _list_software_Zgoubi_624: @@ -51849,7 +53873,7 @@ Zgoubi is a ray-tracing code in use for charged particle beam dynamics simulatio *homepage*: https://zgoubi.sourceforge.io ========= ================== -version toolchain +version toolchain ========= ================== ``6.0.2`` ``GCCcore/10.3.0`` ========= ================== @@ -51865,7 +53889,7 @@ Zero-Inflated Negative binomial Gene Expression in R *homepage*: https://github.com/statOmics/zingeR ============ ============= ============== -version versionsuffix toolchain +version versionsuffix toolchain ============ ============= ============== ``20180131`` ``-R-3.5.1`` ``foss/2018b`` ============ ============= ============== @@ -51881,7 +53905,7 @@ Zip is a compression and file packaging/archive utility. Although highly compati *homepage*: http://www.info-zip.org/Zip.html ======= ========================================================================================================================================================== -version toolchain +version toolchain ======= ========================================================================================================================================================== ``3.0`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.2.0``, ``GCCcore/11.3.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` ======= ========================================================================================================================================================== @@ -51897,13 +53921,13 @@ zlib is designed to be a free, general-purpose, legally unencumbered -- that is, *homepage*: http://www.zlib.net/ ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -version toolchain +version toolchain ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== -``1.2.7`` ``GCC/4.8.1``, ``GCC/4.8.2`` +``1.2.7`` ``GCC/4.8.1``, ``GCC/4.8.2`` ``1.2.8`` ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` -``1.2.10`` ``system`` -``1.2.11`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` -``1.2.12`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0``, ``system`` +``1.2.10`` ``system`` +``1.2.11`` ``FCC/4.5.0``, ``GCCcore/10.1.0``, ``GCCcore/10.2.0``, ``GCCcore/10.3.0``, ``GCCcore/11.1.0``, ``GCCcore/11.2.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/8.4.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/9.3.0``, ``GCCcore/9.4.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` +``1.2.12`` ``GCCcore/11.3.0``, ``GCCcore/12.1.0``, ``GCCcore/12.2.0``, ``GCCcore/9.5.0``, ``system`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== @@ -51917,9 +53941,10 @@ zlib data compression library for the next generation systems *homepage*: https://github.com/zlib-ng/zlib-ng ========= ================== -version toolchain +version toolchain ========= ================== ``2.0.5`` ``GCCcore/10.2.0`` +``2.0.6`` ``GCCcore/10.3.0`` ========= ================== @@ -51933,7 +53958,7 @@ This package uses the source code of zlib-1.2.5 to create libraries for systems *homepage*: https://bioconductor.org/packages/release/bioc/html/zlibbioc.html ========== ============= =============== -version versionsuffix toolchain +version versionsuffix toolchain ========== ============= =============== ``1.18.0`` ``-R-3.2.3`` ``intel/2016a`` ``1.20.0`` ``-R-3.3.1`` ``intel/2016b`` @@ -51949,11 +53974,11 @@ Zopfli Compression Algorithm is a compression library programmed in C to perform *homepage*: https://github.com/google/zopfli -========= ================== -version toolchain -========= ================== -``1.0.3`` ``GCCcore/10.2.0`` -========= ================== +========= ====================================== +version toolchain +========= ====================================== +``1.0.3`` ``GCCcore/10.2.0``, ``GCCcore/10.3.0`` +========= ====================================== .. _list_software_ZPAQ_316: @@ -51966,7 +53991,7 @@ zpaq is a free and open source (GPL v3) incremental, journaling command-line ar *homepage*: http://mattmahoney.net/dc/zpaq.html ======== ============= -version toolchain +version toolchain ======== ============= ``7.00`` ``GCC/4.8.2`` ======== ============= @@ -51982,10 +54007,10 @@ Zsh is a shell designed for interactive use, although it is also a powerful scri *homepage*: https://www.zsh.org/ ========= ========================= -version toolchain +version toolchain ========= ========================= -``5.1.1`` ``GNU/4.9.3-2.25`` -``5.2`` ``foss/2016b`` +``5.1.1`` ``GNU/4.9.3-2.25`` +``5.2`` ``foss/2016b`` ``5.8`` ``GCC/8.3.0``, ``system`` ========= ========================= @@ -52000,14 +54025,14 @@ Zstandard is a real-time compression algorithm, providing high compression ratio *homepage*: https://facebook.github.io/zstd ========= ==================================================== -version toolchain +version toolchain ========= ==================================================== -``1.3.4`` ``foss/2016b`` +``1.3.4`` ``foss/2016b`` ``1.4.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2018b`` -``1.4.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` -``1.4.5`` ``GCCcore/10.2.0`` -``1.4.9`` ``GCCcore/10.3.0`` -``1.5.0`` ``GCCcore/11.2.0`` -``1.5.2`` ``GCCcore/11.3.0`` +``1.4.4`` ``GCCcore/8.3.0``, ``GCCcore/9.3.0`` +``1.4.5`` ``GCCcore/10.2.0`` +``1.4.9`` ``GCCcore/10.3.0`` +``1.5.0`` ``GCCcore/11.2.0`` +``1.5.2`` ``GCCcore/11.3.0``, ``GCCcore/12.2.0`` ========= ==================================================== diff --git a/docs/version-specific/config_file_constants.rst b/docs/version-specific/config_file_constants.rst index 967995c4..dfc42315 100644 --- a/docs/version-specific/config_file_constants.rst +++ b/docs/version-specific/config_file_constants.rst @@ -5,16 +5,15 @@ Constants available (only) in configuration files ------------------------------------------------- - -only in 'DEFAULT' section: +Only in 'DEFAULT' section: -------------------------- ========================== =================================================== =================================================================== -Constant name Constant help Constant value +Constant name Constant help Constant value ========================== =================================================== =================================================================== -``DEFAULT_REPOSITORYPATH`` Default easyconfigs repository path ``/home/example/.local/easybuild/ebfiles_repo`` +``DEFAULT_REPOSITORYPATH`` Default easyconfigs repository path ``/home/example/.local/easybuild/ebfiles_repo`` ``DEFAULT_ROBOT_PATHS`` List of default robot paths (':'-separated) ``/home/example/work/easybuild-easyconfigs/easybuild/easyconfigs`` -``USER`` Current username, translated uid from password file ``example`` -``HOME`` Current user's home directory, expanded '~' ``/home/example`` +``HOME`` Current user's home directory, expanded '~' ``/home/example`` +``USER`` Current username, translated uid from password file ``example`` ========================== =================================================== =================================================================== diff --git a/docs/version-specific/easyblocks.rst b/docs/version-specific/easyblocks.rst index fb54297c..0603daa9 100644 --- a/docs/version-specific/easyblocks.rst +++ b/docs/version-specific/easyblocks.rst @@ -62,6 +62,7 @@ * CrayToolchain * EB_Clang_minus_AOMP * EB_OpenSSL_wrapper + * JuliaBundle * PythonBundle * SystemCompiler * SystemMPI @@ -265,6 +266,7 @@ * ExtensionEasyBlock * EB_Scipion + * JuliaPackage * OCamlPackage * OctavePackage * PerlModule @@ -407,6 +409,7 @@ * ExtensionEasyBlock * EB_Scipion + * JuliaPackage * OCamlPackage * OctavePackage * PerlModule diff --git a/docs/version-specific/easyconfig_constants.rst b/docs/version-specific/easyconfig_constants.rst index 99e684ae..fba9eb79 100644 --- a/docs/version-specific/easyconfig_constants.rst +++ b/docs/version-specific/easyconfig_constants.rst @@ -5,21 +5,21 @@ Constants that can be used in easyconfigs ----------------------------------------- -====================== ============================================================= ================================================================================ -Constant name Constant value Description -====================== ============================================================= ================================================================================ -``ARCH`` ``x86_64`` CPU architecture of current system (aarch64, x86_64, ppc64le, ...) -``EXTERNAL_MODULE`` ``EXTERNAL_MODULE`` External module marker -``HOME`` ``/home/example`` Home directory ($HOME) -``OS_NAME`` ``UNKNOWN`` System name (e.g. 'fedora' or 'RHEL') -``OS_PKG_IBVERBS_DEV`` ``('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')`` OS packages providing ibverbs/infiniband development support -``OS_PKG_OPENSSL_BIN`` ``openssl`` OS packages providing the openSSL binary -``OS_PKG_OPENSSL_DEV`` ``('openssl-devel', 'libssl-dev', 'libopenssl-devel')`` OS packages providing openSSL developement support -``OS_PKG_OPENSSL_LIB`` ``('libssl', 'libopenssl')`` OS packages providing openSSL libraries -``OS_PKG_PAM_DEV`` ``('pam-devel', 'libpam0g-dev')`` OS packages providing Pluggable Authentication Module (PAM) developement support -``OS_TYPE`` ``Darwin`` System type (e.g. 'Linux' or 'Darwin') -``OS_VERSION`` ``UNKNOWN`` System version -``SYSTEM`` ``{'name': 'system', 'version': 'system'}`` System toolchain -``SYS_PYTHON_VERSION`` ``3.9.7`` System Python version (platform.python_version()) -====================== ============================================================= ================================================================================ +====================== ============================================================= =============================================================================== +Constant name Constant value Description +====================== ============================================================= =============================================================================== +``ARCH`` ``aarch64`` CPU architecture of current system (aarch64, x86_64, ppc64le, ...) +``EXTERNAL_MODULE`` ``EXTERNAL_MODULE`` External module marker +``HOME`` ``/home/example`` Home directory ($HOME) +``OS_NAME`` ``UNKNOWN`` System name (e.g. 'fedora' or 'RHEL') +``OS_PKG_IBVERBS_DEV`` ``('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')`` OS packages providing ibverbs/infiniband development support +``OS_PKG_OPENSSL_BIN`` ``openssl`` OS packages providing the openSSL binary +``OS_PKG_OPENSSL_DEV`` ``('openssl-devel', 'libssl-dev', 'libopenssl-devel')`` OS packages providing openSSL development support +``OS_PKG_OPENSSL_LIB`` ``('libssl', 'libopenssl')`` OS packages providing openSSL libraries +``OS_PKG_PAM_DEV`` ``('pam-devel', 'libpam0g-dev')`` OS packages providing Pluggable Authentication Module (PAM) development support +``OS_TYPE`` ``Darwin`` System type (e.g. 'Linux' or 'Darwin') +``OS_VERSION`` ``UNKNOWN`` System version +``SYSTEM`` ``{'name': 'system', 'version': 'system'}`` System toolchain +``SYS_PYTHON_VERSION`` ``3.9.6`` System Python version (platform.python_version()) +====================== ============================================================= =============================================================================== diff --git a/docs/version-specific/easyconfig_license_constants.rst b/docs/version-specific/easyconfig_license_constants.rst index fc9d420c..8ad5ea88 100644 --- a/docs/version-specific/easyconfig_license_constants.rst +++ b/docs/version-specific/easyconfig_license_constants.rst @@ -6,12 +6,12 @@ License constants that can be used in easyconfigs ------------------------------------------------- =================== ============================================================================================================================================================================================================================= ======== -License name License description Version +License name License description Version =================== ============================================================================================================================================================================================================================= ======== -``GCC`` The GNU General Public License is a free, copyleft license for software and other kinds of works. The GCC Runtime Library Exception is an additional permission under section 7 of the GNU General Public License, version 3. ``3`` -``GCCOld`` The GNU General Public License is a free, copyleft license for software and other kinds of works. The GCC Runtime Library Exception is an additional permission under section 7 of the GNU General Public License, version 3. ``2`` -``GPLv2`` The GNU General Public License is a free, copyleft license for software and other kinds of works. ``2`` -``GPLv3`` The GNU General Public License is a free, copyleft license for software and other kinds of works. ``3`` +``GCC`` The GNU General Public License is a free, copyleft license for software and other kinds of works. The GCC Runtime Library Exception is an additional permission under section 7 of the GNU General Public License, version 3. ``3`` +``GCCOld`` The GNU General Public License is a free, copyleft license for software and other kinds of works. The GCC Runtime Library Exception is an additional permission under section 7 of the GNU General Public License, version 3. ``2`` +``GPLv2`` The GNU General Public License is a free, copyleft license for software and other kinds of works. ``2`` +``GPLv3`` The GNU General Public License is a free, copyleft license for software and other kinds of works. ``3`` ``Libpng`` Permission is granted to use, copy, modify, and distribute the source code, or portions hereof, for any purpose, without fee, subject to 3 restrictions; http://libpng.org/pub/png/src/libpng-LICENSE.txt for full license ``None`` ``Unknown`` None ``None`` ``VeryRestrictive`` None ``None`` diff --git a/docs/version-specific/easyconfig_parameters.rst b/docs/version-specific/easyconfig_parameters.rst index 276433e6..7722c260 100644 --- a/docs/version-specific/easyconfig_parameters.rst +++ b/docs/version-specific/easyconfig_parameters.rst @@ -13,14 +13,14 @@ mandatory parameters ========================= ============================================================================= ================= **Parameter name** **Description** **Default value** ========================= ============================================================================= ================= -``description`` A short description of the software None -``docurls`` List of urls with documentation of the software (not necessarily on homepage) None -``homepage`` The homepage of the software None -``name`` Name of software None -``software_license`` Software license None -``software_license_urls`` List of software license locations None -``toolchain`` Name and version of toolchain None -``version`` Version of software None +``description`` A short description of the software None +``docurls`` List of urls with documentation of the software (not necessarily on homepage) None +``homepage`` The homepage of the software None +``name`` Name of software None +``software_license`` Software license None +``software_license_urls`` List of software license locations None +``toolchain`` Name and version of toolchain None +``version`` Version of software None ========================= ============================================================================= ================= @@ -30,8 +30,8 @@ toolchain parameters ================== ================================================================================================================================================================================================================================= ================= **Parameter name** **Description** **Default value** ================== ================================================================================================================================================================================================================================= ================= -``onlytcmod`` Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored). False -``toolchainopts`` Extra options for compilers None +``onlytcmod`` Boolean/string to indicate if the toolchain should only load the environment with module (True) or also set all other variables (False) like compiler CC etc (if string: comma separated list of variables that will be ignored). False +``toolchainopts`` Extra options for compilers None ================== ================================================================================================================================================================================================================================= ================= @@ -41,47 +41,48 @@ build parameters =============================== ========================================================================================================================================= ================= **Parameter name** **Description** **Default value** =============================== ========================================================================================================================================= ================= -``banned_linked_shared_libs`` List of shared libraries (names, file names, or paths) which are not allowed to be linked in any installed binary/library [] -``bin_lib_subdirs`` List of subdirectories for binaries and libraries, which is used during sanity check to check RPATH linking and banned/required libraries [] -``bitbucket_account`` Bitbucket account name to be used to resolve template values in source URLs "%(namelower)s" -``buildopts`` Extra options passed to make step (default already has -j X) "" -``checksums`` Checksums for sources and patches [] -``configopts`` Extra options passed to configure (default already has --prefix) "" -``cuda_compute_capabilities`` List of CUDA compute capabilities to build with (if supported) [] -``download_instructions`` Specify steps to aquire necessary file, if obtaining it is difficult "" -``easyblock`` EasyBlock to use for building; if set to None, an easyblock is selected based on the software name None -``easybuild_version`` EasyBuild-version this spec-file was written for None -``enhance_sanity_check`` Indicate that additional sanity check commands & paths should enhance the existin sanity check, not replace it False -``fix_bash_shebang_for`` List of files for which Bash shebang should be fixed to '#!/usr/bin/env bash' (glob patterns supported) None -``fix_perl_shebang_for`` List of files for which Perl shebang should be fixed to '#!/usr/bin/env perl' (glob patterns supported) None -``fix_python_shebang_for`` List of files for which Python shebang should be fixed to '#!/usr/bin/env python' (glob patterns supported) None -``github_account`` GitHub account name to be used to resolve template values in source URLs "%(namelower)s" -``hidden`` Install module file as 'hidden' by prefixing its version with '.' False -``installopts`` Extra options for installation "" -``maxparallel`` Max degree of parallelism None -``parallel`` Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit) None -``patches`` List of patches to apply [] -``postinstallcmds`` Commands to run after the install step. [] -``postinstallpatches`` Patch files to apply after running the install step. [] -``prebuildopts`` Extra options pre-passed to build command. "" -``preconfigopts`` Extra options pre-passed to configure. "" -``preinstallopts`` Extra prefix options for installation. "" -``pretestopts`` Extra prefix options for test. "" -``required_linked_shared_libs`` List of shared libraries (names, file names, or paths) which must be linked in all installed binaries/libraries [] -``runtest`` Indicates if a test should be run after make; should specify argument after make (for e.g.,"test" for make test) None -``sanity_check_commands`` format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h') [] -``sanity_check_paths`` List of files and directories to check (format: {'files':, 'dirs':}) {} -``skip`` Skip existing software False -``skipsteps`` Skip these steps [] -``source_urls`` List of URLs for source files [] -``sources`` List of source files [] -``stop`` Keyword to halt the build process after a certain step. None -``testopts`` Extra options for test. "" -``tests`` List of test-scripts to run after install. A test script should return a non-zero exit status to fail [] -``unpack_options`` Extra options for unpacking source "" -``unwanted_env_vars`` List of environment variables that shouldn't be set during build [] -``versionprefix`` Additional prefix for software version (placed before version and toolchain name) "" -``versionsuffix`` Additional suffix for software version (placed after toolchain name) "" +``banned_linked_shared_libs`` List of shared libraries (names, file names, or paths) which are not allowed to be linked in any installed binary/library [] +``bin_lib_subdirs`` List of subdirectories for binaries and libraries, which is used during sanity check to check RPATH linking and banned/required libraries [] +``bitbucket_account`` Bitbucket account name to be used to resolve template values in source URLs "%(namelower)s" +``buildopts`` Extra options passed to make step (default already has -j X) "" +``checksums`` Checksums for sources and patches [] +``configopts`` Extra options passed to configure (default already has --prefix) "" +``cuda_compute_capabilities`` List of CUDA compute capabilities to build with (if supported) [] +``download_instructions`` Specify steps to acquire necessary file, if obtaining it is difficult "" +``easyblock`` EasyBlock to use for building; if set to None, an easyblock is selected based on the software name None +``easybuild_version`` EasyBuild-version this spec-file was written for None +``enhance_sanity_check`` Indicate that additional sanity check commands & paths should enhance the existing sanity check, not replace it False +``fix_bash_shebang_for`` List of files for which Bash shebang should be fixed to '#!/usr/bin/env bash' (glob patterns supported) None +``fix_perl_shebang_for`` List of files for which Perl shebang should be fixed to '#!/usr/bin/env perl' (glob patterns supported) None +``fix_python_shebang_for`` List of files for which Python shebang should be fixed to '#!/usr/bin/env python' (glob patterns supported) None +``github_account`` GitHub account name to be used to resolve template values in source URLs "%(namelower)s" +``hidden`` Install module file as 'hidden' by prefixing its version with '.' False +``installopts`` Extra options for installation "" +``maxparallel`` Max degree of parallelism None +``parallel`` Degree of parallelism for e.g. make (default: based on the number of cores, active cpuset and restrictions in ulimit) None +``patches`` List of patches to apply [] +``postinstallcmds`` Commands to run after the install step. [] +``postinstallmsgs`` Messages to print after running the install step. [] +``postinstallpatches`` Patch files to apply after running the install step. [] +``prebuildopts`` Extra options pre-passed to build command. "" +``preconfigopts`` Extra options pre-passed to configure. "" +``preinstallopts`` Extra prefix options for installation. "" +``pretestopts`` Extra prefix options for test. "" +``required_linked_shared_libs`` List of shared libraries (names, file names, or paths) which must be linked in all installed binaries/libraries [] +``runtest`` Indicates if a test should be run after make; should specify argument after make (for e.g.,"test" for make test) None +``sanity_check_commands`` format: [(name, options)] e.g. [('gzip','-h')]. Using a non-tuple is equivalent to (name, '-h') [] +``sanity_check_paths`` List of files and directories to check (format: {'files':, 'dirs':}) {} +``skip`` Skip existing software False +``skipsteps`` Skip these steps [] +``source_urls`` List of URLs for source files [] +``sources`` List of source files [] +``stop`` Keyword to halt the build process after a certain step. None +``testopts`` Extra options for test. "" +``tests`` List of test-scripts to run after install. A test script should return a non-zero exit status to fail [] +``unpack_options`` Extra options for unpacking source "" +``unwanted_env_vars`` List of environment variables that shouldn't be set during build [] +``versionprefix`` Additional prefix for software version (placed before version and toolchain name) "" +``versionsuffix`` Additional suffix for software version (placed after toolchain name) "" =============================== ========================================================================================================================================= ================= @@ -91,13 +92,13 @@ file-management parameters ======================== ============================================================================================================================== ================= **Parameter name** **Description** **Default value** ======================== ============================================================================================================================== ================= -``buildininstalldir`` Boolean to build (True) or not build (False) in the installation directory False -``cleanupoldbuild`` Boolean to remove (True) or backup (False) the previous build directory with identical name or not. True -``cleanupoldinstall`` Boolean to remove (True) or backup (False) the previous install directory with identical name or not. True -``dontcreateinstalldir`` Boolean to create (False) or not create (True) the install directory False -``keeppreviousinstall`` Boolean to keep the previous installation with identical name. Experts only! False -``keepsymlinks`` Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied False -``start_dir`` Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path. None +``buildininstalldir`` Boolean to build (True) or not build (False) in the installation directory False +``cleanupoldbuild`` Boolean to remove (True) or backup (False) the previous build directory with identical name or not. True +``cleanupoldinstall`` Boolean to remove (True) or backup (False) the previous install directory with identical name or not. True +``dontcreateinstalldir`` Boolean to create (False) or not create (True) the install directory False +``keeppreviousinstall`` Boolean to keep the previous installation with identical name. Experts only! False +``keepsymlinks`` Boolean to determine whether symlinks are to be kept during copying or if the content of the files pointed to should be copied False +``start_dir`` Path to start the make in. If the path is absolute, use that path. If not, this is added to the guessed path. None ======================== ============================================================================================================================== ================= @@ -107,14 +108,14 @@ dependencies parameters =========================== ===================================================================== ================= **Parameter name** **Description** **Default value** =========================== ===================================================================== ================= -``allow_system_deps`` Allow listed system dependencies (format: (, )) [] -``builddependencies`` List of build dependencies [] -``dependencies`` List of dependencies [] -``hiddendependencies`` List of dependencies available as hidden modules [] -``moddependpaths`` Absolute path(s) to prepend to MODULEPATH before loading dependencies None -``multi_deps`` Dict of lists of dependency versions over which to iterate {} -``multi_deps_load_default`` Load module for first version listed in multi_deps by default True -``osdependencies`` OS dependencies that should be present on the system [] +``allow_system_deps`` Allow listed system dependencies (format: (, )) [] +``builddependencies`` List of build dependencies [] +``dependencies`` List of dependencies [] +``hiddendependencies`` List of dependencies available as hidden modules [] +``moddependpaths`` Absolute path(s) to prepend to MODULEPATH before loading dependencies None +``multi_deps`` Dict of lists of dependency versions over which to iterate {} +``multi_deps_load_default`` Load module for first version listed in multi_deps by default True +``osdependencies`` OS dependencies that should be present on the system [] =========================== ===================================================================== ================= @@ -124,12 +125,12 @@ license parameters ======================= =================================================================================================================================================== ================= **Parameter name** **Description** **Default value** ======================= =================================================================================================================================================== ================= -``accept_eula`` Accepted End User License Agreement (EULA) for this software False -``group`` Name of the user group for which the software should be available; format: string or 2-tuple with group name + custom error for users outside group None -``key`` Key for installing software None -``license_file`` License file for software None -``license_server`` License server for software None -``license_server_port`` Port for license server None +``accept_eula`` Accepted End User License Agreement (EULA) for this software False +``group`` Name of the user group for which the software should be available; format: string or 2-tuple with group name + custom error for users outside group None +``key`` Key for installing software None +``license_file`` License file for software None +``license_server`` License server for software None +``license_server_port`` Port for license server None ======================= =================================================================================================================================================== ================= @@ -139,12 +140,12 @@ extensions parameters ========================== ========================================================================================================== ================= **Parameter name** **Description** **Default value** ========================== ========================================================================================================== ================= -``exts_classmap`` Map of extension name to class for handling build and installation. {} -``exts_default_options`` List of default options for extensions {} -``exts_defaultclass`` List of module for and name of the default extension class None -``exts_download_dep_fail`` Fail if downloaded dependencies are detected for extensions False -``exts_filter`` Extension filter details: template for cmd and input to cmd (templates for ext_name, ext_version and src). None -``exts_list`` List with extensions added to the base installation [] +``exts_classmap`` Map of extension name to class for handling build and installation. {} +``exts_default_options`` List of default options for extensions {} +``exts_defaultclass`` List of module for and name of the default extension class None +``exts_download_dep_fail`` Fail if downloaded dependencies are detected for extensions False +``exts_filter`` Extension filter details: template for cmd and input to cmd (templates for ext_name, ext_version and src). None +``exts_list`` List with extensions added to the base installation [] ========================== ========================================================================================================== ================= @@ -154,27 +155,27 @@ modules parameters ============================== ================================================================================================================================================================================== ================= **Parameter name** **Description** **Default value** ============================== ================================================================================================================================================================================== ================= -``allow_prepend_abs_path`` Allow specifying absolute paths to prepend in modextrapaths False -``citing`` Free-form text that describes how the software should be cited in publications None -``docpaths`` List of paths for documentation relative to installation directory None -``examples`` Free-form text with examples on using the software None -``include_modpath_extensions`` Include $MODULEPATH extensions specified by module naming scheme. True -``modaliases`` Aliases to be defined in module file {} -``modaltsoftname`` Module name to use (rather than using software name None -``modextrapaths`` Extra paths to be prepended in module file {} -``modextravars`` Extra environment variables to be added to module file {} -``modloadmsg`` Message that should be printed when generated module is loaded {} -``modluafooter`` Footer to include in generated module file (Lua syntax) "" -``modtclfooter`` Footer to include in generated module file (Tcl syntax) "" -``module_depends_on`` Use depends_on (Lmod 7.6.1+) for dependencies in generated module (implies recursive unloading of modules). False -``moduleclass`` Module class to be used for this software "base" -``moduleforceunload`` Force unload of all modules when loading the extension False -``moduleloadnoconflict`` Don't check for conflicts, unload other versions instead False -``recursive_module_unload`` Recursive unload of all dependencies when unloading module (True/False to hard enable/disable; None implies honoring the --recursive-module-unload EasyBuild configuration setting None -``site_contacts`` String/list of strings with site contacts for the software None -``upstream_contacts`` String/list of strings with upstream contact addresses (e.g., support e-mail, mailing list, bugtracker) None -``usage`` Usage instructions for the software None -``whatis`` List of brief (one line) description entries for the software None +``allow_prepend_abs_path`` Allow specifying absolute paths to prepend in modextrapaths False +``citing`` Free-form text that describes how the software should be cited in publications None +``docpaths`` List of paths for documentation relative to installation directory None +``examples`` Free-form text with examples on using the software None +``include_modpath_extensions`` Include $MODULEPATH extensions specified by module naming scheme. True +``modaliases`` Aliases to be defined in module file {} +``modaltsoftname`` Module name to use (rather than using software name None +``modextrapaths`` Extra paths to be prepended in module file {} +``modextravars`` Extra environment variables to be added to module file {} +``modloadmsg`` Message that should be printed when generated module is loaded {} +``modluafooter`` Footer to include in generated module file (Lua syntax) "" +``modtclfooter`` Footer to include in generated module file (Tcl syntax) "" +``module_depends_on`` Use depends_on (Lmod 7.6.1+) for dependencies in generated module (implies recursive unloading of modules). False +``moduleclass`` Module class to be used for this software "base" +``moduleforceunload`` Force unload of all modules when loading the extension False +``moduleloadnoconflict`` Don't check for conflicts, unload other versions instead False +``recursive_module_unload`` Recursive unload of all dependencies when unloading module (True/False to hard enable/disable; None implies honoring the --recursive-module-unload EasyBuild configuration setting None +``site_contacts`` String/list of strings with site contacts for the software None +``upstream_contacts`` String/list of strings with upstream contact addresses (e.g., support e-mail, mailing list, bugtracker) None +``usage`` Usage instructions for the software None +``whatis`` List of brief (one line) description entries for the software None ============================== ================================================================================================================================================================================== ================= @@ -184,9 +185,9 @@ other parameters ================== =========================================================================================================================== ================= **Parameter name** **Description** **Default value** ================== =========================================================================================================================== ================= -``block`` List of other 'block' sections on which this block depends (only relevant in easyconfigs with subblocks) None -``buildstats`` A list of dicts with build statistics None -``deprecated`` String specifying reason why this easyconfig file is deprecated and will be archived in the next major release of EasyBuild False +``block`` List of other 'block' sections on which this block depends (only relevant in easyconfigs with subblocks) None +``buildstats`` A list of dicts with build statistics None +``deprecated`` String specifying reason why this easyconfig file is deprecated and will be archived in the next major release of EasyBuild False ================== =========================================================================================================================== ================= diff --git a/docs/version-specific/easyconfig_templates.rst b/docs/version-specific/easyconfig_templates.rst index 841b377f..a5057736 100644 --- a/docs/version-specific/easyconfig_templates.rst +++ b/docs/version-specific/easyconfig_templates.rst @@ -6,15 +6,15 @@ Template names/values derived from easyconfig instance ------------------------------------------------------ =========================== ============================= -Template name Template value +Template name Template value =========================== ============================= -``%(module_name)s`` Module name +``%(module_name)s`` Module name ``%(nameletter)s`` First letter of software name -``%(toolchain_name)s`` Toolchain name -``%(toolchain_version)s`` Toolchain version -``%(version_major_minor)s`` Major.Minor version -``%(version_major)s`` Major version -``%(version_minor)s`` Minor version +``%(toolchain_name)s`` Toolchain name +``%(toolchain_version)s`` Toolchain version +``%(version_major_minor)s`` Major.Minor version +``%(version_major)s`` Major version +``%(version_minor)s`` Minor version =========================== ============================= @@ -22,20 +22,20 @@ Template names/values for (short) software versions --------------------------------------------------- ==================== ============================================ -Template name Template value +Template name Template value ==================== ============================================ -``%(cudashortver)s`` short version for CUDA (.) -``%(cudaver)s`` full version for CUDA +``%(cudashortver)s`` short version for CUDA (.) +``%(cudaver)s`` full version for CUDA ``%(cudashortver)s`` short version for CUDAcore (.) -``%(cudaver)s`` full version for CUDAcore -``%(javashortver)s`` short version for Java (.) -``%(javaver)s`` full version for Java -``%(perlshortver)s`` short version for Perl (.) -``%(perlver)s`` full version for Perl -``%(pyshortver)s`` short version for Python (.) -``%(pyver)s`` full version for Python -``%(rshortver)s`` short version for R (.) -``%(rver)s`` full version for R +``%(cudaver)s`` full version for CUDAcore +``%(javashortver)s`` short version for Java (.) +``%(javaver)s`` full version for Java +``%(perlshortver)s`` short version for Perl (.) +``%(perlver)s`` full version for Perl +``%(pyshortver)s`` short version for Python (.) +``%(pyver)s`` full version for Python +``%(rshortver)s`` short version for R (.) +``%(rver)s`` full version for R ==================== ============================================ @@ -54,9 +54,9 @@ Lowercase values of template values ----------------------------------- ======================= ================================= -Template name Template value +Template name Template value ======================= ================================= -``%(namelower)s`` lower case of value of name +``%(namelower)s`` lower case of value of name ``%(nameletterlower)s`` lower case of value of nameletter ======================= ================================= @@ -64,9 +64,9 @@ Template values set outside EasyBlock runstep --------------------------------------------- ================== ====================== -Template name Template value +Template name Template value ================== ====================== -``%(builddir)s`` Build directory +``%(builddir)s`` Build directory ``%(installdir)s`` Installation directory ================== ====================== @@ -74,76 +74,76 @@ Template values which are defined dynamically --------------------------------------------- ================================= ========================================================================================================================================================================== -Template name Template value +Template name Template value ================================= ========================================================================================================================================================================== -``%(arch)s`` System architecture (e.g. x86_64, aarch64, ppc64le, ...) -``%(mpi_cmd_prefix)s`` Prefix command for running MPI programs (with default number of ranks) +``%(arch)s`` System architecture (e.g. x86_64, aarch64, ppc64le, ...) +``%(mpi_cmd_prefix)s`` Prefix command for running MPI programs (with default number of ranks) ``%(cuda_compute_capabilities)s`` Comma-separated list of CUDA compute capabilities, as specified via --cuda-compute-capabilities configuration option or via cuda_compute_capabilities easyconfig parameter -``%(cuda_cc_cmake)s`` List of CUDA compute capabilities suitable for use with $CUDAARCHS in CMake 3.18+ -``%(cuda_cc_space_sep)s`` Space-separated list of CUDA compute capabilities -``%(cuda_cc_semicolon_sep)s`` Semicolon-separated list of CUDA compute capabilities -``%(cuda_sm_comma_sep)s`` Comma-separated list of sm_* values that correspond with CUDA compute capabilities -``%(cuda_sm_space_sep)s`` Space-separated list of sm_* values that correspond with CUDA compute capabilities +``%(cuda_cc_cmake)s`` List of CUDA compute capabilities suitable for use with $CUDAARCHS in CMake 3.18+ +``%(cuda_cc_space_sep)s`` Space-separated list of CUDA compute capabilities +``%(cuda_cc_semicolon_sep)s`` Semicolon-separated list of CUDA compute capabilities +``%(cuda_sm_comma_sep)s`` Comma-separated list of sm_* values that correspond with CUDA compute capabilities +``%(cuda_sm_space_sep)s`` Space-separated list of sm_* values that correspond with CUDA compute capabilities ================================= ========================================================================================================================================================================== Template constants that can be used in easyconfigs -------------------------------------------------- ======================== ============================================================================================================= ======================================================================================== -Constant Template value Template name +Constant Template value Template name ======================== ============================================================================================================= ======================================================================================== -``APACHE_SOURCE`` apache.org source url ``https://archive.apache.org/dist/%(namelower)s`` -``BITBUCKET_SOURCE`` bitbucket.org source url (namelower is used if bitbucket_account easyconfig parameter is not specified) ``https://bitbucket.org/%(bitbucket_account)s/%(namelower)s/get`` -``BITBUCKET_DOWNLOADS`` bitbucket.org downloads url (namelower is used if bitbucket_account easyconfig parameter is not specified) ``https://bitbucket.org/%(bitbucket_account)s/%(namelower)s/downloads`` -``CRAN_SOURCE`` CRAN (contrib) source url ``https://cran.r-project.org/src/contrib`` -``FTPGNOME_SOURCE`` http download for gnome ftp server ``https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s`` -``GITHUB_SOURCE`` GitHub source URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(name)s/archive`` -``GITHUB_LOWER_SOURCE`` GitHub source URL (lowercase name, namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(namelower)s/archive`` -``GITHUB_RELEASE`` GitHub release URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(name)s/releases/download/v%(version)s`` -``GITHUB_LOWER_RELEASE`` GitHub release URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s`` -``GNU_SAVANNAH_SOURCE`` download.savannah.gnu.org source url ``https://download-mirror.savannah.gnu.org/releases/%(namelower)s`` -``GNU_SOURCE`` gnu.org source url ``https://ftpmirror.gnu.org/gnu/%(namelower)s`` -``GOOGLECODE_SOURCE`` googlecode.com source url ``http://%(namelower)s.googlecode.com/files`` +``APACHE_SOURCE`` apache.org source url ``https://archive.apache.org/dist/%(namelower)s`` +``BITBUCKET_SOURCE`` bitbucket.org source url (namelower is used if bitbucket_account easyconfig parameter is not specified) ``https://bitbucket.org/%(bitbucket_account)s/%(namelower)s/get`` +``BITBUCKET_DOWNLOADS`` bitbucket.org downloads url (namelower is used if bitbucket_account easyconfig parameter is not specified) ``https://bitbucket.org/%(bitbucket_account)s/%(namelower)s/downloads`` +``CRAN_SOURCE`` CRAN (contrib) source url ``https://cran.r-project.org/src/contrib`` +``FTPGNOME_SOURCE`` http download for gnome ftp server ``https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s`` +``GITHUB_SOURCE`` GitHub source URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(name)s/archive`` +``GITHUB_LOWER_SOURCE`` GitHub source URL (lowercase name, namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(namelower)s/archive`` +``GITHUB_RELEASE`` GitHub release URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(name)s/releases/download/v%(version)s`` +``GITHUB_LOWER_RELEASE`` GitHub release URL (namelower is used if github_account easyconfig parameter is not specified) ``https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s`` +``GNU_SAVANNAH_SOURCE`` download.savannah.gnu.org source url ``https://download-mirror.savannah.gnu.org/releases/%(namelower)s`` +``GNU_SOURCE`` gnu.org source url ``https://ftpmirror.gnu.org/gnu/%(namelower)s`` +``GOOGLECODE_SOURCE`` googlecode.com source url ``http://%(namelower)s.googlecode.com/files`` ``LAUNCHPAD_SOURCE`` launchpad.net source url ``https://launchpad.net/%(namelower)s/%(version_major_minor)s.x/%(version)s/+download/`` -``PYPI_SOURCE`` pypi source url ``https://pypi.python.org/packages/source/%(nameletter)s/%(name)s`` -``PYPI_LOWER_SOURCE`` pypi source url (lowercase name) ``https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s`` -``R_SOURCE`` cran.r-project.org (base) source url ``https://cran.r-project.org/src/base/R-%(version_major)s`` -``SOURCEFORGE_SOURCE`` sourceforge.net source url ``https://download.sourceforge.net/%(namelower)s`` -``XORG_DATA_SOURCE`` xorg data source url ``https://xorg.freedesktop.org/archive/individual/data/`` -``XORG_LIB_SOURCE`` xorg lib source url ``https://xorg.freedesktop.org/archive/individual/lib/`` -``XORG_PROTO_SOURCE`` xorg proto source url ``https://xorg.freedesktop.org/archive/individual/proto/`` -``XORG_UTIL_SOURCE`` xorg util source url ``https://xorg.freedesktop.org/archive/individual/util/`` -``XORG_XCB_SOURCE`` xorg xcb source url ``https://xorg.freedesktop.org/archive/individual/xcb/`` -``SHLIB_EXT`` extension for shared libraries ``dylib`` -``SOURCE_TAR_GZ`` Source .tar.gz bundle ``%(name)s-%(version)s.tar.gz`` -``SOURCELOWER_TAR_GZ`` Source .tar.gz bundle with lowercase name ``%(namelower)s-%(version)s.tar.gz`` -``SOURCE_TAR_XZ`` Source .tar.xz bundle ``%(name)s-%(version)s.tar.xz`` -``SOURCELOWER_TAR_XZ`` Source .tar.xz bundle with lowercase name ``%(namelower)s-%(version)s.tar.xz`` -``SOURCE_TAR_BZ2`` Source .tar.bz2 bundle ``%(name)s-%(version)s.tar.bz2`` -``SOURCELOWER_TAR_BZ2`` Source .tar.bz2 bundle with lowercase name ``%(namelower)s-%(version)s.tar.bz2`` -``SOURCE_TGZ`` Source .tgz bundle ``%(name)s-%(version)s.tgz`` -``SOURCELOWER_TGZ`` Source .tgz bundle with lowercase name ``%(namelower)s-%(version)s.tgz`` -``SOURCE_TXZ`` Source .txz bundle ``%(name)s-%(version)s.txz`` -``SOURCELOWER_TXZ`` Source .txz bundle with lowercase name ``%(namelower)s-%(version)s.txz`` -``SOURCE_TBZ2`` Source .tbz2 bundle ``%(name)s-%(version)s.tbz2`` -``SOURCELOWER_TBZ2`` Source .tbz2 bundle with lowercase name ``%(namelower)s-%(version)s.tbz2`` -``SOURCE_TB2`` Source .tb2 bundle ``%(name)s-%(version)s.tb2`` -``SOURCELOWER_TB2`` Source .tb2 bundle with lowercase name ``%(namelower)s-%(version)s.tb2`` -``SOURCE_GTGZ`` Source .gtgz bundle ``%(name)s-%(version)s.gtgz`` -``SOURCELOWER_GTGZ`` Source .gtgz bundle with lowercase name ``%(namelower)s-%(version)s.gtgz`` -``SOURCE_ZIP`` Source .zip bundle ``%(name)s-%(version)s.zip`` -``SOURCELOWER_ZIP`` Source .zip bundle with lowercase name ``%(namelower)s-%(version)s.zip`` -``SOURCE_TAR`` Source .tar bundle ``%(name)s-%(version)s.tar`` -``SOURCELOWER_TAR`` Source .tar bundle with lowercase name ``%(namelower)s-%(version)s.tar`` -``SOURCE_XZ`` Source .xz bundle ``%(name)s-%(version)s.xz`` -``SOURCELOWER_XZ`` Source .xz bundle with lowercase name ``%(namelower)s-%(version)s.xz`` -``SOURCE_TAR_Z`` Source .tar.Z bundle ``%(name)s-%(version)s.tar.Z`` -``SOURCELOWER_TAR_Z`` Source .tar.Z bundle with lowercase name ``%(namelower)s-%(version)s.tar.Z`` -``SOURCE_WHL`` Generic (non-compiled) Python 2 & Python 3 wheel package ``%(name)s-%(version)s-py2.py3-none-any.whl`` -``SOURCELOWER_WHL`` Generic (non-compiled) Python 2 & Python 3 wheel package with lowercase name ``%(namelower)s-%(version)s-py2.py3-none-any.whl`` -``SOURCE_PY2_WHL`` Generic (non-compiled) Python 2 wheel package ``%(name)s-%(version)s-py2-none-any.whl`` -``SOURCELOWER_PY2_WHL`` Generic (non-compiled) Python 2 wheel package with lowercase name ``%(namelower)s-%(version)s-py2-none-any.whl`` -``SOURCE_PY3_WHL`` Generic (non-compiled) Python 3 wheel package ``%(name)s-%(version)s-py3-none-any.whl`` -``SOURCELOWER_PY3_WHL`` Generic (non-compiled) Python 3 wheel package with lowercase name ``%(namelower)s-%(version)s-py3-none-any.whl`` +``PYPI_SOURCE`` pypi source url ``https://pypi.python.org/packages/source/%(nameletter)s/%(name)s`` +``PYPI_LOWER_SOURCE`` pypi source url (lowercase name) ``https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s`` +``R_SOURCE`` cran.r-project.org (base) source url ``https://cran.r-project.org/src/base/R-%(version_major)s`` +``SOURCEFORGE_SOURCE`` sourceforge.net source url ``https://download.sourceforge.net/%(namelower)s`` +``XORG_DATA_SOURCE`` xorg data source url ``https://xorg.freedesktop.org/archive/individual/data/`` +``XORG_LIB_SOURCE`` xorg lib source url ``https://xorg.freedesktop.org/archive/individual/lib/`` +``XORG_PROTO_SOURCE`` xorg proto source url ``https://xorg.freedesktop.org/archive/individual/proto/`` +``XORG_UTIL_SOURCE`` xorg util source url ``https://xorg.freedesktop.org/archive/individual/util/`` +``XORG_XCB_SOURCE`` xorg xcb source url ``https://xorg.freedesktop.org/archive/individual/xcb/`` +``SHLIB_EXT`` extension for shared libraries ``dylib`` +``SOURCE_TAR_GZ`` Source .tar.gz bundle ``%(name)s-%(version)s.tar.gz`` +``SOURCELOWER_TAR_GZ`` Source .tar.gz bundle with lowercase name ``%(namelower)s-%(version)s.tar.gz`` +``SOURCE_TAR_XZ`` Source .tar.xz bundle ``%(name)s-%(version)s.tar.xz`` +``SOURCELOWER_TAR_XZ`` Source .tar.xz bundle with lowercase name ``%(namelower)s-%(version)s.tar.xz`` +``SOURCE_TAR_BZ2`` Source .tar.bz2 bundle ``%(name)s-%(version)s.tar.bz2`` +``SOURCELOWER_TAR_BZ2`` Source .tar.bz2 bundle with lowercase name ``%(namelower)s-%(version)s.tar.bz2`` +``SOURCE_TGZ`` Source .tgz bundle ``%(name)s-%(version)s.tgz`` +``SOURCELOWER_TGZ`` Source .tgz bundle with lowercase name ``%(namelower)s-%(version)s.tgz`` +``SOURCE_TXZ`` Source .txz bundle ``%(name)s-%(version)s.txz`` +``SOURCELOWER_TXZ`` Source .txz bundle with lowercase name ``%(namelower)s-%(version)s.txz`` +``SOURCE_TBZ2`` Source .tbz2 bundle ``%(name)s-%(version)s.tbz2`` +``SOURCELOWER_TBZ2`` Source .tbz2 bundle with lowercase name ``%(namelower)s-%(version)s.tbz2`` +``SOURCE_TB2`` Source .tb2 bundle ``%(name)s-%(version)s.tb2`` +``SOURCELOWER_TB2`` Source .tb2 bundle with lowercase name ``%(namelower)s-%(version)s.tb2`` +``SOURCE_GTGZ`` Source .gtgz bundle ``%(name)s-%(version)s.gtgz`` +``SOURCELOWER_GTGZ`` Source .gtgz bundle with lowercase name ``%(namelower)s-%(version)s.gtgz`` +``SOURCE_ZIP`` Source .zip bundle ``%(name)s-%(version)s.zip`` +``SOURCELOWER_ZIP`` Source .zip bundle with lowercase name ``%(namelower)s-%(version)s.zip`` +``SOURCE_TAR`` Source .tar bundle ``%(name)s-%(version)s.tar`` +``SOURCELOWER_TAR`` Source .tar bundle with lowercase name ``%(namelower)s-%(version)s.tar`` +``SOURCE_XZ`` Source .xz bundle ``%(name)s-%(version)s.xz`` +``SOURCELOWER_XZ`` Source .xz bundle with lowercase name ``%(namelower)s-%(version)s.xz`` +``SOURCE_TAR_Z`` Source .tar.Z bundle ``%(name)s-%(version)s.tar.Z`` +``SOURCELOWER_TAR_Z`` Source .tar.Z bundle with lowercase name ``%(namelower)s-%(version)s.tar.Z`` +``SOURCE_WHL`` Generic (non-compiled) Python 2 & Python 3 wheel package ``%(name)s-%(version)s-py2.py3-none-any.whl`` +``SOURCELOWER_WHL`` Generic (non-compiled) Python 2 & Python 3 wheel package with lowercase name ``%(namelower)s-%(version)s-py2.py3-none-any.whl`` +``SOURCE_PY2_WHL`` Generic (non-compiled) Python 2 wheel package ``%(name)s-%(version)s-py2-none-any.whl`` +``SOURCELOWER_PY2_WHL`` Generic (non-compiled) Python 2 wheel package with lowercase name ``%(namelower)s-%(version)s-py2-none-any.whl`` +``SOURCE_PY3_WHL`` Generic (non-compiled) Python 3 wheel package ``%(name)s-%(version)s-py3-none-any.whl`` +``SOURCELOWER_PY3_WHL`` Generic (non-compiled) Python 3 wheel package with lowercase name ``%(namelower)s-%(version)s-py3-none-any.whl`` ======================== ============================================================================================================= ======================================================================================== diff --git a/docs/version-specific/generic_easyblocks.rst b/docs/version-specific/generic_easyblocks.rst index de762df2..f037e59b 100644 --- a/docs/version-specific/generic_easyblocks.rst +++ b/docs/version-specific/generic_easyblocks.rst @@ -10,7 +10,7 @@ Overview of generic easyblocks ============================== -:ref:`BinariesTarball` - :ref:`Binary` - :ref:`BuildEnv` - :ref:`Bundle` - :ref:`CMakeMake` - :ref:`CMakeMakeCp` - :ref:`CMakeNinja` - :ref:`CMakePythonPackage` - :ref:`CmdCp` - :ref:`Conda` - :ref:`ConfigureMake` - :ref:`ConfigureMakePythonPackage` - :ref:`CrayToolchain` - :ref:`FortranPythonPackage` - :ref:`GoPackage` - :ref:`IntelBase` - :ref:`JAR` - :ref:`MakeCp` - :ref:`MesonNinja` - :ref:`ModuleRC` - :ref:`OCamlPackage` - :ref:`OctavePackage` - :ref:`PackedBinary` - :ref:`PerlModule` - :ref:`PythonBundle` - :ref:`PythonPackage` - :ref:`RPackage` - :ref:`Rpm` - :ref:`RubyGem` - :ref:`SCons` - :ref:`SystemCompiler` - :ref:`SystemMPI` - :ref:`Tarball` - :ref:`Toolchain` - :ref:`VSCPythonPackage` - :ref:`VersionIndependentPythonPackage` - :ref:`Waf` +:ref:`BinariesTarball` - :ref:`Binary` - :ref:`BuildEnv` - :ref:`Bundle` - :ref:`CMakeMake` - :ref:`CMakeMakeCp` - :ref:`CMakeNinja` - :ref:`CMakePythonPackage` - :ref:`CmdCp` - :ref:`Conda` - :ref:`ConfigureMake` - :ref:`ConfigureMakePythonPackage` - :ref:`CrayToolchain` - :ref:`FortranPythonPackage` - :ref:`GoPackage` - :ref:`IntelBase` - :ref:`JAR` - :ref:`JuliaBundle` - :ref:`JuliaPackage` - :ref:`MakeCp` - :ref:`MesonNinja` - :ref:`ModuleRC` - :ref:`OCamlPackage` - :ref:`OctavePackage` - :ref:`PackedBinary` - :ref:`PerlModule` - :ref:`PythonBundle` - :ref:`PythonPackage` - :ref:`RPackage` - :ref:`Rpm` - :ref:`RubyGem` - :ref:`SCons` - :ref:`SystemCompiler` - :ref:`SystemMPI` - :ref:`Tarball` - :ref:`Toolchain` - :ref:`VSCPythonPackage` - :ref:`VersionIndependentPythonPackage` - :ref:`Waf` .. _BinariesTarball: @@ -27,9 +27,9 @@ Extra easyconfig parameters specific to ``BinariesTarball`` easyblock ==================== ============================================================================================================================================================= ============= easyconfig parameter description default value ==================== ============================================================================================================================================================= ============= -``install_type`` Defaults to extract tarball into clean directory. Options: 'merge' merges tarball to existing directory, 'subdir' extracts tarball into its own sub-directory ``None`` -``options`` Dictionary with extension options. ``{}`` -``preinstall_cmd`` Command to execute before installation ``None`` +``install_type`` Defaults to extract tarball into clean directory. Options: 'merge' merges tarball to existing directory, 'subdir' extracts tarball into its own sub-directory ``None`` +``options`` Dictionary with extension options. ``{}`` +``preinstall_cmd`` Command to execute before installation ``None`` ==================== ============================================================================================================================================================= ============= Customised steps in ``BinariesTarball`` easyblock @@ -52,10 +52,10 @@ Extra easyconfig parameters specific to ``Binary`` easyblock ==================== =============================================================================================================================================== ============= easyconfig parameter description default value ==================== =============================================================================================================================================== ============= -``extract_sources`` Whether or not to extract sources ``False`` -``install_cmd`` Install command to be used. ``None`` -``prepend_to_path`` Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself. ``['']`` -``staged_install`` Perform staged installation via subdirectory of build directory ``False`` +``extract_sources`` Whether or not to extract sources ``False`` +``install_cmd`` Install command to be used. ``None`` +``prepend_to_path`` Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself. ``['']`` +``staged_install`` Perform staged installation via subdirectory of build directory ``False`` ==================== =============================================================================================================================================== ============= Customised steps in ``Binary`` easyblock @@ -107,13 +107,13 @@ Extra easyconfig parameters specific to ``BuildEnv`` easyblock =============================== =========================================================================== ============= easyconfig parameter description default value =============================== =========================================================================== ============= -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -``sanity_check_all_components`` Enable sanity checks for all components ``False`` -``sanity_check_components`` List of components for which to run sanity checks ``[]`` +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` =============================== =========================================================================== ============= .. _Bundle: @@ -131,13 +131,13 @@ Extra easyconfig parameters specific to ``Bundle`` easyblock =============================== =========================================================================== ============= easyconfig parameter description default value =============================== =========================================================================== ============= -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -``sanity_check_all_components`` Enable sanity checks for all components ``False`` -``sanity_check_components`` List of components for which to run sanity checks ``[]`` +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` =============================== =========================================================================== ============= Customised steps in ``Bundle`` easyblock @@ -182,27 +182,28 @@ Support for configuring build with CMake instead of traditional configure script Extra easyconfig parameters specific to ``CMakeMake`` easyblock --------------------------------------------------------------- -========================= ================================================================================================================================================================================================== ================== -easyconfig parameter description default value -========================= ================================================================================================================================================================================================== ================== -``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` -``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` -``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` -``configure_cmd`` Configure command to use ``"cmake"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``generator`` Build file generator to use. None to use CMakes default ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Install command to use ``"make install"`` -``install_target_subdir`` Subdirectory to use as installation target ``None`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``separate_build_dir`` Perform build in a separate directory ``True`` -``srcdir`` Source directory location to provide to cmake command ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` -========================= ================================================================================================================================================================================================== ================== +================================ ================================================================================================================================================================================================== ================== +easyconfig parameter description default value +================================ ================================================================================================================================================================================================== ================== +``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` +``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` +``configure_cmd`` Configure command to use ``"cmake"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``configure_without_installdir`` Avoid passing an install directory to the configure command (such as via --prefix) ``False`` +``generator`` Build file generator to use. None to use CMakes default ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Install command to use ``"make install"`` +``install_target_subdir`` Subdirectory to use as installation target ``None`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``separate_build_dir`` Perform build in a separate directory ``True`` +``srcdir`` Source directory location to provide to cmake command ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` +================================ ================================================================================================================================================================================================== ================== Customised steps in ``CMakeMake`` easyblock ------------------------------------------- @@ -260,29 +261,30 @@ Software configured with CMake but without 'make install' step Extra easyconfig parameters specific to ``CMakeMakeCp`` easyblock ----------------------------------------------------------------- -========================= ================================================================================================================================================================================================== ================== -easyconfig parameter description default value -========================= ================================================================================================================================================================================================== ================== -``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` -``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` -``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` -``configure_cmd`` Configure command to use ``"cmake"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``files_to_copy`` List of files or dirs to copy ``None`` -``generator`` Build file generator to use. None to use CMakes default ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Install command to use ``"make install"`` -``install_target_subdir`` Subdirectory to use as installation target ``None`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``separate_build_dir`` Perform build in a separate directory ``True`` -``srcdir`` Source directory location to provide to cmake command ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` -``with_configure`` Run configure script before building ``False`` -========================= ================================================================================================================================================================================================== ================== +================================ ================================================================================================================================================================================================== ================== +easyconfig parameter description default value +================================ ================================================================================================================================================================================================== ================== +``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` +``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` +``configure_cmd`` Configure command to use ``"cmake"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``configure_without_installdir`` Avoid passing an install directory to the configure command (such as via --prefix) ``False`` +``files_to_copy`` List of files or dirs to copy ``None`` +``generator`` Build file generator to use. None to use CMakes default ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Install command to use ``"make install"`` +``install_target_subdir`` Subdirectory to use as installation target ``None`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``separate_build_dir`` Perform build in a separate directory ``True`` +``srcdir`` Source directory location to provide to cmake command ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` +``with_configure`` Run configure script before building ``False`` +================================ ================================================================================================================================================================================================== ================== Customised steps in ``CMakeMakeCp`` easyblock --------------------------------------------- @@ -301,27 +303,28 @@ Support for configuring with CMake, building and installing with MesonNinja. Extra easyconfig parameters specific to ``CMakeNinja`` easyblock ---------------------------------------------------------------- -========================= ================================================================================================================================================================================================== ================== -easyconfig parameter description default value -========================= ================================================================================================================================================================================================== ================== -``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` -``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` -``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` -``configure_cmd`` Configure command to use ``"cmake"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``generator`` Build file generator to use. None to use CMakes default ``"Ninja"`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Install command to use ``"make install"`` -``install_target_subdir`` Subdirectory to use as installation target ``None`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``separate_build_dir`` Perform build in a separate directory ``True`` -``srcdir`` Source directory location to provide to cmake command ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` -========================= ================================================================================================================================================================================================== ================== +================================ ================================================================================================================================================================================================== ================== +easyconfig parameter description default value +================================ ================================================================================================================================================================================================== ================== +``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` +``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` +``configure_cmd`` Configure command to use ``"cmake"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``configure_without_installdir`` Avoid passing an install directory to the configure command (such as via --prefix) ``False`` +``generator`` Build file generator to use. None to use CMakes default ``"Ninja"`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Install command to use ``"make install"`` +``install_target_subdir`` Subdirectory to use as installation target ``None`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``separate_build_dir`` Perform build in a separate directory ``True`` +``srcdir`` Source directory location to provide to cmake command ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` +================================ ================================================================================================================================================================================================== ================== Customised steps in ``CMakeNinja`` easyblock -------------------------------------------- @@ -347,48 +350,49 @@ Build a Python package and module with cmake. Extra easyconfig parameters specific to ``CMakePythonPackage`` easyblock ------------------------------------------------------------------------ -========================= ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -easyconfig parameter description default value -========================= ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` -``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` -``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` -``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``configure_cmd`` Configure command to use ``"cmake"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``generator`` Build file generator to use. None to use CMakes default ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Install command to use ``"make install"`` -``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``install_target_subdir`` Subdirectory to use as installation target ``None`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``None`` -``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``separate_build_dir`` Perform build in a separate directory ``True`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``srcdir`` Source directory location to provide to cmake command ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``zipped_egg`` Install as a zipped eggs ``False`` -========================= ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +================================ ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +================================ ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +``abs_path_compilers`` Specify compilers via absolute file path (not via command names) ``False`` +``allow_system_boost`` Always allow CMake to pick up on Boost installed in OS (even if Boost is included as a dependency) ``False`` +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_shared_libs`` Build shared library (instead of static library)None can be used to add no flag (usually results in static library) ``None`` +``build_type`` Build type for CMake, e.g. Release.Defaults to 'Release' or 'Debug' depending on toolchainopts[debug] ``None`` +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``configure_cmd`` Configure command to use ``"cmake"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``configure_without_installdir`` Avoid passing an install directory to the configure command (such as via --prefix) ``False`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``generator`` Build file generator to use. None to use CMakes default ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Install command to use ``"make install"`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``install_target_subdir`` Subdirectory to use as installation target ``None`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``None`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``separate_build_dir`` Perform build in a separate directory ``True`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``srcdir`` Source directory location to provide to cmake command ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` +================================ ======================================================================================================================================================================================================================================================================================================================== ======================================================================= Customised steps in ``CMakePythonPackage`` easyblock ---------------------------------------------------- @@ -408,23 +412,24 @@ Software with no configure, no make, and no make install step. Extra easyconfig parameters specific to ``CmdCp`` easyblock ----------------------------------------------------------- -======================== =================================================================================================================================================================================================== ==================================================== -easyconfig parameter description default value -======================== =================================================================================================================================================================================================== ==================================================== -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``cmds_map`` List of regex/template command (with 'source'/'target' fields) tuples ``[('.*', '$CC $CFLAGS %(source)s -o %(target)s')]`` -``configure_cmd`` Configure command to use ``"./configure"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``files_to_copy`` List of files or dirs to copy ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Install command to use ``"make install"`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` -``with_configure`` Run configure script before building ``False`` -======================== =================================================================================================================================================================================================== ==================================================== +================================ =================================================================================================================================================================================================== ==================================================== +easyconfig parameter description default value +================================ =================================================================================================================================================================================================== ==================================================== +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``cmds_map`` List of regex/template command (with 'source'/'target' fields) tuples ``[('.*', '$CC $CFLAGS %(source)s -o %(target)s')]`` +``configure_cmd`` Configure command to use ``"./configure"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``configure_without_installdir`` Avoid passing an install directory to the configure command (such as via --prefix) ``False`` +``files_to_copy`` List of files or dirs to copy ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Install command to use ``"make install"`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` +``with_configure`` Run configure script before building ``False`` +================================ =================================================================================================================================================================================================== ==================================================== Customised steps in ``CmdCp`` easyblock --------------------------------------- @@ -447,14 +452,14 @@ Extra easyconfig parameters specific to ``Conda`` easyblock ====================== =============================================================================================================================================== ============= easyconfig parameter description default value ====================== =============================================================================================================================================== ============= -``channels`` List of conda channels to pass to 'conda install' ``None`` -``environment_file`` Conda environment.yml file to use with 'conda env create' ``None`` -``extract_sources`` Whether or not to extract sources ``False`` -``install_cmd`` Install command to be used. ``None`` -``prepend_to_path`` Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself. ``['']`` -``remote_environment`` Remote conda environment to use with 'conda env create' ``None`` -``requirements`` Requirements specification to pass to 'conda install' ``None`` -``staged_install`` Perform staged installation via subdirectory of build directory ``False`` +``channels`` List of conda channels to pass to 'conda install' ``None`` +``environment_file`` Conda environment.yml file to use with 'conda env create' ``None`` +``extract_sources`` Whether or not to extract sources ``False`` +``install_cmd`` Install command to be used. ``None`` +``prepend_to_path`` Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself. ``['']`` +``remote_environment`` Remote conda environment to use with 'conda env create' ``None`` +``requirements`` Requirements specification to pass to 'conda install' ``None`` +``staged_install`` Perform staged installation via subdirectory of build directory ``False`` ====================== =============================================================================================================================================== ============= Customised steps in ``Conda`` easyblock @@ -473,30 +478,31 @@ Support for building and installing applications with configure/make/make instal Extra easyconfig parameters specific to ``ConfigureMake`` easyblock ------------------------------------------------------------------- -======================== =================================================================================================================================================================================================== ================== -easyconfig parameter description default value -======================== =================================================================================================================================================================================================== ================== -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``configure_cmd`` Configure command to use ``"./configure"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Install command to use ``"make install"`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` -======================== =================================================================================================================================================================================================== ================== +================================ =================================================================================================================================================================================================== ================== +easyconfig parameter description default value +================================ =================================================================================================================================================================================================== ================== +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``configure_cmd`` Configure command to use ``"./configure"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``configure_without_installdir`` Avoid passing an install directory to the configure command (such as via --prefix) ``False`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Install command to use ``"make install"`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` +================================ =================================================================================================================================================================================================== ================== Commonly used easyconfig parameters with ``ConfigureMake`` easyblock -------------------------------------------------------------------- ==================== ================================================================ -easyconfig parameter description +easyconfig parameter description ==================== ================================================================ configopts Extra options passed to configure (default already has --prefix) -buildopts Extra options passed to make step (default already has -j X) -installopts Extra options for installation +buildopts Extra options passed to make step (default already has -j X) +installopts Extra options for installation ==================== ================================================================ @@ -542,9 +548,10 @@ Example easyconfig for ``ConfigureMake`` easyblock (derives from :ref:`ConfigureMake`, :ref:`PythonPackage`) -Build a Python package and module with 'python configure/make/make install'. +Build a Python package and module with ``python configure``/``make``/``make install``. Implemented by using: + - a custom implementation of configure_step - using the build_step and install_step from ConfigureMake - using the sanity_check_step and make_module_extra from PythonPackage @@ -552,47 +559,48 @@ Build a Python package and module with 'python configure/make/make install'. Extra easyconfig parameters specific to ``ConfigureMakePythonPackage`` easyblock -------------------------------------------------------------------------------- -======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -easyconfig parameter description default value -======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``configure_cmd`` Configure command to use ``"./configure"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Install command to use ``"make install"`` -``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` -``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``zipped_egg`` Install as a zipped eggs ``False`` -======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +================================ ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +easyconfig parameter description default value +================================ ======================================================================================================================================================================================================================================================================================================================== ======================================================================= +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``configure_cmd`` Configure command to use ``"./configure"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``configure_without_installdir`` Avoid passing an install directory to the configure command (such as via --prefix) ``False`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Install command to use ``"make install"`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` +================================ ======================================================================================================================================================================================================================================================================================================================== ======================================================================= Customised steps in ``ConfigureMakePythonPackage`` easyblock ------------------------------------------------------------ -* ``build_step`` - Build Python package with 'make'. -* ``configure_step`` - Configure build using 'python configure'. -* ``install_step`` - Install with 'make install'. +* ``build_step`` - Build Python package with ``make``. +* ``configure_step`` - Configure build using ``python configure``. +* ``install_step`` - Install with ``make install``. Example easyconfig for ``ConfigureMakePythonPackage`` easyblock --------------------------------------------------------------- @@ -645,13 +653,13 @@ Extra easyconfig parameters specific to ``CrayToolchain`` easyblock =============================== =========================================================================== ============= easyconfig parameter description default value =============================== =========================================================================== ============= -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -``sanity_check_all_components`` Enable sanity checks for all components ``False`` -``sanity_check_components`` List of components for which to run sanity checks ``[]`` +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` =============================== =========================================================================== ============= .. _FortranPythonPackage: @@ -667,29 +675,29 @@ Extra easyconfig parameters specific to ``FortranPythonPackage`` easyblock -------------------------------------------------------------------------- ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -easyconfig parameter description default value +easyconfig parameter description default value ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``zipped_egg`` Install as a zipped eggs ``False`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= Customised steps in ``FortranPythonPackage`` easyblock @@ -713,8 +721,8 @@ Extra easyconfig parameters specific to ``GoPackage`` easyblock ==================== ===================================================================== ============= easyconfig parameter description default value ==================== ===================================================================== ============= -``forced_deps`` Force specific version of Go package, when building non-native module ``None`` -``modulename`` Module name of the Go package, when building non-native module ``None`` +``forced_deps`` Force specific version of Go package, when building non-native module ``None`` +``modulename`` Module name of the Go package, when building non-native module ``None`` ==================== ===================================================================== ============= Customised steps in ``GoPackage`` easyblock @@ -731,6 +739,7 @@ Customised steps in ``GoPackage`` easyblock (derives from EasyBlock) Base class for Intel software + - no configure/make : binary release - add license_file variable @@ -738,14 +747,14 @@ Extra easyconfig parameters specific to ``IntelBase`` easyblock --------------------------------------------------------------- ============================ =============================================================== ==================== -easyconfig parameter description default value +easyconfig parameter description default value ============================ =============================================================== ==================== -``components`` List of components to install ``None`` +``components`` List of components to install ``None`` ``license_activation`` License activation type ``"license_server"`` -``m32`` Enable 32-bit toolchain ``False`` -``requires_runtime_license`` Boolean indicating whether or not a runtime license is required ``True`` -``serial_number`` Serial number for the product ``None`` -``usetmppath`` Use temporary path for installation ``False`` +``m32`` Enable 32-bit toolchain ``False`` +``requires_runtime_license`` Boolean indicating whether or not a runtime license is required ``True`` +``serial_number`` Serial number for the product ``None`` +``usetmppath`` Use temporary path for installation ``False`` ============================ =============================================================== ==================== Customised steps in ``IntelBase`` easyblock @@ -769,12 +778,64 @@ Extra easyconfig parameters specific to ``JAR`` easyblock ==================== =============================================================================================================================================== ============= easyconfig parameter description default value ==================== =============================================================================================================================================== ============= -``extract_sources`` Whether or not to extract sources ``False`` -``install_cmd`` Install command to be used. ``None`` -``prepend_to_path`` Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself. ``['']`` -``staged_install`` Perform staged installation via subdirectory of build directory ``False`` +``extract_sources`` Whether or not to extract sources ``False`` +``install_cmd`` Install command to be used. ``None`` +``prepend_to_path`` Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself. ``['']`` +``staged_install`` Perform staged installation via subdirectory of build directory ``False`` ==================== =============================================================================================================================================== ============= +.. _JuliaBundle: + +``JuliaBundle`` +=============== + +(derives from :ref:`Bundle`) + +Bundle of JuliaPackages: install Julia packages as extensions in a bundle + Defines custom sanity checks and module environment + +Extra easyconfig parameters specific to ``JuliaBundle`` easyblock +----------------------------------------------------------------- + +=============================== =========================================================================== ============= +easyconfig parameter description default value +=============================== =========================================================================== ============= +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``download_pkg_deps`` Let Julia download and bundle all needed dependencies for this installation ``False`` +``options`` Dictionary with extension options. ``{}`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` +=============================== =========================================================================== ============= + +.. _JuliaPackage: + +``JuliaPackage`` +================ + +(derives from ExtensionEasyBlock) + +Builds and installs Julia Packages. + +Extra easyconfig parameters specific to ``JuliaPackage`` easyblock +------------------------------------------------------------------ + +===================== =========================================================================== ============= +easyconfig parameter description default value +===================== =========================================================================== ============= +``download_pkg_deps`` Let Julia download and bundle all needed dependencies for this installation ``False`` +``options`` Dictionary with extension options. ``{}`` +===================== =========================================================================== ============= + +Customised steps in ``JuliaPackage`` easyblock +---------------------------------------------- +* ``build_step`` - No separate build procedure for JuliaPackage. +* ``configure_step`` - No separate configuration for JuliaPackage. +* ``install_step`` - Install Julia package with Pkg + .. _MakeCp: ``MakeCp`` @@ -787,22 +848,23 @@ Software with no configure and no make install step. Extra easyconfig parameters specific to ``MakeCp`` easyblock ------------------------------------------------------------ -======================== =================================================================================================================================================================================================== ================== -easyconfig parameter description default value -======================== =================================================================================================================================================================================================== ================== -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``configure_cmd`` Configure command to use ``"./configure"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``files_to_copy`` List of files or dirs to copy ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Install command to use ``"make install"`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` -``with_configure`` Run configure script before building ``False`` -======================== =================================================================================================================================================================================================== ================== +================================ =================================================================================================================================================================================================== ================== +easyconfig parameter description default value +================================ =================================================================================================================================================================================================== ================== +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``configure_cmd`` Configure command to use ``"./configure"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``configure_without_installdir`` Avoid passing an install directory to the configure command (such as via --prefix) ``False`` +``files_to_copy`` List of files or dirs to copy ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Install command to use ``"make install"`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` +``with_configure`` Run configure script before building ``False`` +================================ =================================================================================================================================================================================================== ================== Customised steps in ``MakeCp`` easyblock ---------------------------------------- @@ -824,7 +886,7 @@ Extra easyconfig parameters specific to ``MesonNinja`` easyblock ====================== ===================================== ============= easyconfig parameter description default value ====================== ===================================== ============= -``separate_build_dir`` Perform build in a separate directory ``True`` +``separate_build_dir`` Perform build in a separate directory ``True`` ====================== ===================================== ============= Customised steps in ``MesonNinja`` easyblock @@ -863,7 +925,7 @@ Extra easyconfig parameters specific to ``OCamlPackage`` easyblock ==================== ================================== ============= easyconfig parameter description default value ==================== ================================== ============= -``options`` Dictionary with extension options. ``{}`` +``options`` Dictionary with extension options. ``{}`` ==================== ================================== ============= Customised steps in ``OCamlPackage`` easyblock @@ -886,7 +948,7 @@ Extra easyconfig parameters specific to ``OctavePackage`` easyblock ==================== ================================== ============= easyconfig parameter description default value ==================== ================================== ============= -``options`` Dictionary with extension options. ``{}`` +``options`` Dictionary with extension options. ``{}`` ==================== ================================== ============= Customised steps in ``OctavePackage`` easyblock @@ -910,10 +972,10 @@ Extra easyconfig parameters specific to ``PackedBinary`` easyblock ==================== =============================================================================================================================================== ============= easyconfig parameter description default value ==================== =============================================================================================================================================== ============= -``extract_sources`` Whether or not to extract sources ``False`` -``install_cmd`` Install command to be used. ``None`` -``prepend_to_path`` Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself. ``['']`` -``staged_install`` Perform staged installation via subdirectory of build directory ``False`` +``extract_sources`` Whether or not to extract sources ``False`` +``install_cmd`` Install command to be used. ``None`` +``prepend_to_path`` Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself. ``['']`` +``staged_install`` Perform staged installation via subdirectory of build directory ``False`` ==================== =============================================================================================================================================== ============= Customised steps in ``PackedBinary`` easyblock @@ -935,8 +997,8 @@ Extra easyconfig parameters specific to ``PerlModule`` easyblock ==================== ================================== ============= easyconfig parameter description default value ==================== ================================== ============= -``options`` Dictionary with extension options. ``{}`` -``runtest`` Run unit tests. ``"test"`` +``options`` Dictionary with extension options. ``{}`` +``runtest`` Run unit tests. ``"test"`` ==================== ================================== ============= Customised steps in ``PerlModule`` easyblock @@ -952,42 +1014,43 @@ Customised steps in ``PerlModule`` easyblock (derives from :ref:`Bundle`) -Bundle of modules: only generate module files, nothing to build/install +Bundle of PythonPackages: install Python packages as extensions in a bundle + Defines custom sanity checks and module environment Extra easyconfig parameters specific to ``PythonBundle`` easyblock ------------------------------------------------------------------ =============================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -easyconfig parameter description default value +easyconfig parameter description default value =============================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_check_all_components`` Enable sanity checks for all components ``False`` -``sanity_check_components`` List of components for which to run sanity checks ``[]`` -``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``zipped_egg`` Install as a zipped eggs ``False`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` =============================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= .. _PythonPackage: @@ -1003,29 +1066,29 @@ Extra easyconfig parameters specific to ``PythonPackage`` easyblock ------------------------------------------------------------------- ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -easyconfig parameter description default value +easyconfig parameter description default value ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``zipped_egg`` Install as a zipped eggs ``False`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= Customised steps in ``PythonPackage`` easyblock @@ -1049,9 +1112,9 @@ Extra easyconfig parameters specific to ``RPackage`` easyblock ==================== ======================================================== ============= easyconfig parameter description default value ==================== ======================================================== ============= -``exts_subdir`` Subdirectory where R extensions should be installed info ``""`` -``options`` Dictionary with extension options. ``{}`` -``unpack_sources`` Unpack sources before installation ``False`` +``exts_subdir`` Subdirectory where R extensions should be installed info ``""`` +``options`` Dictionary with extension options. ``{}`` +``unpack_sources`` Unpack sources before installation ``False`` ==================== ======================================================== ============= Customised steps in ``RPackage`` easyblock @@ -1068,6 +1131,7 @@ Customised steps in ``RPackage`` easyblock (derives from :ref:`Binary`) Support for installing RPM files. + - sources is a list of rpms - installation is with --nodeps (so the sources list has to be complete) @@ -1077,14 +1141,14 @@ Extra easyconfig parameters specific to ``Rpm`` easyblock ==================== =============================================================================================================================================== ============= easyconfig parameter description default value ==================== =============================================================================================================================================== ============= -``extract_sources`` Whether or not to extract sources ``False`` -``force`` Use force ``False`` -``install_cmd`` Install command to be used. ``None`` -``makesymlinks`` Create symlinks for listed paths ``[]`` -``postinstall`` Enable post install ``False`` -``preinstall`` Enable pre install ``False`` -``prepend_to_path`` Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself. ``['']`` -``staged_install`` Perform staged installation via subdirectory of build directory ``False`` +``extract_sources`` Whether or not to extract sources ``False`` +``force`` Use force ``False`` +``install_cmd`` Install command to be used. ``None`` +``makesymlinks`` Create symlinks for listed paths ``[]`` +``postinstall`` Enable post install ``False`` +``preinstall`` Enable pre install ``False`` +``prepend_to_path`` Prepend the given directories (relative to install-dir) to the environment variable PATH in the module file. Default is the install-dir itself. ``['']`` +``staged_install`` Perform staged installation via subdirectory of build directory ``False`` ==================== =============================================================================================================================================== ============= Customised steps in ``Rpm`` easyblock @@ -1107,8 +1171,8 @@ Extra easyconfig parameters specific to ``RubyGem`` easyblock ==================== ==================================== ============= easyconfig parameter description default value ==================== ==================================== ============= -``gem_file`` Path to gem file in unpacked sources ``None`` -``options`` Dictionary with extension options. ``{}`` +``gem_file`` Path to gem file in unpacked sources ``None`` +``options`` Dictionary with extension options. ``{}`` ==================== ==================================== ============= Customised steps in ``RubyGem`` easyblock @@ -1158,48 +1222,49 @@ Support for generating a module file for the system compiler with specified name Extra easyconfig parameters specific to ``SystemCompiler`` easyblock -------------------------------------------------------------------- -=============================== =================================================================================================================================================================================================== ==================== -easyconfig parameter description default value -=============================== =================================================================================================================================================================================================== ==================== -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``clooguseisl`` Use ISL with CLooG or not ``False`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``configure_cmd`` Configure command to use ``"./configure"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -``generate_standalone_module`` Add known path/library extensions and environment variables for the compiler to the final module ``False`` -``generic`` Build GCC and support libraries such that it runs on all processors of the target architecture (use False to enforce non-generic regardless of configuration) ``None`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Install command to use ``"make install"`` -``languages`` List of languages to build GCC for (--enable-languages) ``[]`` -``license_activation`` License activation type ``"license_server"`` -``m32`` Enable 32-bit toolchain ``False`` -``multilib`` Build multilib gcc (both i386 and x86_64) ``False`` -``pplwatchdog`` Enable PPL watchdog ``False`` -``prefer_lib_subdir`` Configure GCC to prefer 'lib' subdirs over 'lib64' when linking ``False`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``profiled`` Bootstrap GCC with profile-guided optimizations ``False`` -``requires_runtime_license`` Boolean indicating whether or not a runtime license is required ``True`` -``sanity_check_all_components`` Enable sanity checks for all components ``False`` -``sanity_check_components`` List of components for which to run sanity checks ``[]`` -``serial_number`` Serial number for the product ``None`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` -``use_gold_linker`` Configure GCC to use GOLD as default linker (default: enable automatically for GCC < 11.3.0, except on RISC-V) ``None`` -``usetmppath`` Use temporary path for installation ``False`` -``withamdgcn`` Build GCC with AMD GCN offload support ``False`` -``withcloog`` Build GCC with CLooG support ``False`` -``withisl`` Build GCC with ISL support ``False`` -``withlibiberty`` Enable installing of libiberty ``False`` -``withlto`` Enable LTO support ``True`` -``withnvptx`` Build GCC with NVPTX offload support ``False`` -``withppl`` Build GCC with PPL support ``False`` -=============================== =================================================================================================================================================================================================== ==================== +================================ =================================================================================================================================================================================================== ==================== +easyconfig parameter description default value +================================ =================================================================================================================================================================================================== ==================== +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``clooguseisl`` Use ISL with CLooG or not ``False`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``configure_cmd`` Configure command to use ``"./configure"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``configure_without_installdir`` Avoid passing an install directory to the configure command (such as via --prefix) ``False`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``generate_standalone_module`` Add known path/library extensions and environment variables for the compiler to the final module ``False`` +``generic`` Build GCC and support libraries such that it runs on all processors of the target architecture (use False to enforce non-generic regardless of configuration) ``None`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Install command to use ``"make install"`` +``languages`` List of languages to build GCC for (--enable-languages) ``[]`` +``license_activation`` License activation type ``"license_server"`` +``m32`` Enable 32-bit toolchain ``False`` +``multilib`` Build multilib gcc (both i386 and x86_64) ``False`` +``pplwatchdog`` Enable PPL watchdog ``False`` +``prefer_lib_subdir`` Configure GCC to prefer 'lib' subdirs over 'lib64' when linking ``False`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``profiled`` Bootstrap GCC with profile-guided optimizations ``False`` +``requires_runtime_license`` Boolean indicating whether or not a runtime license is required ``True`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` +``serial_number`` Serial number for the product ``None`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` +``use_gold_linker`` Configure GCC to use GOLD as default linker (default: enable automatically for GCC < 11.3.0, except on RISC-V) ``None`` +``usetmppath`` Use temporary path for installation ``False`` +``withamdgcn`` Build GCC with AMD GCN offload support ``False`` +``withcloog`` Build GCC with CLooG support ``False`` +``withisl`` Build GCC with ISL support ``False`` +``withlibiberty`` Enable installing of libiberty ``False`` +``withlto`` Enable LTO support ``True`` +``withnvptx`` Build GCC with NVPTX offload support ``False`` +``withppl`` Build GCC with PPL support ``False`` +================================ =================================================================================================================================================================================================== ==================== .. _SystemMPI: @@ -1219,38 +1284,39 @@ Extra easyconfig parameters specific to ``SystemMPI`` easyblock --------------------------------------------------------------- ================================= =================================================================================================================================================================================================== ==================== -easyconfig parameter description default value +easyconfig parameter description default value ================================= =================================================================================================================================================================================================== ==================== -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``build_cmd`` Build command to use ``"make"`` -``build_cmd_targets`` Target name (string) or list of target names to build ``""`` -``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``configure_cmd`` Configure command to use ``"./configure"`` -``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -``generate_standalone_module`` Add known path extensions and environment variables for the MPI installation to the final module ``False`` -``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` -``install_cmd`` Install command to use ``"make install"`` -``libfabric_configopts`` Configure options for the provided libfabric ``""`` -``libfabric_rebuild`` Try to rebuild internal libfabric instead of using provided binary ``True`` +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``build_cmd`` Build command to use ``"make"`` +``build_cmd_targets`` Target name (string) or list of target names to build ``""`` +``build_type`` Value to provide to --build option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``configure_cmd`` Configure command to use ``"./configure"`` +``configure_cmd_prefix`` Prefix to be glued before ./configure ``""`` +``configure_without_installdir`` Avoid passing an install directory to the configure command (such as via --prefix) ``False`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``generate_standalone_module`` Add known path extensions and environment variables for the MPI installation to the final module ``False`` +``host_type`` Value to provide to --host option of configure script, e.g., x86_64-pc-linux-gnu (determined by config.guess shipped with EasyBuild if None, False implies to leave it up to the configure script) ``None`` +``install_cmd`` Install command to use ``"make install"`` +``libfabric_configopts`` Configure options for the provided libfabric ``""`` +``libfabric_rebuild`` Try to rebuild internal libfabric instead of using provided binary ``True`` ``license_activation`` License activation type ``"license_server"`` -``m32`` Enable 32-bit toolchain ``False`` -``ofi_internal`` Use internal shipped libfabric instead of external libfabric ``True`` -``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` -``requires_runtime_license`` Boolean indicating whether or not a runtime license is required ``True`` -``sanity_check_all_components`` Enable sanity checks for all components ``False`` -``sanity_check_components`` List of components for which to run sanity checks ``[]`` -``serial_number`` Serial number for the product ``None`` -``set_mpi_wrapper_aliases_gcc`` Set compiler for mpigcc/mpigxx via aliases ``False`` -``set_mpi_wrapper_aliases_intel`` Set compiler for mpiicc/mpiicpc/mpiifort via aliases ``False`` -``set_mpi_wrappers_all`` Set (default) compiler for all MPI wrapper commands ``False`` -``set_mpi_wrappers_compiler`` Override default compiler used by MPI wrapper commands ``False`` -``tar_config_opts`` Override tar settings as determined by configure. ``False`` -``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` -``usetmppath`` Use temporary path for installation ``False`` +``m32`` Enable 32-bit toolchain ``False`` +``ofi_internal`` Use internal shipped libfabric instead of external libfabric ``True`` +``prefix_opt`` Prefix command line option for configure script ('--prefix=' if None) ``None`` +``requires_runtime_license`` Boolean indicating whether or not a runtime license is required ``True`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` +``serial_number`` Serial number for the product ``None`` +``set_mpi_wrapper_aliases_gcc`` Set compiler for mpigcc/mpigxx via aliases ``False`` +``set_mpi_wrapper_aliases_intel`` Set compiler for mpiicc/mpiicpc/mpiifort via aliases ``False`` +``set_mpi_wrappers_all`` Set (default) compiler for all MPI wrapper commands ``False`` +``set_mpi_wrappers_compiler`` Override default compiler used by MPI wrapper commands ``False`` +``tar_config_opts`` Override tar settings as determined by configure. ``False`` +``test_cmd`` Test command to use ('runtest' value is appended) ``"make"`` +``usetmppath`` Use temporary path for installation ``False`` ================================= =================================================================================================================================================================================================== ==================== .. _Tarball: @@ -1260,8 +1326,7 @@ easyconfig parameter description (derives from ExtensionEasyBlock) -Precompiled software supplied as a tarball: - - will unpack binary and copy it to the install dir +Precompiled software supplied as a tarball: will unpack binary and copy it to the install dir Extra easyconfig parameters specific to ``Tarball`` easyblock ------------------------------------------------------------- @@ -1269,9 +1334,9 @@ Extra easyconfig parameters specific to ``Tarball`` easyblock ==================== ============================================================================================================================================================= ============= easyconfig parameter description default value ==================== ============================================================================================================================================================= ============= -``install_type`` Defaults to extract tarball into clean directory. Options: 'merge' merges tarball to existing directory, 'subdir' extracts tarball into its own sub-directory ``None`` -``options`` Dictionary with extension options. ``{}`` -``preinstall_cmd`` Command to execute before installation ``None`` +``install_type`` Defaults to extract tarball into clean directory. Options: 'merge' merges tarball to existing directory, 'subdir' extracts tarball into its own sub-directory ``None`` +``options`` Dictionary with extension options. ``{}`` +``preinstall_cmd`` Command to execute before installation ``None`` ==================== ============================================================================================================================================================= ============= Customised steps in ``Tarball`` easyblock @@ -1295,14 +1360,14 @@ Extra easyconfig parameters specific to ``Toolchain`` easyblock =============================== =========================================================================================================== ============= easyconfig parameter description default value =============================== =========================================================================================================== ============= -``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` -``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` -``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` -``default_component_specs`` Default specs to use for every component ``{}`` -``default_easyblock`` Default easyblock to use for components ``None`` -``sanity_check_all_components`` Enable sanity checks for all components ``False`` -``sanity_check_components`` List of components for which to run sanity checks ``[]`` -``set_env_external_modules`` Include setenv statements for toolchain components that use an external module, based on available metadata ``False`` +``altroot`` Software name of dependency to use to define $EBROOT for this bundle ``None`` +``altversion`` Software name of dependency to use to define $EBVERSION for this bundle ``None`` +``components`` List of components to install: tuples w/ name, version and easyblock to use ``()`` +``default_component_specs`` Default specs to use for every component ``{}`` +``default_easyblock`` Default easyblock to use for components ``None`` +``sanity_check_all_components`` Enable sanity checks for all components ``False`` +``sanity_check_components`` List of components for which to run sanity checks ``[]`` +``set_env_external_modules`` Include setenv statements for toolchain components that use an external module, based on available metadata ``False`` =============================== =========================================================================================================== ============= .. _VSCPythonPackage: @@ -1318,29 +1383,29 @@ Extra easyconfig parameters specific to ``VSCPythonPackage`` easyblock ---------------------------------------------------------------------- ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -easyconfig parameter description default value +easyconfig parameter description default value ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``zipped_egg`` Install as a zipped eggs ``False`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= .. _VersionIndependentPythonPackage: @@ -1356,29 +1421,29 @@ Extra easyconfig parameters specific to ``VersionIndependentPythonPackage`` easy ------------------------------------------------------------------------------------- ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -easyconfig parameter description default value +easyconfig parameter description default value ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= -``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` -``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` -``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` -``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` -``install_target`` Option to pass to setup.py ``"install"`` -``options`` Dictionary with extension options. ``{}`` -``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` -``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` -``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` -``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` -``runtest`` Run unit tests. ``True`` -``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` +``buildcmd`` Command for building the package (e.g. for custom builds resulting in a whl file). When using setup.py this will be passed to setup.py and defaults to 'build'. Otherwise it will be used as-is. A value of None then skips the build step. The template %(python)s will be replace by the currently used Python binary. ``None`` +``check_ldshared`` Check Python value of $LDSHARED, correct if needed to "$CC -shared" ``None`` +``download_dep_fail`` Fail if downloaded dependencies are detected ``None`` +``install_src`` Source path to pass to the install command (e.g. a whl file).Defaults to '.' for unpacked sources or the first source file specified ``None`` +``install_target`` Option to pass to setup.py ``"install"`` +``options`` Dictionary with extension options. ``{}`` +``pip_ignore_installed`` Let pip ignore installed Python packages (i.e. don't remove them) ``True`` +``pip_no_index`` Pass --no-index to pip to disable connecting to PyPi entirely which also disables the pip version check. Enabled by default when pip_ignore_installed=True ``None`` +``req_py_majver`` Required major Python version (only relevant when using system Python) ``None`` +``req_py_minver`` Required minor Python version (only relevant when using system Python) ``None`` +``runtest`` Run unit tests. ``True`` +``sanity_pip_check`` Run 'python -m pip check' to ensure all required Python packages are installed and check for any package with an invalid (0.0.0) version. ``False`` ``source_urls`` List of URLs for source files ``['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s']`` -``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` -``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` -``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` -``use_pip_editable`` Install using 'pip install --editable' ``False`` -``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` -``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` -``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` -``zipped_egg`` Install as a zipped eggs ``False`` +``unpack_sources`` Unpack sources prior to build/install. Defaults to 'True' except for whl files ``None`` +``unversioned_packages`` List of packages that don't have a version at all, i.e. show 0.0.0 ``[]`` +``use_pip`` Install using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``None`` +``use_pip_editable`` Install using 'pip install --editable' ``False`` +``use_pip_extras`` String with comma-separated list of 'extras' to install via pip ``None`` +``use_pip_for_deps`` Install dependencies using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' ``False`` +``use_pip_requirement`` Install using 'python -m pip install --requirement'. The sources is expected to be the requirements file. ``False`` +``zipped_egg`` Install as a zipped eggs ``False`` ======================== ======================================================================================================================================================================================================================================================================================================================== ======================================================================= Customised steps in ``VersionIndependentPythonPackage`` easyblock diff --git a/docs/version-specific/help.rst b/docs/version-specific/help.rst index 309526a9..3d275410 100644 --- a/docs/version-specific/help.rst +++ b/docs/version-specific/help.rst @@ -18,22 +18,22 @@ Provide one or more easyconfigs or directories, use -H or --help more informatio Help options ------------ ========================================== ====================================== -Option flag Option description +Option flag Option description ========================================== ====================================== ``--version`` show program's version number and exit -``-h, --shorthelp`` show short help message and exit -``-H OUTPUT_FORMAT, --help=OUTPUT_FORMAT`` show full help message and exit -``--confighelp`` show help as annotated configfile +``-h, --shorthelp`` show short help message and exit +``-H OUTPUT_FORMAT, --help=OUTPUT_FORMAT`` show full help message and exit +``--confighelp`` show help as annotated configfile ========================================== ====================================== Debug and logging options (configfile section MAIN) --------------------------------------------------- =============== ============================================== -Option flag Option description +Option flag Option description =============== ============================================== -``-d, --debug`` Enable debug log mode (default: False) -``--info`` Enable info log mode (default: False) +``-d, --debug`` Enable debug log mode (default: False) +``--info`` Enable info log mode (default: False) ``--quiet`` Enable quiet/warning log mode (default: False) =============== ============================================== @@ -41,336 +41,339 @@ Option flag Option description Configfile options ------------------ ========================================= ===================================================================== -Option flag Option description +Option flag Option description ========================================= ===================================================================== ``--configfiles=CONFIGFILES`` Parse (additional) configfiles (type comma-separated list; default: ) -``--ignoreconfigfiles=IGNORECONFIGFILES`` Ignore configfiles (type comma-separated list) +``--ignoreconfigfiles=IGNORECONFIGFILES`` Ignore configfiles (type comma-separated list) ========================================= ===================================================================== Basic options ------------- ======================================= ======================================================================================================================================================================================================================================================= -Option flag Option description +Option flag Option description ======================================= ======================================================================================================================================================================================================================================================= -``--dry-run`` Print build overview incl. dependencies (full paths) (default: False) -``-D, --dry-run-short`` Print build overview incl. dependencies (short paths) (default: False) -``-x, --extended-dry-run`` Print build environment and (expected) build procedure that will be performed (default: False) -``--extended-dry-run-ignore-errors`` Ignore errors that occur during dry run (default: True; disable with --disable-extended-dry-run-ignore-errors) -``-f, --force`` Force to rebuild software even if it's already installed (i.e. if it can be found as module), and skipping check for OS dependencies (default: False) -``--ignore-locks`` Ignore locks that prevent two identical installations running in parallel (default: False) -``--job`` Submit the build as a job (default: False) -``--locks-dir=LOCKS-DIR`` Directory to store lock files (should be on a shared filesystem); None implies .locks subdirectory of software installation directory -``-l, --logtostdout`` Redirect main log to stdout (default: False) -``-M, --missing-modules`` Print list of missing modules for dependencies of specified easyconfigs (default: False) -``-b BLOCKS, --only-blocks=BLOCKS`` Only build listed blocks (type comma-separated list) -``--rebuild`` Rebuild software, even if module already exists (don't skip OS dependencies checks) (default: False) -``-r PATH[:PATH], --robot=PATH[:PATH]`` Enable dependency resolution, using easyconfigs in specified paths (type pathsep-separated list; default: ) -``--robot-paths=PATH[:PATH]`` Additional paths to consider by robot for easyconfigs (--robot paths get priority) (type pathsep-separated list; default: /home/example/work/easybuild-easyconfigs/easybuild/easyconfigs) -``--search-paths=PATH[:PATH]`` Additional locations to consider in --search (next to --robot and --robot-paths paths) (type pathsep-separated list; default: ) -``-k, --skip`` Skip existing software (useful for installing additional packages) (default: False) +``--dry-run`` Print build overview incl. dependencies (full paths) (default: False) +``-D, --dry-run-short`` Print build overview incl. dependencies (short paths) (default: False) +``-x, --extended-dry-run`` Print build environment and (expected) build procedure that will be performed (default: False) +``--extended-dry-run-ignore-errors`` Ignore errors that occur during dry run (default: True; disable with --disable-extended-dry-run-ignore-errors) +``-f, --force`` Force to rebuild software even if it's already installed (i.e. if it can be found as module), and skipping check for OS dependencies (default: False) +``--ignore-locks`` Ignore locks that prevent two identical installations running in parallel (default: False) +``--job`` Submit the build as a job (default: False) +``--locks-dir=LOCKS-DIR`` Directory to store lock files (should be on a shared filesystem); None implies .locks subdirectory of software installation directory +``-l, --logtostdout`` Redirect main log to stdout (default: False) +``-M, --missing-modules`` Print list of missing modules for dependencies of specified easyconfigs (default: False) +``-b BLOCKS, --only-blocks=BLOCKS`` Only build listed blocks (type comma-separated list) +``--rebuild`` Rebuild software, even if module already exists (don't skip OS dependencies checks) (default: False) +``-r PATH[:PATH], --robot=PATH[:PATH]`` Enable dependency resolution, using easyconfigs in specified paths (type pathsep-separated list; default: ) +``--robot-paths=PATH[:PATH]`` Additional paths to consider by robot for easyconfigs (--robot paths get priority) (type pathsep-separated list; default: /home/example/work/easybuild-easyconfigs/easybuild/easyconfigs) +``--search-paths=PATH[:PATH]`` Additional locations to consider in --search (next to --robot and --robot-paths paths) (type pathsep-separated list; default: ) +``-k, --skip`` Skip existing software (useful for installing additional packages) (default: False) ``-s STOP, --stop=STOP`` Stop the installation after certain step (type choice; default: source) (choices: fetch, ready, source, patch, prepare, configure, build, test, install, extensions, postiter, postproc, sanitycheck, cleanup, module, permissions, package, testcases) -``--strict=STRICT`` Set strictness level (type choice; default: warn) (choices: ignore, warn, error) +``--strict=STRICT`` Set strictness level (type choice; default: warn) (choices: ignore, warn, error) ======================================= ======================================================================================================================================================================================================================================================= Configuration options --------------------- ================================================================= ==================================================================================================================================================================================================================================================================================== -Option flag Option description +Option flag Option description ================================================================= ==================================================================================================================================================================================================================================================================================== -``--avail-module-naming-schemes`` Show all supported module naming schemes (default: False) -``--avail-modules-tools`` Show all supported module tools (default: False) -``--avail-repositories`` Show all repository types (incl. non-usable) (default: False) -``--buildpath=BUILDPATH`` Temporary build path (default: /home/example/.local/easybuild/build) -``--containerpath=CONTAINERPATH`` Location where container recipe & image will be stored (default: /home/example/.local/easybuild/containers) -``--envvars-user-modules=ENVVARS-USER-MODULES`` List of environment variables that hold the base paths for which user-specific modules will be installed relative to (type comma-separated list; default: HOME) -``--external-modules-metadata=EXTERNAL-MODULES-METADATA`` List of (glob patterns for) paths to files specifying metadata for external modules (INI format) (type comma-separated list) -``--hooks=HOOKS`` Location of Python module with hook implementations (type str) -``--ignore-dirs=IGNORE-DIRS`` Directory names to ignore when searching for files/dirs (type comma-separated list; default: .git,.svn) -``--include-easyblocks=INCLUDE-EASYBLOCKS`` Location(s) of extra or customized easyblocks (type comma-separated list; default: ) -``--include-module-naming-schemes=INCLUDE-MODULE-NAMING-SCHEMES`` Location(s) of extra or customized module naming schemes (type comma-separated list; default: ) -``--include-toolchains=INCLUDE-TOOLCHAINS`` Location(s) of extra or customized toolchains or toolchain components (type comma-separated list; default: ) -``--installpath=INSTALLPATH`` Install path for software and modules (default: /home/example/.local/easybuild) -``--installpath-modules=INSTALLPATH-MODULES`` Install path for modules (if None, combine --installpath and --subdir-modules) -``--installpath-software=INSTALLPATH-SOFTWARE`` Install path for software (if None, combine --installpath and --subdir-software) -``--job-backend=JOB-BACKEND`` Backend to use for submitting jobs (type choice; default: GC3Pie) (choices: GC3Pie, PbsPython, Slurm) -``--logfile-format=DIR,FORMAT`` Directory name and format of the log file (type comma-separated tuple; default: easybuild,easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log) -``--module-depends-on`` Use depends_on (Lmod 7.6.1+) for dependencies in all generated modules (implies recursive unloading of modules). (default: False) -``--module-extensions`` Include 'extensions' statement in generated module file (Lua syntax only) (default: False) -``--module-naming-scheme=MODULE-NAMING-SCHEME`` Module naming scheme to use (default: EasyBuildMNS) -``--module-syntax=MODULE-SYNTAX`` Syntax to be used for module files (type choice; default: Lua) (choices: Lua, Tcl) +``--avail-module-naming-schemes`` Show all supported module naming schemes (default: False) +``--avail-modules-tools`` Show all supported module tools (default: False) +``--avail-repositories`` Show all repository types (incl. non-usable) (default: False) +``--buildpath=BUILDPATH`` Temporary build path (default: /home/example/.local/easybuild/build) +``--containerpath=CONTAINERPATH`` Location where container recipe & image will be stored (default: /home/example/.local/easybuild/containers) +``--envvars-user-modules=ENVVARS-USER-MODULES`` List of environment variables that hold the base paths for which user-specific modules will be installed relative to (type comma-separated list; default: HOME) +``--external-modules-metadata=EXTERNAL-MODULES-METADATA`` List of (glob patterns for) paths to files specifying metadata for external modules (INI format) (type comma-separated list) +``--hooks=HOOKS`` Location of Python module with hook implementations (type str) +``--ignore-dirs=IGNORE-DIRS`` Directory names to ignore when searching for files/dirs (type comma-separated list; default: .git,.svn) +``--include-easyblocks=INCLUDE-EASYBLOCKS`` Location(s) of extra or customized easyblocks (type comma-separated list; default: ) +``--include-module-naming-schemes=INCLUDE-MODULE-NAMING-SCHEMES`` Location(s) of extra or customized module naming schemes (type comma-separated list; default: ) +``--include-toolchains=INCLUDE-TOOLCHAINS`` Location(s) of extra or customized toolchains or toolchain components (type comma-separated list; default: ) +``--installpath=INSTALLPATH`` Install path for software and modules (default: /home/example/.local/easybuild) +``--installpath-modules=INSTALLPATH-MODULES`` Install path for modules (if None, combine --installpath and --subdir-modules) +``--installpath-software=INSTALLPATH-SOFTWARE`` Install path for software (if None, combine --installpath and --subdir-software) +``--job-backend=JOB-BACKEND`` Backend to use for submitting jobs (type choice; default: GC3Pie) (choices: GC3Pie, PbsPython, Slurm) +``--logfile-format=DIR,FORMAT`` Directory name and format of the log file (type comma-separated tuple; default: easybuild,easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log) +``--module-depends-on`` Use depends_on (Lmod 7.6.1+) for dependencies in all generated modules (implies recursive unloading of modules). (default: False) +``--module-extensions`` Include 'extensions' statement in generated module file (Lua syntax only) (default: False) +``--module-naming-scheme=MODULE-NAMING-SCHEME`` Module naming scheme to use (default: EasyBuildMNS) +``--module-syntax=MODULE-SYNTAX`` Syntax to be used for module files (type choice; default: Lua) (choices: Lua, Tcl) ``--moduleclasses=MODULECLASSES`` Extend supported module classes (For more info on the default classes, use --show-default-moduleclasses) (type comma-separated list; default: base,ai,astro,bio,cae,chem,compiler,data,debugger,devel,geo,ide,lang,lib,math,mpi,numlib,perf,quantum,phys,system,toolchain,tools,vis) -``--modules-footer=PATH`` Path to file containing footer to be added to all generated module files -``--modules-header=PATH`` Path to file containing header to be added to all generated module files -``--modules-tool=MODULES-TOOL`` Modules tool to use (type choice; default: Lmod) (choices: EnvironmentModules, EnvironmentModulesC, EnvironmentModulesTcl, Lmod) -``--package-naming-scheme=PACKAGE-NAMING-SCHEME`` Packaging naming scheme choice (type choice; default: EasyBuildPNS) (choices: EasyBuildPNS) -``--packagepath=PACKAGEPATH`` The destination path for the packages built by package-tool (default: /home/example/.local/easybuild/packages) -``--prefix=PREFIX`` Change prefix for buildpath, installpath, sourcepath and repositorypath (used prefix for defaults /home/example/.local/easybuild) -``--recursive-module-unload`` Enable generating of modules that unload recursively. (default: False) -``--repository=REPOSITORY`` Repository type, using repositorypath (type choice; default: FileRepository) (choices: FileRepository) -``--repositorypath=REPOSITORYPATH`` Repository path, used by repository (is passed as list of arguments to create the repository instance). For more info, use --avail-repositories. (type comma-separated list; default: /home/example/.local/easybuild/ebfiles_repo) -``--sourcepath=SOURCEPATH`` Path(s) to where sources should be downloaded (string, colon-separated) (default: /home/example/.local/easybuild/sources) -``--subdir-modules=SUBDIR-MODULES`` Installpath subdir for modules (default: modules) -``--subdir-software=SUBDIR-SOFTWARE`` Installpath subdir for software (default: software) -``--subdir-user-modules=SUBDIR-USER-MODULES`` Base path of user-specific modules relative to --envvars-user-modules -``--suffix-modules-path=SUFFIX-MODULES-PATH`` Suffix for module files install path (default: all) -``--testoutput=TESTOUTPUT`` Path to where a job should place the output (to be set within jobscript) -``--tmp-logdir=TMP-LOGDIR`` Log directory where temporary log files are stored -``--tmpdir=TMPDIR`` Directory to use for temporary storage +``--modules-footer=PATH`` Path to file containing footer to be added to all generated module files +``--modules-header=PATH`` Path to file containing header to be added to all generated module files +``--modules-tool=MODULES-TOOL`` Modules tool to use (type choice; default: Lmod) (choices: EnvironmentModules, EnvironmentModulesC, EnvironmentModulesTcl, Lmod) +``--package-naming-scheme=PACKAGE-NAMING-SCHEME`` Packaging naming scheme choice (type choice; default: EasyBuildPNS) (choices: EasyBuildPNS) +``--packagepath=PACKAGEPATH`` The destination path for the packages built by package-tool (default: /home/example/.local/easybuild/packages) +``--prefix=PREFIX`` Change prefix for buildpath, installpath, sourcepath and repositorypath (used prefix for defaults /home/example/.local/easybuild) +``--recursive-module-unload`` Enable generating of modules that unload recursively. (default: False) +``--repository=REPOSITORY`` Repository type, using repositorypath (type choice; default: FileRepository) (choices: FileRepository) +``--repositorypath=REPOSITORYPATH`` Repository path, used by repository (is passed as list of arguments to create the repository instance). For more info, use --avail-repositories. (type comma-separated list; default: /home/example/.local/easybuild/ebfiles_repo) +``--sourcepath=SOURCEPATH`` Path(s) to where sources should be downloaded (string, colon-separated) (default: /home/example/.local/easybuild/sources) +``--subdir-modules=SUBDIR-MODULES`` Installpath subdir for modules (default: modules) +``--subdir-software=SUBDIR-SOFTWARE`` Installpath subdir for software (default: software) +``--subdir-user-modules=SUBDIR-USER-MODULES`` Base path of user-specific modules relative to --envvars-user-modules +``--suffix-modules-path=SUFFIX-MODULES-PATH`` Suffix for module files install path (default: all) +``--testoutput=TESTOUTPUT`` Path to where a job should place the output (to be set within jobscript) +``--tmp-logdir=TMP-LOGDIR`` Log directory where temporary log files are stored +``--tmpdir=TMPDIR`` Directory to use for temporary storage ================================================================= ==================================================================================================================================================================================================================================================================================== Container options ----------------- =============================================== =========================================================================================================== -Option flag Option description +Option flag Option description =============================================== =========================================================================================================== -``--container-build-image`` Build container image (requires sudo privileges!) (default: False) -``--container-config=CONFIG`` Configuration for container image (type ) -``--container-image-format=IMAGE-FORMAT`` Container image format (type choice) (choices: ext3, sandbox, sif, squashfs) -``--container-image-name=IMAGE-NAME`` Custom name for container image (defaults to name of easyconfig) -``--container-template-recipe=TEMPLATE-RECIPE`` Template recipe for container image (type ) -``--container-tmpdir=TMPDIR`` Temporary directory where container image is built +``--container-build-image`` Build container image (requires sudo privileges!) (default: False) +``--container-config=CONFIG`` Configuration for container image (type ) +``--container-image-format=IMAGE-FORMAT`` Container image format (type choice) (choices: ext3, sandbox, sif, squashfs) +``--container-image-name=IMAGE-NAME`` Custom name for container image (defaults to name of easyconfig) +``--container-template-recipe=TEMPLATE-RECIPE`` Template recipe for container image (type ) +``--container-tmpdir=TMPDIR`` Temporary directory where container image is built ``--container-type=TYPE`` Type of container recipe/image to create (type choice; default: singularity) (choices: docker, singularity) =============================================== =========================================================================================================== Options for Easyconfigs ----------------------- -=================================================== ===================================================================================================================================================================================================================================================== -Option flag Option description -=================================================== ===================================================================================================================================================================================================================================================== -``--create-index=CREATE-INDEX`` Create index for files in specified directory -``--fix-deprecated-easyconfigs`` Fix use of deprecated functionality in specified easyconfig files. (default: False) -``--ignore-index`` Ignore index when searching for files (default: False) -``--index-max-age=INDEX-MAX-AGE`` Maximum age for index before it is considered stale (in seconds) (type ; default: 604800) -``--inject-checksums=INJECT-CHECKSUMS`` Inject checksums of specified type for sources/patches into easyconfig file(s) (type choice; default: sha256) (choices: adler32, crc32, md5, sha1, sha256, sha512, size) -``--local-var-naming-check=LOCAL-VAR-NAMING-CHECK`` Mode to use when checking whether local variables follow the recommended naming scheme ('log': only log warnings (no printed messages); 'warn': print warnings; 'error': fail with an error) (type choice; default: warn) (choices: error, log, warn) -=================================================== ===================================================================================================================================================================================================================================================== +======================================================= ===================================================================================================================================================================================================================================================== +Option flag Option description +======================================================= ===================================================================================================================================================================================================================================================== +``--create-index=CREATE-INDEX`` Create index for files in specified directory +``--fix-deprecated-easyconfigs`` Fix use of deprecated functionality in specified easyconfig files. (default: False) +``--ignore-index`` Ignore index when searching for files (default: False) +``--index-max-age=INDEX-MAX-AGE`` Maximum age for index before it is considered stale (in seconds) (type ; default: 604800) +``--inject-checksums=INJECT-CHECKSUMS`` Inject checksums of specified type for sources/patches into easyconfig file(s) (type choice; default: sha256) (choices: adler32, crc32, md5, sha1, sha256, sha512, size) +``--inject-checksums-to-json=INJECT-CHECKSUMS-TO-JSON`` Inject checksums of specified type for sources/patches into checksums.json (type choice; default: sha256) (choices: adler32, crc32, md5, sha1, sha256, sha512, size) +``--local-var-naming-check=LOCAL-VAR-NAMING-CHECK`` Mode to use when checking whether local variables follow the recommended naming scheme ('log': only log warnings (no printed messages); 'warn': print warnings; 'error': fail with an error) (type choice; default: warn) (choices: error, log, warn) +======================================================= ===================================================================================================================================================================================================================================================== GitHub integration options -------------------------- ======================================================= ================================================================================================================================= -Option flag Option description +Option flag Option description ======================================================= ================================================================================================================================= -``--add-pr-labels=PR#`` Try to add labels to PR based on files changed (type ) -``--check-contrib`` Runs checks to see whether the given easyconfigs are ready to be contributed back (default: False) -``--check-github`` Check status of GitHub integration, and report back (default: False) -``--check-style`` Run a style check on the given easyconfigs (default: False) -``--cleanup-easyconfigs`` Clean up easyconfig files for pull request (default: True; disable with --disable-cleanup-easyconfigs) -``--close-pr=PR#`` Close pull request (type ) -``--close-pr-msg=CLOSE-PR-MSG`` Custom close message for pull request closed with --close-pr; (type ) +``--add-pr-labels=PR#`` Try to add labels to PR based on files changed (type ) +``--check-contrib`` Runs checks to see whether the given easyconfigs are ready to be contributed back (default: False) +``--check-github`` Check status of GitHub integration, and report back (default: False) +``--check-style`` Run a style check on the given easyconfigs (default: False) +``--cleanup-easyconfigs`` Clean up easyconfig files for pull request (default: True; disable with --disable-cleanup-easyconfigs) +``--close-pr=PR#`` Close pull request (type ) +``--close-pr-msg=CLOSE-PR-MSG`` Custom close message for pull request closed with --close-pr; (type ) ``--close-pr-reasons=CLOSE-PR-REASONS`` Close reason for pull request closed with --close-pr; supported values: archived, inactive, obsolete, retest (type ) -``--dump-test-report=DUMP-TEST-REPORT`` Dump test report to specified path (default: test_report.md) -``--from-pr=PR#`` Obtain easyconfigs from specified PR (type comma-separated list; default: ) -``--git-working-dirs-path=GIT-WORKING-DIRS-PATH`` Path to Git working directories for EasyBuild repositories (type ) -``--github-org=GITHUB-ORG`` GitHub organization (type ) -``--github-user=GITHUB-USER`` GitHub username (type ) -``--include-easyblocks-from-pr=PR#`` Include easyblocks from specified PR (type comma-separated list; default: ) -``--install-github-token`` Install GitHub token (requires --github-user) (default: False) -``--list-prs=STATE,ORDER,DIRECTION`` List pull requests (type ; default: open,created,desc) -``--merge-pr=PR#`` Merge pull request (type ) -``--new-branch-github`` Create new branch in GitHub in preparation for a PR (default: False) -``--new-pr`` Open a new pull request (default: False) -``--new-pr-from-branch=NEW-PR-FROM-BRANCH`` Open a new pull request from branch in GitHub (type ) -``--pr-branch-name=PR-BRANCH-NAME`` Branch name to use for new PRs; '_new_pr_' if unspecified (type ) -``--pr-commit-msg=PR-COMMIT-MSG`` Commit message for new/updated pull request created with --new-pr (type ) -``--pr-descr=PR-DESCR`` Description for new pull request created with --new-pr (type ) -``--pr-target-account=PR-TARGET-ACCOUNT`` Target account for new PRs (type ; default: easybuilders) -``--pr-target-branch=PR-TARGET-BRANCH`` Target branch for new PRs (type ; default: develop) -``--pr-target-repo=PR-TARGET-REPO`` Target repository for new/updating PRs (default: auto-detect based on provided files) (type ) -``--pr-title=PR-TITLE`` Title for new pull request created with --new-pr (type ) -``--preview-pr`` Preview a new pull request (default: False) -``--review-pr=PR#`` Review specified pull request (type ) -``--review-pr-filter=REVIEW-PR-FILTER`` Regex used to filter out easyconfigs to diff against in --review-pr -``--review-pr-max=REVIEW-PR-MAX`` Maximum number of easyconfigs to diff against in --review-pr (type ) -``--sync-branch-with-develop=SYNC-BRANCH-WITH-DEVELOP`` Sync branch with current 'develop' branch (type ) -``--sync-pr-with-develop=PR#`` Sync pull request with current 'develop' branch (type ) -``--test-report-env-filter=TEST-REPORT-ENV-FILTER`` Regex used to filter out variables in environment dump of test report -``--update-branch-github=UPDATE-BRANCH-GITHUB`` Update specified branch in GitHub (type ) -``--update-pr=PR#`` Update an existing pull request (type ) -``-u, --upload-test-report`` Upload full test report as a gist on GitHub (default: False) +``--dump-test-report=DUMP-TEST-REPORT`` Dump test report to specified path (default: test_report.md) +``--from-pr=PR#`` Obtain easyconfigs from specified PR (type comma-separated list; default: ) +``--git-working-dirs-path=GIT-WORKING-DIRS-PATH`` Path to Git working directories for EasyBuild repositories (type ) +``--github-org=GITHUB-ORG`` GitHub organization (type ) +``--github-user=GITHUB-USER`` GitHub username (type ) +``--include-easyblocks-from-pr=PR#`` Include easyblocks from specified PR (type comma-separated list; default: ) +``--install-github-token`` Install GitHub token (requires --github-user) (default: False) +``--list-prs=STATE,ORDER,DIRECTION`` List pull requests (type ; default: open,created,desc) +``--merge-pr=PR#`` Merge pull request (type ) +``--new-branch-github`` Create new branch in GitHub in preparation for a PR (default: False) +``--new-pr`` Open a new pull request (default: False) +``--new-pr-from-branch=NEW-PR-FROM-BRANCH`` Open a new pull request from branch in GitHub (type ) +``--pr-branch-name=PR-BRANCH-NAME`` Branch name to use for new PRs; '_new_pr_' if unspecified (type ) +``--pr-commit-msg=PR-COMMIT-MSG`` Commit message for new/updated pull request created with --new-pr (type ) +``--pr-descr=PR-DESCR`` Description for new pull request created with --new-pr (type ) +``--pr-target-account=PR-TARGET-ACCOUNT`` Target account for new PRs (type ; default: easybuilders) +``--pr-target-branch=PR-TARGET-BRANCH`` Target branch for new PRs (type ; default: develop) +``--pr-target-repo=PR-TARGET-REPO`` Target repository for new/updating PRs (default: auto-detect based on provided files) (type ) +``--pr-title=PR-TITLE`` Title for new pull request created with --new-pr (type ) +``--preview-pr`` Preview a new pull request (default: False) +``--review-pr=PR#`` Review specified pull request (type ) +``--review-pr-filter=REVIEW-PR-FILTER`` Regex used to filter out easyconfigs to diff against in --review-pr +``--review-pr-max=REVIEW-PR-MAX`` Maximum number of easyconfigs to diff against in --review-pr (type ) +``--sync-branch-with-develop=SYNC-BRANCH-WITH-DEVELOP`` Sync branch with current 'develop' branch (type ) +``--sync-pr-with-develop=PR#`` Sync pull request with current 'develop' branch (type ) +``--test-report-env-filter=TEST-REPORT-ENV-FILTER`` Regex used to filter out variables in environment dump of test report +``--update-branch-github=UPDATE-BRANCH-GITHUB`` Update specified branch in GitHub (type ) +``--update-pr=PR#`` Update an existing pull request (type ) +``-u, --upload-test-report`` Upload full test report as a gist on GitHub (default: False) ======================================================= ================================================================================================================================= Informative options ------------------- ===================================================== ================================================================================================ -Option flag Option description +Option flag Option description ===================================================== ================================================================================================ -``--avail-cfgfile-constants`` Show all constants that can be used in configuration files (default: False) -``--avail-easyconfig-constants`` Show all constants that can be used in easyconfigs (default: False) -``--avail-easyconfig-licenses`` Show all license constants that can be used in easyconfigs (default: False) -``-a, --avail-easyconfig-params`` Show all easyconfig parameters (include easyblock-specific ones by using -e) (default: False) +``--avail-cfgfile-constants`` Show all constants that can be used in configuration files (default: False) +``--avail-easyconfig-constants`` Show all constants that can be used in easyconfigs (default: False) +``--avail-easyconfig-licenses`` Show all license constants that can be used in easyconfigs (default: False) +``-a, --avail-easyconfig-params`` Show all easyconfig parameters (include easyblock-specific ones by using -e) (default: False) ``--avail-easyconfig-templates`` Show all template names and template constants that can be used in easyconfigs. (default: False) -``--avail-hooks`` Show list of known hooks (default: False) -``--avail-toolchain-opts=AVAIL-TOOLCHAIN-OPTS`` Show options for toolchain (type str) -``--check-conflicts`` Check for version conflicts in dependency graphs (default: False) -``--check-eb-deps`` Check presence and version of (required and optional) EasyBuild dependencies (default: False) -``--dep-graph=depgraph.`` Create dependency graph -``--dump-env-script`` Dump source script to set up build environment based on toolchain/dependencies (default: False) -``--easystack=EASYSTACK`` Path to easystack file in YAML format, specifying details of a software stack -``--last-log`` Print location to EasyBuild log file of last (failed) session (default: False) -``--list-easyblocks=LIST-EASYBLOCKS`` Show list of available easyblocks (type choice; default: simple) (choices: simple, detailed) -``--list-installed-software=LIST-INSTALLED-SOFTWARE`` Show list of installed software (type choice; default: simple) (choices: simple, detailed) -``--list-software=LIST-SOFTWARE`` Show list of supported software (type choice; default: simple) (choices: simple, detailed) -``--list-toolchains`` Show list of known toolchains (default: False) -``--search=REGEX`` Search for easyconfig files in the robot search path, print full paths -``--search-filename=REGEX`` Search for easyconfig files in the robot search path, print only filenames -``-S REGEX, --search-short=REGEX`` Search for easyconfig files in the robot search path, print short paths -``--show-config`` Show current EasyBuild configuration (only non-default + selected settings) (default: False) -``--show-default-configfiles`` Show list of default config files (default: False) -``--show-default-moduleclasses`` Show default module classes with description (default: False) -``--show-ec`` Show contents of specified easyconfig(s) (default: False) -``--show-full-config`` Show current EasyBuild configuration (all settings) (default: False) -``--show-system-info`` Show system information relevant to EasyBuild (default: False) -``--terse`` Terse output (machine-readable) (default: False) +``--avail-hooks`` Show list of known hooks (default: False) +``--avail-toolchain-opts=AVAIL-TOOLCHAIN-OPTS`` Show options for toolchain (type str) +``--check-conflicts`` Check for version conflicts in dependency graphs (default: False) +``--check-eb-deps`` Check presence and version of (required and optional) EasyBuild dependencies (default: False) +``--dep-graph=depgraph.`` Create dependency graph +``--dump-env-script`` Dump source script to set up build environment based on toolchain/dependencies (default: False) +``--easystack=EASYSTACK`` Path to easystack file in YAML format, specifying details of a software stack +``--last-log`` Print location to EasyBuild log file of last (failed) session (default: False) +``--list-easyblocks=LIST-EASYBLOCKS`` Show list of available easyblocks (type choice; default: simple) (choices: simple, detailed) +``--list-installed-software=LIST-INSTALLED-SOFTWARE`` Show list of installed software (type choice; default: simple) (choices: simple, detailed) +``--list-software=LIST-SOFTWARE`` Show list of supported software (type choice; default: simple) (choices: simple, detailed) +``--list-toolchains`` Show list of known toolchains (default: False) +``--search=REGEX`` Search for easyconfig files in the robot search path, print full paths +``--search-filename=REGEX`` Search for easyconfig files in the robot search path, print only filenames +``-S REGEX, --search-short=REGEX`` Search for easyconfig files in the robot search path, print short paths +``--show-config`` Show current EasyBuild configuration (only non-default + selected settings) (default: False) +``--show-default-configfiles`` Show list of default config files (default: False) +``--show-default-moduleclasses`` Show default module classes with description (default: False) +``--show-ec`` Show contents of specified easyconfig(s) (default: False) +``--show-full-config`` Show current EasyBuild configuration (all settings) (default: False) +``--show-system-info`` Show system information relevant to EasyBuild (default: False) +``--terse`` Terse output (machine-readable) (default: False) ===================================================== ================================================================================================ Options for job backend ----------------------- =========================================== =========================================================================================================================== -Option flag Option description +Option flag Option description =========================================== =========================================================================================================================== -``--job-backend-config=BACKEND-CONFIG`` Configuration file for job backend -``--job-cores=CORES`` Number of cores to request per job (type int) +``--job-backend-config=BACKEND-CONFIG`` Configuration file for job backend +``--job-cores=CORES`` Number of cores to request per job (type int) ``--job-deps-type=DEPS-TYPE`` Type of dependency to set between jobs (default depends on job backend) (type choice) (choices: abort_on_error, always_run) -``--job-eb-cmd=EB-CMD`` EasyBuild command to use in jobs (type str; default: eb) -``--job-max-jobs=MAX-JOBS`` Maximum number of concurrent jobs (queued and running, 0 = unlimited) (type int; default: 0) -``--job-max-walltime=MAX-WALLTIME`` Maximum walltime for jobs (in hours) (type int; default: 24) -``--job-output-dir=OUTPUT-DIR`` Output directory for jobs (default: current directory) (default: /Volumes/work/easybuild/docs) -``--job-polling-interval=POLLING-INTERVAL`` Interval between polls for status of jobs (in seconds) (type ; default: 30.0) -``--job-target-resource=TARGET-RESOURCE`` Target resource for jobs +``--job-eb-cmd=EB-CMD`` EasyBuild command to use in jobs (type str; default: eb) +``--job-max-jobs=MAX-JOBS`` Maximum number of concurrent jobs (queued and running, 0 = unlimited) (type int; default: 0) +``--job-max-walltime=MAX-WALLTIME`` Maximum walltime for jobs (in hours) (type int; default: 24) +``--job-output-dir=OUTPUT-DIR`` Output directory for jobs (default: current directory) (default: /Volumes/work/easybuild/docs) +``--job-polling-interval=POLLING-INTERVAL`` Interval between polls for status of jobs (in seconds) (type ; default: 30.0) +``--job-target-resource=TARGET-RESOURCE`` Target resource for jobs =========================================== =========================================================================================================================== Override options ---------------- -========================================================================= ================================================================================================================================================================================================================================================================================ -Option flag Option description -========================================================================= ================================================================================================================================================================================================================================================================================ -``--accept-eula=ACCEPT-EULA`` Accept EULA for specified software [DEPRECATED, use --accept-eula-for instead!] (type comma-separated list; default: ) -``--accept-eula-for=ACCEPT-EULA-FOR`` Accept EULA for specified software (type comma-separated list; default: ) -``--add-dummy-to-minimal-toolchains`` Include dummy toolchain in minimal toolchain searches [DEPRECATED, use --add-system-to-minimal-toolchains instead!) (default: False) -``--add-system-to-minimal-toolchains`` Include system toolchain in minimal toolchain searches (default: False) -``--allow-loaded-modules=ALLOW-LOADED-MODULES`` List of software names for which to allow loaded modules in initial environment (type comma-separated list; default: EasyBuild) -``--allow-modules-tool-mismatch`` Allow mismatch of modules tool and definition of 'module' function (default: False) -``--allow-use-as-root-and-accept-consequences`` Allow using of EasyBuild as root (NOT RECOMMENDED!) (default: False) -``--backup-modules`` Back up an existing module file, if any. Only works when using --module-only -``--backup-patched-files`` Create a backup (*.orig) file when applying a patch (default: False) -``--banned-linked-shared-libs=BANNED-LINKED-SHARED-LIBS`` Comma-separated list of shared libraries (names, file names, or paths) which are not allowed to be linked in any installed binary/library (type comma-separated list) -``--check-ebroot-env-vars=CHECK-EBROOT-ENV-VARS`` Action to take when defined $EBROOT* environment variables are found for which there is no matching loaded module; supported values: error, ignore, unset, warn (default: warn) -``--cleanup-builddir`` Cleanup build dir after successful installation. (default: True; disable with --disable-cleanup-builddir) -``--cleanup-tmpdir`` Cleanup tmp dir after successful run. (default: True; disable with --disable-cleanup-tmpdir) -``--color=WHEN`` Colorize output (type choice; default: auto) (choices: auto, always, never) -``--consider-archived-easyconfigs`` Also consider archived easyconfigs (default: False) -``-C, --containerize`` Generate container recipe/image (default: False) -``--copy-ec`` Copy specified easyconfig(s) to specified location (default: False) -``--cuda-cache-dir=PATH`` Path to CUDA cache dir to use if enabled. Defaults to a path inside the build dir. (type ) -``--cuda-cache-maxsize=CUDA-CACHE-MAXSIZE`` Maximum size of the CUDA cache (in MiB) used for JIT compilation of PTX code. Leave value empty to let EasyBuild choose a value or '0' to disable the cache (type ) -``--cuda-compute-capabilities=CUDA-COMPUTE-CAPABILITIES`` List of CUDA compute capabilities to use when building GPU software; values should be specified as digits separated by a dot, for example: 3.5,5.0,7.2 (type comma-separated list) -``--debug-lmod`` Run Lmod modules tool commands in debug module (default: False) -``--default-opt-level=DEFAULT-OPT-LEVEL`` Specify default optimisation level (type choice; default: defaultopt) (choices: noopt, lowopt, defaultopt, opt) -``--deprecated=DEPRECATED`` Run pretending to be (future) version, to test removal of deprecated code. -``--detect-loaded-modules=DETECT-LOADED-MODULES`` Detect loaded EasyBuild-generated modules, act accordingly; supported values: error, ignore, purge, unload, warn (default: warn) -``--devel`` Enable including of development log messages (default: False) -``--download-timeout=DOWNLOAD-TIMEOUT`` Timeout for initiating downloads (in seconds) (type ) -``--dump-autopep8`` Reformat easyconfigs using autopep8 when dumping them (default: False) -``-e CLASS, --easyblock=CLASS`` easyblock to use for processing the spec file or dumping the options -``--enforce-checksums`` Enforce availability of checksums for all sources/patches, so they can be verified (default: False) -``--env-for-shebang=ENV-FOR-SHEBANG`` Define the env command to use when fixing shebangs (default: /usr/bin/env) -``--experimental`` Allow experimental code (with behaviour that can be changed/removed at any given time). (default: False) -``--extra-modules=EXTRA-MODULES`` List of extra modules to load after setting up the build environment (type comma-separated list) -``--fetch`` Allow downloading sources ignoring OS and modules tool dependencies, implies --stop=fetch, --ignore-osdeps and ignore modules tool (default: False) -``--filter-deps=FILTER-DEPS`` List of dependencies that you do *not* want to install with EasyBuild, because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses) (type comma-separated list) -``--filter-ecs=FILTER-ECS`` List of easyconfigs (given as glob patterns) to *ignore* when given on command line or auto-selected when building with --from-pr. (e.g. --filter-ecs=*intel*) (type comma-separated list) -``--filter-env-vars=FILTER-ENV-VARS`` List of names of environment variables that should *not* be defined/updated by module files generated by EasyBuild (type comma-separated list) -``--fixed-installdir-naming-scheme`` Use fixed naming scheme for installation directories (default: True; disable with --disable-fixed-installdir-naming-scheme) -``--force-download=FORCE-DOWNLOAD`` Force re-downloading of sources and/or patches, even if they are available already in source path (type choice; default: sources) (choices: all, patches, sources) -``--generate-devel-module`` Generate a develop module file, implies --force if disabled (default: True; disable with --disable-generate-devel-module) -``--group=GROUP`` Group to be used for software installations (only verified, not set) -``--group-writable-installdir`` Enable group write permissions on installation directory after installation (default: False) -``--hidden`` Install 'hidden' module file(s) by prefixing their version with '.' (default: False) -``--hide-deps=HIDE-DEPS`` Comma separated list of dependencies that you want automatically hidden, (e.g. --hide-deps=zlib,ncurses) (type comma-separated list) -``--hide-toolchains=HIDE-TOOLCHAINS`` Comma separated list of toolchains that you want automatically hidden, (e.g. --hide-toolchains=GCCcore) (type comma-separated list) +========================================================================= ========================================================================================================================================================================================================================================================================================================================================================================== +Option flag Option description +========================================================================= ========================================================================================================================================================================================================================================================================================================================================================================== +``--accept-eula=ACCEPT-EULA`` Accept EULA for specified software [DEPRECATED, use --accept-eula-for instead!] (type comma-separated list; default: ) +``--accept-eula-for=ACCEPT-EULA-FOR`` Accept EULA for specified software (type comma-separated list; default: ) +``--add-dummy-to-minimal-toolchains`` Include dummy toolchain in minimal toolchain searches [DEPRECATED, use --add-system-to-minimal-toolchains instead!) (default: False) +``--add-system-to-minimal-toolchains`` Include system toolchain in minimal toolchain searches (default: False) +``--allow-loaded-modules=ALLOW-LOADED-MODULES`` List of software names for which to allow loaded modules in initial environment (type comma-separated list; default: EasyBuild) +``--allow-modules-tool-mismatch`` Allow mismatch of modules tool and definition of 'module' function (default: False) +``--allow-use-as-root-and-accept-consequences`` Allow using of EasyBuild as root (NOT RECOMMENDED!) (default: False) +``--backup-modules`` Back up an existing module file, if any. Only works when using --module-only +``--backup-patched-files`` Create a backup (*.orig) file when applying a patch (default: False) +``--banned-linked-shared-libs=BANNED-LINKED-SHARED-LIBS`` Comma-separated list of shared libraries (names, file names, or paths) which are not allowed to be linked in any installed binary/library (type comma-separated list) +``--check-ebroot-env-vars=CHECK-EBROOT-ENV-VARS`` Action to take when defined $EBROOT* environment variables are found for which there is no matching loaded module; supported values: error, ignore, unset, warn (default: warn) +``--checksum-priority=CHECKSUM-PRIORITY`` When checksums are found in both the EasyConfig and the checksums.json fileDefine which one to use. (type choice; default: easyconfig) (choices: json, easyconfig) +``--cleanup-builddir`` Cleanup build dir after successful installation. (default: True; disable with --disable-cleanup-builddir) +``--cleanup-tmpdir`` Cleanup tmp dir after successful run. (default: True; disable with --disable-cleanup-tmpdir) +``--color=WHEN`` Colorize output (type choice; default: auto) (choices: auto, always, never) +``--consider-archived-easyconfigs`` Also consider archived easyconfigs (default: False) +``-C, --containerize`` Generate container recipe/image (default: False) +``--copy-ec`` Copy specified easyconfig(s) to specified location (default: False) +``--cuda-cache-dir=PATH`` Path to CUDA cache dir to use if enabled. Defaults to a path inside the build dir. (type ) +``--cuda-cache-maxsize=CUDA-CACHE-MAXSIZE`` Maximum size of the CUDA cache (in MiB) used for JIT compilation of PTX code. Leave value empty to let EasyBuild choose a value or '0' to disable the cache (type ) +``--cuda-compute-capabilities=CUDA-COMPUTE-CAPABILITIES`` List of CUDA compute capabilities to use when building GPU software; values should be specified as digits separated by a dot, for example: 3.5,5.0,7.2 (type comma-separated list) +``--debug-lmod`` Run Lmod modules tool commands in debug module (default: False) +``--default-opt-level=DEFAULT-OPT-LEVEL`` Specify default optimisation level (type choice; default: defaultopt) (choices: noopt, lowopt, defaultopt, opt) +``--deprecated=DEPRECATED`` Run pretending to be (future) version, to test removal of deprecated code. +``--detect-loaded-modules=DETECT-LOADED-MODULES`` Detect loaded EasyBuild-generated modules, act accordingly; supported values: error, ignore, purge, unload, warn (default: warn) +``--devel`` Enable including of development log messages (default: False) +``--download-timeout=DOWNLOAD-TIMEOUT`` Timeout for initiating downloads (in seconds) (type ) +``--dump-autopep8`` Reformat easyconfigs using autopep8 when dumping them (default: False) +``-e CLASS, --easyblock=CLASS`` easyblock to use for processing the spec file or dumping the options +``--enforce-checksums`` Enforce availability of checksums for all sources/patches, so they can be verified (default: False) +``--env-for-shebang=ENV-FOR-SHEBANG`` Define the env command to use when fixing shebangs (default: /usr/bin/env) +``--experimental`` Allow experimental code (with behaviour that can be changed/removed at any given time). (default: False) +``--extra-modules=EXTRA-MODULES`` List of extra modules to load after setting up the build environment (type comma-separated list) +``--fetch`` Allow downloading sources ignoring OS and modules tool dependencies, implies --stop=fetch, --ignore-osdeps and ignore modules tool (default: False) +``--filter-deps=FILTER-DEPS`` List of dependencies that you do *not* want to install with EasyBuild, because equivalent OS packages are installed. (e.g. --filter-deps=zlib,ncurses) (type comma-separated list) +``--filter-ecs=FILTER-ECS`` List of easyconfigs (given as glob patterns) to *ignore* when given on command line or auto-selected when building with --from-pr. (e.g. --filter-ecs=*intel*) (type comma-separated list) +``--filter-env-vars=FILTER-ENV-VARS`` List of names of environment variables that should *not* be defined/updated by module files generated by EasyBuild (type comma-separated list) +``--filter-rpath-sanity-libs=FILTER-RPATH-SANITY-LIBS`` List of libraries that should be ignored by the RPATH sanity check. I.e. if these libraries are not RPATH-ed, that will be accepted by the RPATH sanity check. Note that you'll need to provide the exact library name, as it is returned by 'ldd', including any version (type comma-separated list; default: libcuda.so,libcuda.so.1,libnvidia-ml.so,libnvidia-ml.so.1) +``--fixed-installdir-naming-scheme`` Use fixed naming scheme for installation directories (default: True; disable with --disable-fixed-installdir-naming-scheme) +``--force-download=FORCE-DOWNLOAD`` Force re-downloading of sources and/or patches, even if they are available already in source path (type choice; default: sources) (choices: all, patches, sources) +``--generate-devel-module`` Generate a develop module file, implies --force if disabled (default: True; disable with --disable-generate-devel-module) +``--group=GROUP`` Group to be used for software installations (only verified, not set) +``--group-writable-installdir`` Enable group write permissions on installation directory after installation (default: False) +``--hidden`` Install 'hidden' module file(s) by prefixing their version with '.' (default: False) +``--hide-deps=HIDE-DEPS`` Comma separated list of dependencies that you want automatically hidden, (e.g. --hide-deps=zlib,ncurses) (type comma-separated list) +``--hide-toolchains=HIDE-TOOLCHAINS`` Comma separated list of toolchains that you want automatically hidden, (e.g. --hide-toolchains=GCCcore) (type comma-separated list) ``--http-header-fields-urlpat=[URLPAT::][HEADER:]FILE|FIELD`` Set extra HTTP header FIELDs when downloading files from URL PATterns. To not log sensitive values, specify a file containing newline separated FIELDs. e.g. "^https://www.example.com::/path/to/headers.txt" or "client[A-z0-9]*.example.com': ['Authorization: Basic token']". -``--ignore-checksums`` Ignore failing checksum verification (default: False) -``--ignore-osdeps`` Ignore any listed OS dependencies (default: False) -``--ignore-test-failure`` Ignore a failing test step (default: False) -``--insecure-download`` Don't check the server certificate against the available certificate authorities. (default: False) -``--install-latest-eb-release`` Install latest known version of easybuild (default: False) -``--lib-lib64-symlink`` Automatically create symlinks for lib/ pointing to lib64/ if the former is missing (default: True; disable with --disable-lib-lib64-symlink) -``--lib64-fallback-sanity-check`` Fallback in sanity check to lib64/ equivalent for missing libraries (default: True; disable with --disable-lib64-fallback-sanity-check) -``--lib64-lib-symlink`` Automatically create symlinks for lib64/ pointing to lib/ if the former is missing (default: True; disable with --disable-lib64-lib-symlink) -``--max-fail-ratio-adjust-permissions=MAX-FAIL-RATIO-ADJUST-PERMISSIONS`` Maximum ratio for failures to allow when adjusting permissions (type float; default: 0.5) -``--minimal-build-env=MINIMAL-BUILD-ENV`` Minimal build environment to define when using system toolchain, specified as a comma-separated list that defines a mapping between name of environment variable and its value separated by a colon (':') (default: CC:gcc,CXX:g++) -``--minimal-toolchains`` Use minimal toolchain when resolving dependencies (default: False) -``--module-only`` Only generate module file(s); skip all steps except for module, prepare, ready, postiter, sanitycheck (default: False) -``--modules-tool-version-check`` Check version of modules tool being used (default: True; disable with --disable-modules-tool-version-check) -``--mpi-cmd-template=MPI-CMD-TEMPLATE`` Template for MPI commands (template keys: %(nr_ranks)s, %(cmd)s) -``--mpi-tests`` Run MPI tests (when relevant) (default: True; disable with --disable-mpi-tests) -``--optarch=OPTARCH`` Set architecture optimization, overriding native architecture optimizations -``--output-format=OUTPUT-FORMAT`` Set output format (type choice; default: txt) (choices: txt, rst) -``--output-style=OUTPUT-STYLE`` Control output style; auto implies using Rich if available to produce rich output, with fallback to basic colored output (type choice; default: auto) (choices: auto, basic, no_color, rich) -``--parallel=PARALLEL`` Specify (maximum) level of parallellism used during build procedure (type int) -``--parallel-extensions-install`` Install list of extensions in parallel (if supported) (default: False) -``--pre-create-installdir`` Create installation directory before submitting build jobs (default: True; disable with --disable-pre-create-installdir) -``-p, --pretend`` Does the build/installation in a test directory located in $HOME/easybuildinstall (default: False) -``--read-only-installdir`` Set read-only permissions on installation directory after installation (default: False) -``--remove-ghost-install-dirs`` Remove ghost installation directories when --force or --rebuild is used, rather than just warning about them (default: False) -``--required-linked-shared-libs=REQUIRED-LINKED-SHARED-LIBS`` Comma-separated list of shared libraries (names, file names, or paths) which must be linked in all installed binaries/libraries (type comma-separated list) -``--rpath`` Enable use of RPATH for linking with libraries (default: False) -``--rpath-filter=RPATH-FILTER`` List of regex patterns to use for filtering out RPATH paths (type comma-separated list) -``--rpath-override-dirs=RPATH-OVERRIDE-DIRS`` Path(s) to be prepended when linking with RPATH (string, colon-separated) -``--sanity-check-only`` Only run sanity check (module is expected to be installed already (default: False) -``--set-default-module`` Set the generated module as default (default: False) -``--set-gid-bit`` Set group ID bit on newly created directories (default: False) -``--show-progress-bar`` Show progress bar in terminal output (default: True; disable with --disable-show-progress-bar) -``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` Silence specified deprecation warnings (type comma-separated list) -``--skip-extensions`` Skip installation of extensions (default: False) -``-t, --skip-test-cases`` Skip running test cases (default: False) -``--skip-test-step`` Skip running the test step (e.g. unit tests) (default: False) -``--sticky-bit`` Set sticky bit on newly created directories (default: False) -``--sysroot=SYSROOT`` Location root directory of system, prefix for standard paths like /usr/lib and /usr/include -``-T, --trace`` Provide more information in output to stdout on progress (default: False) -``--umask=UMASK`` umask to use (e.g. '022'); non-user write permissions on install directories are removed -``--unit-testing-mode`` Run in unit test mode (default: False) -``--update-modules-tool-cache`` Update modules tool cache file(s) after generating module file (default: False) -``--use-ccache=PATH`` Enable use of ccache to speed up compilation, with specified cache dir (type ; default: False) -``--use-existing-modules`` Use existing modules when resolving dependencies with minimal toolchains (default: False) -``--use-f90cache=PATH`` Enable use of f90cache to speed up compilation, with specified cache dir (type ; default: False) -``--verify-easyconfig-filenames`` Verify whether filename of specified easyconfigs matches with contents (default: False) -``--wait-on-lock=WAIT-ON-LOCK`` Wait for lock to be released; 0 implies no waiting (exit with an error if the lock already exists), non-zero value specified waiting interval [DEPRECATED: use --wait-on-lock-interval and --wait-on-lock-limit instead] (type ) -``--wait-on-lock-interval=WAIT-ON-LOCK-INTERVAL`` Wait interval (in seconds) to use when waiting for existing lock to be removed (type ; default: 60) -``--wait-on-lock-limit=WAIT-ON-LOCK-LIMIT`` Maximum amount of time (in seconds) to wait until lock is released (0 means no waiting at all, exit with error; -1 means no waiting limit, keep waiting) (type ; default: 0) -``--zip-logs=ZIP-LOGS`` Zip logs that are copied to install directory, using specified command (default: gzip) -========================================================================= ================================================================================================================================================================================================================================================================================ +``--ignore-checksums`` Ignore failing checksum verification (default: False) +``--ignore-osdeps`` Ignore any listed OS dependencies (default: False) +``--ignore-test-failure`` Ignore a failing test step (default: False) +``--insecure-download`` Don't check the server certificate against the available certificate authorities. (default: False) +``--install-latest-eb-release`` Install latest known version of easybuild (default: False) +``--lib-lib64-symlink`` Automatically create symlinks for lib/ pointing to lib64/ if the former is missing (default: True; disable with --disable-lib-lib64-symlink) +``--lib64-fallback-sanity-check`` Fallback in sanity check to lib64/ equivalent for missing libraries (default: True; disable with --disable-lib64-fallback-sanity-check) +``--lib64-lib-symlink`` Automatically create symlinks for lib64/ pointing to lib/ if the former is missing (default: True; disable with --disable-lib64-lib-symlink) +``--max-fail-ratio-adjust-permissions=MAX-FAIL-RATIO-ADJUST-PERMISSIONS`` Maximum ratio for failures to allow when adjusting permissions (type float; default: 0.5) +``--minimal-build-env=MINIMAL-BUILD-ENV`` Minimal build environment to define when using system toolchain, specified as a comma-separated list that defines a mapping between name of environment variable and its value separated by a colon (':') (default: CC:gcc,CXX:g++) +``--minimal-toolchains`` Use minimal toolchain when resolving dependencies (default: False) +``--module-only`` Only generate module file(s); skip all steps except for module, prepare, ready, postiter, sanitycheck (default: False) +``--modules-tool-version-check`` Check version of modules tool being used (default: True; disable with --disable-modules-tool-version-check) +``--mpi-cmd-template=MPI-CMD-TEMPLATE`` Template for MPI commands (template keys: %(nr_ranks)s, %(cmd)s) +``--mpi-tests`` Run MPI tests (when relevant) (default: True; disable with --disable-mpi-tests) +``--optarch=OPTARCH`` Set architecture optimization, overriding native architecture optimizations +``--output-format=OUTPUT-FORMAT`` Set output format (type choice; default: txt) (choices: md, rst, txt) +``--output-style=OUTPUT-STYLE`` Control output style; auto implies using Rich if available to produce rich output, with fallback to basic colored output (type choice; default: auto) (choices: auto, basic, no_color, rich) +``--parallel=PARALLEL`` Specify (maximum) level of parallellism used during build procedure (type int) +``--parallel-extensions-install`` Install list of extensions in parallel (if supported) (default: False) +``--pre-create-installdir`` Create installation directory before submitting build jobs (default: True; disable with --disable-pre-create-installdir) +``-p, --pretend`` Does the build/installation in a test directory located in $HOME/easybuildinstall (default: False) +``--read-only-installdir`` Set read-only permissions on installation directory after installation (default: False) +``--remove-ghost-install-dirs`` Remove ghost installation directories when --force or --rebuild is used, rather than just warning about them (default: False) +``--required-linked-shared-libs=REQUIRED-LINKED-SHARED-LIBS`` Comma-separated list of shared libraries (names, file names, or paths) which must be linked in all installed binaries/libraries (type comma-separated list) +``--rpath`` Enable use of RPATH for linking with libraries (default: False) +``--rpath-filter=RPATH-FILTER`` List of regex patterns to use for filtering out RPATH paths (type comma-separated list) +``--rpath-override-dirs=RPATH-OVERRIDE-DIRS`` Path(s) to be prepended when linking with RPATH (string, colon-separated) +``--sanity-check-only`` Only run sanity check (module is expected to be installed already (default: False) +``--set-default-module`` Set the generated module as default (default: False) +``--set-gid-bit`` Set group ID bit on newly created directories (default: False) +``--show-progress-bar`` Show progress bar in terminal output (default: True; disable with --disable-show-progress-bar) +``--silence-deprecation-warnings=SILENCE-DEPRECATION-WARNINGS`` Silence specified deprecation warnings (type comma-separated list) +``--skip-extensions`` Skip installation of extensions (default: False) +``-t, --skip-test-cases`` Skip running test cases (default: False) +``--skip-test-step`` Skip running the test step (e.g. unit tests) (default: False) +``--sticky-bit`` Set sticky bit on newly created directories (default: False) +``--sysroot=SYSROOT`` Location root directory of system, prefix for standard paths like /usr/lib and /usr/include +``-T, --trace`` Provide more information in output to stdout on progress (default: False) +``--umask=UMASK`` umask to use (e.g. '022'); non-user write permissions on install directories are removed +``--unit-testing-mode`` Run in unit test mode (default: False) +``--update-modules-tool-cache`` Update modules tool cache file(s) after generating module file (default: False) +``--use-ccache=PATH`` Enable use of ccache to speed up compilation, with specified cache dir (type ; default: False) +``--use-existing-modules`` Use existing modules when resolving dependencies with minimal toolchains (default: False) +``--use-f90cache=PATH`` Enable use of f90cache to speed up compilation, with specified cache dir (type ; default: False) +``--verify-easyconfig-filenames`` Verify whether filename of specified easyconfigs matches with contents (default: False) +``--wait-on-lock=WAIT-ON-LOCK`` Wait for lock to be released; 0 implies no waiting (exit with an error if the lock already exists), non-zero value specified waiting interval [DEPRECATED: use --wait-on-lock-interval and --wait-on-lock-limit instead] (type ) +``--wait-on-lock-interval=WAIT-ON-LOCK-INTERVAL`` Wait interval (in seconds) to use when waiting for existing lock to be removed (type ; default: 60) +``--wait-on-lock-limit=WAIT-ON-LOCK-LIMIT`` Maximum amount of time (in seconds) to wait until lock is released (0 means no waiting at all, exit with error; -1 means no waiting limit, keep waiting) (type ; default: 0) +``--zip-logs=ZIP-LOGS`` Zip logs that are copied to install directory, using specified command (default: gzip) +========================================================================= ========================================================================================================================================================================================================================================================================================================================================================================== Package options --------------- =============================================== ============================================== -Option flag Option description +Option flag Option description =============================================== ============================================== -``--package`` Enabling packaging (default: False) -``--package-release=PACKAGE-RELEASE`` Package release iteration number (default: 1) -``--package-tool=PACKAGE-TOOL`` Packaging tool to use (default: fpm) +``--package`` Enabling packaging (default: False) +``--package-release=PACKAGE-RELEASE`` Package release iteration number (default: 1) +``--package-tool=PACKAGE-TOOL`` Packaging tool to use (default: fpm) ``--package-tool-options=PACKAGE-TOOL-OPTIONS`` Extra options for packaging tool (default: '') -``--package-type=PACKAGE-TYPE`` Type of package to generate (default: rpm) +``--package-type=PACKAGE-TYPE`` Type of package to generate (default: rpm) =============================================== ============================================== Regression test options ----------------------- ============================ ========================================================================== -Option flag Option description +Option flag Option description ============================ ========================================================================== ``--aggregate-regtest=DIR`` Collect all the xmls inside the given directory and generate a single file -``--regtest`` Enable regression test mode (default: False) -``--regtest-output-dir=DIR`` Set output directory for test-run +``--regtest`` Enable regression test mode (default: False) +``--regtest-output-dir=DIR`` Set output directory for test-run ``--sequential`` Specify this option if you want to prevent parallel build (default: False) ============================ ========================================================================== @@ -378,32 +381,32 @@ Option flag Option description Software search and build options --------------------------------- =================================== =================================================================================================================================================================== -Option flag Option description +Option flag Option description =================================== =================================================================================================================================================================== -``--amend=VAR=VALUE[,VALUE]`` Specify additional search and build parameters (can be used multiple times); for example: versionprefix=foo or patches=one.patch,two.patch) -``--map-toolchains`` Enable mapping of (sub)toolchains when --try-toolchain(-version) is used (default: True; disable with --disable-map-toolchains) -``--software=NAME,VERSION`` Search and build software with given name and version (type comma-separated list) -``--software-name=NAME`` Search and build software with given name -``--software-version=VERSION`` Search and build software with given version -``--toolchain=NAME,VERSION`` Search and build with given toolchain (name and version) (type comma-separated list) -``--toolchain-name=NAME`` Search and build with given toolchain name -``--toolchain-version=VERSION`` Search and build with given toolchain version +``--amend=VAR=VALUE[,VALUE]`` Specify additional search and build parameters (can be used multiple times); for example: versionprefix=foo or patches=one.patch,two.patch) +``--map-toolchains`` Enable mapping of (sub)toolchains when --try-toolchain(-version) is used (default: True; disable with --disable-map-toolchains) +``--software=NAME,VERSION`` Search and build software with given name and version (type comma-separated list) +``--software-name=NAME`` Search and build software with given name +``--software-version=VERSION`` Search and build software with given version +``--toolchain=NAME,VERSION`` Search and build with given toolchain (name and version) (type comma-separated list) +``--toolchain-name=NAME`` Search and build with given toolchain name +``--toolchain-version=VERSION`` Search and build with given toolchain version ``--try-amend=VAR=VALUE[,VALUE]`` Try to specify additional search and build parameters (can be used multiple times); for example: versionprefix=foo or patches=one.patch,two.patch) (USE WITH CARE!) -``--try-ignore-versionsuffixes`` Ignore versionsuffix differences when --try-update-deps is used (default: False) -``--try-software=NAME,VERSION`` Try to search and build software with given name and version (USE WITH CARE!) (type comma-separated list) -``--try-software-name=NAME`` Try to search and build software with given name (USE WITH CARE!) -``--try-software-version=VERSION`` Try to search and build software with given version (USE WITH CARE!) -``--try-toolchain=NAME,VERSION`` Try to search and build with given toolchain (name and version) (USE WITH CARE!) (type comma-separated list) -``--try-toolchain-name=NAME`` Try to search and build with given toolchain name (USE WITH CARE!) -``--try-toolchain-version=VERSION`` Try to search and build with given toolchain version (USE WITH CARE!) -``--try-update-deps`` Try to update versions of the dependencies of an easyconfig based on what is available in the robot path (default: False) +``--try-ignore-versionsuffixes`` Ignore versionsuffix differences when --try-update-deps is used (default: False) +``--try-software=NAME,VERSION`` Try to search and build software with given name and version (USE WITH CARE!) (type comma-separated list) +``--try-software-name=NAME`` Try to search and build software with given name (USE WITH CARE!) +``--try-software-version=VERSION`` Try to search and build software with given version (USE WITH CARE!) +``--try-toolchain=NAME,VERSION`` Try to search and build with given toolchain (name and version) (USE WITH CARE!) (type comma-separated list) +``--try-toolchain-name=NAME`` Try to search and build with given toolchain name (USE WITH CARE!) +``--try-toolchain-version=VERSION`` Try to search and build with given toolchain version (USE WITH CARE!) +``--try-update-deps`` Try to update versions of the dependencies of an easyconfig based on what is available in the robot path (default: False) =================================== =================================================================================================================================================================== Unittest options ---------------- ======================== ================================= -Option flag Option description +Option flag Option description ======================== ================================= ``--unittest-file=FILE`` Log to this file in unittest mode ======================== ================================= diff --git a/docs/version-specific/toolchain_opts.rst b/docs/version-specific/toolchain_opts.rst index b0534e95..3c670be6 100644 --- a/docs/version-specific/toolchain_opts.rst +++ b/docs/version-specific/toolchain_opts.rst @@ -5,7 +5,7 @@ Available toolchain options (by toolchain) *(see also* ``eb --avail-toolchain-opts `` *)* -ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gfbf_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpit_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - nvompi_ - nvompic_ - nvpsmpi_ - nvpsmpic_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ +ClangGCC_ - CrayCCE_ - CrayGNU_ - CrayIntel_ - CrayPGI_ - FCC_ - Fujitsu_ - GCC_ - GCCcore_ - GNU_ - NVHPC_ - PGI_ - cgmpich_ - cgmpolf_ - cgmvapich2_ - cgmvolf_ - cgompi_ - cgoolf_ - ffmpi_ - foss_ - fosscuda_ - gcccuda_ - gfbf_ - gimkl_ - gimpi_ - gimpic_ - giolf_ - giolfc_ - gmacml_ - gmkl_ - gmklc_ - gmpich2_ - gmpich_ - gmpit_ - gmpolf_ - gmvapich2_ - gmvolf_ - goalf_ - gobff_ - goblf_ - gofbf_ - golf_ - golfc_ - gomkl_ - gomklc_ - gompi_ - gompic_ - goolf_ - goolfc_ - gpsmpi_ - gpsolf_ - gqacml_ - gsmpi_ - gsolf_ - iccifort_ - iccifortcuda_ - ictce_ - iibff_ - iimkl_ - iimklc_ - iimpi_ - iimpic_ - iiqmpi_ - impich_ - impmkl_ - intel-compilers_ - intel-para_ - intel_ - intelcuda_ - iomkl_ - iomklc_ - iompi_ - iompic_ - ipsmpi_ - iqacml_ - ismkl_ - nvofbf_ - nvompi_ - nvompic_ - nvpsmpi_ - nvpsmpic_ - pmkl_ - pomkl_ - pompi_ - system_ - xlcxlf_ - xlmpich2_ - xlmpich_ - xlmvapich2_ - xlompi_ .. _ClangGCC: @@ -13,20 +13,20 @@ Available options for ClangGCC toolchain ---------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``basic-block-vectorize`` Basic block vectorization ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -35,17 +35,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -57,20 +57,20 @@ Available options for CrayCCE toolchain --------------------------------------- ========================= =============================================================================================================================================================================================================================================================== ========= -option description default +option description default ========================= =============================================================================================================================================================================================================================================================== ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``dynamic`` Generate dynamically linked executable ``True`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``dynamic`` Generate dynamically linked executable ``True`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -84,14 +84,14 @@ option description ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` -``verbose`` Verbose output ``True`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``True`` ``veryloose`` Very loose precision ``False`` ========================= =============================================================================================================================================================================================================================================================== ========= @@ -102,20 +102,20 @@ Available options for CrayGNU toolchain --------------------------------------- ========================= =============================================================================================================================================================================================================================================================== ========= -option description default +option description default ========================= =============================================================================================================================================================================================================================================================== ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``dynamic`` Generate dynamically linked executable ``True`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``dynamic`` Generate dynamically linked executable ``True`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -129,14 +129,14 @@ option description ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` -``verbose`` Verbose output ``True`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``True`` ``veryloose`` Very loose precision ``False`` ========================= =============================================================================================================================================================================================================================================================== ========= @@ -147,20 +147,20 @@ Available options for CrayIntel toolchain ----------------------------------------- ========================= =============================================================================================================================================================================================================================================================== ========= -option description default +option description default ========================= =============================================================================================================================================================================================================================================================== ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``dynamic`` Generate dynamically linked executable ``True`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``dynamic`` Generate dynamically linked executable ``True`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -174,14 +174,14 @@ option description ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` -``verbose`` Verbose output ``True`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``True`` ``veryloose`` Very loose precision ``False`` ========================= =============================================================================================================================================================================================================================================================== ========= @@ -192,20 +192,20 @@ Available options for CrayPGI toolchain --------------------------------------- ========================= =============================================================================================================================================================================================================================================================== ========= -option description default +option description default ========================= =============================================================================================================================================================================================================================================================== ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``dynamic`` Generate dynamically linked executable ``True`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``dynamic`` Generate dynamically linked executable ``True`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -219,14 +219,14 @@ option description ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` -``verbose`` Verbose output ``True`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``True`` ``veryloose`` Very loose precision ``False`` ========================= =============================================================================================================================================================================================================================================================== ========= @@ -237,19 +237,19 @@ Available options for FCC toolchain ----------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -257,17 +257,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -279,19 +279,19 @@ Available options for Fujitsu toolchain --------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -299,18 +299,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -322,19 +322,19 @@ Available options for GCC toolchain ----------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -345,17 +345,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -367,19 +367,19 @@ Available options for GCCcore toolchain --------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -390,17 +390,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -412,19 +412,19 @@ Available options for GNU toolchain ----------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -435,17 +435,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -457,19 +457,19 @@ Available options for NVHPC toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -477,17 +477,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -499,19 +499,19 @@ Available options for PGI toolchain ----------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -519,17 +519,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -541,20 +541,20 @@ Available options for cgmpich toolchain --------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``basic-block-vectorize`` Basic block vectorization ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -563,18 +563,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -586,20 +586,20 @@ Available options for cgmpolf toolchain --------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``basic-block-vectorize`` Basic block vectorization ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -608,18 +608,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -631,20 +631,20 @@ Available options for cgmvapich2 toolchain ------------------------------------------ ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``basic-block-vectorize`` Basic block vectorization ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -653,18 +653,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -676,20 +676,20 @@ Available options for cgmvolf toolchain --------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``basic-block-vectorize`` Basic block vectorization ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -698,18 +698,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -721,20 +721,20 @@ Available options for cgompi toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``basic-block-vectorize`` Basic block vectorization ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -743,18 +743,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -766,20 +766,20 @@ Available options for cgoolf toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``basic-block-vectorize`` Basic block vectorization ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loop-vectorize`` Loop vectorization ``False`` @@ -788,18 +788,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -811,19 +811,19 @@ Available options for ffmpi toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -831,18 +831,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -854,19 +854,19 @@ Available options for foss toolchain ------------------------------------ ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -877,18 +877,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -900,19 +900,19 @@ Available options for fosscuda toolchain ---------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -923,18 +923,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -946,19 +946,19 @@ Available options for gcccuda toolchain --------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -969,17 +969,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -991,19 +991,19 @@ Available options for gfbf toolchain ------------------------------------ ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1014,17 +1014,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1036,19 +1036,19 @@ Available options for gimkl toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1059,18 +1059,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1082,19 +1082,19 @@ Available options for gimpi toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1105,18 +1105,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1128,19 +1128,19 @@ Available options for gimpic toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1151,18 +1151,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1174,19 +1174,19 @@ Available options for giolf toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1197,18 +1197,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1220,19 +1220,19 @@ Available options for giolfc toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1243,18 +1243,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1266,19 +1266,19 @@ Available options for gmacml toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1289,18 +1289,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1312,19 +1312,19 @@ Available options for gmkl toolchain ------------------------------------ ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1335,17 +1335,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1357,19 +1357,19 @@ Available options for gmklc toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1380,17 +1380,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1402,19 +1402,19 @@ Available options for gmpich2 toolchain --------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1425,18 +1425,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1448,19 +1448,19 @@ Available options for gmpich toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1471,18 +1471,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1494,19 +1494,19 @@ Available options for gmpit toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1517,18 +1517,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1540,19 +1540,19 @@ Available options for gmpolf toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1563,18 +1563,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1586,19 +1586,19 @@ Available options for gmvapich2 toolchain ----------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1609,18 +1609,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1632,19 +1632,19 @@ Available options for gmvolf toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1655,18 +1655,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1678,19 +1678,19 @@ Available options for goalf toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1701,18 +1701,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1724,19 +1724,19 @@ Available options for gobff toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1747,18 +1747,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1770,19 +1770,19 @@ Available options for goblf toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1793,18 +1793,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1816,19 +1816,19 @@ Available options for gofbf toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1839,18 +1839,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1862,19 +1862,19 @@ Available options for golf toolchain ------------------------------------ ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1885,17 +1885,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1907,19 +1907,19 @@ Available options for golfc toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1930,17 +1930,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1952,19 +1952,19 @@ Available options for gomkl toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -1975,18 +1975,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -1998,19 +1998,19 @@ Available options for gomklc toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -2021,18 +2021,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2044,19 +2044,19 @@ Available options for gompi toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -2067,18 +2067,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2090,19 +2090,19 @@ Available options for gompic toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -2113,18 +2113,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2136,19 +2136,19 @@ Available options for goolf toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -2159,18 +2159,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2182,19 +2182,19 @@ Available options for goolfc toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -2205,18 +2205,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2228,19 +2228,19 @@ Available options for gpsmpi toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -2251,18 +2251,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2274,19 +2274,19 @@ Available options for gpsolf toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -2297,18 +2297,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2320,19 +2320,19 @@ Available options for gqacml toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -2343,18 +2343,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2366,19 +2366,19 @@ Available options for gsmpi toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -2389,18 +2389,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2412,19 +2412,19 @@ Available options for gsolf toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``f2c`` Generate code compatible with f2c and f77 ``False`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -2435,18 +2435,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2458,20 +2458,20 @@ Available options for iccifort toolchain ---------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2481,17 +2481,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2503,20 +2503,20 @@ Available options for iccifortcuda toolchain -------------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2526,17 +2526,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2547,46 +2547,48 @@ option description Available options for ictce toolchain ------------------------------------- -========================= ======================================================================= ========= -option description default -========================= ======================================================================= ========= -``32bit`` Compile 32bit target ``False`` -``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` -``debug`` Enable debug ``False`` -``defaultopt`` Default compiler optimizations ``False`` -``defaultprec`` Default precision ``False`` -``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` -``i8`` Integers are 8 byte integers ``False`` -``ieee`` Adhere to IEEE-754 rules ``False`` -``intel-static`` Link Intel provided libraries statically ``False`` -``loose`` Loose precision ``False`` -``lowopt`` Low compiler optimizations ``False`` -``no-icc`` Don't set Intel specific macros ``False`` -``noopt`` Disable compiler optimizations ``False`` -``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` -``openmp`` Enable OpenMP ``False`` -``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` -``packed-linker-options`` Pack the linker options as comma separated list ``False`` -``pic`` Use PIC ``False`` -``precise`` High precision ``False`` -``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` -``shared`` Build shared library ``False`` -``static`` Build static library ``False`` -``strict`` Strict (highest) precision ``False`` -``unroll`` Unroll loops ``False`` -``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` -``verbose`` Verbose output ``False`` -``veryloose`` Very loose precision ``False`` -========================= ======================================================================= ========= +========================= ========================================================================================================================================== ========= +option description default +========================= ========================================================================================================================================== ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``intel-static`` Link Intel provided libraries statically ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``no-icc`` Don't set Intel specific macros ``False`` +``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``None`` +``oneapi_c_cxx`` Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer) ``None`` +``oneapi_fortran`` Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ========================================================================================================================================== ========= .. _iibff: @@ -2594,46 +2596,48 @@ option description Available options for iibff toolchain ------------------------------------- -========================= ======================================================================= ========= -option description default -========================= ======================================================================= ========= -``32bit`` Compile 32bit target ``False`` -``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` -``debug`` Enable debug ``False`` -``defaultopt`` Default compiler optimizations ``False`` -``defaultprec`` Default precision ``False`` -``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` -``i8`` Integers are 8 byte integers ``False`` -``ieee`` Adhere to IEEE-754 rules ``False`` -``intel-static`` Link Intel provided libraries statically ``False`` -``loose`` Loose precision ``False`` -``lowopt`` Low compiler optimizations ``False`` -``no-icc`` Don't set Intel specific macros ``False`` -``noopt`` Disable compiler optimizations ``False`` -``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` -``openmp`` Enable OpenMP ``False`` -``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` -``packed-linker-options`` Pack the linker options as comma separated list ``False`` -``pic`` Use PIC ``False`` -``precise`` High precision ``False`` -``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` -``shared`` Build shared library ``False`` -``static`` Build static library ``False`` -``strict`` Strict (highest) precision ``False`` -``unroll`` Unroll loops ``False`` -``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` -``verbose`` Verbose output ``False`` -``veryloose`` Very loose precision ``False`` -========================= ======================================================================= ========= +========================= ========================================================================================================================================== ========= +option description default +========================= ========================================================================================================================================== ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``intel-static`` Link Intel provided libraries statically ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``no-icc`` Don't set Intel specific macros ``False`` +``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``None`` +``oneapi_c_cxx`` Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer) ``None`` +``oneapi_fortran`` Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ========================================================================================================================================== ========= .. _iimkl: @@ -2641,44 +2645,47 @@ option description Available options for iimkl toolchain ------------------------------------- -========================= ======================================================================= ========= -option description default -========================= ======================================================================= ========= -``32bit`` Compile 32bit target ``False`` -``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` -``debug`` Enable debug ``False`` -``defaultopt`` Default compiler optimizations ``False`` -``defaultprec`` Default precision ``False`` -``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` -``i8`` Integers are 8 byte integers ``False`` -``ieee`` Adhere to IEEE-754 rules ``False`` -``intel-static`` Link Intel provided libraries statically ``False`` -``loose`` Loose precision ``False`` -``lowopt`` Low compiler optimizations ``False`` -``no-icc`` Don't set Intel specific macros ``False`` -``noopt`` Disable compiler optimizations ``False`` -``openmp`` Enable OpenMP ``False`` -``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` -``packed-linker-options`` Pack the linker options as comma separated list ``False`` -``pic`` Use PIC ``False`` -``precise`` High precision ``False`` -``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` -``shared`` Build shared library ``False`` -``static`` Build static library ``False`` -``strict`` Strict (highest) precision ``False`` -``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` -``verbose`` Verbose output ``False`` -``veryloose`` Very loose precision ``False`` -========================= ======================================================================= ========= +========================= ========================================================================================================================================== ========= +option description default +========================= ========================================================================================================================================== ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``intel-static`` Link Intel provided libraries statically ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``no-icc`` Don't set Intel specific macros ``False`` +``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``None`` +``oneapi_c_cxx`` Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer) ``None`` +``oneapi_fortran`` Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ========================================================================================================================================== ========= .. _iimklc: @@ -2686,44 +2693,47 @@ option description Available options for iimklc toolchain -------------------------------------- -========================= ======================================================================= ========= -option description default -========================= ======================================================================= ========= -``32bit`` Compile 32bit target ``False`` -``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` -``debug`` Enable debug ``False`` -``defaultopt`` Default compiler optimizations ``False`` -``defaultprec`` Default precision ``False`` -``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` -``i8`` Integers are 8 byte integers ``False`` -``ieee`` Adhere to IEEE-754 rules ``False`` -``intel-static`` Link Intel provided libraries statically ``False`` -``loose`` Loose precision ``False`` -``lowopt`` Low compiler optimizations ``False`` -``no-icc`` Don't set Intel specific macros ``False`` -``noopt`` Disable compiler optimizations ``False`` -``openmp`` Enable OpenMP ``False`` -``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` -``packed-linker-options`` Pack the linker options as comma separated list ``False`` -``pic`` Use PIC ``False`` -``precise`` High precision ``False`` -``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` -``shared`` Build shared library ``False`` -``static`` Build static library ``False`` -``strict`` Strict (highest) precision ``False`` -``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` -``verbose`` Verbose output ``False`` -``veryloose`` Very loose precision ``False`` -========================= ======================================================================= ========= +========================= ========================================================================================================================================== ========= +option description default +========================= ========================================================================================================================================== ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``intel-static`` Link Intel provided libraries statically ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``no-icc`` Don't set Intel specific macros ``False`` +``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``None`` +``oneapi_c_cxx`` Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer) ``None`` +``oneapi_fortran`` Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ========================================================================================================================================== ========= .. _iimpi: @@ -2731,46 +2741,48 @@ option description Available options for iimpi toolchain ------------------------------------- -========================= ======================================================================= ========= -option description default -========================= ======================================================================= ========= -``32bit`` Compile 32bit target ``False`` -``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` -``debug`` Enable debug ``False`` -``defaultopt`` Default compiler optimizations ``False`` -``defaultprec`` Default precision ``False`` -``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` -``i8`` Integers are 8 byte integers ``False`` -``ieee`` Adhere to IEEE-754 rules ``False`` -``intel-static`` Link Intel provided libraries statically ``False`` -``loose`` Loose precision ``False`` -``lowopt`` Low compiler optimizations ``False`` -``no-icc`` Don't set Intel specific macros ``False`` -``noopt`` Disable compiler optimizations ``False`` -``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` -``openmp`` Enable OpenMP ``False`` -``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` -``packed-linker-options`` Pack the linker options as comma separated list ``False`` -``pic`` Use PIC ``False`` -``precise`` High precision ``False`` -``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` -``shared`` Build shared library ``False`` -``static`` Build static library ``False`` -``strict`` Strict (highest) precision ``False`` -``unroll`` Unroll loops ``False`` -``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` -``verbose`` Verbose output ``False`` -``veryloose`` Very loose precision ``False`` -========================= ======================================================================= ========= +========================= ========================================================================================================================================== ========= +option description default +========================= ========================================================================================================================================== ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``intel-static`` Link Intel provided libraries statically ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``no-icc`` Don't set Intel specific macros ``False`` +``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``None`` +``oneapi_c_cxx`` Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer) ``None`` +``oneapi_fortran`` Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ========================================================================================================================================== ========= .. _iimpic: @@ -2779,20 +2791,20 @@ Available options for iimpic toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2802,18 +2814,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2825,20 +2837,20 @@ Available options for iiqmpi toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2848,18 +2860,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2871,20 +2883,20 @@ Available options for impich toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2894,18 +2906,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2917,20 +2929,20 @@ Available options for impmkl toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -2940,18 +2952,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -2962,45 +2974,47 @@ option description Available options for intel-compilers toolchain ----------------------------------------------- -========================= ======================================================================= ========= -option description default -========================= ======================================================================= ========= -``32bit`` Compile 32bit target ``False`` -``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` -``debug`` Enable debug ``False`` -``defaultopt`` Default compiler optimizations ``False`` -``defaultprec`` Default precision ``False`` -``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` -``i8`` Integers are 8 byte integers ``False`` -``ieee`` Adhere to IEEE-754 rules ``False`` -``intel-static`` Link Intel provided libraries statically ``False`` -``loose`` Loose precision ``False`` -``lowopt`` Low compiler optimizations ``False`` -``no-icc`` Don't set Intel specific macros ``False`` -``noopt`` Disable compiler optimizations ``False`` -``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` -``openmp`` Enable OpenMP ``False`` -``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` -``packed-linker-options`` Pack the linker options as comma separated list ``False`` -``pic`` Use PIC ``False`` -``precise`` High precision ``False`` -``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` -``shared`` Build shared library ``False`` -``static`` Build static library ``False`` -``strict`` Strict (highest) precision ``False`` -``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` -``verbose`` Verbose output ``False`` -``veryloose`` Very loose precision ``False`` -========================= ======================================================================= ========= +========================= ========================================================================================================================================== ========= +option description default +========================= ========================================================================================================================================== ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``intel-static`` Link Intel provided libraries statically ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``no-icc`` Don't set Intel specific macros ``False`` +``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``None`` +``oneapi_c_cxx`` Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer) ``None`` +``oneapi_fortran`` Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ========================================================================================================================================== ========= .. _intel-para: @@ -3009,20 +3023,20 @@ Available options for intel-para toolchain ------------------------------------------ ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -3032,18 +3046,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3054,46 +3068,48 @@ option description Available options for intel toolchain ------------------------------------- -========================= ======================================================================= ========= -option description default -========================= ======================================================================= ========= -``32bit`` Compile 32bit target ``False`` -``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` -``debug`` Enable debug ``False`` -``defaultopt`` Default compiler optimizations ``False`` -``defaultprec`` Default precision ``False`` -``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` -``i8`` Integers are 8 byte integers ``False`` -``ieee`` Adhere to IEEE-754 rules ``False`` -``intel-static`` Link Intel provided libraries statically ``False`` -``loose`` Loose precision ``False`` -``lowopt`` Low compiler optimizations ``False`` -``no-icc`` Don't set Intel specific macros ``False`` -``noopt`` Disable compiler optimizations ``False`` -``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` -``openmp`` Enable OpenMP ``False`` -``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` -``packed-linker-options`` Pack the linker options as comma separated list ``False`` -``pic`` Use PIC ``False`` -``precise`` High precision ``False`` -``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` -``shared`` Build shared library ``False`` -``static`` Build static library ``False`` -``strict`` Strict (highest) precision ``False`` -``unroll`` Unroll loops ``False`` -``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` -``verbose`` Verbose output ``False`` -``veryloose`` Very loose precision ``False`` -========================= ======================================================================= ========= +========================= ========================================================================================================================================== ========= +option description default +========================= ========================================================================================================================================== ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``intel-static`` Link Intel provided libraries statically ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``no-icc`` Don't set Intel specific macros ``False`` +``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``None`` +``oneapi_c_cxx`` Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer) ``None`` +``oneapi_fortran`` Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ========================================================================================================================================== ========= .. _intelcuda: @@ -3102,20 +3118,20 @@ Available options for intelcuda toolchain ----------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -3125,18 +3141,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3147,46 +3163,48 @@ option description Available options for iomkl toolchain ------------------------------------- -========================= ======================================================================= ========= -option description default -========================= ======================================================================= ========= -``32bit`` Compile 32bit target ``False`` -``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` -``debug`` Enable debug ``False`` -``defaultopt`` Default compiler optimizations ``False`` -``defaultprec`` Default precision ``False`` -``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` -``i8`` Integers are 8 byte integers ``False`` -``ieee`` Adhere to IEEE-754 rules ``False`` -``intel-static`` Link Intel provided libraries statically ``False`` -``loose`` Loose precision ``False`` -``lowopt`` Low compiler optimizations ``False`` -``no-icc`` Don't set Intel specific macros ``False`` -``noopt`` Disable compiler optimizations ``False`` -``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` -``openmp`` Enable OpenMP ``False`` -``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` -``packed-linker-options`` Pack the linker options as comma separated list ``False`` -``pic`` Use PIC ``False`` -``precise`` High precision ``False`` -``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` -``shared`` Build shared library ``False`` -``static`` Build static library ``False`` -``strict`` Strict (highest) precision ``False`` -``unroll`` Unroll loops ``False`` -``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` -``verbose`` Verbose output ``False`` -``veryloose`` Very loose precision ``False`` -========================= ======================================================================= ========= +========================= ========================================================================================================================================== ========= +option description default +========================= ========================================================================================================================================== ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``intel-static`` Link Intel provided libraries statically ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``no-icc`` Don't set Intel specific macros ``False`` +``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``None`` +``oneapi_c_cxx`` Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer) ``None`` +``oneapi_fortran`` Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ========================================================================================================================================== ========= .. _iomklc: @@ -3195,20 +3213,20 @@ Available options for iomklc toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -3218,18 +3236,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3240,21 +3258,70 @@ option description Available options for iompi toolchain ------------------------------------- +========================= ========================================================================================================================================== ========= +option description default +========================= ========================================================================================================================================== ========= +``32bit`` Compile 32bit target ``False`` +``cciscxx`` Use CC as CXX ``False`` +``cstd`` Specify C standard ``None`` +``debug`` Enable debug ``False`` +``defaultopt`` Default compiler optimizations ``False`` +``defaultprec`` Default precision ``False`` +``error-unknown-option`` Error instead of warning for unknown options ``False`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` +``i8`` Integers are 8 byte integers ``False`` +``ieee`` Adhere to IEEE-754 rules ``False`` +``intel-static`` Link Intel provided libraries statically ``False`` +``loose`` Loose precision ``False`` +``lowopt`` Low compiler optimizations ``False`` +``no-icc`` Don't set Intel specific macros ``False`` +``noopt`` Disable compiler optimizations ``False`` +``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``None`` +``oneapi_c_cxx`` Use oneAPI C/C++ compilers icx/icpx instead of classic Intel C/C++ compilers (auto-enabled for Intel compilers version 2022.2.0, or newer) ``None`` +``oneapi_fortran`` Use oneAPI Fortran compiler ifx instead of classic Intel Fortran compiler ``False`` +``openmp`` Enable OpenMP ``False`` +``opt`` High compiler optimizations ``False`` +``optarch`` Enable architecture optimizations ``True`` +``packed-linker-options`` Pack the linker options as comma separated list ``False`` +``pic`` Use PIC ``False`` +``precise`` High precision ``False`` +``r8`` Real is 8 byte real ``False`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``shared`` Build shared library ``False`` +``static`` Build static library ``False`` +``strict`` Strict (highest) precision ``False`` +``unroll`` Unroll loops ``False`` +``usempi`` Use MPI compiler as default compiler ``False`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``verbose`` Verbose output ``False`` +``veryloose`` Very loose precision ``False`` +========================= ========================================================================================================================================== ========= + + +.. _iompic: + +Available options for iompic toolchain +-------------------------------------- + ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -3262,46 +3329,45 @@ option description ``lowopt`` Low compiler optimizations ``False`` ``no-icc`` Don't set Intel specific macros ``False`` ``noopt`` Disable compiler optimizations ``False`` -``oneapi`` Use oneAPI compilers icx/icpx/ifx instead of classic compilers ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= -.. _iompic: +.. _ipsmpi: -Available options for iompic toolchain +Available options for ipsmpi toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -3311,43 +3377,43 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= -.. _ipsmpi: +.. _iqacml: -Available options for ipsmpi toolchain +Available options for iqacml toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -3357,43 +3423,43 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= -.. _iqacml: +.. _ismkl: -Available options for iqacml toolchain --------------------------------------- +Available options for ismkl toolchain +------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``intel-static`` Link Intel provided libraries statically ``False`` @@ -3403,64 +3469,61 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= -.. _ismkl: +.. _nvofbf: -Available options for ismkl toolchain -------------------------------------- +Available options for nvofbf toolchain +-------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` -``intel-static`` Link Intel provided libraries statically ``False`` ``loose`` Loose precision ``False`` ``lowopt`` Low compiler optimizations ``False`` -``no-icc`` Don't set Intel specific macros ``False`` ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3472,19 +3535,19 @@ Available options for nvompi toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -3492,18 +3555,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3515,19 +3578,19 @@ Available options for nvompic toolchain --------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -3535,18 +3598,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3558,19 +3621,19 @@ Available options for nvpsmpi toolchain --------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -3578,18 +3641,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3601,19 +3664,19 @@ Available options for nvpsmpic toolchain ---------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -3621,18 +3684,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3644,19 +3707,19 @@ Available options for pmkl toolchain ------------------------------------ ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -3664,17 +3727,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3686,19 +3749,19 @@ Available options for pomkl toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -3706,18 +3769,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3729,19 +3792,19 @@ Available options for pompi toolchain ------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -3749,18 +3812,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3772,19 +3835,19 @@ Available options for system toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` ``loose`` Loose precision ``False`` @@ -3792,17 +3855,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3814,20 +3877,20 @@ Available options for xlcxlf toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ibm-static`` Link IBM XL provided libraries statically ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -3836,17 +3899,17 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3858,20 +3921,20 @@ Available options for xlmpich2 toolchain ---------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ibm-static`` Link IBM XL provided libraries statically ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -3880,18 +3943,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3903,20 +3966,20 @@ Available options for xlmpich toolchain --------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ibm-static`` Link IBM XL provided libraries statically ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -3925,18 +3988,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3948,20 +4011,20 @@ Available options for xlmvapich2 toolchain ------------------------------------------ ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ibm-static`` Link IBM XL provided libraries statically ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -3970,18 +4033,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= @@ -3993,20 +4056,20 @@ Available options for xlompi toolchain -------------------------------------- ========================= ======================================================================= ========= -option description default +option description default ========================= ======================================================================= ========= ``32bit`` Compile 32bit target ``False`` ``cciscxx`` Use CC as CXX ``False`` -``cstd`` Specify C standard ``None`` +``cstd`` Specify C standard ``None`` ``debug`` Enable debug ``False`` ``defaultopt`` Default compiler optimizations ``False`` ``defaultprec`` Default precision ``False`` ``error-unknown-option`` Error instead of warning for unknown options ``False`` -``extra_cflags`` Specify extra CFLAGS options. ``None`` -``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` -``extra_f90flags`` Specify extra F90FLAGS options. ``None`` -``extra_fcflags`` Specify extra FCFLAGS options. ``None`` -``extra_fflags`` Specify extra FFLAGS options. ``None`` +``extra_cflags`` Specify extra CFLAGS options. ``None`` +``extra_cxxflags`` Specify extra CXXFLAGS options. ``None`` +``extra_f90flags`` Specify extra F90FLAGS options. ``None`` +``extra_fcflags`` Specify extra FCFLAGS options. ``None`` +``extra_fflags`` Specify extra FFLAGS options. ``None`` ``i8`` Integers are 8 byte integers ``False`` ``ibm-static`` Link IBM XL provided libraries statically ``False`` ``ieee`` Adhere to IEEE-754 rules ``False`` @@ -4015,18 +4078,18 @@ option description ``noopt`` Disable compiler optimizations ``False`` ``openmp`` Enable OpenMP ``False`` ``opt`` High compiler optimizations ``False`` -``optarch`` Enable architecture optimizations ``True`` +``optarch`` Enable architecture optimizations ``True`` ``packed-linker-options`` Pack the linker options as comma separated list ``False`` ``pic`` Use PIC ``False`` ``precise`` High precision ``False`` ``r8`` Real is 8 byte real ``False`` -``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` +``rpath`` Use RPATH wrappers when --rpath is enabled in EasyBuild configuration ``True`` ``shared`` Build shared library ``False`` ``static`` Build static library ``False`` ``strict`` Strict (highest) precision ``False`` ``unroll`` Unroll loops ``False`` ``usempi`` Use MPI compiler as default compiler ``False`` -``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` +``vectorize`` Enable compiler auto-vectorization, default except for noopt and lowopt ``None`` ``verbose`` Verbose output ``False`` ``veryloose`` Very loose precision ``False`` ========================= ======================================================================= ========= diff --git a/docs/version-specific/toolchains.rst b/docs/version-specific/toolchains.rst index b42d7525..7ff35346 100644 --- a/docs/version-specific/toolchains.rst +++ b/docs/version-specific/toolchains.rst @@ -4,14 +4,14 @@ List of known toolchains ------------------------ =================== ================ ============= ========================= ======== -Name Compiler(s) MPI Linear algebra FFT +Name Compiler(s) MPI Linear algebra FFT =================== ================ ============= ========================= ======== **cgmpich** Clang, GCC MPICH *(none)* *(none)* -**cgmpolf** Clang, GCC MPICH OpenBLAS, ScaLAPACK FFTW +**cgmpolf** Clang, GCC MPICH OpenBLAS, ScaLAPACK FFTW **cgmvapich2** Clang, GCC MVAPICH2 *(none)* *(none)* -**cgmvolf** Clang, GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW +**cgmvolf** Clang, GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW **cgompi** Clang, GCC OpenMPI *(none)* *(none)* -**cgoolf** Clang, GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**cgoolf** Clang, GCC OpenMPI OpenBLAS, ScaLAPACK FFTW **ClangGCC** Clang, GCC *(none)* *(none)* *(none)* **CrayCCE** PrgEnv-cray cray-mpich cray-libsci *(none)* **CrayGNU** PrgEnv-gnu cray-mpich cray-libsci *(none)* @@ -19,75 +19,76 @@ Name Compiler(s) MPI Linear algebra **CrayPGI** PrgEnv-pgi cray-mpich cray-libsci *(none)* **FCC** lang *(none)* *(none)* *(none)* **ffmpi** FCC *(none)* *(none)* *(none)* -**foss** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW -**fosscuda** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW -**Fujitsu** FCC *(none)* *(none)* FFTW +**foss** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**fosscuda** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW +**Fujitsu** FCC *(none)* *(none)* FFTW **GCC** GCC *(none)* *(none)* *(none)* **GCCcore** GCCcore *(none)* *(none)* *(none)* **gcccuda** GCC, CUDA *(none)* *(none)* *(none)* -**gfbf** GCC *(none)* FlexiBLAS FFTW -**gimkl** GCC impi imkl imkl +**gfbf** GCC *(none)* FlexiBLAS FFTW +**gimkl** GCC impi imkl imkl **gimpi** GCC impi *(none)* *(none)* **gimpic** GCC, CUDA impi *(none)* *(none)* -**giolf** GCC impi OpenBLAS, ScaLAPACK FFTW -**giolfc** GCC, CUDA impi OpenBLAS, ScaLAPACK FFTW -**gmacml** GCC MVAPICH2 ACML, ScaLAPACK FFTW -**gmkl** GCC *(none)* imkl imkl -**gmklc** GCC, CUDA *(none)* imkl imkl +**giolf** GCC impi OpenBLAS, ScaLAPACK FFTW +**giolfc** GCC, CUDA impi OpenBLAS, ScaLAPACK FFTW +**gmacml** GCC MVAPICH2 ACML, ScaLAPACK FFTW +**gmkl** GCC *(none)* imkl imkl +**gmklc** GCC, CUDA *(none)* imkl imkl **gmpich** GCC MPICH *(none)* *(none)* **gmpich2** GCC MPICH2 *(none)* *(none)* **gmpit** GCC MPItrampoline *(none)* *(none)* -**gmpolf** GCC MPICH OpenBLAS, ScaLAPACK FFTW +**gmpolf** GCC MPICH OpenBLAS, ScaLAPACK FFTW **gmvapich2** GCC MVAPICH2 *(none)* *(none)* -**gmvolf** GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW +**gmvolf** GCC MVAPICH2 OpenBLAS, ScaLAPACK FFTW **GNU** GCC *(none)* *(none)* *(none)* -**goalf** GCC OpenMPI ATLAS, ScaLAPACK FFTW -**gobff** GCC OpenMPI BLIS, libFLAME, ScaLAPACK FFTW -**goblf** GCC OpenMPI BLIS, LAPACK, ScaLAPACK FFTW -**gofbf** GCC OpenMPI FlexiBLAS, ScaLAPACK FFTW -**golf** GCC *(none)* OpenBLAS FFTW -**golfc** GCC, CUDA *(none)* OpenBLAS FFTW -**gomkl** GCC OpenMPI imkl imkl -**gomklc** GCC, CUDA OpenMPI imkl imkl +**goalf** GCC OpenMPI ATLAS, ScaLAPACK FFTW +**gobff** GCC OpenMPI BLIS, libFLAME, ScaLAPACK FFTW +**goblf** GCC OpenMPI BLIS, LAPACK, ScaLAPACK FFTW +**gofbf** GCC OpenMPI FlexiBLAS, ScaLAPACK FFTW +**golf** GCC *(none)* OpenBLAS FFTW +**golfc** GCC, CUDA *(none)* OpenBLAS FFTW +**gomkl** GCC OpenMPI imkl imkl +**gomklc** GCC, CUDA OpenMPI imkl imkl **gompi** GCC OpenMPI *(none)* *(none)* **gompic** GCC, CUDA OpenMPI *(none)* *(none)* -**goolf** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW -**goolfc** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW +**goolf** GCC OpenMPI OpenBLAS, ScaLAPACK FFTW +**goolfc** GCC, CUDA OpenMPI OpenBLAS, ScaLAPACK FFTW **gpsmpi** GCC psmpi *(none)* *(none)* -**gpsolf** GCC psmpi OpenBLAS, ScaLAPACK FFTW -**gqacml** GCC QLogicMPI ACML, ScaLAPACK FFTW +**gpsolf** GCC psmpi OpenBLAS, ScaLAPACK FFTW +**gqacml** GCC QLogicMPI ACML, ScaLAPACK FFTW **gsmpi** GCC SpectrumMPI *(none)* *(none)* -**gsolf** GCC SpectrumMPI OpenBLAS, ScaLAPACK FFTW +**gsolf** GCC SpectrumMPI OpenBLAS, ScaLAPACK FFTW **iccifort** icc, ifort *(none)* *(none)* *(none)* **iccifortcuda** icc, ifort, CUDA *(none)* *(none)* *(none)* -**ictce** icc, ifort impi imkl imkl -**iibff** icc, ifort impi BLIS, libFLAME, ScaLAPACK FFTW -**iimkl** icc, ifort *(none)* imkl imkl -**iimklc** icc, ifort, CUDA *(none)* imkl imkl +**ictce** icc, ifort impi imkl imkl +**iibff** icc, ifort impi BLIS, libFLAME, ScaLAPACK FFTW +**iimkl** icc, ifort *(none)* imkl imkl +**iimklc** icc, ifort *(none)* imkl imkl **iimpi** icc, ifort impi *(none)* *(none)* **iimpic** icc, ifort, CUDA impi *(none)* *(none)* **iiqmpi** icc, ifort QLogicMPI *(none)* *(none)* **impich** icc, ifort MPICH *(none)* *(none)* -**impmkl** icc, ifort MPICH imkl imkl -**intel** icc, ifort impi imkl imkl +**impmkl** icc, ifort MPICH imkl imkl +**intel** icc, ifort impi imkl imkl **intel-compilers** intel-compilers *(none)* *(none)* *(none)* -**intel-para** icc, ifort psmpi imkl imkl -**intelcuda** icc, ifort, CUDA impi imkl imkl -**iomkl** icc, ifort OpenMPI imkl imkl -**iomklc** icc, ifort, CUDA OpenMPI imkl imkl +**intel-para** icc, ifort psmpi imkl imkl +**intelcuda** icc, ifort, CUDA impi imkl imkl +**iomkl** icc, ifort OpenMPI imkl imkl +**iomklc** icc, ifort, CUDA OpenMPI imkl imkl **iompi** icc, ifort OpenMPI *(none)* *(none)* **iompic** icc, ifort, CUDA OpenMPI *(none)* *(none)* **ipsmpi** icc, ifort psmpi *(none)* *(none)* -**iqacml** icc, ifort QLogicMPI ACML, ScaLAPACK FFTW -**ismkl** icc, ifort MPICH2 imkl imkl +**iqacml** icc, ifort QLogicMPI ACML, ScaLAPACK FFTW +**ismkl** icc, ifort MPICH2 imkl imkl **NVHPC** NVHPC *(none)* *(none)* *(none)* +**nvofbf** NVHPC OpenMPI FlexiBLAS, ScaLAPACK FFTW **nvompi** NVHPC OpenMPI *(none)* *(none)* **nvompic** NVHPC OpenMPI *(none)* *(none)* **nvpsmpi** NVHPC psmpi *(none)* *(none)* **nvpsmpic** NVHPC psmpi *(none)* *(none)* **PGI** PGI *(none)* *(none)* *(none)* -**pmkl** PGI *(none)* imkl imkl -**pomkl** PGI OpenMPI imkl imkl +**pmkl** PGI *(none)* imkl imkl +**pomkl** PGI OpenMPI imkl imkl **pompi** PGI OpenMPI *(none)* *(none)* **system** *(none)* *(none)* *(none)* *(none)* **xlcxlf** xlc, xlf *(none)* *(none)* *(none)* From e3baa65b2a80a6831fe8e079e2f092089ea695ea Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 9 Jan 2023 14:53:46 +0100 Subject: [PATCH 259/286] update release notes and changelog for EasyBuild v4.7.0 + bump version to 4.7.0 --- docs/Changelog.rst | 1 + docs/Release_notes.rst | 221 +++++++++++++++++++++++++++++++++++++++++ docs/conf.py | 4 +- 3 files changed, 224 insertions(+), 2 deletions(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index e3c517ea..2babf34e 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,6 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) +* **release 20221021.01** (`Jan 9th 2023`): update release notes for EasyBuild v4.7.0 (see :ref:`release_notes_eb470`) * **release 20221021.01** (`Oct 21st 2022`): update release notes for EasyBuild v4.6.2 (see :ref:`release_notes_eb462`) * **release 20220912.01** (`Sep 12th 2022`): update release notes for EasyBuild v4.6.1 (see :ref:`release_notes_eb461`) * **release 20220708.01** (`Jul 8th 2022`): update release notes for EasyBuild v4.6.0 (see :ref:`release_notes_eb460`) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index c3ed0e46..f131a9ba 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -9,6 +9,227 @@ alongside 15,535 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. + +.. _release_notes_eb470: + +EasyBuild v4.7.0 (Januar 9th 2023) +---------------------------------- + +feature release + +**framework** + +* print deprecation warning with running EasyBuild with Python 2 (`#4136 `_) + +* various enhancements, including: + + * add support for checksums specified in external ``checksums.json`` file (`#3749 `_) + * vendor ``distutils.version.LooseVersion`` as ``easybuild.tools.LooseVersion`` (since distutils is deprecated in Python 3.10) (`#3794 `_, `#4156 `_) + * take into account custom configuration options specified in easystack file (`#4057 `_) + * add support for using ``--output-format=md`` (MarkDown) (`#4117 `_, `#4155 `_) + * add support for `--filter-rpath-sanity-libs` to skip RPATH sanity check for designated libraries (`#4119 `_) + * add sanity_check_load_module method to EasyBlock to provide control over when module is loaded during sanity check step (`#4125 `_) + * add ``eb_bash_completion_local.bash`` script to ``setup.py`` (`#4127 `_) + * check whether ``nvidia-smi/rocm-smi`` command is available before trying to run it in ``get_gpu_info`` (`#4131 `_) + * add ``gfbf`` as subtoolchain of foss (`#4143 `_) + * add support for ``postinstallmsgs`` (`#4145 `_) + * make ``iimkl`` toolchain aware of ``intel-compilers`` (`#4146 `_) + * add definition for ``nvofbf`` toolchain (`#4157 `_, `#4163 `_) + +* various bug fixes, including: + + * also use EasyConfig instances cache in process_easyconfig when ``build_specs`` is empty dict (`#4107 `_) + * fix build options that should have empty list as default value (`#4108 `_) + * catch easyconfig parsing failure so we can generate and post a test report (`#4109 `_) + * add explicit return when no checksums match those specified in a tuple (`#4112 `_) + * tweak ``findPythonDeps.py`` script to use canonical package names (`#4118 `_) + * add ``-fdefault-double-8`` to ``r8`` toolchain compiler option for GCC (to be consistent with Intel) (`#4121 `_) + * always start with empty list for banned/requires libraries to avoid that corresponding build option is updated in-place (`#4137 `_) + * fix container tests by using EPEL archive URL for downloading Singularity RPM (`#4138 `_) + * use ``-march=x86-64 -mtune=generic`` instead of ``-xSSE2`` when using Intel oneAPI compilers (`#4147 `_) + * partially ``skip test_det_copy_ec_specs`` if no GitHub token is available (`#4149 `_) + +* other changes: + + * drop support for easystack files using ``'software'`` top-level key (`#4057 `_) + * also run unit tests with Python 3.11 + add Python 3.11 to classifiers in ``setup.py`` (`#4092 `_, `#4141 `_) + * use new EasyBuild logo in README (`#4123 `_) + * automatically cancel Github Action workflow runs for outdated commits (`#4132 `_) + * auto-enable use of oneAPI C/C++ compilers for intel-compilers >= 2022.2.0 (`#4135 `_) + * trim CI test configurations to avoid hitting GitHub rate limits (`#4148 `_) + * various tweaks to docstrings and help messages to fix problems with auto-generated documentation in MarkDown format (`#4129 `_, `#4130 `_, `#4154 `_, `#4160 `_, `#4162 `_, `#4168 `_) + * update copyright lines for 2023 (`#4161 `_) + +**easyblocks** + +* add generic easyblocks for installing (bundle of) Julia packages: JuliaPackage (`#2816 `_) and JuliaBundle (`#2830 `_) + +* minor enhancements and updates, including: + + * enhance TensorFlow easyblock to take into account provided OpenSSL dependency (`#2575 `_) + * add fix_shebang to ``install_step`` of PythonPackage easyblock so that we can fix shebangs when installing extensions (`#2680 `_) + * update PETSc easyblock for newer versions (>= 3.17) (`#2796 `_) + * update Clang easyblock to add support for new directory structure in Clang versions >= 14 + support Flang (`#2800 `_) + * update Xmipp easyblock since versions >= 3.20.07 use ``noAsk`` option to configure (`#2809 `_) + * add ``include/opencv4`` to ``$CPATH`` for OpenCV versions >= 4.0 (`#2818 `_) + * add extra option for disabling LAPACK in ESMF (`#2821 `_) + * enable building of static libraries for libxml2 >= 2.10 (`#2825 `_) + * update Xmipp easyblock to handle effects of CUDA at SYSTEM level and newer CUDA version requirements for stdc++ (`#2831 `_) + * update LLVM easyblock to put ``'cmake'`` symlink in place so separate CMake modules required for LLVM 15+ can be found (`#2832 `_) + * set ``$TEMPDIRPATH`` for testsuite in the BerkeleyGW easyblock, to avoid polluting ``/tmp`` (`#2836 `_) + * add ``configure_no_prefix`` option to skip addition of prefix to configure command in ConfigureMake easyblock (`#2842 `_) + * update ``qscintilla.py`` to be compatible with EB install of PyQt5 >= 5.15 (`#2845 `_) + * add UCC to known_dependencies in OpenMPI EasyBlock (`#2847 `_) + * update Clang-AOMP easyblock to handle version 5.2 and newer (`#2851 `_) + +* various bug fixes, including: + + * fix installing of Clang with RPATH linking (`#2799 `_) + * fix ``--module-only`` for Clang + fix sanity check for Clang 11.x (`#2800 `_) + * create ``$XDG_CACHE_HOME`` for PyTorch tests (`#2806 `_) + * make PythonPackage easyblock compatible with ``--sanity-check-only`` by loading module early during sanity check step (`#2828 `_) + * fix docstring of PythonBundle generic easyblock (`#2833 `_) + * fix counting of failures in PyTorch tests (`#2834 `_, `#2840 `_) + * make sure that ANSYS INSTALL script has execute permissions (`#2852 `_, `#2853 `_) + +* other changes: + + * remove useless ``-openmp`` build option for MRtrix v3.x (`#2822 `_) + * update HDF5 easyblock to use ``--enable-threadsafe`` configure option to make C API thread safe (`#2824 `_) + * use new EasyBuild logo in README (`#2827 `_) + * automatically cancel Github Action workflow runs for outdated commits (`#2835 `_) + * use fixed names for ``bazel/wrapper`` subdirectories used when building TensorFlow, to make debugging easier (`#2841 `_) + * also run unit tests with Python 3.11 (`#2844 `_) + * tweak docstring in some generic easyblocks so it renders nicely in auto-generated documentation (`#2849 `_) + * update copyright lines for 2023 (`#2850 `_) + +**easyconfigs** + +* added easyconfigs for ``foss/2022b``, ``intel/2022b`` common toolchains (`#16961 `_ and `#16962 `_) + + * see also https://docs.easybuild.io/en/latest/Common-toolchains.html + +* added easyconfigs for NVHPC-based toolchains ``nvompi/2022.07`` and ``nvofbf/2022.07`` (`#16724 `_) + +* added example easyconfig files for 107 new software packages: + + * Alfred (`#16780 `_), attrdict3 (`#16856 `_), bamFilters (`#16735 `_), bcl-convert (`#16351 `_), Beagle (`#346 `_), Boost.MPI (`#15757 `_), + captum (`#16477 `_), CAT-BAT (`#16577 `_, `#16634 `_), cdo-bindings (`#16669 `_), Chemaxon-Marvin (`#13954 `_), CliMetLab (`#16842 `_), + CloudCompare (`#16944 `_), cmocean (`#16659 `_), COBRApy (`#16616 `_), CodAn (`#16902 `_), CoSymLib (`#17049 `_), CPPE (`#16749 `_), + cryoCARE (`#16534 `_), CTPL (`#16498 `_), CUDA-Samples (`#16914 `_), cwltool (`#16503 `_), Cytoscape (`#16682 `_), DeepLabCut (`#16391 `_), + DeepMod2 (`#17008 `_), Dice (`#16752 `_), dlb (`#16845 `_), DRAGMAP (`#16532 `_), ecBuild (`#16842 `_), EGTtools (`#16704 `_), + ESM-2 (`#16528 `_), flair-NLP (`#15588 `_), FMS (`#16965 `_), Godon (`#16574 `_), gsw (`#16643 `_), HighFive (`#16737 `_), humann (`#16853 `_), + HyperQueue (`#16753 `_), IJulia (`#16494 `_, `#16665 `_), infercnvpy (`#16712 `_), InParanoid (`#16572 `_), jupyter-server (`#14844 `_), + KaHIP (`#16861 `_), KITE (`#16550 `_), lagrangian-filtering (`#16654 `_), LHAPDF (`#17028 `_), librttopo (`#16856 `_), libwpe (`#16088 `_), + Magics (`#16842 `_), matlab-proxy (`#14270 `_), mcu (`#16566 `_), MEMOTE (`#16772 `_), memtester (`#16763 `_), meson-python (`#16911 `_), + minizip (`#16856 `_), MITgcmutils (`#16623 `_), MONAI (`#16519 `_), MOOSE (`#13824 `_), mstore (`#16892 `_, `#17029 `_), + MultilevelEstimators (`#15630 `_, `#16665 `_), n2v (`#16535 `_), NanoLyse (`#16575 `_), napari (`#16468 `_), NECI (`#16751 `_), + nf-core-mag (`#16613 `_), oceanspy (`#16640 `_), olego (`#16909 `_), OmegaFold (`#16698 `_), OVITO (`#16811 `_), Panedr (`#16564 `_), + Parcels (`#16838 `_), polars (`#16989 `_), PsiCLASS (`#16906 `_), pyccel (`#16823 `_), PyCheMPS2 (`#16710 `_), PyDamage (`#16576 `_), + PyImageJ (`#16757 `_), pysteps (`#16783 `_), python-libsbml (`#16610 `_), python-telegram-bot (`#16442 `_), pyWannier90 (`#16447 `_), + resolos (`#16649 `_), RLCard (`#16695 `_), SAP (`#5200 `_), scikit-misc (`#16457 `_), scvi-tools (`#16457 `_), SELFIES (`#17032 `_), + SeuratDisk (`#16951 `_), sfftk (`#16466 `_), simint (`#16886 `_), SISSO++ (`#15759 `_), slamdunk (`#15197 `_), spaCy (`#17027 `_), + Sphinx-RTD-Theme (`#16736 `_), SPOOLES (`#16756 `_), Squidpy (`#16880 `_), svist4get (`#16505 `_), task-spooler (`#17048 `_), + TBA (`#16497 `_), TensorFlow-Datasets (`#16421 `_), TFEA (`#16476 `_), TinyXML (`#16992 `_), tokenizers (`#15587 `_), + torchsampler (`#16464 `_), trimesh (`#16858 `_), UCX-ROCm (`#17033 `_), wpebackend-fdo (`#16093 `_), xmitgcm (`#16637 `_) + +* added additional easyconfigs for various supported software packages, including: + + * Albumentations 1.3.0, ANSYS 2022R2, AOCC 4.0.0, archspec 0.1.4, ArviZ 0.12.1, ASAP 2.1, astropy 5.1.1, + basemap 1.3.6, BBMap 39.01, BEDOPS 2.4.41, Blender 3.3.1, Blosc 1.21.3, Blosc2 2.4.3, bokeh 2.4.3, Bonnie++ 2.00a, + boto3 1.26.37, BRAKER 2.1.6, CDO 2.1.1, cdsapi 0.5.1, CharLS 2.4.1, CheMPS2 1.8.12, CMake 3.24.3, CubeGUI 4.8, + CubeLib 4.8, CubeWriter 4.8, CUDA 11.8.0 + 12.0.0, cuDNN 8.6.0.163 + 8.7.0.84, cURL 7.86.0, cutadapt 4.2, + cuTENSOR 1.6.1.5, dask 2022.10.0, DAS_Tool 1.1.3, DBus 1.15.2, dcm2niix 1.0.20220720, DCMTK 3.6.7, deepdiff 5.8.1, + dm-reverb 0.7.0, double-conversion 3.2.1, Doxygen 1.9.5, ecCodes 2.27.0, exiv2 0.27.5, Fiji 2.9.0, Filtlong 0.2.1, + FLANN 1.9.1, FlexiBLAS 3.2.1, fontconfig 2.14.1, FreeXL 1.0.6, g2clib 1.7.0, GATK 4.3.0.0, GD 2.75, GDCM 3.0.20, + Gdk-Pixbuf 2.42.10, GeneMark-ET 4.71, gensim 4.2.0, geopandas 0.12.2, gettext 0.21.1, gh 2.20.2, Ghostscript 10.0.0, + git 2.38.1, GLib 2.75.0, GlobalArrays 5.8.2, GnuTLS 3.7.8, GObject-Introspection 1.74.0, GRASS 8.2.0, GTK3 3.24.35, + HarfBuzz 5.3.1, HTSeq 2.0.2, hwloc 2.8.0, Hyperopt 0.2.7, ICU 72.1, imagecodecs 2022.9.26, imageio 2.22.2, + ImageMagick 7.1.0-53, imbalanced-learn 0.9.0, JasPer 4.0.0, jax 0.3.23, JupyterLab 3.5.0, Leptonica 1.83.0, + libavif 0.11.1, libdap 3.20.11, libdeflate 1.15, libdrm 2.4.114, libfabric 1.16.1, libffi 3.4.4, libglvnd 1.6.0, + libgpg-error 1.46, libidn 1.41, libjpeg-turbo 2.1.4, LibLZF 3.6, libpciaccess 0.17, libpng 1.6.38, librsvg 2.55.1, + LibSoup 3.0.8, libspatialindex 1.9.3, libspatialite 5.0.1, libtasn1 4.19.0, LibTIFF 4.4.0, libxml2 2.10.3, + libxml2-python 2.9.13, line_profiler 4.0.0, LittleCMS 2.14, LLVM 15.0.5, lz4 1.9.4, makedepend 1.0.7, Mako 1.2.4, + MATLAB-Engine 2021b, Mesa 22.2.4, Meson 0.64.0, MIGRATE-N 5.0.4, Miniconda3 4.12.0, mold 1.7.1, Molden 7.1, + MotionCor2 1.5.0, MoviePy 1.0.3, MRChem 1.1.1, MRCPP 1.4.1, nano 7.0, NanoFilt 2.8.0, nanoget 1.18.1, + nanomath 1.2.1, ncbi-vdb 3.0.0, NCCL 2.16.2, NCCL-tests 2.13.6, NCO 5.1.3, nglview 3.0.3, NiBabel 4.0.2, + Ninja 1.11.1, nodejs 18.12.1, NSPR 4.35, NSS 3.85, NVHPC 22.7, NVSHMEM 2.7.0, Octave 7.1.0, OPARI2 2.0.7, + OpenFOAM 10, OpenFold 1.0.1, OpenImageIO 2.3.17.0, OpenMolcas 22.10, openpyxl 3.0.10, openslide-python 1.2.0, + OpenStackClient 6.0.0, OSU-Micro-Benchmarks 6.2, OTF2 3.0.2, Pango 1.50.12, PAPI 7.0.0, pauvre 0.2.3, PETSc 3.17.4, + phonopy 2.16.3, pigz 2.7, Pillow 9.2.0, Pint 0.19.2, pixman 0.42.2, PMIx 4.2.2, poppler 22.12.0, psutil 5.9.3, + pybedtools 0.9.0, PyBerny 0.6.3, pydantic 1.10.2, pydicom 2.3.0, pyproj 3.4.0, PyQt5 5.15.5, pytest 7.1.3, + Python 3.10.8, python-isal 1.1.0, PyTorch 1.12.1, PyTorch-Geometric 2.1.0, PyTorch-Lightning 1.8.4, QCA 2.3.5, + QGIS 3.28.1, QIIME2 2022.8, QScintilla 2.11.6, Qt5 5.15.7, Qtconsole 5.3.2, QtKeychain 0.13.2, QtPy 2.2.1, + rasterio 1.3.4, re2c 3.0, ReFrame 3.12.0, RStudio-Server 2022.07.2+576, Ruby 3.0.5, Rust 1.65.0, SAP 1.1.3, + scanpy 1.9.1, scikit-image 0.19.3, SCons 4.4.0, Score-P 8.0, Seaborn 0.12.1, SentencePiece 0.1.97, Seurat 4.3.0, + SignalP 6.0g, SimPEG 0.18.1, SLEPc 3.17.2, SNAP 2.0.1, SpaceRanger 2.0.0, SQLite 3.39.4, STAR-CCM+ 17.06.007, + SuperLU_DIST 8.1.0, tensorboardX 2.5.1, TensorFlow 2.8.4, tensorflow-probability 0.16.0, tesseract 5.3.0, + texinfo 6.8, TM-align 20190822, tmux 3.3a, TOBIAS 0.14.0, TOML-Fortran 0.3.1, Transformers 4.24.0, + typing-extensions 4.4.0, UCC 1.1.0, UCX-CUDA 1.13.1, util-linux 2.38.1, Valgrind 3.20.0, Vim 9.0.0950, VTK 9.2.2, + wandb 0.13.6, WebKitGTK+ 2.37.1, WPS 4.4, WRF 4.4, wxPython 4.2.0, wxWidgets 3.2.0, X11 20221110, xarray 2022.9.0, + XCFun 2.1.1, XGBoost 1.7.2, Xmipp 3.22.07, XZ 5.2.7, yaml-cpp 0.7.0, zarr 2.13.3, zlib-ng 2.0.6 + +* minor enhancements, including: + + * enable building of dev tools in recent PyQt5 easyconfigs (`#16469 `_) + * add extensions to R v4.2.1: LMERConvenienceFunctions (`#16512 `_), HGNChelper 4.2.1 (`#16744 `_) + * add extensions to R-bundle-Bioconductor 3.15: SPOTlight (`#16569 `_), HiCcompare (`#16581 `_), ROntoTools (`#16636 `_), + scDblFinder (`#16686 `_), numbat (`#16777 `_), HiCBricks (`#16913 `_), zellkonverter (`#16952 `_) + * add libmad dependency to SoX v14.4.2 (`#16758 `_) + * also install subtree support in recent git easyconfigs (`#16784 `_, `#16785 `_) + * add extensions to ESM-2 to enhance it for esmfold (`#16841 `_) + * add libwebp dependency to Pillow-SIMD 9.2.0 to add webp support (`#16844 `_) + * add KaHIP dependency to OpenFOAM v2206 (`#16974 `_) + * enable dataset support for recent versions of Arrow (`#16956 `_) + +* various bug fixes, including: + + * define ``$JUPYTER_PATH`` via modextrapaths rather than modextravars for IRkernel 1.x (`#15776 `_) + * add patches to fix PyTorch 1.10.0 build on POWER (`#15904 `_) + * fix installation of Python 2.7.18 with GCCcore/11.2.0 (was broken due to 0.0.0 version for some extensions) (`#16485 `_) + * add patch for M4 1.4.18 to fix glibc v2.34 ``SIGSTKSZ`` compatibility (`#16486 `_) + * add patch for pybind11 2.6.0 to fix failing test due to extra whitespace (`#16487 `_) + * work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml (`#16490 `_) + * fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x (`#16502 `_) + * add OpenBLAS patches to disable FMA in ``[cz]cal`` and fix crash in ``zdot`` (`#16510 `_) + * add missing Perl build dependency GStreamer + add patch to skip trying to make files suid (`#16516 `_) + * build nodejs with OpenSSL and ICU provided as proper dependencies (`#16529 `_) + * also define ``$JUPYTER_CONFIG_PATH`` in IPython and JupyterLab easyconfigs (`#16556 `_) + * define ``$GTKDOCIZE`` as ``'echo'`` before generating configure script for recent HarfBuzz versions (`#16570 `_) + * disable use of ``-Werror`` in recent NSS easyconfigs (`#16571 `_) + * use 'cpan.metacpan.org' rather than 'www.cpan.org' in extension source_urls for recent Perl easyconfigs (`#16611 `_) + * avoid that zlib + htslib are downloaded and built during installation of MetaBAT (`#16624 `_) + * add patch to fix installation of MetaBAT 2.15 on non-x86_64 systems (`#16633 `_) + * add missing pyWannier90 dependency for mcu + enhance sanity check (`#16667 `_) + * fix ``source_urls`` for colossalai 0.1.8 (no longer available via PyPI, only via GitHub repo) (`#16693 `_) + * add patches to fix or skip PyTorch 1.12.1 tests (`#16793 `_) + * fix checksum for cell2location 0.05-alpha and add missing build dependency on flex (`#16819 `_) + * upgrade dependency on libdeflate to common v1.8 in fastp and vt easyconfigs using GCC(core)/10.3.0 (`#16839 `_) + * fix checksum for dlllogger extension in OpenFold v1.0.0 (`#16694 `_) + * make sure that Python dependency is actually used for VTK 9.0.1 (`#16741 `_) + * fix homepage for pocl v1.8 (`#16857 `_) + * fix source_urls in MUMPS easyconfigs (`#16931 `_, `#16932 `_) + * fix installation of Bowtie2 v2.4.4+ on non-x86_64 systems (`#16946 `_) + * add missing OpenSSL dependency to DCMTK 3.6.7 (`#16979 `_) + * fix source URL for PCRE2 (`#16987 `_) + * add pkgconf dependency for ICU and add patch to avoid trouble with long path names for nodejs-16.15.1/GCCcore-11.3.0 (`#16990 `_) + * add patch for libwpe 1.13.3 to avoid build issues on CentOS 7 (`#17001 `_) + * add missing zlib and zstd to GnuTLS (`#17013 `_) + * add missing pkgconf build dependency to Transformers v4.24.0 (`#17020 `_) + * fix checksums for ``xxx-rocm-4.5.0.tar.gz`` source tarballs for Clang-AOMP 4.5.0 (`#17042 `_) + * replace useless test step for simint 0.7 with (lightweight) sanity check command (`#17044 `_) + +* other changes: + + * only give read permissions in GitHub Actions workflows (`#16263 `_) + * remove ExomeDepth from recent R-bundle-Bioconductor easyconfigs (`#16492 `_) + * include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0 (`#16578 `_) + * use new EasyBuild logo in README (`#16641 `_) + * rename hyperopt to Hyperopt, to be consistent with existing Hyperopt easyconfigs (`#16697 `_) + * automatically cancel Github Action workflow runs for outdated commits (`#16754 `_) + * use geo moduleclass for SimPEG 0.14.1 (`#16847 `_) + + .. _release_notes_eb462: EasyBuild v4.6.2 (October 21st 2022) diff --git a/docs/conf.py b/docs/conf.py index f465205a..a2cd2473 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -41,9 +41,9 @@ # other places throughout the built documents. # # The short X.Y version. -version = '4.6.2' # this is meant to reference the version of EasyBuild +version = '4.7.0' # this is meant to reference the version of EasyBuild # The full version, including alpha/beta/rc tags. -release = '20221021.0' # this is meant to reference the version of the documentation itself +release = '20230109.0' # this is meant to reference the version of the documentation itself # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: From 5d68d72e88cb5abcacbac2c0a86ed6a96cfa15c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Jan 2023 15:37:45 +0100 Subject: [PATCH 260/286] fix typo: Januar to January --- docs/Release_notes.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index f131a9ba..13cc510f 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -12,8 +12,8 @@ alongside 15,535 easyconfig files. .. _release_notes_eb470: -EasyBuild v4.7.0 (Januar 9th 2023) ----------------------------------- +EasyBuild v4.7.0 (January 9th 2023) +----------------------------------- feature release From 88a8d17095964055e4ee60cc88d11de083ab0b1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Jan 2023 16:23:03 +0100 Subject: [PATCH 261/286] update version to 4.7.0 in setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 71ca46d3..5847d16a 100644 --- a/setup.py +++ b/setup.py @@ -36,7 +36,7 @@ # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware -VERSION = '4.6.2' +VERSION = '4.7.0' # Utility function to read README file From a467f23ebf91bdde95e8b1f3a0e3c67b6cf27553 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Jan 2023 19:30:29 +0100 Subject: [PATCH 262/286] update counts on top of release notes for EasyBuild v4.7.0 --- docs/Release_notes.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/Release_notes.rst b/docs/Release_notes.rst index 13cc510f..484bf420 100644 --- a/docs/Release_notes.rst +++ b/docs/Release_notes.rst @@ -3,9 +3,9 @@ EasyBuild release notes ======================= -The latest version of EasyBuild provides support for building and installing **2,798** different software packages, -including 37 different (compiler) toolchains. It contains 248 software-specific easyblocks and 37 generic easyblocks, -alongside 15,535 easyconfig files. +The latest version of EasyBuild provides support for building and installing **2,904** different software packages, +including 39 different (compiler) toolchains. It contains 248 software-specific easyblocks and 39 generic easyblocks, +alongside 16,138 easyconfig files. .. note:: See also the :ref:`concise overview of major changes in EasyBuild v4.0 `. From 362413b66881472a218147de8a65111aea4e6524 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 14 Jan 2023 10:37:58 +0000 Subject: [PATCH 263/286] correct date in changelog entry for EB 4.7.0 --- docs/Changelog.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Changelog.rst b/docs/Changelog.rst index 2babf34e..4d34fe0a 100644 --- a/docs/Changelog.rst +++ b/docs/Changelog.rst @@ -5,7 +5,7 @@ Changelog for EasyBuild documentation (for EasyBuild release notes, see :ref:`release_notes`) -* **release 20221021.01** (`Jan 9th 2023`): update release notes for EasyBuild v4.7.0 (see :ref:`release_notes_eb470`) +* **release 20230109.01** (`Jan 9th 2023`): update release notes for EasyBuild v4.7.0 (see :ref:`release_notes_eb470`) * **release 20221021.01** (`Oct 21st 2022`): update release notes for EasyBuild v4.6.2 (see :ref:`release_notes_eb462`) * **release 20220912.01** (`Sep 12th 2022`): update release notes for EasyBuild v4.6.1 (see :ref:`release_notes_eb461`) * **release 20220708.01** (`Jul 8th 2022`): update release notes for EasyBuild v4.6.0 (see :ref:`release_notes_eb460`) From a1decbc7962f47b3484de597084221207bf8b9c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 20 Jan 2023 15:37:15 +0100 Subject: [PATCH 264/286] fix indentation for easystack examples --- docs/Easystack-files.rst | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/docs/Easystack-files.rst b/docs/Easystack-files.rst index fc1a30e8..950cb240 100644 --- a/docs/Easystack-files.rst +++ b/docs/Easystack-files.rst @@ -70,13 +70,13 @@ For example: easyconfigs: - PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb: - options: - from-pr: 15924 - debug: True + options: + from-pr: 15924 + debug: True - Hypre-2.25.0-foss-2022a.eb: - OpenFOAM-v2206-foss-2022a.eb: - options: - installpath: /my/custom/installpath + options: + installpath: /my/custom/installpath .. note:: You need to take care with some values in YAML, especially integers, booleans, etc. @@ -108,8 +108,8 @@ Specifying short options in an easystack file is allowed, for example: easyconfigs: - OpenFOAM-v2206-foss-2022a.eb: - options: - D: True + options: + D: True This is not recommended however, as short options are more difficult to interpret by humans. @@ -127,9 +127,9 @@ These apply to *all* items in the easystack file. For example, if you have an ea easyconfigs: - PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb: - options: - from-pr: 15924 - debug: True + options: + from-pr: 15924 + debug: True - OpenFOAM-v2206-foss-2022a.eb: and you run with @@ -180,8 +180,8 @@ In the future, we are planning to support additional also global options specifi robot: True easyconfigs: - - PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb - - OpenFOAM-v2206-foss-2022a.eb + - PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb + - OpenFOAM-v2206-foss-2022a.eb would installed both ``PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb`` and ``OpenFOAM-v2206-foss-2022a.eb`` using ``--robot`` (see `issue #4105 `_). From 1a826bb4fbbbe3a66ba14ac6d8eb0d3b322c648d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 29 Jan 2023 12:17:53 +0100 Subject: [PATCH 265/286] fix website/docs links in README + don't mention IRC anymore --- README.rst | 25 ++++++++++--------------- 1 file changed, 10 insertions(+), 15 deletions(-) diff --git a/README.rst b/README.rst index 0f5ababf..f77356b9 100644 --- a/README.rst +++ b/README.rst @@ -5,7 +5,7 @@ .. image:: https://github.com/easybuilders/easybuild/actions/workflows/doc_build.yml/badge.svg :target: https://github.com/easybuilders/easybuild/actions/workflows/doc_build.yml -`EasyBuild `_ is a software build +`EasyBuild `_ is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. @@ -29,24 +29,23 @@ Corresponding Python packages are available via PyPi: Documentation ~~~~~~~~~~~~~ -Read the fine manual (RTFM!) at http://easybuild.readthedocs.org . +Read the fine manual (RTFM!) at http://docs.easybuild.io . Getting started ~~~~~~~~~~~~~~~ -The recommended way of installing EasyBuild is via the -`documented bootstrap procedure `_ -You should `configure `_ +The recommended way of installing EasyBuild is `using pip `_. +You should `configure `_ EasyBuild to behave as you prefer, subsequently. That is all that is needed to get started with installing (scientific) software with ease. -Take a look at the `typical workflow `_ +Take a look at the `typical workflow `_ example in the EasyBuild documentation that shows how to make EasyBuild build and **install WRF with a single command**. Quick demo for the impatient ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -After `installing EasyBuild `_, +After `installing EasyBuild `_, you can build and install **HPL** on top of a compiler toolchain that consists of open source components (GCC, OpenMPI, etc.) by running the following commands:: @@ -60,7 +59,7 @@ This should install a module file for HPL which you can load to start using it:: $ module load HPL For more information on using EasyBuild, see the -`EasyBuild documentation `_ +`EasyBuild documentation `_ Contact info ~~~~~~~~~~~~ @@ -78,15 +77,11 @@ have any questions or suggestions, you can post them there. Only members can post to this mailinglist. To request membership, see https://lists.ugent.be/wws/info/easybuild. -Slack/IRC -^^^^^^^^^ +Slack +^^^^^ Contact the EasyBuild community via Slack: https://easybuild.slack.com, -self-request an invite via https://easybuild-slack.herokuapp.com. - -An IRC channel #easybuild has been set up on the FreeNode network. - -Just connect your IRC client to the chat.freenode.net server, and join the #easybuild channel. +self-request an invite via https://easybuild.io/join-slack. Twitter ^^^^^^^ From ce76957f68eebfb7ae14799246f906e51cfabc07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Jan 2023 19:43:54 +0100 Subject: [PATCH 266/286] remove old EasyBuild documentation, refer to https://docs.easybuild.io on landing page --- docs/Archived-easyconfigs.rst | 78 - docs/Backup_modules.rst | 98 - docs/Changelog.rst | 253 - docs/Code_style.rst | 38 - docs/Common-toolchains.rst | 279 - docs/Concepts_and_Terminology.rst | 187 - docs/Configuration.rst | 731 - docs/Configuration_Legacy.rst | 123 - docs/Containers.rst | 694 - docs/Contributing.rst | 710 - ...ontrolling_compiler_optimization_flags.rst | 163 - docs/Cray-support.rst | 165 - docs/Deprecated-easyconfigs.rst | 180 - docs/Deprecated-functionality.rst | 145 - docs/Detecting_loaded_modules.rst | 293 - docs/EasyBuild4-overview-of-changes.rst | 256 - ...overview-relocated-functions-constants.rst | 237 - docs/Easyconfig-files-local-variables.rst | 161 - docs/Easyconfigs_index.rst | 175 - docs/Easystack-files.rst | 199 - docs/Experimental_features.rst | 18 - docs/Extended_dry_run.rst | 732 - docs/Extended_dry_run_examples.rst | 522 - docs/Hooks.rst | 319 - docs/Implementing-easyblocks.rst | 562 - docs/Including_additional_Python_modules.rst | 164 - docs/Installation.rst | 560 - docs/Installation_Alternative.rst | 217 - ...stalling-Lmod-without-root-permissions.rst | 97 - ...nment-modules-without-root-permissions.rst | 121 - docs/Installing_extensions_in_parallel.rst | 109 - docs/Integration_with_GitHub.rst | 872 - docs/Introduction.rst | 46 - docs/Locks.rst | 102 - docs/Logfiles.rst | 114 - docs/Maintainers.rst | 156 - docs/Manipulating_dependencies.rst | 207 - docs/Packaging_support.rst | 178 - docs/Partial_installations.rst | 306 - docs/Progress_bars.rst | 140 - docs/Python-2-3-compatibility.rst | 245 - docs/RPATH-support.rst | 154 - docs/Release_notes.rst | 10795 --- docs/Removed-functionality.rst | 664 - docs/Submitting_jobs.rst | 417 - docs/System_toolchain.rst | 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docs/version-specific/eb_help.txt delete mode 100644 docs/version-specific/eb_list_easyblocks.txt delete mode 100644 docs/version-specific/generic_easyblocks.rst delete mode 100644 docs/version-specific/help.rst delete mode 100644 docs/version-specific/index.rst delete mode 100644 docs/version-specific/toolchain_opts.rst delete mode 100644 docs/version-specific/toolchains.rst diff --git a/docs/Archived-easyconfigs.rst b/docs/Archived-easyconfigs.rst deleted file mode 100644 index 0e7c59db..00000000 --- a/docs/Archived-easyconfigs.rst +++ /dev/null @@ -1,78 +0,0 @@ -.. _archived_easyconfigs: - -Archived easyconfigs -==================== - -Since EasyBuild v3.0.0, easyconfig files using deprecated (i.e., old and inactive) toolchains are *archived*. - -.. contents:: - :depth: 3 - :backlinks: none - -.. _archived_easyconfigs_toolchain_deprecation: - -Toolchain deprecation ----------------------- - -Once in a blue moon, we review the list of toolchains (& versions) that are included in EasyBuild. - -Easyconfig files that use toolchains that become *deprecated* are then moved to the *easyconfigs archive*, -i.e. the ``__archive__`` subdirectory in the ``easybuild-easyconfigs`` repository -(see https://github.com/easybuilders/easybuild-easyconfigs/tree/main/easybuild/easyconfigs/__archive__). - -.. _archived_easyconfigs_deprecated_toolchains_what: - -What are deprecated toolchains? -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Toolchains become deprecated if: - -* no easyconfig files using that toolchain have been contributed recently (e.g., in the last year) -* that toolchain is considered to be inactive, after consulting the EasyBuild community (via mailing list, bi-weekly conf calls) - -Deprecating a toolchain implies that all easyconfigs using that toolchain are moved to the easyconfigs archive, -and that they are no longer included in the EasyBuild regression test. -In addition, these easyconfigs are 'hidden' from plain sight, in the sense that you need to use ``--consider-archived-easyconfigs`` -to make EasyBuild consider them when it is looking for easyconfigs (e.g., with ```--search`` or ``--robot``). - -This does *not* mean that the support for using these toolchains is removed from the EasyBuild framework, -although not testing them anymore may imply that using them may no longer work at some point in time. - -For toolchains for which no active versions are available (outside of the easyconfigs archive), -it is possible that they will be reactivated, if a new toolchain version is contributed. - -.. _archived_easyconfigs_deprecated_toolchains_why: - -Why are toolchains being deprecated? -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -* using old toolchains (incl. old compilers and/or libraries) is likely to become more and more difficult on modern operating systems -* these toolchains put a significant burden on the regression testing for EasyBuild releases -* easyconfigs using old toolchains are likely to be for old software versions, which may no longer be relevant anyway - -.. _archived_easyconfigs_consider: - -Using ``--consider-archived-easyconfigs`` ------------------------------------------ - -To make EasyBuild consider archived easyconfig files, you need to enable the ``--consider-archived-easyconfigs`` configuration option:: - - $ eb -S '^goolfc' - CFGS=/home/example/work/easybuild-easyconfigs/easybuild/easyconfigs - * $CFGS1/g/goolfc/goolfc-2016.08.eb - * $CFGS1/g/goolfc/goolfc-2016.10.eb - - Note: 6 matching archived easyconfig(s) found, use --consider-archived-easyconfigs to see them - -.. code:: - - $ eb -S '^goolfc' --consider-archived-easyconfigs - CFGS=/home/example/easybuild-easyconfigs/easybuild/easyconfigs - * $CFGS/g/goolfc/goolfc-2016.08.eb - * $CFGS/g/goolfc/goolfc-2016.10.eb - - Matching archived easyconfigs: - - * $CFGS/__archive__/g/goolfc/goolfc-1.3.12.eb - * $CFGS/__archive__/g/goolfc/goolfc-1.4.10.eb - * $CFGS/__archive__/g/goolfc/goolfc-2.6.10.eb diff --git a/docs/Backup_modules.rst b/docs/Backup_modules.rst deleted file mode 100644 index 3a745af2..00000000 --- a/docs/Backup_modules.rst +++ /dev/null @@ -1,98 +0,0 @@ -.. _backup_modules: - -Backing up of existing modules (``--backup-modules``) ------------------------------------------------------ - -While regenerating existing module files, you may want to preserve the existing module files -to compare and assess that the changes in the newly generated module file match expectations. - -Backing up of existing modules can be enabled with ``--backup-modules``. - -Backups are stored in the same directory as where the module file was located, -and the files are given an additional extension of the form ``.bak_``. - -* With module files in Tcl syntax, the backup module file is hidden by adding a leading dot to the filename; - this is done to avoid that it is displayed as a normal module in ``module avail``. -* With module files in Lua syntax, the backup module file is not made hidden (unless Lmod 6.x is used), - since the additional ``.bak_*`` extension prevents from picking it up as a valid module file; - only files ending in ``.lua`` are considered to be module files by Lmod 7+ . - -The location of the backed up module file will be printed, as well as a "unified diff" comparison -(very similar to what ``diff -u`` produces) between the backed up module file and the newly generated module file -(or a message mentioning that no differences were found). - - -.. _backup_modules_disable: - -Disabling automatic backup of modules -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -When ``--skip`` or ``--module-only`` is used, backing up of existing modules is enabled automatically. - -This can be disabled with ``--disable-backup-modules``. - - -.. _backup_modules_example: - -Example -~~~~~~~ - -Suppose existing modules in both Tcl & Lua syntax are present (``bzip2/1.0.6``). - -Both these module files are missing an update statement for $PATH -because the ``/bin`` subdirectory was missing in the installation, -for the purpose of this example:: - - $ ls -la $EASYBUILD_PREFIX/modules/all/bzip2 - total 16 - drwxr-xr-x 2 example example 136 Aug 24 10:20 . - drwxr-xr-x 3 example example 102 Aug 24 10:18 .. - -rw-r--r-- 1 example example 1256 Aug 24 10:19 1.0.6 - -rw-r--r-- 1 example example 1303 Aug 24 10:18 1.0.6.lua - - -Using ``--force`` and ``--backup-modules``, we can reinstall the ``bzip2/1.0.6`` modules -and get a clear view on what has changed. - -To reinstall the ``bzip2/1.0.6`` module in Lua syntax while retaining a backup of the existing module:: - - $ eb bzip2-1.0.6.eb --module-syntax=Lua --force --backup-modules - ... - == creating build dir, resetting environment... - == backup of existing module file stored at /example/modules/all/bzip2/1.0.6.lua.bak_20170824102603 - ... - == creating module... - == comparing module file with backup /example/modules/all/bzip2/1.0.6.lua.bak_20170824102603; diff is: - --- /example/modules/all/bzip2/1.0.6.lua.bak_20170824102603 - +++ /example/modules/all/bzip2/1.0.6.lua - @@ -25,9 +25,10 @@ - prepend_path("LD_LIBRARY_PATH", pathJoin(root, "lib")) - prepend_path("LIBRARY_PATH", pathJoin(root, "lib")) - prepend_path("MANPATH", pathJoin(root, "man")) - +prepend_path("PATH", pathJoin(root, "bin")) - setenv("EBROOTBZIP2", root) - setenv("EBVERSIONBZIP2", "1.0.6") - setenv("EBDEVELBZIP2", pathJoin(root, "easybuild/bzip2-1.0.6-easybuild-devel")) - - ... - -Equivalently, we can reinstall the module in Tcl syntax using:: - - $ eb bzip2-1.0.6.eb --module-syntax=Tcl --force --backup-modules - -Afterwards, both the newly generated modules and the backups are in place:: - - $ ls -la $EASYBUILD_PREFIX/modules/all/bzip2 - total 32 - drwxr-xr-x 2 example example 204 Aug 24 10:26 . - drwxr-xr-x 3 example example 102 Jul 11 10:18 .. - -rw-r--r-- 1 example example 1227 Aug 24 10:24 .1.0.6.bak_20170824102412 - -rw-r--r-- 1 example example 1256 Jul 11 01:24 1.0.6 - -rw-r--r-- 1 example example 1303 Jul 11 01:26 1.0.6.lua - -rw-r--r-- 1 example example 1259 Aug 24 10:26 1.0.6.lua.bak_20170824102603 - -Cleaning up the backup module files can be done with the following command (for example):: - - $ find $EASYBUILD_PREFIX/modules/all/bzip2 -name '*.bak*' | xargs rm -v - /example/modules/all/bzip2/.1.0.6.bak_20170824102412 - /example/modules/all/bzip2/1.0.6.lua.bak_20170824102603 diff --git a/docs/Changelog.rst b/docs/Changelog.rst deleted file mode 100644 index 4d34fe0a..00000000 --- a/docs/Changelog.rst +++ /dev/null @@ -1,253 +0,0 @@ -.. _changelog: - -Changelog for EasyBuild documentation -------------------------------------- - -(for EasyBuild release notes, see :ref:`release_notes`) - -* **release 20230109.01** (`Jan 9th 2023`): update release notes for EasyBuild v4.7.0 (see :ref:`release_notes_eb470`) -* **release 20221021.01** (`Oct 21st 2022`): update release notes for EasyBuild v4.6.2 (see :ref:`release_notes_eb462`) -* **release 20220912.01** (`Sep 12th 2022`): update release notes for EasyBuild v4.6.1 (see :ref:`release_notes_eb461`) -* **release 20220708.01** (`Jul 8th 2022`): update release notes for EasyBuild v4.6.0 (see :ref:`release_notes_eb460`) -* **release 20220608.01** (`Jun 8th 2022`): update release notes for EasyBuild v4.5.5 (see :ref:`release_notes_eb455`) -* **release 20220331.01** (`Mar 31st 2022`): update release notes for EasyBuild v4.5.4 (see :ref:`release_notes_eb454`) -* **release 20220211.01** (`Feb 11th 2022`): update release notes for EasyBuild v4.5.3 (see :ref:`release_notes_eb453`) -* **release 20220124.01** (`Jan 24th 2022`): update release notes for EasyBuild v4.5.2 (see :ref:`release_notes_eb452`) -* **release 20211213.01** (`Dec 13th 2021`): update release notes for EasyBuild v4.5.1 (see :ref:`release_notes_eb451`) -* **release 20211029.01** (`Oct 29th 2021`): update release notes for EasyBuild v4.5.0 (see :ref:`release_notes_eb450`) -* **release 20210907.01** (`Sep 7th 2021`): update release notes for EasyBuild v4.4.2 (see :ref:`release_notes_eb442`) -* **release 20210706.01** (`Jul 6th 2021`): update release notes for EasyBuild v4.4.1 (see :ref:`release_notes_eb441`) -* **release 20210602.01** (`Jun 2nd 2021`): update release notes for EasyBuild v4.4.0 (see :ref:`release_notes_eb440`) -* **release 20210409.01** (`Apr 9th 2021`): update release notes for EasyBuild v4.3.4 (see :ref:`release_notes_eb434`) -* **release 20210223.01** (`Feb 23rd 2021`): update release notes for EasyBuild v4.3.3 (see :ref:`release_notes_eb433`) -* **release 20201210.01** (`Dec 10th 2020`): update release notes for EasyBuild v4.3.2 (see :ref:`release_notes_eb432`) -* **release 20201029.01** (`Oct 29th 2020`): update release notes for EasyBuild v4.3.1 (see :ref:`release_notes_eb431`) -* **release 20200913.01** (`Sep 13th 2020`): update release notes for EasyBuild v4.3.0 (see :ref:`release_notes_eb430`) -* **release 20200708.01** (`July 8th 2020`): update release notes for EasyBuild v4.2.2 (see :ref:`release_notes_eb422`) -* **release 20200520.01** (`May 20th 2020`): update release notes for EasyBuild v4.2.1 (see :ref:`release_notes_eb421`) -* **release 20200414.01** (`Apr 14th 2020`): - - * document new EasyBuild locking mechanism (see :ref:`locks`) - * document support for creating index files (see :ref:`easyconfigs_index`) - * update release notes for EasyBuild v4.2.0 (see :ref:`release_notes_eb420`) -* **release 20200316.01** (`Mar 16th 2020`): update release notes for EasyBuild v4.1.2 (see :ref:`release_notes_eb412`) -* **release 20200116.01** (`Jan 16th 2020`): update release notes for EasyBuild v4.1.1 (see :ref:`release_notes_eb411`) -* **release 20191204.01** (`Dec 4th 2019`): update release notes for EasyBuild v4.1.0 (see :ref:`release_notes_eb410`) -* **release 20191015.01** (`Oct 15th 2019`): update release notes for EasyBuild v4.0.1 (see :ref:`release_notes_eb401`) -* **release 20190920.01** (`Sep 20th 2019`): update release notes for EasyBuild v4.0.0 (see :ref:`release_notes_eb400`); see also :ref:`eb4_changes_overview` -* **release 20190823.01** (`Aug 23rd 2019`): update release notes for EasyBuild v3.9.4 (see :ref:`release_notes_eb394`) -* **release 20190708.01** (`Jul 8th 2019`): update release notes for EasyBuild v3.9.3 (see :ref:`release_notes_eb393`) -* **release 20190609.01** (`Jun 9th 2019`): update release notes for EasyBuild v3.9.2 (see :ref:`release_notes_eb392`) -* **release 20190908.01** (`Jun 8th 2019`): update documentation on support for generating (Singularity) container recipes/images (see :ref:`containers`) -* **release 20190520.01** (`May 20th 2019`): update release notes for EasyBuild v3.9.1 (see :ref:`release_notes_eb391`) -* **release 20190412.01** (`Apr 12th 2019`): update release notes for EasyBuild v3.9.0 (see :ref:`release_notes_eb390`) -* **release 20190129.01** (`Jan 29th 2019`): update release notes for EasyBuild v3.8.1 (see :ref:`release_notes_eb381`) -* **release 20190124.01** (`Jan 24th 2019`): add definitions for ``2019a`` common toolchains (see :ref:`common_toolchains`) -* **release 20181218.01** (`Dec 18th 2018`): update release notes for EasyBuild v3.8.0 (see :ref:`release_notes_eb380`) -* **release 20181114.01** (`Nov 14th 2018`): add documentation on deprecated easyconfigs & toolchains (:ref:`deprecated_easyconfigs`) -* **release 20181104.01** (`Nov 4th 2018`): update ``--job`` documentation to also cover ``Slurm`` job backend (see :ref:`submitting_jobs`) -* **release 20181018.01** (`Oct 18th 2018`): update release notes for EasyBuild v3.7.1 (see :ref:`release_notes_eb371`) -* **release 20180925.01** (`Sep 25th 2018`): update release notes for EasyBuild v3.7.0 (see :ref:`release_notes_eb370`) -* **release 20180921.01** (`Sep 21st 2018`): document support for wrapping dependencies (see :ref:`wrapping_dependencies`) -* **release 20180920.01** (`Sep 20th 2018`): document support for downloading sources directly from a Git repository (see :ref:`common_easyconfig_param_sources_git_config`) -* **release 20180711.01** (`Jul 11th 2018`): update release notes for EasyBuild v3.6.2 (see :ref:`release_notes_eb362`) -* **release 20180710.01** (`Jul 10th 2018`): add definitions for ``2018b`` common toolchains (see :ref:`common_toolchains`) -* **release 20180528.01** (`May 28th 2018`): update release notes for EasyBuild v3.6.1 (see :ref:`release_notes_eb361`) -* **release 20180427.01** (`Apr 27th 2018`): update release notes for EasyBuild v3.6.0 (see :ref:`release_notes_eb360`) -* **release 20180425.01** (`Apr 25th 2018`): add documentation on support for generating container recipes & images (see :ref:`containers`) -* **release 20180307.01** (`Mar 7th 2018`): update release notes for EasyBuild v3.5.3 (see :ref:`release_notes_eb353`) -* **release 20180302.01** (`Mar 2nd 2018`): update release notes for EasyBuild v3.5.2 (see :ref:`release_notes_eb352`) -* **release 20180116.01** (`Jan 16th 2018`): update release notes for EasyBuild v3.5.1 (see :ref:`release_notes_eb351`) -* **release 20180112.01** (`Jan 12th 2018`): add definitions for ``2018a`` common toolchains (see :ref:`common_toolchains`) -* **release 20171215.01** (`Dec 15th 2017`): update release notes for EasyBuild v3.5.0 (see :ref:`release_notes_eb350`) -* **release 20171208.01** (`Dec 8th 2017`): document support for user-defined hooks (see :ref:`hooks`) -* **release 20171017.01** (`Oct 17th 2017`): update release notes for EasyBuild v3.4.1 (see :ref:`release_notes_eb341`) -* **release 20170910.01** (`Sept 10th 2017`): update release notes for EasyBuild v3.4.0 (see :ref:`release_notes_eb340`) -* **release 20170906.01** (`Sept 6th 2017`): document ``--trace`` (see :ref:`trace`) -* **release 20170824.02** (`Aug 24th 2017`): document ``--inject-checksums`` (see :ref:`inject_checksums`) -* **release 20170824.01** (`Aug 24th 2017`): document ``--backup-modules`` (see :ref:`backup_modules`) -* **release 20170712.01** (`July 12th 2017`): update release notes for EasyBuild v3.3.1 (see :ref:`release_notes_eb331`) -* **release 20170708.01** (`July 8th 2017`): add documentation on :ref:`github_merge_pr` -* **release 20170705.01** (`July 5th 2017`): clarify :ref:`contributing_review_process_pr_requirements`, add page listing :ref:`maintainers` -* **release 20170626.01** (`June 26th 2017`): update release notes for EasyBuild v3.3.0 (see :ref:`release_notes_eb330`) -* **release 20170623.01** (`June 23rd 2017`): document use of ``checksums`` & alternative formats for ``sources`` (see :ref:`common_easyconfig_param_sources`) -* **release 20170622.01** (`June 22nd 2017`): document support for detecting loaded modules (see :ref:`detect_loaded_modules`) -* **release 20170522.01** (`May 22nd 2017`): document deprecated behaviour in EasyBuild v3.2.0 (see :ref:`overview_deprecated`) -* **release 20170512.01** (`May 12th 2017`): update release notes for EasyBuild v3.2.1 (see :ref:`release_notes_eb321`) -* **release 20170505.01** (`May 5th 2017`): update release notes for EasyBuild v3.2.0 (see :ref:`release_notes_eb320`) -* **release 20170320.01** (`Mar 20th 2017`): update release notes for EasyBuild v3.1.2 (see :ref:`release_notes_eb312`) -* **release 20170307.01** (`Mar 7th 2017`): update release notes for EasyBuild v3.1.1 (see :ref:`release_notes_eb311`) -* **release 20170221.01** (`Feb 21st 2017`): add documentation on :ref:`contributing` -* **release 20170209.01** (`Feb 9th 2017`): add documentation on implementing easyblocks (see :ref:`implementing_easyblocks`) -* **release 20170203.01** (`Feb 3rd 2017`): update release notes for EasyBuild v3.1.0 (see :ref:`release_notes_eb310`) -* **release 20170129.01** (`Jan 29th 2017`): update ``--optarch`` documentation (see :ref:`controlling_compiler_optimization_flags_optarch_per_compiler`) -* **release 20170109.01** (`Jan 9th 2017`): add documentation on :ref:`common_toolchains` -* **release 20161222.01** (`Dec 22nd 2016`): update documentation and release notes for EasyBuild v3.0.2 (see :ref:`release_notes_eb302`) -* **release 20161218.01** (`Dec 18th 2016`): document need to download ``vsc-*`` source tarballs from PyPI (see :ref:`bootstrap_offline`) -* **release 20161202.01** (`Dec 2nd 2016`): add documentation on Cray support (see :ref:`cray_support`) -* **release 20161130.01** (`Nov 16th 2016`): update release notes for EasyBuild v3.0.1 (see :ref:`release_notes_eb301`) -* **release 20161117.01** (`Nov 17th 2016`): update mentions of default configuration according to updated default in EasyBuild v3.0.0 -* **release 20161116.01** (`Nov 16th 2016`): update documentation and release notes for EasyBuild v3.0.0 (see :ref:`release_notes_eb300`) - - * :ref:`archived_easyconfigs` - * :ref:`rpath_support` - -* **release 20161028.01** (`Oct 28th 2016`): recommend using ``--rebuild`` rather than ``--force`` (see :ref:`rebuild_option`) -* **release 20161023.01** (`Oct 24th 2016`): add section on iterating over configure/build/install options (see :ref:`configure_build_install_command_options_iterate`) -* **release 20161014.01** (`Oct 14th 2016`): update documentation on deprecated functionality (see :ref:`deprecated`) -* **release 20161010.01** (`Oct 10th 2016`): add page for EasyBuild demos (see :ref:`demos`) -* **release 20160923.02** (`Sept 23rd 2016`): update release notes for EasyBuild v2.9.0 (see :ref:`release_notes_eb290`) -* **release 20160923.01** (`Sept 23rd 2016`): add generated list of supported software (see :ref:`list_software`) -* **release 20160713.01** (`July 13th 2016`): update release notes for EasyBuild v2.8.2 (see :ref:`release_notes_eb282`) -* **release 20160613.01** (`June 13th 2016`): clarify required dependencies (setuptools, vsc-install) (see :ref:`required_python_packages`) -* **release 20160607.01** (`June 7th 2016`): update/complete documentation on GitHub integration (see :ref:`integration_with_github`) -* **release 20160530.01** (`May 30th 2016`): update release notes for EasyBuild v2.8.1 (see :ref:`release_notes_eb281`) -* **release 20160518.01** (`May 18th 2016`): update release notes for EasyBuild v2.8.0 (see :ref:`release_notes_eb280`) -* **release 20160429.01** (`April 29th 2016`): add section on updating EasyBuild, see :ref:`updating` -* **release 20160320.01** (`March 20th 2016`): update release notes for EasyBuild v2.7.0 (see :ref:`release_notes_eb270`) -* **release 20160228.01** (`February 28th 2016`): - - * update documentation on external modules metadata (see :ref:`using_external_modules_metadata`) - -* **release 20160214.01** (`February 14th 2016`): - - * add section on ``--show-config`` (see :ref:`configuration_show_config`) - -* **release 20160126.02** (`January 26th 2016`): packaging support is stable since EasyBuild v2.5.0 (see :ref:`packaging_support`) -* **release 20160126.01** (`January 26th 2016`): update release notes for EasyBuild v2.6.0 (see :ref:`release_notes_eb260`) -* **release 20151217.01** (`December 17th 2015`): update release notes for EasyBuild v2.5.0 (see :ref:`release_notes_eb250`) -* **release 20151209.01** (`December 9th 2015`): - - * add documentation on controlling compiler optimizations flags, see :ref:`controlling_compiler_optimization_flags` - -* **release 20151110.01** (`November 10th 2015`): update release notes for EasyBuild v2.4.0 (see :ref:`release_notes_eb240`) -* **release 20151108.01** (`November 8th 2015`): - - * document (experimental) support for using minimal toolchains (see :ref:`minimal_toolchains`) - -* **release 20151028.01** (`October 28th 2015`): document extended dry run mechanism (see :ref:`extended_dry_run`) -* **release 20151021.01** (`October 21st 2015`): - - * include initial documentation on experimental support for easyconfig files in YAML syntax (``.yeb``), - see :ref:`easyconfig_yeb_format` - -* **release 20150902.01** (`September 2nd 2015`): update release notes for EasyBuild v2.3.0 (see :ref:`release_notes_eb230`) -* **release 20150715.01** (`July 15th 2015`): update release notes for EasyBuild v2.2.0 (see :ref:`release_notes_eb220`) -* **release 20150714.01** (`July 14th 2015`): add documentation on :ref:`packaging_support` -* **release 20150709.01** (`July 9th 2015`): add documentation on :ref:`submitting_jobs` -* **release 20150708.01** (`July 8th 2015`): - - * add documentation on ``--include-*`` options (see :ref:`including_additional_python_modules`) - -* **release 20150703.01** (`July 3rd 2015`): - - * fix outdated documentation on ``easyblock`` parameter (see :ref:`writing_easyconfigs_easyblock_spec`) - -* **release 20150624.01** (`June 24th 2015`): mention ``MigrateFromEBToHMNS`` module naming scheme in section on - ``--module-only`` (see :ref:`module_only_additional`) -* **release 20150610.01** (`June 10th 2015`): update :ref:`installing_lmod` for Lmod v6.0 - -* **release 20150518.01** (`May 18th 2015`): - - * update section on ``--search``: better examples + highlight ability to search via regular expression (see :ref:`searching_for_easyconfigs`) - * update release notes for EasyBuild v2.1.1 (see :ref:`release_notes_eb211`) - -* **release 20150506.01** (`May 6th 2015`): updated documentation for EasyBuild v2.1.1 - - * add note on ``$LMOD_CMD`` fallback to find full path to ``lmod`` binary (see :ref:`required_modules_tool`) - -* **release 20150430.01** (`Apr 30th 2015`): updated documentation for EasyBuild v2.1.0 - - * also cover extensions in page on concepts and terminology (see :ref:`extensions`) - * add documentation on :ref:`partial_installations`, covering ``--stop``, ``--skip`` and ``--module-only`` - * add documentation on :ref:`manipulating_dependencies`, covering ``--filter-deps`` and ``--hide-deps`` - * document ``-module-syntax`` configuration option (see :ref:`module_syntax`) - * add note on detection of unknown ``$EASYBUILD``-prefixed environment variables (see :ref:`configuration_env_vars`) - * mention support for prepending/appending to ``--robot-paths`` (see :ref:`robot_search_path_prepend_append`) - * update release notes for EasyBuild v2.1.0 (see :ref:`release_notes`) - -* **release 20150425.01** (`Apr 25th 2015`): - - * add documentation on :ref:`using_external_modules` - -* **release 20150407.01** (`Apr 7th 2015`): - - * add link to :ref:`unit_tests` page in dedicated section at :ref:`installation` page - (see :ref:`install_running_unit_tests`) - * clarify relation between ``--installpath``, ``--prefix``, ``-subdir-*`` and ``--installpath-*`` - configuration options (see :ref:`installpath`) - * mention ``--show-default-configfiles`` command line option in relevant section - (see :ref:`default_configuration_files`) - -* **release 20150327.01** (`Mar 27th 2015`): - - * documented deprecated functionality w.r.t. error reporting (see :ref:`depr_error_reporting`) -* **release 20150316.01** (`Mar 16th 2015`): - - * include list of EasyBuild repositories cloned by ``install-EasyBuild-develop.sh`` script - (see :ref:`install_latest_develop_using_script`) -* **release 20150312.01** (`Mar 12th 2015`): - - * enhance documentation w.r.t. template values in configuration files (see :ref:`configuration_file_templates_constants`) - * improve documentation on ``--robot`` and ``--robot-paths`` (see :ref:`controlling_robot_search_path`) -* **release 20150310.01** (`Mar 10th 2015`): - - * document peculiarties w.r.t. dependencies in combination with a ``dummy`` toolchain (see :ref:`dependency_specs`) - * document ``clean_gists.py`` script (see :ref:`clean_gists_script`) - * mention taking into account of proxy settings for downloading sources (see :ref:`common_easyconfig_param_sources`) -* **release 20150306.03** (`Mar 6th 2015`): add release notes for EasyBuild v2.0.0 (see :ref:`release_notes`) -* **release 20150306.02** (`Mar 6th 2015`): - - * add documentation on GitHub integration features (see :ref:`integration_with_github`), mainly ``--from-pr`` (see :ref:`from_pr`) - * document locations where (specified) easyconfig files are being searched for (see :ref:`specifying_easyconfigs`) -* **release 20150306.01** (`Mar 6th 2015`): - - * add documentation on removed functionality (see :ref:`removed_functionality`) - * clean up documentation on deprecated functionality (see :ref:`deprecated`) - * add documentation on provided scripts, in particular ``fix-broken-easyconfigs.py`` (see :ref:`useful_scripts`) -* **release 20150302.01** (`Mar 2nd 2015`): update/cleanup documentation on :ref:`alt_inst_methods` -* **release 20150227.02** (`Feb 27th 2015`): add documentation on the EasyBuild unit test suites, see :ref:`unit_tests` -* **release 20150227.01** (`Feb 27th 2015`): enhance documentation w.r.t. to (optional dependencies), see :ref:`installation` -* **release 20150220.01** (`Feb 20th 2015`): - - * document new advanced bootstrapping options: skipping stage 0 and providing source tarballs (see :ref:`installation`) -* **release 20150219.01** (`Feb 19th 2015`): first updates for EasyBuild v2.0.0 - - * extend section on (default) EasyBuild configuration files to also cover ``$XDG_CONFIG_DIRS`` (see :ref:`configuration_file:`) -* **release 20150205.01** (`Feb 5th 2015`): include information on deprecated functionality in (generic) easyblocks (see :ref:`deprecated`) -* **release 20150126.01** (`Jan 26th 2015`): - - * fix ``pip`` installation prefix option (:ref:`alt_inst_methods`) - * clarify need to have modules tool binary available in ``$PATH`` (:ref:`installation`) -* **release 20150112.01** (`Jan 12th 2015`): mention need to escape ``%`` when setting log file format via config file (see :ref:`logfile_format`) -* **release 20150107.01** (`Jan 7th 2015`): document behaviour of `dummy` toolchain (:ref:`dummy_toolchain`) -* **release 20141219.01** (`Dec 19th 2014`): add release notes for EasyBuild v1.16.1 (see :ref:`release_notes`) -* **release 20141218.01** (`Dec 18th 2014`): add release notes for EasyBuild v1.16.0 (see :ref:`release_notes`) -* **release 20141217.01** (`Dec 17th 2014`): document deprecated functionality in EasyBuild v1.x (:ref:`deprecated`) -* **release 20141204.02** (`Dec 4th 2014`): add EasyBuild release notes (see :ref:`release_notes`) -* **release 20141204.01** (`Dec 4th 2014`): updates for EasyBuild v1.16.0 - - * document details w.r.t. (controlling of) robot search path, incl. ``--robot-paths`` (:ref:`using_the_easybuild_command_line`) - * document use of templates and constants in EasyBuild configuration files (:ref:`configuring_easybuild`) - * bump EasyBuild version to 1.16.0 - * changed release number scheme for documentation (based on datestamp) -* **release 1.0.3** (`Dec 3rd 2014`): add page on :ref:`code_style` -* **release 1.0.2** (`Nov 6th 2014`): typo and grammar fixes, update Lmod installation instructions for Lmod v5.8 -* **release 1.0.1** (`Nov 4th 2014`): fix issues with Changelog -* **release 1.0.0** `(Nov 4th 2014)`: initial release of revamped EasyBuild documentation - @ http://easybuild.readthedocs.org, covering basic topics: - - * introductory topics: - - * :ref:`what_is_easybuild` - * :ref:`concepts_and_terminology` - * :ref:`typical_workflow` - * getting started: - - * :ref:`installation` - * :ref:`configuring_easybuild` - * basic usage topics: - - * :ref:`using_the_easybuild_command_line` - * :ref:`writing_easyconfig_files` - * :ref:`understanding_easyBuild_logs` diff --git a/docs/Code_style.rst b/docs/Code_style.rst deleted file mode 100644 index b29decaf..00000000 --- a/docs/Code_style.rst +++ /dev/null @@ -1,38 +0,0 @@ - -.. _code_style: - -Code style -========== - -The code style we follow in the EasyBuild code repository is mainly dictated by the Python standard `PEP8`_. - -Highlighted PEP8 code style rules: - -* use **4 spaces** for indentation, **do not use tabs** - for example, use ``:set tabstop 4`` and ``:set expandtab`` in Vim -* indent items in a list at an extra 4 spaces - nested lists can be indented at the same indentation as the first item in the list if it is on the first line, closing brackets must match visual indentation -* use `optional underscores`, not camelCase, for variable, function and method names (i.e. ``poll.get_unique_voters()``, - **not** ``poll.getUniqueVoters``) -* use ``InitialCaps`` for class names -* in docstrings, don't use "action words" - -The only (major) exception to PEP8 is our preference for longer line lengths: line lengths **must be limited to 120 characters**, and should by preference be `shorter than 100 characters` (as opposed to the 80-character limit in PEP8). - -.. _PEP8: http://www.python.org/dev/peps/pep-0008 - - -Notes -~~~~~ - -Code style in easyconfig files can be **automatically checked** using ``--check-contrib``, -for example: ``eb --check-contrib sympy-1.3-intel-2018a-Python-2.7.14.eb`` -(see :ref:`contributing_review_process_code_style` for more details). - -Style guides that go a step beyond PEP8: - * http://www.gramps-project.org/wiki/index.php?title=Programming_guidelines - * http://code.google.com/p/volatility/wiki/StyleGuide - -Automatic rewriting of Python code: http://pypi.python.org/pypi/PythonTidy/1.22 - -``pep8`` might be a useful tool to check PEP8 compliance: https://github.com/jcrocholl/pep8 diff --git a/docs/Common-toolchains.rst b/docs/Common-toolchains.rst deleted file mode 100644 index d2e988b6..00000000 --- a/docs/Common-toolchains.rst +++ /dev/null @@ -1,279 +0,0 @@ -.. _common_toolchains: - -Common toolchains -================= - -This page documents the concept of *common toolchains* in the EasyBuild community; -for a more general definition of what (compiler) toolchains are, see :ref:`toolchains`. - -.. contents:: - :depth: 3 - :backlinks: none - - -.. _common_toolchains_what: - -Definition and motivation -------------------------- - -Picking a :ref:`compiler toolchain ` to use is one of the first things you (need to) do when starting to use EasyBuild. -This can be a daunting task, since a whole bunch of toolchains and different toolchain versions -are readily available in EasyBuild. It may be difficult to determine which toolchain would be most rewarding to use, -in terms of stability, performance of the resulting binaries and readily available easyconfig files. - -In an attempt to focus the effort of the EasyBuild community, -the concept of so-called *common toolchains* was introduced. - -The idea is to compose and maintain a limited set of specific compiler toolchains, -and try and convince many HPC sites to employ these toolchains. -This helps in assuring stability of these toolchains w.r.t. which software can be built (correctly) with them, -since they get significantly more testing. In addition, the expectation/hope is that more easyconfigs are -contributed back to the central easyconfigs repository (https://github.com/easybuilders/easybuild-easyconfigs), -resulting in a wide range of readily available easyconfig files using the common toolchains. - -The intention is to revise/update the definitions of the common toolchains regularly -(see :ref:`common_toolchains_update_cycle`), which again can be a joint effort -that benefits many HPC sites. - -Currently, two different common toolchains are being maintained: ``foss`` and ``intel``; -see below for more details, and also :ref:`common_toolchains_overview`. - - -.. _common_toolchains_foss: - -``foss`` toolchain -~~~~~~~~~~~~~~~~~~ - -The ``foss`` common compiler toolchain consists entirely of open source software (hence the name, -derived from the common term 'FOSS', which is short for "Free and Open Source Software"). - -This toolchain consists of: - -* binutils (https://www.gnu.org/software/binutils/) - -* the GNU Compiler Collection (GCC, https://gcc.gnu.org/), - i.e. ``gcc`` (C), ``g++`` (C++) and ``gfortran`` (Fortran) - -* the Open MPI library (https://www.open-mpi.org/) - -* the OpenBLAS (http://www.openblas.net/) + LAPACK (http://netlib.org/lapack) libraries (for ``foss`` < 2021a) - -* the FlexiBLAS library (https://www.mpi-magdeburg.mpg.de/projects/flexiblas), with OpenBLAS + LAPACK as backend (for ``foss`` >= 2021a) - -* the ScaLAPACK (http://netlib.org/scalapack) library is also included - -* the FFTW library (http://fftw.org/) - -.. note:: The toolchain name was deliberately chosen to be generic, to allow for swapping - any of the toolchain components with a better (open source) alternative in the future, - should the need or opportunity arise. - - -.. _common_toolchains_intel: - -``intel`` toolchain -~~~~~~~~~~~~~~~~~~~ - -The ``intel`` common compiler toolchain consists of the Intel compilers and libraries, i.e.: - -* the Intel C/C++/Fortran compilers (https://software.intel.com/en-us/intel-compilers), - i.e. ``icc``, ``icpc`` and ``ifort``, - - * binutils and GCC, which serve as a base for the Intel compilers, are also included - -* the Intel MPI library (https://software.intel.com/en-us/intel-mpi-library) - -* the Intel Math Kernel Library (MKL, https://software.intel.com/en-us/intel-mkl) for BLAS/LAPACK/FFT functionality - -.. note:: This compiler toolchain includes licensed software; - valid licenses must be available to install and use it. - - -.. _common_toolchains_versioning_scheme: - -Versioning scheme for common toolchains ---------------------------------------- - -The common toolchains follow a specific versioning scheme, which takes the -:ref:`6-month update cycle ` into account. - -Each revision of the common toolchains is versioned as the *year* in which it -was defined, plus an additional '``a``' or '``b``' to indicate whether the toolchain -was defined at the start of the year ('``a``') or halfway through the year ('``b``'); -in short, the common toolchains are versioned as ``{a,b}``. - -For example, ``foss/2016b`` is a revision of the ``foss`` that was composed mid-2016. - -A full historic overview of the ``foss`` and ``intel`` common toolchains is -available in :ref:`common_toolchains_overview`. - -.. note:: Next to the versions that follow the ``{a,b}`` versioning scheme, - additional versions of the ``foss`` and ``intel`` versions are available - as well. - - These versions are **not** considered to be part of the series of common - toolchains (even though they consists of the same toolchain components). - These versions may be site-specific, or compositions that were put in - place to evaluate a potential future common toolchain. - - Typically, they are versioned as ``.``, indicating when - the most recent component included was released, or when that particular - toolchain composition was defined. - - -.. _common_toolchains_update_cycle: - -Update cycle for common toolchains ----------------------------------- - -The intention is to revise and update the common toolchains every 6 months: -once in late December/early January (version ``a``), -and once in late June/early July (version ``b``). - -This is meant be to be a community effort, in the sense that a proposal -for an updated composition is shared and discussed before it is set in stone. - -Recent versions of each of the toolchain components are considered, taking -into account stability, performance improvements, added features, -known bugs/issues and experiences with those versions. - -Moreover, the proposed toolchain compositions are tested extensively, -typically by rebuilding all available easyconfigs that are using the -most recent revision of the common toolchains at that time. - -.. _common_toolchains_overview: - -Overview of common toolchains ------------------------------ - -.. _common_toolchains_overview_foss: - -Component versions in ``foss`` toolchain -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``foss`` | *date* |*binutils* | *GCC* | *Open MPI* | *FlexiBLAS* | *OpenBLAS* | *LAPACK* | *ScaLAPACK* | *FFTW* | -+================+=============+============+===========+============+=============+============+=======================+==============+=============+ -| ``2019a`` | Jan '19 | 2.31.1 | 8.2.0 | 3.1.3 | *(none)* | 0.3.5 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2019b`` | Sept '19 | 2.32 | 8.3.0 | 3.1.4 | *(none)* | 0.3.7 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2020a`` | May '20 | 2.34 | 9.3.0 | 4.0.3 | *(none)* | 0.3.9 | (incl. with OpenBLAS) | 2.1.0 | 3.3.8 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2020b`` | Nov '20 | 2.35 | 10.2.0 | 4.0.5 | *(none)* | 0.3.12 | (incl. with OpenBLAS) | 2.1.0 | 3.3.8 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2021a`` | May '21 | 2.36.1 | 10.3.0 | 4.1.1 | 3.0.4 | 0.3.15 | (incl. with OpenBLAS) | 2.1.0 | 3.3.9 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2021b`` | Oct '21 | 2.37 | 11.2.0 | 4.1.1 | 3.0.4 | 0.3.18 | (incl. with OpenBLAS) | 2.1.0 | 3.3.10 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2022a`` | Jun '22 | 2.38 | 11.3.0 | 4.1.4 | 3.2.0 | 0.3.20 | (incl. with OpenBLAS) | 2.2.0 | 3.3.10 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2022b`` | Dec '22 | 2.39 | 12.2.0 | 4.1.4 | 3.2.1 | 0.3.21 | (incl. with OpenBLAS) | 2.2.0 | 3.3.10 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ - -*(components marked with* * *were patched)* - -.. _common_toolchains_overview_intel: - -Component versions in ``intel`` toolchain -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``intel`` | *date* | *binutils* | *GCC* | *Intel compilers* | *Intel MPI* | *Intel MKL* | -+================+=============+=============+===========+====================+=============+==============+ -| ``2019a`` | Jan '19 | 2.31.1 | 8.2.0 | 2019.1.144 | 2018.4.274 | 2019.1.144 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2019b`` | Sept '19 | 2.32 | 8.3.0 | 2019.5.281 | 2018.5.288 | 2019.5.281 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2020a`` | May'20 | 2.34 | 9.3.0 | 2020.1.217 | 2019.7.217 | 2020.1.217 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2020b`` | Nov'20 | 2.35 | 10.2.0 | 2020.4.304 | 2019.9.304 | 2020.4.304 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2021a`` | May'21 | 2.36.1 | 10.3.0 | 2021.2.0 | 2021.2.0 | 2021.2.0 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2021b`` | Oct'21 | 2.37 | 11.2.0 | 2021.4.0 | 2021.4.0 | 2021.4.0 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2022a`` | Jun'22 | 2.38 | 11.3.0 | 2022.1.0 | 2021.6.0 | 2022.1.0 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2022b`` | Dec'22 | 2.39 | 12.2.0 | 2022.2.1 | 2021.7.1 | 2022.2.1 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ - -.. _common_toolchains_overview_deprecated: - -Overview of common toolchains (deprecated versions) ---------------------------------------------------- - -.. _common_toolchains_overview_foss_deprecated: - -Component versions in ``foss`` toolchain (deprecated versions) -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``foss`` | *date* |*binutils* | *GCC* | *Open MPI* | *FlexiBLAS* | *OpenBLAS* | *LAPACK* | *ScaLAPACK* | *FFTW* | -+================+=============+============+===========+============+=============+============+=======================+==============+=============+ -| ``2014b`` | Jul '14 | '*(none)* | 4.8.3 | 1.8.1 | *(none)* | 0.2.9 | 3.5.0 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2015a`` | Jan '15 | '*(none)* | 4.9.2 | 1.8.4 | *(none)* | 0.2.13 | 3.5.0 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2015b`` | Jul '15 | 2.25 | 4.9.3 | 1.8.8 | *(none)* | 0.2.14 | 3.5.0 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2016a`` | Jan '16 | 2.25 | 4.9.3 | 1.10.2 | *(none)* | 0.2.15 | 3.6.0 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2016b`` | Jul '16 | 2.26 | 5.4.0 | 1.10.3 | *(none)* | 0.2.18 | 3.6.1 | 2.0.2 | 3.3.4 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2017a`` | Jan '17 | 2.27 | 6.3.0 | 2.0.2 | *(none)* | 0.2.19 | 3.7.0 | 2.0.2 | 3.3.6(-pl2) | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2017b`` | Jul '17 | 2.28 | 6.4.0 | 2.1.1 | *(none)* | 0.2.20* | (incl. with OpenBLAS) | 2.0.2 | 3.3.6(-pl2) | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2018a`` | Jan '18 | 2.28 | 6.4.0 | 2.1.2 | *(none)* | 0.2.20* | (incl. with OpenBLAS) | 2.0.2 | 3.3.7 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ -| ``2018b`` | Jul '18 | 2.30 | 7.3.0 | 3.1.1 | *(none)* | 0.3.1 | (incl. with OpenBLAS) | 2.0.2 | 3.3.8 | -+----------------+-------------+------------+-----------+------------+-------------+------------+-----------------------+--------------+-------------+ - -.. _common_toolchains_overview_intel_deprecated: - -Component versions in ``intel`` toolchain (deprecated versions) -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``intel`` | *date* | *binutils* | *GCC* | *Intel compilers* | *Intel MPI* | *Intel MKL* | -+================+=============+=============+===========+====================+=============+==============+ -| ``2014b`` | Jul '14 | '*(none)* | 4.8.3 | 2013.5.192 | 4.1.3.049 | 11.1.2.144 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2015a`` | Jan '15 | '*(none)* | 4.9.2 | 2015.1.133 | 5.0.2.044 | 11.2.1.133 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2015b`` | Jul '15 | 2.25 | 4.9.3 | 2015.3.187 | 5.0.3.048 | 11.2.3.187 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2016a`` | Jan '16 | 2.26 | 4.9.3 | 2016.1.150 | 5.1.2.150 | 11.3.1.150 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2016b`` | Jul '16 | 2.26 | 5.4.0 | 2016.3.210 | 5.1.3.181 | 11.3.3.210 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2017a`` | Jan '17 | 2.27 | 6.3.0 | 2017.1.132 | 2017.1.132 | 2017.1.132 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2017b`` | Jul '17 | 2.28 | 6.4.0 | 2017.4.196 | 2017.3.196 | 2017.3.196 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2018a`` | Jan '18 | 2.28 | 6.4.0 | 2018.1.163 | 2018.1.163 | 2018.1.163 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ -| ``2018b`` | Jul '18 | 2.30 | 7.3.0 | 2018.3.222 | 2018.3.222 | 2018.3.222 | -+----------------+-------------+-------------+-----------+--------------------+-------------+--------------+ - -.. _common_toolchains_customizing: - -Customizing common toolchains ------------------------------ - - -Sometimes the need arises to customize one or more components of a common toolchain w.r.t. site-specific aspects. -One common example is using additional configuration options for Open MPI. - -To customize a toolchain component, you should copy the corresponding easyconfig file, -modify according to your needs, and make sure it is included in a location in the robot search path -that precedes the location of the easyconfig files that are included with EasyBuild -(see also :ref:`robot_search_path`), before building and installation the toolchain. - -More information about toolchains ---------------------------------- - -Please see the :ref:`toolchains_table` for how to obtain a listing of the currently known toolchains. - -For a detailed listing of the compiler options available with each toolchain, please see :ref:`avail_toolchain_opts`. diff --git a/docs/Concepts_and_Terminology.rst b/docs/Concepts_and_Terminology.rst deleted file mode 100644 index 541e977c..00000000 --- a/docs/Concepts_and_Terminology.rst +++ /dev/null @@ -1,187 +0,0 @@ -.. _concepts_and_terminology: - -Concepts and terminology -======================== - - -EasyBuild consists of a collection of Python modules and packages that interact with each other, -dynamically picking up additional Python modules as needed for building and installing -a (stack of) software package(s) specified via simple specification files. - -Or, in EasyBuild terminology: **the EasyBuild framework leverages easyblocks to automatically -build and install software using particular compiler toolchains, as specified by one or multiple easyconfig files**. - -.. contents:: - :depth: 3 - :backlinks: none - -.. _framework: - -EasyBuild framework -------------------- - -The EasyBuild **framework** embodies the core of the tool, providing functionality commonly -needed when installing scientific software on HPC systems. For example, it deals with downloading, -unpacking and patching of sources, loading module files for dependencies, -setting up the build environment, autonomously running (interactive) shell commands, -creating module files that match the specification files, etc. - -Included in the framework is an `abstract` implementation of a software build and install procedure, -which is split up into different `steps`: - -* unpacking sources -* configuration -* build -* installation -* module generation -* etc. - -Most of these steps, i.e., the ones which are generally more-or-less -analogous across different software packages, have appropriate (default) implementations. -The only exceptions are the configuration, build and installation steps that are purposely -left unimplemented (since there is no common procedure for them). - -Each of the steps can be -tweaked and steered via different parameters known to the framework, for which values are -either obtained from the provided specification files or set to reasonable default values. -See :ref:`easyconfig_files`. - -.. XXX - UPDATE BY VERSION FIXME - -In EasyBuild version |version| the framework source code consists of about 19000 lines of code, -organized across about 125 Python modules in roughly a dozen Python package directories, -next to almost 7000 lines of code for tests. This provides some notion of the size of the -EasyBuild framework and the amount of supporting functionality it has to offer. - - -.. _Easyblocks: - -Easyblocks ----------- - -The implementation of a particular software build and install procedure is done in a Python module, -which is aptly referred to as an **easyblock**. - -Each easyblock ties in with the framework API -by defining (or extending/replacing) one or more of the step functions that are part -of the abstract procedure used by the EasyBuild framework. Easyblocks typically heavily -rely on the supporting functionality provided by the framework, for example for -(autonomously) executing (interactive) shell commands and obtaining the command's output and exit code. - -A distinction is made between **software-specific** and **generic** easyblocks. Software-specific -easyblocks implement a build and install procedure which is entirely custom to one particular -software package (e.g., WRF), while generic easyblocks implement a procedure using standard -tools (e.g., CMake). Since easyblocks are implemented in an object-oriented scheme, the step -methods implemented by a particular easyblock can be reused in others via inheritance, -enabling code reuse across build procedure implementations. - -For each software package being built, the EasyBuild framework will determine which easyblock -should be used, based on the name of the software package or the value of the ``easyblock`` -specification parameter (see :ref:`writing_easyconfigs_easyblock_spec`). -Since EasyBuild v2.0, an easyblock *must* be specified in case no matching easyblock is found based on the -software name (cfr. :ref:`depr_ConfigureMake_fallback_eb1`). - -.. XXX - UPDATE BY VERSION FIXME - -EasyBuild version 2.4.0 includes 154 software-specific easyblocks and 28 generic -easyblocks (see also :ref:`basic_usage_easyblocks`), providing support for automatically installing a wide range -of software packages. Examples range from fairly easy-to-build programs like gzip, other basic tools -like compilers, various MPI stacks and commonly used libraries, primarily for x86_64 architecture systems, -to large scientific software packages that are notorious for their involved and tedious install procedures, such as: -`CP2K`, `NWChem`, `OpenFOAM`, `QuantumESPRESSO`, `WRF`. - -.. _toolchains: - -Toolchains ----------- - -EasyBuild employs so-called **compiler toolchains** or, simply `toolchains` for short, -which are a major concept in handling the build and installation processes. - -A typical toolchain consists of one or more compilers, usually put together with some libraries for specific functionality, -e.g., for using an MPI stack for distributed computing, or which provide optimized routines for commonly -used math operations, e.g., the well-known BLAS/LAPACK APIs for linear algebra routines. - -For each software package being built, the toolchain to be used must be specified in some way. - -The EasyBuild framework prepares the `build environment` for the different toolchain components, -by loading their respective modules and defining environment variables to specify compiler commands -(e.g., via ``$F90``), compiler and linker options (e.g., via ``$CFLAGS`` and ``$LDFLAGS``), the list -of library names to supply to the linker (via ``$LIBS``), etc. This enables making easyblocks largely -`toolchain-agnostic` since they can simply rely on these environment variables; that is, unless they -need to be aware of, for example, the particular compiler being used to determine the build configuration options. - -Recent releases of EasyBuild include out-of-the-box toolchain support for: - -- various compilers, including GCC, Intel, Clang, CUDA -- common MPI libraries, such as Intel MPI, MPICH, MVAPICH2, OpenMPI -- various numerical libraries, including ATLAS, Intel MKL, OpenBLAS, ScalaPACK, FFTW - -Please see the :ref:`common_toolchains` page for details about the two most common toolchains, -one for "free and open source software" (``foss``) based on GCC and one based on the Intel compilers -(``intel``). - -.. _system_toolchain: - -``system`` toolchain -~~~~~~~~~~~~~~~~~~~ - -The ``system`` toolchain is a special case. It is an *empty* toolchain, i.e. a toolchain without any components, -and corresponds to using the readily available compilers and libraries (e.g., the ones provided by the operating -system, or by modules which were loaded before issuing the ``eb`` command). - -When the ``system`` toolchain is used, a corresponding ``system`` module file is not required/loaded and no build -environment is being defined. - - -.. _dummy_toolchain: - -``dummy`` toolchain *(DEPRECATED)* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -The ``dummy`` toolchain has been deprecated in EasyBuild v4.0, and replaced by the :ref:`system_toolchain`. - - -Common toolchains -~~~~~~~~~~~~~~~~~ - -For more information on the concept of *common toolchains*, see :ref:`common_toolchains`. - -.. _easyconfig_files: - -Easyconfig files ----------------- - -The specification files that are supplied to EasyBuild are referred to as **easyconfig files** -(or simply `easyconfigs`), which are basically plain text files containing (mostly) -key-value assignments for build parameters supported by the framework, also referred -to as **easyconfig parameters** (see :doc:`Writing_easyconfig_files` for more information). - -Note that easyconfig files only provide the bits of information required -to determine the corresponding module name; the module name itself is computed by EasyBuild -framework by querying the module naming scheme being used. The complete -list of supported easyconfig parameters can be easily obtained via the EasyBuild command line using -``eb -a`` (see also :ref:`avail_easyconfig_params`). - -As such, each easyconfig file provides a complete specification of which particular software -package should be installed, and which settings should be used for building it. After completing -an installation, EasyBuild copies the used easyconfig file to the install directory, as a template, -and also supports maintaining an easyconfig archive which is updated on every successful installation. -Therefore, reproducing installations becomes trivial. - -.. _extensions: - -Extensions ----------- - -Some software packages support installing additional add-ons alongside the 'main' software, either in the same -installation prefix, or in a separate location. - -In EasyBuild, we use the neutral term '**extensions**' to refer these add-ons. - -Well-known examples include: - -* Perl modules (http://www.cpan.org/modules/) -* Python packages (https://pypi.python.org/pypi) -* R libraries (http://cran.r-project.org/web/packages/) -* Ruby gems (http://guides.rubygems.org/what-is-a-gem/) diff --git a/docs/Configuration.rst b/docs/Configuration.rst deleted file mode 100644 index a971b821..00000000 --- a/docs/Configuration.rst +++ /dev/null @@ -1,731 +0,0 @@ -.. _configuring_easybuild: - -Configuring EasyBuild -===================== - -This page discusses the recommended style of configuring -EasyBuild, which is supported since EasyBuild v1.3.0. - -A demo on configuring EasyBuild is available :ref:`here `. - -.. contents:: - :depth: 3 - :backlinks: none - -.. _configuration_types: - -Supported configuration types ------------------------------ - -Configuring EasyBuild can be done by: - -* using ``eb`` with **command line arguments** -* setting **environment variables** (``$EASYBUILD_...``) -* providing one or more **configuration files** - -Of course, combining any of these types of configuration works too (and -is even fairly common). - -The order of preference for the different configuration types is as listed above, that is: - -* environment variables override the corresponding entries in the configuration file -* command line arguments in turn override the corresponding environment variables *and* matching entries in the - configuration file - - -.. _configuration_consistency: - -Consistency across supported configuration types -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Note that the various available configuration options are handled -**consistently** across the supported configuration types. - -For example: to configure EasyBuild to use Lmod as modules tool, the following alternatives are available: - -* configuration file entry (key-value assignment): - - .. code:: ini - - [config] - modules-tool = Lmod - -* environment variable (upper case, ``EASYBUILD_`` prefix, ``-``'s becomes ``_``'s): - - .. code:: - - $ export EASYBUILD_MODULES_TOOL=Lmod - -* command line argument (long options preceded by ``--`` and (optionally) using ``=``): - - .. code:: - - $ eb --modules-tool=Lmod - - or - - .. code:: - - $ eb --modules-tool Lmod - -For more details w.r.t. each of the supported configuration types, see below. - - -.. _configuration_file: - -Configuration file(s) -~~~~~~~~~~~~~~~~~~~~~ - -.. _list_of_configuration_files: - -List of used configuration files -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -The list of configuration files that will be used by EasyBuild is determined in the following order of preference: - -* the path(s) specified via the **command line argument** ``--configfiles`` -* the path(s) specified via the ``$EASYBUILD_CONFIGFILES`` **environment variable** -* the **default paths** for EasyBuild configuration files - -.. _default_configuration_files: - -Default configuration files -+++++++++++++++++++++++++++ - -By default, EasyBuild will use existing configuration files at the following paths: - -* ``$dir/easybuild.d/*.cfg``, for each directory ``$dir`` listed in ``$XDG_CONFIG_DIRS`` (where ``$XDG_CONFIG_DIRS`` - defaults to ``/etc``) -* ``$XDG_CONFIG_HOME/easybuild/config.cfg`` (where ``$XDG_CONFIG_HOME`` defaults to ``$HOME/.config``) - -Hence, if ``$XDG_CONFIG_HOME`` and ``$XDG_CONFIG_DIRS`` are not defined, EasyBuild will only consider default -configuration files at ``/etc/easybuild.d/*.cfg`` and ``$HOME/.config/easybuild/config.cfg``. - -The configuration file located in ``$XDG_CONFIG_HOME`` will be listed *after* the ones obtained via ``$XDG_CONFIG_DIRS``, -such that user-defined configuration settings have preference over system defaults. - -A detailed overview of the list of default configuration files is available via ``eb --show-default-configfiles`` -(available since EasyBuild v2.1.0). For example:: - - $ XDG_CONFIG_DIRS=/tmp/etc:/tmp/moreetc eb --show-default-configfiles - Default list of configuration files: - - [with $XDG_CONFIG_HOME: (not set), $XDG_CONFIG_DIRS: /tmp/etc:/tmp/moreetc] - - * user-level: ${XDG_CONFIG_HOME:-$HOME/.config}/easybuild/config.cfg - -> /home/example/.config/easybuild/config.cfg => found - * system-level: ${XDG_CONFIG_DIRS:-/etc}/easybuild.d/*.cfg - -> {/tmp/etc, /tmp/moreetc}/easybuild.d/*.cfg => /tmp/etc/easybuild.d/config.cfg, /tmp/moreetc/easybuild.d/bar.cfg, /tmp/moreetc/easybuild.d/foo.cfg - - Default list of existing configuration files (4): /tmp/etc/easybuild.d/config.cfg, /tmp/moreetc/easybuild.d/bar.cfg, /tmp/moreetc/easybuild.d/foo.cfg, /home/example/.config/easybuild/config.cfg - -Multiple configuration files -++++++++++++++++++++++++++++ - -If multiple configuration files are listed via a mechanism listed above, the settings in the last -configuration file have preference over the others. - -Each available configuration file will be used, and the configuration settings specified in these files -will be retained according to the order of preference as indicated above: settings in configuration files specified via -``--configfiles`` override those in configuration files specified via ``$EASYBUILD_CONFIGFILES``, which in turns override -settings in default configuration files. - -Ignored configuration files -+++++++++++++++++++++++++++ - -On top of this, the ``--ignoreconfigfiles`` configuration option allows to specify configuration files that should be -*ignored* by EasyBuild (regardless of whether they are specified via any of the options above). - - -Configuration file format -^^^^^^^^^^^^^^^^^^^^^^^^^ - -The EasyBuild configuration file follows the default Python -configuration format as parsed by the ``configparser`` module -(see `http://docs.python.org/2/library/configparser.html`_). - -Configuration files are organized in sections, the section name for a -particular configuration setting is indicated in the output of ``eb --help``. -Some examples sections are: ``MAIN``, ``basic``, ``config``, -``informative``, ``override``, ``regtest``, ``software``, ``unittest``, etc. - -Sections are indicated by specifying the section name in square brackets -on a dedicated line, e.g., ``[basic]``. - -Configuration settings are specified in a ``key = value`` or -``key: value`` format, **without using quotes for string-like values**. -For boolean configuration settings, values that evaluated to ``True`` -(e.g., ``true``, ``1``, …) are all equivalent to enabling the setting. - -Comment lines start with a hash character ``#`` (just like in Python code). - -An example configuration file that should make everything clear is shown below. - -.. code:: python - - [basic] - # always enable logging to stdout - logtostdout = true - [config] - # use Lmod as modules tool - modules-tool: Lmod - # use different default installation path - prefix=/home/you/work/easybuild/ - -.. _configuration_file_templates_constants: - -Templates and constants supported in configuration files -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Two types of template values ``%(...)s`` are supported in configuration files: - -* for configuration options defined in the configuration file (and only those) - - * *syntax:* ``%(opt)s``, i.e., using the (lowercase) name of the configuration option - -* for the default value of selected configuration options (see ``eb --avail-cfgfile-constants``) - - * *syntax:* ``%(DEFAULT_OPT)s``, i.e., using the uppercase name of the configuration option and prefixed with ``DEFAULT_`` - - -.. note:: - These template values are only supported in configuration files, *not* in environment variable values or - command line option values. - -.. note:: - Using an unknown template value, i.e. either one for a configuration option that was not defined in the - configuration file, or a non-existing one for a particular default value, will result in an error like: - ``ConfigParser.InterpolationMissingOptionError: Bad value substitution``. - -Example -+++++++ - -To include both the (custom) location for the easyconfigs archive repository and the default list of robot search -paths in the active robot search path, the following configuration file entry can be used, featuring the template -for the ``repositorypath`` configuration option and the provided ``DEFAULT_ROBOT_PATHS`` constant:: - - [basic] - repositorypath = /home/example/easybuild/easyconfigs_archive - robot-paths = %(repositorypath)s:%(DEFAULT_ROBOT_PATHS)s - -See also :ref:`controlling_robot_search_path`. - -Generating a template configuration file -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Since EasyBuild v1.10, a command line option ``--confighelp`` is -available that prints out the help text as an annotated configuration -file. This can be used as an empty template configuration file: - -.. code:: shell-session - - $ mkdir -p $HOME/.config/easybuild - $ eb --confighelp > $HOME/.config/easybuild/config.cfg - -.. code:: shell-session - - $ head $HOME/.easybuild/config.cfg - [MAIN] - # Enable debug log mode (def False) - #debug= - # Enable info log mode (def False) - #info= - # Enable info quiet/warning mode (def False) - #quiet= - - [basic] - # Print build overview incl. dependencies (full paths) (def False) - -.. _configuration_env_vars: - -Environment variables -~~~~~~~~~~~~~~~~~~~~~ - -All configuration settings listed as long options in ``eb --help`` can -also be specified via ``EASYBUILD_``-prefixed environment variables. - -Configuration settings specified this way always override the -corresponding setting specified in a configuration file. - -For example, to enable debug logging using an environment variable: - -.. code:: shell-session - - $ export EASYBUILD_DEBUG=1 - -More examples of using environment variables to configure EasyBuild are -shown in the sections below. - -.. tip:: Any configuration option of EasyBuild which can be tuned by command line - or via the configuration file, can also be tuned via a corresponding environment variable. - -.. note:: If any ``$EASYBUILD``-prefixed environment variables are defined that do not correspond to a known - configuration option, EasyBuild will report an error message and exit. - -.. _configuration_cmdline: - -Command line arguments -~~~~~~~~~~~~~~~~~~~~~~ - -The configuration type with the highest precedence are the ``eb`` -command line arguments, which override settings specified through environment variables or in configuration files. - -For some configuration options, both short and long command line -arguments are available (see ``eb --help``); the long options indicate -how the configuration setting should be specified in a configuration file -or via an environment variable (``$EASYBUILD_``). - -For boolean configuration settings, both the ``--

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